Starting phenix.real_space_refine on Wed Sep 25 02:31:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sag_10130/09_2024/6sag_10130.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sag_10130/09_2024/6sag_10130.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sag_10130/09_2024/6sag_10130.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sag_10130/09_2024/6sag_10130.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sag_10130/09_2024/6sag_10130.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sag_10130/09_2024/6sag_10130.cif" } resolution = 2.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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: 7 Type Number sf(0) Gaussians Ca 40 9.91 5 P 120 5.49 5 Mg 160 5.21 5 S 40 5.16 5 C 31640 2.51 5 N 9000 2.21 5 O 13080 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 160 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 54080 Number of models: 1 Model: "" Number of chains: 84 Chain: "A" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "R" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "I" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "K" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "M" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "O" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "P" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "Q" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "S" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "T" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "U" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "V" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "W" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "X" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "Y" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "Z" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "0" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "1" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "2" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "3" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "4" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "5" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "6" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "7" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "8" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "9" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "a" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "b" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "c" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "d" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "e" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "f" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "g" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "h" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "i" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "j" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "k" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "l" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "m" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "n" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "o" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "p" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "q" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "r" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "s" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "t" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "u" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "v" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "w" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "x" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "y" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "z" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "AA" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1209 Unusual residues: {'ACE': 1} Classifications: {'peptide': 153, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 7, 'TRANS': 145} Chain: "AA" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "AA" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "AB" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "AC" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "AD" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "AE" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "AF" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "AG" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "AH" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "AI" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "AJ" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "AK" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "AL" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "AN" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "AN" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "AM" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "AN" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "AO" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "AP" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "AQ" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "AR" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Restraints were copied for chains: AC, AE, AG, AM, AO, 0, 2, 4, 6, 8, AK, A, B, D, F, H, J, L, N, P, S, U, W, Y, a, AQ, c, e, g, i, k, m, o, q, s, u, w, y, AI, AH, AJ, AB, AD, AL, AF, 1, 3, 5, 7, 9, C, E, G, I, K, M, O, Q, R, T, V, X, AP, Z, b, d, f, h, j, l, n, p, r, t, v, x, z, AR Time building chain proxies: 9.92, per 1000 atoms: 0.18 Number of scatterers: 54080 At special positions: 0 Unit cell: (188.21, 188.21, 101.442, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 40 19.99 S 40 16.00 P 120 15.00 Mg 160 11.99 O 13080 8.00 N 9000 7.00 C 31640 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.39 Conformation dependent library (CDL) restraints added in 4.7 seconds 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11840 Finding SS restraints... Secondary structure from input PDB file: 280 helices and 40 sheets defined 64.7% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 13.83 Creating SS restraints... Processing helix chain 'A' and resid 6 through 14 removed outlier: 3.705A pdb=" N PHE A 10 " --> pdb=" O PRO A 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL A 11 " --> pdb=" O SER A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 31 removed outlier: 3.620A pdb=" N LEU A 31 " --> pdb=" O CYS A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 51 Processing helix chain 'A' and resid 75 through 87 removed outlier: 4.079A pdb=" N LEU A 79 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 97 removed outlier: 3.529A pdb=" N GLU A 95 " --> pdb=" O ASN A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 134 removed outlier: 3.703A pdb=" N GLU A 131 " --> pdb=" O ASN A 127 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG A 134 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 149 Processing helix chain 'B' and resid 6 through 14 removed outlier: 3.705A pdb=" N PHE B 10 " --> pdb=" O PRO B 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL B 11 " --> pdb=" O SER B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 31 removed outlier: 3.621A pdb=" N LEU B 31 " --> pdb=" O CYS B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 51 Processing helix chain 'B' and resid 75 through 87 removed outlier: 4.079A pdb=" N LEU B 79 " --> pdb=" O VAL B 75 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 97 removed outlier: 3.529A pdb=" N GLU B 95 " --> pdb=" O ASN B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 134 removed outlier: 3.703A pdb=" N GLU B 131 " --> pdb=" O ASN B 127 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG B 134 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 149 Processing helix chain 'D' and resid 6 through 14 removed outlier: 3.705A pdb=" N PHE D 10 " --> pdb=" O PRO D 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL D 11 " --> pdb=" O SER D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 31 removed outlier: 3.620A pdb=" N LEU D 31 " --> pdb=" O CYS D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 51 Processing helix chain 'D' and resid 75 through 87 removed outlier: 4.080A pdb=" N LEU D 79 " --> pdb=" O VAL D 75 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE D 87 " --> pdb=" O LEU D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 97 removed outlier: 3.529A pdb=" N GLU D 95 " --> pdb=" O ASN D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 134 removed outlier: 3.703A pdb=" N GLU D 131 " --> pdb=" O ASN D 127 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG D 134 " --> pdb=" O VAL D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 149 Processing helix chain 'F' and resid 6 through 14 removed outlier: 3.706A pdb=" N PHE F 10 " --> pdb=" O PRO F 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL F 11 " --> pdb=" O SER F 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 31 removed outlier: 3.620A pdb=" N LEU F 31 " --> pdb=" O CYS F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 51 Processing helix chain 'F' and resid 75 through 87 removed outlier: 4.080A pdb=" N LEU F 79 " --> pdb=" O VAL F 75 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE F 87 " --> pdb=" O LEU F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 97 removed outlier: 3.529A pdb=" N GLU F 95 " --> pdb=" O ASN F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 134 removed outlier: 3.703A pdb=" N GLU F 131 " --> pdb=" O ASN F 127 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG F 134 " --> pdb=" O VAL F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 149 Processing helix chain 'H' and resid 6 through 14 removed outlier: 3.705A pdb=" N PHE H 10 " --> pdb=" O PRO H 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL H 11 " --> pdb=" O SER H 8 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 31 removed outlier: 3.619A pdb=" N LEU H 31 " --> pdb=" O CYS H 27 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 51 Processing helix chain 'H' and resid 75 through 87 removed outlier: 4.080A pdb=" N LEU H 79 " --> pdb=" O VAL H 75 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE H 87 " --> pdb=" O LEU H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 97 removed outlier: 3.529A pdb=" N GLU H 95 " --> pdb=" O ASN H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 134 removed outlier: 3.704A pdb=" N GLU H 131 " --> pdb=" O ASN H 127 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG H 134 " --> pdb=" O VAL H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 149 Processing helix chain 'J' and resid 6 through 14 removed outlier: 3.705A pdb=" N PHE J 10 " --> pdb=" O PRO J 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL J 11 " --> pdb=" O SER J 8 " (cutoff:3.500A) Processing helix chain 'J' and resid 19 through 31 removed outlier: 3.620A pdb=" N LEU J 31 " --> pdb=" O CYS J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 51 Processing helix chain 'J' and resid 75 through 87 removed outlier: 4.079A pdb=" N LEU J 79 " --> pdb=" O VAL J 75 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE J 87 " --> pdb=" O LEU J 83 " (cutoff:3.500A) Processing helix chain 'J' and resid 91 through 97 removed outlier: 3.529A pdb=" N GLU J 95 " --> pdb=" O ASN J 91 " (cutoff:3.500A) Processing helix chain 'J' and resid 103 through 134 removed outlier: 3.703A pdb=" N GLU J 131 " --> pdb=" O ASN J 127 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG J 134 " --> pdb=" O VAL J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 140 through 149 Processing helix chain 'L' and resid 6 through 14 removed outlier: 3.705A pdb=" N PHE L 10 " --> pdb=" O PRO L 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL L 11 " --> pdb=" O SER L 8 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 31 removed outlier: 3.620A pdb=" N LEU L 31 " --> pdb=" O CYS L 27 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 51 Processing helix chain 'L' and resid 75 through 87 removed outlier: 4.080A pdb=" N LEU L 79 " --> pdb=" O VAL L 75 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE L 87 " --> pdb=" O LEU L 83 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 97 removed outlier: 3.529A pdb=" N GLU L 95 " --> pdb=" O ASN L 91 " (cutoff:3.500A) Processing helix chain 'L' and resid 103 through 134 removed outlier: 3.703A pdb=" N GLU L 131 " --> pdb=" O ASN L 127 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG L 134 " --> pdb=" O VAL L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 140 through 149 Processing helix chain 'N' and resid 6 through 14 removed outlier: 3.705A pdb=" N PHE N 10 " --> pdb=" O PRO N 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL N 11 " --> pdb=" O SER N 8 " (cutoff:3.500A) Processing helix chain 'N' and resid 19 through 31 removed outlier: 3.620A pdb=" N LEU N 31 " --> pdb=" O CYS N 27 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 51 Processing helix chain 'N' and resid 75 through 87 removed outlier: 4.079A pdb=" N LEU N 79 " --> pdb=" O VAL N 75 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE N 87 " --> pdb=" O LEU N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 91 through 97 removed outlier: 3.528A pdb=" N GLU N 95 " --> pdb=" O ASN N 91 " (cutoff:3.500A) Processing helix chain 'N' and resid 103 through 134 removed outlier: 3.703A pdb=" N GLU N 131 " --> pdb=" O ASN N 127 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG N 134 " --> pdb=" O VAL N 130 " (cutoff:3.500A) Processing helix chain 'N' and resid 140 through 149 Processing helix chain 'P' and resid 6 through 14 removed outlier: 3.705A pdb=" N PHE P 10 " --> pdb=" O PRO P 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL P 11 " --> pdb=" O SER P 8 " (cutoff:3.500A) Processing helix chain 'P' and resid 19 through 31 removed outlier: 3.620A pdb=" N LEU P 31 " --> pdb=" O CYS P 27 " (cutoff:3.500A) Processing helix chain 'P' and resid 37 through 51 Processing helix chain 'P' and resid 75 through 87 removed outlier: 4.079A pdb=" N LEU P 79 " --> pdb=" O VAL P 75 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE P 87 " --> pdb=" O LEU P 83 " (cutoff:3.500A) Processing helix chain 'P' and resid 91 through 97 removed outlier: 3.529A pdb=" N GLU P 95 " --> pdb=" O ASN P 91 " (cutoff:3.500A) Processing helix chain 'P' and resid 103 through 134 removed outlier: 3.702A pdb=" N GLU P 131 " --> pdb=" O ASN P 127 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG P 134 " --> pdb=" O VAL P 130 " (cutoff:3.500A) Processing helix chain 'P' and resid 140 through 149 Processing helix chain 'S' and resid 6 through 14 removed outlier: 3.705A pdb=" N PHE S 10 " --> pdb=" O PRO S 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL S 11 " --> pdb=" O SER S 8 " (cutoff:3.500A) Processing helix chain 'S' and resid 19 through 31 removed outlier: 3.619A pdb=" N LEU S 31 " --> pdb=" O CYS S 27 " (cutoff:3.500A) Processing helix chain 'S' and resid 37 through 51 Processing helix chain 'S' and resid 75 through 87 removed outlier: 4.080A pdb=" N LEU S 79 " --> pdb=" O VAL S 75 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE S 87 " --> pdb=" O LEU S 83 " (cutoff:3.500A) Processing helix chain 'S' and resid 91 through 97 removed outlier: 3.528A pdb=" N GLU S 95 " --> pdb=" O ASN S 91 " (cutoff:3.500A) Processing helix chain 'S' and resid 103 through 134 removed outlier: 3.704A pdb=" N GLU S 131 " --> pdb=" O ASN S 127 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG S 134 " --> pdb=" O VAL S 130 " (cutoff:3.500A) Processing helix chain 'S' and resid 140 through 149 Processing helix chain 'U' and resid 6 through 14 removed outlier: 3.704A pdb=" N PHE U 10 " --> pdb=" O PRO U 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL U 11 " --> pdb=" O SER U 8 " (cutoff:3.500A) Processing helix chain 'U' and resid 19 through 31 removed outlier: 3.620A pdb=" N LEU U 31 " --> pdb=" O CYS U 27 " (cutoff:3.500A) Processing helix chain 'U' and resid 37 through 51 Processing helix chain 'U' and resid 75 through 87 removed outlier: 4.079A pdb=" N LEU U 79 " --> pdb=" O VAL U 75 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE U 87 " --> pdb=" O LEU U 83 " (cutoff:3.500A) Processing helix chain 'U' and resid 91 through 97 removed outlier: 3.529A pdb=" N GLU U 95 " --> pdb=" O ASN U 91 " (cutoff:3.500A) Processing helix chain 'U' and resid 103 through 134 removed outlier: 3.703A pdb=" N GLU U 131 " --> pdb=" O ASN U 127 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG U 134 " --> pdb=" O VAL U 130 " (cutoff:3.500A) Processing helix chain 'U' and resid 140 through 149 Processing helix chain 'W' and resid 6 through 14 removed outlier: 3.705A pdb=" N PHE W 10 " --> pdb=" O PRO W 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL W 11 " --> pdb=" O SER W 8 " (cutoff:3.500A) Processing helix chain 'W' and resid 19 through 31 removed outlier: 3.619A pdb=" N LEU W 31 " --> pdb=" O CYS W 27 " (cutoff:3.500A) Processing helix chain 'W' and resid 37 through 51 Processing helix chain 'W' and resid 75 through 87 removed outlier: 4.079A pdb=" N LEU W 79 " --> pdb=" O VAL W 75 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE W 87 " --> pdb=" O LEU W 83 " (cutoff:3.500A) Processing helix chain 'W' and resid 91 through 97 removed outlier: 3.528A pdb=" N GLU W 95 " --> pdb=" O ASN W 91 " (cutoff:3.500A) Processing helix chain 'W' and resid 103 through 134 removed outlier: 3.703A pdb=" N GLU W 131 " --> pdb=" O ASN W 127 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG W 134 " --> pdb=" O VAL W 130 " (cutoff:3.500A) Processing helix chain 'W' and resid 140 through 149 Processing helix chain 'Y' and resid 6 through 14 removed outlier: 3.705A pdb=" N PHE Y 10 " --> pdb=" O PRO Y 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL Y 11 " --> pdb=" O SER Y 8 " (cutoff:3.500A) Processing helix chain 'Y' and resid 19 through 31 removed outlier: 3.620A pdb=" N LEU Y 31 " --> pdb=" O CYS Y 27 " (cutoff:3.500A) Processing helix chain 'Y' and resid 37 through 51 Processing helix chain 'Y' and resid 75 through 87 removed outlier: 4.079A pdb=" N LEU Y 79 " --> pdb=" O VAL Y 75 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE Y 87 " --> pdb=" O LEU Y 83 " (cutoff:3.500A) Processing helix chain 'Y' and resid 91 through 97 removed outlier: 3.529A pdb=" N GLU Y 95 " --> pdb=" O ASN Y 91 " (cutoff:3.500A) Processing helix chain 'Y' and resid 103 through 134 removed outlier: 3.703A pdb=" N GLU Y 131 " --> pdb=" O ASN Y 127 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG Y 134 " --> pdb=" O VAL Y 130 " (cutoff:3.500A) Processing helix chain 'Y' and resid 140 through 149 Processing helix chain '0' and resid 6 through 14 removed outlier: 3.705A pdb=" N PHE 0 10 " --> pdb=" O PRO 0 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL 0 11 " --> pdb=" O SER 0 8 " (cutoff:3.500A) Processing helix chain '0' and resid 19 through 31 removed outlier: 3.620A pdb=" N LEU 0 31 " --> pdb=" O CYS 0 27 " (cutoff:3.500A) Processing helix chain '0' and resid 37 through 51 Processing helix chain '0' and resid 75 through 87 removed outlier: 4.079A pdb=" N LEU 0 79 " --> pdb=" O VAL 0 75 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE 0 87 " --> pdb=" O LEU 0 83 " (cutoff:3.500A) Processing helix chain '0' and resid 91 through 97 removed outlier: 3.528A pdb=" N GLU 0 95 " --> pdb=" O ASN 0 91 " (cutoff:3.500A) Processing helix chain '0' and resid 103 through 134 removed outlier: 3.703A pdb=" N GLU 0 131 " --> pdb=" O ASN 0 127 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG 0 134 " --> pdb=" O VAL 0 130 " (cutoff:3.500A) Processing helix chain '0' and resid 140 through 149 Processing helix chain '2' and resid 6 through 14 removed outlier: 3.705A pdb=" N PHE 2 10 " --> pdb=" O PRO 2 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL 2 11 " --> pdb=" O SER 2 8 " (cutoff:3.500A) Processing helix chain '2' and resid 19 through 31 removed outlier: 3.620A pdb=" N LEU 2 31 " --> pdb=" O CYS 2 27 " (cutoff:3.500A) Processing helix chain '2' and resid 37 through 51 Processing helix chain '2' and resid 75 through 87 removed outlier: 4.080A pdb=" N LEU 2 79 " --> pdb=" O VAL 2 75 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE 2 87 " --> pdb=" O LEU 2 83 " (cutoff:3.500A) Processing helix chain '2' and resid 91 through 97 removed outlier: 3.528A pdb=" N GLU 2 95 " --> pdb=" O ASN 2 91 " (cutoff:3.500A) Processing helix chain '2' and resid 103 through 134 removed outlier: 3.703A pdb=" N GLU 2 131 " --> pdb=" O ASN 2 127 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG 2 134 " --> pdb=" O VAL 2 130 " (cutoff:3.500A) Processing helix chain '2' and resid 140 through 149 Processing helix chain '4' and resid 6 through 14 removed outlier: 3.704A pdb=" N PHE 4 10 " --> pdb=" O PRO 4 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL 4 11 " --> pdb=" O SER 4 8 " (cutoff:3.500A) Processing helix chain '4' and resid 19 through 31 removed outlier: 3.620A pdb=" N LEU 4 31 " --> pdb=" O CYS 4 27 " (cutoff:3.500A) Processing helix chain '4' and resid 37 through 51 Processing helix chain '4' and resid 75 through 87 removed outlier: 4.080A pdb=" N LEU 4 79 " --> pdb=" O VAL 4 75 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE 4 87 " --> pdb=" O LEU 4 83 " (cutoff:3.500A) Processing helix chain '4' and resid 91 through 97 removed outlier: 3.528A pdb=" N GLU 4 95 " --> pdb=" O ASN 4 91 " (cutoff:3.500A) Processing helix chain '4' and resid 103 through 134 removed outlier: 3.703A pdb=" N GLU 4 131 " --> pdb=" O ASN 4 127 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG 4 134 " --> pdb=" O VAL 4 130 " (cutoff:3.500A) Processing helix chain '4' and resid 140 through 149 Processing helix chain '6' and resid 6 through 14 removed outlier: 3.705A pdb=" N PHE 6 10 " --> pdb=" O PRO 6 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL 6 11 " --> pdb=" O SER 6 8 " (cutoff:3.500A) Processing helix chain '6' and resid 19 through 31 removed outlier: 3.619A pdb=" N LEU 6 31 " --> pdb=" O CYS 6 27 " (cutoff:3.500A) Processing helix chain '6' and resid 37 through 51 Processing helix chain '6' and resid 75 through 87 removed outlier: 4.079A pdb=" N LEU 6 79 " --> pdb=" O VAL 6 75 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE 6 87 " --> pdb=" O LEU 6 83 " (cutoff:3.500A) Processing helix chain '6' and resid 91 through 97 removed outlier: 3.529A pdb=" N GLU 6 95 " --> pdb=" O ASN 6 91 " (cutoff:3.500A) Processing helix chain '6' and resid 103 through 134 removed outlier: 3.703A pdb=" N GLU 6 131 " --> pdb=" O ASN 6 127 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG 6 134 " --> pdb=" O VAL 6 130 " (cutoff:3.500A) Processing helix chain '6' and resid 140 through 149 Processing helix chain '8' and resid 6 through 14 removed outlier: 3.705A pdb=" N PHE 8 10 " --> pdb=" O PRO 8 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL 8 11 " --> pdb=" O SER 8 8 " (cutoff:3.500A) Processing helix chain '8' and resid 19 through 31 removed outlier: 3.620A pdb=" N LEU 8 31 " --> pdb=" O CYS 8 27 " (cutoff:3.500A) Processing helix chain '8' and resid 37 through 51 Processing helix chain '8' and resid 75 through 87 removed outlier: 4.079A pdb=" N LEU 8 79 " --> pdb=" O VAL 8 75 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE 8 87 " --> pdb=" O LEU 8 83 " (cutoff:3.500A) Processing helix chain '8' and resid 91 through 97 removed outlier: 3.529A pdb=" N GLU 8 95 " --> pdb=" O ASN 8 91 " (cutoff:3.500A) Processing helix chain '8' and resid 103 through 134 removed outlier: 3.703A pdb=" N GLU 8 131 " --> pdb=" O ASN 8 127 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG 8 134 " --> pdb=" O VAL 8 130 " (cutoff:3.500A) Processing helix chain '8' and resid 140 through 149 Processing helix chain 'a' and resid 6 through 14 removed outlier: 3.705A pdb=" N PHE a 10 " --> pdb=" O PRO a 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL a 11 " --> pdb=" O SER a 8 " (cutoff:3.500A) Processing helix chain 'a' and resid 19 through 31 removed outlier: 3.620A pdb=" N LEU a 31 " --> pdb=" O CYS a 27 " (cutoff:3.500A) Processing helix chain 'a' and resid 37 through 51 Processing helix chain 'a' and resid 75 through 87 removed outlier: 4.079A pdb=" N LEU a 79 " --> pdb=" O VAL a 75 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE a 87 " --> pdb=" O LEU a 83 " (cutoff:3.500A) Processing helix chain 'a' and resid 91 through 97 removed outlier: 3.529A pdb=" N GLU a 95 " --> pdb=" O ASN a 91 " (cutoff:3.500A) Processing helix chain 'a' and resid 103 through 134 removed outlier: 3.703A pdb=" N GLU a 131 " --> pdb=" O ASN a 127 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG a 134 " --> pdb=" O VAL a 130 " (cutoff:3.500A) Processing helix chain 'a' and resid 140 through 149 Processing helix chain 'c' and resid 6 through 14 removed outlier: 3.705A pdb=" N PHE c 10 " --> pdb=" O PRO c 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL c 11 " --> pdb=" O SER c 8 " (cutoff:3.500A) Processing helix chain 'c' and resid 19 through 31 removed outlier: 3.620A pdb=" N LEU c 31 " --> pdb=" O CYS c 27 " (cutoff:3.500A) Processing helix chain 'c' and resid 37 through 51 Processing helix chain 'c' and resid 75 through 87 removed outlier: 4.080A pdb=" N LEU c 79 " --> pdb=" O VAL c 75 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE c 87 " --> pdb=" O LEU c 83 " (cutoff:3.500A) Processing helix chain 'c' and resid 91 through 97 removed outlier: 3.528A pdb=" N GLU c 95 " --> pdb=" O ASN c 91 " (cutoff:3.500A) Processing helix chain 'c' and resid 103 through 134 removed outlier: 3.703A pdb=" N GLU c 131 " --> pdb=" O ASN c 127 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG c 134 " --> pdb=" O VAL c 130 " (cutoff:3.500A) Processing helix chain 'c' and resid 140 through 149 Processing helix chain 'e' and resid 6 through 14 removed outlier: 3.705A pdb=" N PHE e 10 " --> pdb=" O PRO e 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL e 11 " --> pdb=" O SER e 8 " (cutoff:3.500A) Processing helix chain 'e' and resid 19 through 31 removed outlier: 3.620A pdb=" N LEU e 31 " --> pdb=" O CYS e 27 " (cutoff:3.500A) Processing helix chain 'e' and resid 37 through 51 Processing helix chain 'e' and resid 75 through 87 removed outlier: 4.080A pdb=" N LEU e 79 " --> pdb=" O VAL e 75 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE e 87 " --> pdb=" O LEU e 83 " (cutoff:3.500A) Processing helix chain 'e' and resid 91 through 97 removed outlier: 3.529A pdb=" N GLU e 95 " --> pdb=" O ASN e 91 " (cutoff:3.500A) Processing helix chain 'e' and resid 103 through 134 removed outlier: 3.704A pdb=" N GLU e 131 " --> pdb=" O ASN e 127 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG e 134 " --> pdb=" O VAL e 130 " (cutoff:3.500A) Processing helix chain 'e' and resid 140 through 149 Processing helix chain 'g' and resid 6 through 14 removed outlier: 3.705A pdb=" N PHE g 10 " --> pdb=" O PRO g 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL g 11 " --> pdb=" O SER g 8 " (cutoff:3.500A) Processing helix chain 'g' and resid 19 through 31 removed outlier: 3.619A pdb=" N LEU g 31 " --> pdb=" O CYS g 27 " (cutoff:3.500A) Processing helix chain 'g' and resid 37 through 51 Processing helix chain 'g' and resid 75 through 87 removed outlier: 4.079A pdb=" N LEU g 79 " --> pdb=" O VAL g 75 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE g 87 " --> pdb=" O LEU g 83 " (cutoff:3.500A) Processing helix chain 'g' and resid 91 through 97 removed outlier: 3.529A pdb=" N GLU g 95 " --> pdb=" O ASN g 91 " (cutoff:3.500A) Processing helix chain 'g' and resid 103 through 134 removed outlier: 3.704A pdb=" N GLU g 131 " --> pdb=" O ASN g 127 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG g 134 " --> pdb=" O VAL g 130 " (cutoff:3.500A) Processing helix chain 'g' and resid 140 through 149 Processing helix chain 'i' and resid 6 through 14 removed outlier: 3.705A pdb=" N PHE i 10 " --> pdb=" O PRO i 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL i 11 " --> pdb=" O SER i 8 " (cutoff:3.500A) Processing helix chain 'i' and resid 19 through 31 removed outlier: 3.620A pdb=" N LEU i 31 " --> pdb=" O CYS i 27 " (cutoff:3.500A) Processing helix chain 'i' and resid 37 through 51 Processing helix chain 'i' and resid 75 through 87 removed outlier: 4.080A pdb=" N LEU i 79 " --> pdb=" O VAL i 75 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE i 87 " --> pdb=" O LEU i 83 " (cutoff:3.500A) Processing helix chain 'i' and resid 91 through 97 removed outlier: 3.529A pdb=" N GLU i 95 " --> pdb=" O ASN i 91 " (cutoff:3.500A) Processing helix chain 'i' and resid 103 through 134 removed outlier: 3.704A pdb=" N GLU i 131 " --> pdb=" O ASN i 127 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG i 134 " --> pdb=" O VAL i 130 " (cutoff:3.500A) Processing helix chain 'i' and resid 140 through 149 Processing helix chain 'k' and resid 6 through 14 removed outlier: 3.705A pdb=" N PHE k 10 " --> pdb=" O PRO k 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL k 11 " --> pdb=" O SER k 8 " (cutoff:3.500A) Processing helix chain 'k' and resid 19 through 31 removed outlier: 3.620A pdb=" N LEU k 31 " --> pdb=" O CYS k 27 " (cutoff:3.500A) Processing helix chain 'k' and resid 37 through 51 Processing helix chain 'k' and resid 75 through 87 removed outlier: 4.079A pdb=" N LEU k 79 " --> pdb=" O VAL k 75 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE k 87 " --> pdb=" O LEU k 83 " (cutoff:3.500A) Processing helix chain 'k' and resid 91 through 97 removed outlier: 3.529A pdb=" N GLU k 95 " --> pdb=" O ASN k 91 " (cutoff:3.500A) Processing helix chain 'k' and resid 103 through 134 removed outlier: 3.703A pdb=" N GLU k 131 " --> pdb=" O ASN k 127 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG k 134 " --> pdb=" O VAL k 130 " (cutoff:3.500A) Processing helix chain 'k' and resid 140 through 149 Processing helix chain 'm' and resid 6 through 14 removed outlier: 3.705A pdb=" N PHE m 10 " --> pdb=" O PRO m 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL m 11 " --> pdb=" O SER m 8 " (cutoff:3.500A) Processing helix chain 'm' and resid 19 through 31 removed outlier: 3.620A pdb=" N LEU m 31 " --> pdb=" O CYS m 27 " (cutoff:3.500A) Processing helix chain 'm' and resid 37 through 51 Processing helix chain 'm' and resid 75 through 87 removed outlier: 4.080A pdb=" N LEU m 79 " --> pdb=" O VAL m 75 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE m 87 " --> pdb=" O LEU m 83 " (cutoff:3.500A) Processing helix chain 'm' and resid 91 through 97 removed outlier: 3.529A pdb=" N GLU m 95 " --> pdb=" O ASN m 91 " (cutoff:3.500A) Processing helix chain 'm' and resid 103 through 134 removed outlier: 3.703A pdb=" N GLU m 131 " --> pdb=" O ASN m 127 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG m 134 " --> pdb=" O VAL m 130 " (cutoff:3.500A) Processing helix chain 'm' and resid 140 through 149 Processing helix chain 'o' and resid 6 through 14 removed outlier: 3.705A pdb=" N PHE o 10 " --> pdb=" O PRO o 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL o 11 " --> pdb=" O SER o 8 " (cutoff:3.500A) Processing helix chain 'o' and resid 19 through 31 removed outlier: 3.620A pdb=" N LEU o 31 " --> pdb=" O CYS o 27 " (cutoff:3.500A) Processing helix chain 'o' and resid 37 through 51 Processing helix chain 'o' and resid 75 through 87 removed outlier: 4.079A pdb=" N LEU o 79 " --> pdb=" O VAL o 75 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE o 87 " --> pdb=" O LEU o 83 " (cutoff:3.500A) Processing helix chain 'o' and resid 91 through 97 removed outlier: 3.529A pdb=" N GLU o 95 " --> pdb=" O ASN o 91 " (cutoff:3.500A) Processing helix chain 'o' and resid 103 through 134 removed outlier: 3.703A pdb=" N GLU o 131 " --> pdb=" O ASN o 127 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG o 134 " --> pdb=" O VAL o 130 " (cutoff:3.500A) Processing helix chain 'o' and resid 140 through 149 Processing helix chain 'q' and resid 6 through 14 removed outlier: 3.704A pdb=" N PHE q 10 " --> pdb=" O PRO q 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL q 11 " --> pdb=" O SER q 8 " (cutoff:3.500A) Processing helix chain 'q' and resid 19 through 31 removed outlier: 3.619A pdb=" N LEU q 31 " --> pdb=" O CYS q 27 " (cutoff:3.500A) Processing helix chain 'q' and resid 37 through 51 Processing helix chain 'q' and resid 75 through 87 removed outlier: 4.079A pdb=" N LEU q 79 " --> pdb=" O VAL q 75 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE q 87 " --> pdb=" O LEU q 83 " (cutoff:3.500A) Processing helix chain 'q' and resid 91 through 97 removed outlier: 3.529A pdb=" N GLU q 95 " --> pdb=" O ASN q 91 " (cutoff:3.500A) Processing helix chain 'q' and resid 103 through 134 removed outlier: 3.703A pdb=" N GLU q 131 " --> pdb=" O ASN q 127 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG q 134 " --> pdb=" O VAL q 130 " (cutoff:3.500A) Processing helix chain 'q' and resid 140 through 149 Processing helix chain 's' and resid 6 through 14 removed outlier: 3.705A pdb=" N PHE s 10 " --> pdb=" O PRO s 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL s 11 " --> pdb=" O SER s 8 " (cutoff:3.500A) Processing helix chain 's' and resid 19 through 31 removed outlier: 3.620A pdb=" N LEU s 31 " --> pdb=" O CYS s 27 " (cutoff:3.500A) Processing helix chain 's' and resid 37 through 51 Processing helix chain 's' and resid 75 through 87 removed outlier: 4.079A pdb=" N LEU s 79 " --> pdb=" O VAL s 75 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE s 87 " --> pdb=" O LEU s 83 " (cutoff:3.500A) Processing helix chain 's' and resid 91 through 97 removed outlier: 3.528A pdb=" N GLU s 95 " --> pdb=" O ASN s 91 " (cutoff:3.500A) Processing helix chain 's' and resid 103 through 134 removed outlier: 3.703A pdb=" N GLU s 131 " --> pdb=" O ASN s 127 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG s 134 " --> pdb=" O VAL s 130 " (cutoff:3.500A) Processing helix chain 's' and resid 140 through 149 Processing helix chain 'u' and resid 6 through 14 removed outlier: 3.704A pdb=" N PHE u 10 " --> pdb=" O PRO u 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL u 11 " --> pdb=" O SER u 8 " (cutoff:3.500A) Processing helix chain 'u' and resid 19 through 31 removed outlier: 3.619A pdb=" N LEU u 31 " --> pdb=" O CYS u 27 " (cutoff:3.500A) Processing helix chain 'u' and resid 37 through 51 Processing helix chain 'u' and resid 75 through 87 removed outlier: 4.079A pdb=" N LEU u 79 " --> pdb=" O VAL u 75 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE u 87 " --> pdb=" O LEU u 83 " (cutoff:3.500A) Processing helix chain 'u' and resid 91 through 97 removed outlier: 3.529A pdb=" N GLU u 95 " --> pdb=" O ASN u 91 " (cutoff:3.500A) Processing helix chain 'u' and resid 103 through 134 removed outlier: 3.703A pdb=" N GLU u 131 " --> pdb=" O ASN u 127 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG u 134 " --> pdb=" O VAL u 130 " (cutoff:3.500A) Processing helix chain 'u' and resid 140 through 149 Processing helix chain 'w' and resid 6 through 14 removed outlier: 3.705A pdb=" N PHE w 10 " --> pdb=" O PRO w 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL w 11 " --> pdb=" O SER w 8 " (cutoff:3.500A) Processing helix chain 'w' and resid 19 through 31 removed outlier: 3.619A pdb=" N LEU w 31 " --> pdb=" O CYS w 27 " (cutoff:3.500A) Processing helix chain 'w' and resid 37 through 51 Processing helix chain 'w' and resid 75 through 87 removed outlier: 4.079A pdb=" N LEU w 79 " --> pdb=" O VAL w 75 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE w 87 " --> pdb=" O LEU w 83 " (cutoff:3.500A) Processing helix chain 'w' and resid 91 through 97 removed outlier: 3.529A pdb=" N GLU w 95 " --> pdb=" O ASN w 91 " (cutoff:3.500A) Processing helix chain 'w' and resid 103 through 134 removed outlier: 3.703A pdb=" N GLU w 131 " --> pdb=" O ASN w 127 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG w 134 " --> pdb=" O VAL w 130 " (cutoff:3.500A) Processing helix chain 'w' and resid 140 through 149 Processing helix chain 'y' and resid 6 through 14 removed outlier: 3.705A pdb=" N PHE y 10 " --> pdb=" O PRO y 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL y 11 " --> pdb=" O SER y 8 " (cutoff:3.500A) Processing helix chain 'y' and resid 19 through 31 removed outlier: 3.620A pdb=" N LEU y 31 " --> pdb=" O CYS y 27 " (cutoff:3.500A) Processing helix chain 'y' and resid 37 through 51 Processing helix chain 'y' and resid 75 through 87 removed outlier: 4.079A pdb=" N LEU y 79 " --> pdb=" O VAL y 75 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE y 87 " --> pdb=" O LEU y 83 " (cutoff:3.500A) Processing helix chain 'y' and resid 91 through 97 removed outlier: 3.529A pdb=" N GLU y 95 " --> pdb=" O ASN y 91 " (cutoff:3.500A) Processing helix chain 'y' and resid 103 through 134 removed outlier: 3.702A pdb=" N GLU y 131 " --> pdb=" O ASN y 127 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG y 134 " --> pdb=" O VAL y 130 " (cutoff:3.500A) Processing helix chain 'y' and resid 140 through 149 Processing helix chain 'AA' and resid 6 through 14 removed outlier: 3.705A pdb=" N PHEAA 10 " --> pdb=" O PROAA 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VALAA 11 " --> pdb=" O SERAA 8 " (cutoff:3.500A) Processing helix chain 'AA' and resid 19 through 31 removed outlier: 3.619A pdb=" N LEUAA 31 " --> pdb=" O CYSAA 27 " (cutoff:3.500A) Processing helix chain 'AA' and resid 37 through 51 Processing helix chain 'AA' and resid 75 through 87 removed outlier: 4.079A pdb=" N LEUAA 79 " --> pdb=" O VALAA 75 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHEAA 87 " --> pdb=" O LEUAA 83 " (cutoff:3.500A) Processing helix chain 'AA' and resid 91 through 97 removed outlier: 3.529A pdb=" N GLUAA 95 " --> pdb=" O ASNAA 91 " (cutoff:3.500A) Processing helix chain 'AA' and resid 103 through 134 removed outlier: 3.704A pdb=" N GLUAA 131 " --> pdb=" O ASNAA 127 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARGAA 134 " --> pdb=" O VALAA 130 " (cutoff:3.500A) Processing helix chain 'AA' and resid 140 through 149 Processing helix chain 'AC' and resid 6 through 14 removed outlier: 3.704A pdb=" N PHEAC 10 " --> pdb=" O PROAC 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VALAC 11 " --> pdb=" O SERAC 8 " (cutoff:3.500A) Processing helix chain 'AC' and resid 19 through 31 removed outlier: 3.619A pdb=" N LEUAC 31 " --> pdb=" O CYSAC 27 " (cutoff:3.500A) Processing helix chain 'AC' and resid 37 through 51 Processing helix chain 'AC' and resid 75 through 87 removed outlier: 4.080A pdb=" N LEUAC 79 " --> pdb=" O VALAC 75 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHEAC 87 " --> pdb=" O LEUAC 83 " (cutoff:3.500A) Processing helix chain 'AC' and resid 91 through 97 removed outlier: 3.529A pdb=" N GLUAC 95 " --> pdb=" O ASNAC 91 " (cutoff:3.500A) Processing helix chain 'AC' and resid 103 through 134 removed outlier: 3.703A pdb=" N GLUAC 131 " --> pdb=" O ASNAC 127 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARGAC 134 " --> pdb=" O VALAC 130 " (cutoff:3.500A) Processing helix chain 'AC' and resid 140 through 149 Processing helix chain 'AE' and resid 6 through 14 removed outlier: 3.705A pdb=" N PHEAE 10 " --> pdb=" O PROAE 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VALAE 11 " --> pdb=" O SERAE 8 " (cutoff:3.500A) Processing helix chain 'AE' and resid 19 through 31 removed outlier: 3.620A pdb=" N LEUAE 31 " --> pdb=" O CYSAE 27 " (cutoff:3.500A) Processing helix chain 'AE' and resid 37 through 51 Processing helix chain 'AE' and resid 75 through 87 removed outlier: 4.079A pdb=" N LEUAE 79 " --> pdb=" O VALAE 75 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHEAE 87 " --> pdb=" O LEUAE 83 " (cutoff:3.500A) Processing helix chain 'AE' and resid 91 through 97 removed outlier: 3.528A pdb=" N GLUAE 95 " --> pdb=" O ASNAE 91 " (cutoff:3.500A) Processing helix chain 'AE' and resid 103 through 134 removed outlier: 3.703A pdb=" N GLUAE 131 " --> pdb=" O ASNAE 127 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARGAE 134 " --> pdb=" O VALAE 130 " (cutoff:3.500A) Processing helix chain 'AE' and resid 140 through 149 Processing helix chain 'AG' and resid 6 through 14 removed outlier: 3.705A pdb=" N PHEAG 10 " --> pdb=" O PROAG 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VALAG 11 " --> pdb=" O SERAG 8 " (cutoff:3.500A) Processing helix chain 'AG' and resid 19 through 31 removed outlier: 3.620A pdb=" N LEUAG 31 " --> pdb=" O CYSAG 27 " (cutoff:3.500A) Processing helix chain 'AG' and resid 37 through 51 Processing helix chain 'AG' and resid 75 through 87 removed outlier: 4.079A pdb=" N LEUAG 79 " --> pdb=" O VALAG 75 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHEAG 87 " --> pdb=" O LEUAG 83 " (cutoff:3.500A) Processing helix chain 'AG' and resid 91 through 97 removed outlier: 3.529A pdb=" N GLUAG 95 " --> pdb=" O ASNAG 91 " (cutoff:3.500A) Processing helix chain 'AG' and resid 103 through 134 removed outlier: 3.703A pdb=" N GLUAG 131 " --> pdb=" O ASNAG 127 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARGAG 134 " --> pdb=" O VALAG 130 " (cutoff:3.500A) Processing helix chain 'AG' and resid 140 through 149 Processing helix chain 'AI' and resid 6 through 14 removed outlier: 3.705A pdb=" N PHEAI 10 " --> pdb=" O PROAI 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VALAI 11 " --> pdb=" O SERAI 8 " (cutoff:3.500A) Processing helix chain 'AI' and resid 19 through 31 removed outlier: 3.619A pdb=" N LEUAI 31 " --> pdb=" O CYSAI 27 " (cutoff:3.500A) Processing helix chain 'AI' and resid 37 through 51 Processing helix chain 'AI' and resid 75 through 87 removed outlier: 4.080A pdb=" N LEUAI 79 " --> pdb=" O VALAI 75 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHEAI 87 " --> pdb=" O LEUAI 83 " (cutoff:3.500A) Processing helix chain 'AI' and resid 91 through 97 removed outlier: 3.528A pdb=" N GLUAI 95 " --> pdb=" O ASNAI 91 " (cutoff:3.500A) Processing helix chain 'AI' and resid 103 through 134 removed outlier: 3.703A pdb=" N GLUAI 131 " --> pdb=" O ASNAI 127 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARGAI 134 " --> pdb=" O VALAI 130 " (cutoff:3.500A) Processing helix chain 'AI' and resid 140 through 149 Processing helix chain 'AK' and resid 6 through 14 removed outlier: 3.705A pdb=" N PHEAK 10 " --> pdb=" O PROAK 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VALAK 11 " --> pdb=" O SERAK 8 " (cutoff:3.500A) Processing helix chain 'AK' and resid 19 through 31 removed outlier: 3.620A pdb=" N LEUAK 31 " --> pdb=" O CYSAK 27 " (cutoff:3.500A) Processing helix chain 'AK' and resid 37 through 51 Processing helix chain 'AK' and resid 75 through 87 removed outlier: 4.079A pdb=" N LEUAK 79 " --> pdb=" O VALAK 75 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHEAK 87 " --> pdb=" O LEUAK 83 " (cutoff:3.500A) Processing helix chain 'AK' and resid 91 through 97 removed outlier: 3.529A pdb=" N GLUAK 95 " --> pdb=" O ASNAK 91 " (cutoff:3.500A) Processing helix chain 'AK' and resid 103 through 134 removed outlier: 3.703A pdb=" N GLUAK 131 " --> pdb=" O ASNAK 127 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARGAK 134 " --> pdb=" O VALAK 130 " (cutoff:3.500A) Processing helix chain 'AK' and resid 140 through 149 Processing helix chain 'AM' and resid 6 through 14 removed outlier: 3.706A pdb=" N PHEAM 10 " --> pdb=" O PROAM 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VALAM 11 " --> pdb=" O SERAM 8 " (cutoff:3.500A) Processing helix chain 'AM' and resid 19 through 31 removed outlier: 3.619A pdb=" N LEUAM 31 " --> pdb=" O CYSAM 27 " (cutoff:3.500A) Processing helix chain 'AM' and resid 37 through 51 Processing helix chain 'AM' and resid 75 through 87 removed outlier: 4.080A pdb=" N LEUAM 79 " --> pdb=" O VALAM 75 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHEAM 87 " --> pdb=" O LEUAM 83 " (cutoff:3.500A) Processing helix chain 'AM' and resid 91 through 97 removed outlier: 3.528A pdb=" N GLUAM 95 " --> pdb=" O ASNAM 91 " (cutoff:3.500A) Processing helix chain 'AM' and resid 103 through 134 removed outlier: 3.704A pdb=" N GLUAM 131 " --> pdb=" O ASNAM 127 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARGAM 134 " --> pdb=" O VALAM 130 " (cutoff:3.500A) Processing helix chain 'AM' and resid 140 through 149 Processing helix chain 'AO' and resid 6 through 14 removed outlier: 3.705A pdb=" N PHEAO 10 " --> pdb=" O PROAO 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VALAO 11 " --> pdb=" O SERAO 8 " (cutoff:3.500A) Processing helix chain 'AO' and resid 19 through 31 removed outlier: 3.620A pdb=" N LEUAO 31 " --> pdb=" O CYSAO 27 " (cutoff:3.500A) Processing helix chain 'AO' and resid 37 through 51 Processing helix chain 'AO' and resid 75 through 87 removed outlier: 4.079A pdb=" N LEUAO 79 " --> pdb=" O VALAO 75 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHEAO 87 " --> pdb=" O LEUAO 83 " (cutoff:3.500A) Processing helix chain 'AO' and resid 91 through 97 removed outlier: 3.529A pdb=" N GLUAO 95 " --> pdb=" O ASNAO 91 " (cutoff:3.500A) Processing helix chain 'AO' and resid 103 through 134 removed outlier: 3.704A pdb=" N GLUAO 131 " --> pdb=" O ASNAO 127 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARGAO 134 " --> pdb=" O VALAO 130 " (cutoff:3.500A) Processing helix chain 'AO' and resid 140 through 149 Processing helix chain 'AQ' and resid 6 through 14 removed outlier: 3.704A pdb=" N PHEAQ 10 " --> pdb=" O PROAQ 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VALAQ 11 " --> pdb=" O SERAQ 8 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 19 through 31 removed outlier: 3.619A pdb=" N LEUAQ 31 " --> pdb=" O CYSAQ 27 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 37 through 51 Processing helix chain 'AQ' and resid 75 through 87 removed outlier: 4.080A pdb=" N LEUAQ 79 " --> pdb=" O VALAQ 75 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHEAQ 87 " --> pdb=" O LEUAQ 83 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 91 through 97 removed outlier: 3.528A pdb=" N GLUAQ 95 " --> pdb=" O ASNAQ 91 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 103 through 134 removed outlier: 3.703A pdb=" N GLUAQ 131 " --> pdb=" O ASNAQ 127 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARGAQ 134 " --> pdb=" O VALAQ 130 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 140 through 149 Processing sheet with id=1, first strand: chain 'A' and resid 17 through 18 Processing sheet with id=2, first strand: chain 'B' and resid 17 through 18 Processing sheet with id=3, first strand: chain 'D' and resid 17 through 18 Processing sheet with id=4, first strand: chain 'F' and resid 17 through 18 Processing sheet with id=5, first strand: chain 'H' and resid 17 through 18 Processing sheet with id=6, first strand: chain 'J' and resid 17 through 18 Processing sheet with id=7, first strand: chain 'L' and resid 17 through 18 Processing sheet with id=8, first strand: chain 'N' and resid 17 through 18 Processing sheet with id=9, first strand: chain 'P' and resid 17 through 18 Processing sheet with id=10, first strand: chain 'S' and resid 17 through 18 Processing sheet with id=11, first strand: chain 'U' and resid 17 through 18 Processing sheet with id=12, first strand: chain 'W' and resid 17 through 18 Processing sheet with id=13, first strand: chain 'Y' and resid 17 through 18 Processing sheet with id=14, first strand: chain '0' and resid 17 through 18 Processing sheet with id=15, first strand: chain '2' and resid 17 through 18 Processing sheet with id=16, first strand: chain '4' and resid 17 through 18 Processing sheet with id=17, first strand: chain '6' and resid 17 through 18 Processing sheet with id=18, first strand: chain '8' and resid 17 through 18 Processing sheet with id=19, first strand: chain 'a' and resid 17 through 18 Processing sheet with id=20, first strand: chain 'c' and resid 17 through 18 Processing sheet with id=21, first strand: chain 'e' and resid 17 through 18 Processing sheet with id=22, first strand: chain 'g' and resid 17 through 18 Processing sheet with id=23, first strand: chain 'i' and resid 17 through 18 Processing sheet with id=24, first strand: chain 'k' and resid 17 through 18 Processing sheet with id=25, first strand: chain 'm' and resid 17 through 18 Processing sheet with id=26, first strand: chain 'o' and resid 17 through 18 Processing sheet with id=27, first strand: chain 'q' and resid 17 through 18 Processing sheet with id=28, first strand: chain 's' and resid 17 through 18 Processing sheet with id=29, first strand: chain 'u' and resid 17 through 18 Processing sheet with id=30, first strand: chain 'w' and resid 17 through 18 Processing sheet with id=31, first strand: chain 'y' and resid 17 through 18 Processing sheet with id=32, first strand: chain 'AA' and resid 17 through 18 Processing sheet with id=33, first strand: chain 'AC' and resid 17 through 18 Processing sheet with id=34, first strand: chain 'AE' and resid 17 through 18 Processing sheet with id=35, first strand: chain 'AG' and resid 17 through 18 Processing sheet with id=36, first strand: chain 'AI' and resid 17 through 18 Processing sheet with id=37, first strand: chain 'AK' and resid 17 through 18 Processing sheet with id=38, first strand: chain 'AM' and resid 17 through 18 Processing sheet with id=39, first strand: chain 'AO' and resid 17 through 18 Processing sheet with id=40, first strand: chain 'AQ' and resid 17 through 18 2720 hydrogen bonds defined for protein. 7560 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: 15.35 Time building geometry restraints manager: 12.20 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: 16683 1.34 - 1.45: 7642 1.45 - 1.57: 27755 1.57 - 1.68: 200 1.68 - 1.80: 40 Bond restraints: 52320 Sorted by residual: bond pdb=" C ACEAQ 0 " pdb=" O ACEAQ 0 " ideal model delta sigma weight residual 1.199 1.229 -0.030 2.00e-02 2.50e+03 2.31e+00 bond pdb=" C ACE a 0 " pdb=" O ACE a 0 " ideal model delta sigma weight residual 1.199 1.229 -0.030 2.00e-02 2.50e+03 2.30e+00 bond pdb=" C ACE F 0 " pdb=" O ACE F 0 " ideal model delta sigma weight residual 1.199 1.229 -0.030 2.00e-02 2.50e+03 2.29e+00 bond pdb=" C ACE 6 0 " pdb=" O ACE 6 0 " ideal model delta sigma weight residual 1.199 1.229 -0.030 2.00e-02 2.50e+03 2.28e+00 bond pdb=" C ACEAG 0 " pdb=" O ACEAG 0 " ideal model delta sigma weight residual 1.199 1.229 -0.030 2.00e-02 2.50e+03 2.28e+00 ... (remaining 52315 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 68291 1.29 - 2.58: 2995 2.58 - 3.86: 554 3.86 - 5.15: 80 5.15 - 6.44: 80 Bond angle restraints: 72000 Sorted by residual: angle pdb=" C PRO 6 54 " pdb=" N SER 6 55 " pdb=" CA SER 6 55 " ideal model delta sigma weight residual 121.80 116.10 5.70 2.44e+00 1.68e-01 5.47e+00 angle pdb=" C PROAE 54 " pdb=" N SERAE 55 " pdb=" CA SERAE 55 " ideal model delta sigma weight residual 121.80 116.10 5.70 2.44e+00 1.68e-01 5.45e+00 angle pdb=" C PRO B 54 " pdb=" N SER B 55 " pdb=" CA SER B 55 " ideal model delta sigma weight residual 121.80 116.11 5.69 2.44e+00 1.68e-01 5.44e+00 angle pdb=" C PRO a 54 " pdb=" N SER a 55 " pdb=" CA SER a 55 " ideal model delta sigma weight residual 121.80 116.11 5.69 2.44e+00 1.68e-01 5.43e+00 angle pdb=" C PRO k 54 " pdb=" N SER k 55 " pdb=" CA SER k 55 " ideal model delta sigma weight residual 121.80 116.12 5.68 2.44e+00 1.68e-01 5.43e+00 ... (remaining 71995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.45: 27680 14.45 - 28.89: 2498 28.89 - 43.34: 404 43.34 - 57.78: 338 57.78 - 72.23: 200 Dihedral angle restraints: 31120 sinusoidal: 13040 harmonic: 18080 Sorted by residual: dihedral pdb=" CA ASP 0 66 " pdb=" C ASP 0 66 " pdb=" N PHE 0 67 " pdb=" CA PHE 0 67 " ideal model delta harmonic sigma weight residual 180.00 160.70 19.30 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA ASP W 66 " pdb=" C ASP W 66 " pdb=" N PHE W 67 " pdb=" CA PHE W 67 " ideal model delta harmonic sigma weight residual 180.00 160.70 19.30 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA ASP H 66 " pdb=" C ASP H 66 " pdb=" N PHE H 67 " pdb=" CA PHE H 67 " ideal model delta harmonic sigma weight residual 180.00 160.71 19.29 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 31117 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 5769 0.039 - 0.079: 2271 0.079 - 0.118: 435 0.118 - 0.157: 5 0.157 - 0.196: 40 Chirality restraints: 8520 Sorted by residual: chirality pdb=" CA SER 0 55 " pdb=" N SER 0 55 " pdb=" C SER 0 55 " pdb=" CB SER 0 55 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.63e-01 chirality pdb=" CA SERAI 55 " pdb=" N SERAI 55 " pdb=" C SERAI 55 " pdb=" CB SERAI 55 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.60e-01 chirality pdb=" CA SER u 55 " pdb=" N SER u 55 " pdb=" C SER u 55 " pdb=" CB SER u 55 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.60e-01 ... (remaining 8517 not shown) Planarity restraints: 8920 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASNAC 101 " -0.025 5.00e-02 4.00e+02 3.84e-02 2.36e+00 pdb=" N PROAC 102 " 0.066 5.00e-02 4.00e+02 pdb=" CA PROAC 102 " -0.020 5.00e-02 4.00e+02 pdb=" CD PROAC 102 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN i 101 " -0.025 5.00e-02 4.00e+02 3.84e-02 2.35e+00 pdb=" N PRO i 102 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO i 102 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO i 102 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN o 101 " 0.025 5.00e-02 4.00e+02 3.83e-02 2.35e+00 pdb=" N PRO o 102 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO o 102 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO o 102 " 0.021 5.00e-02 4.00e+02 ... (remaining 8917 not shown) Histogram of nonbonded interaction distances: 0.35 - 1.26: 109 1.26 - 2.17: 187 2.17 - 3.08: 41689 3.08 - 3.99: 174797 3.99 - 4.90: 304030 Warning: very small nonbonded interaction distances. Nonbonded interactions: 520812 Sorted by model distance: nonbonded pdb=" O3' A C 6 " pdb=" OP1 G E 4 " model vdw 0.351 3.040 nonbonded pdb=" O3' A v 6 " pdb=" OP1 G x 4 " model vdw 0.351 3.040 nonbonded pdb=" O3' AAJ 6 " pdb=" OP1 GAL 4 " model vdw 0.352 3.040 nonbonded pdb=" O3' A h 6 " pdb=" OP1 G j 4 " model vdw 0.352 3.040 nonbonded pdb=" O3' A Q 6 " pdb=" OP1 G T 4 " model vdw 0.352 3.040 ... (remaining 520807 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '0' selection = chain '2' selection = chain '4' selection = chain '6' selection = chain '8' selection = chain 'A' selection = chain 'AA' selection = chain 'AC' selection = chain 'AE' selection = chain 'AG' selection = chain 'AI' selection = chain 'AK' selection = chain 'AM' selection = chain 'AO' selection = chain 'AQ' selection = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'Y' selection = chain 'a' selection = chain 'c' selection = chain 'e' selection = chain 'g' selection = chain 'i' selection = chain 'k' selection = chain 'm' selection = chain 'o' selection = chain 'q' selection = chain 's' selection = chain 'u' selection = chain 'w' selection = chain 'y' } ncs_group { reference = chain '1' selection = chain '3' selection = chain '5' selection = chain '7' selection = chain '9' selection = chain 'AB' selection = chain 'AD' selection = chain 'AF' selection = chain 'AH' selection = chain 'AJ' selection = chain 'AL' selection = chain 'AN' selection = chain 'AP' selection = chain 'AR' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'Z' selection = chain 'b' selection = chain 'd' selection = chain 'f' selection = chain 'h' selection = chain 'j' selection = chain 'l' selection = chain 'n' selection = chain 'p' selection = chain 'r' selection = chain 't' selection = chain 'v' selection = chain 'x' selection = chain 'z' } 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 individual isotropic 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: 4.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.580 Check model and map are aligned: 0.310 Set scattering table: 0.370 Process input model: 82.460 Find NCS groups from input model: 1.840 Set up NCS constraints: 0.610 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 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 0.030 52320 Z= 0.248 Angle : 0.646 6.439 72000 Z= 0.364 Chirality : 0.041 0.196 8520 Planarity : 0.005 0.038 8920 Dihedral : 13.897 72.230 19280 Min Nonbonded Distance : 0.351 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.10), residues: 6040 helix: 0.38 (0.08), residues: 3440 sheet: None (None), residues: 0 loop : -0.96 (0.10), residues: 2600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP a 17 PHE 0.010 0.002 PHE B 35 TYR 0.013 0.002 TYRAI 72 ARG 0.004 0.001 ARGAO 122 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 894 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 894 time to evaluate : 4.499 Fit side-chains REVERT: F 72 TYR cc_start: 0.8443 (m-80) cc_final: 0.8110 (m-80) REVERT: 2 79 LEU cc_start: 0.8597 (mt) cc_final: 0.8332 (mt) REVERT: 4 145 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8185 (mt-10) REVERT: 8 128 LEU cc_start: 0.8229 (tp) cc_final: 0.7914 (mt) REVERT: i 128 LEU cc_start: 0.8258 (tp) cc_final: 0.7832 (mp) REVERT: q 84 LEU cc_start: 0.8805 (mt) cc_final: 0.8589 (mt) outliers start: 0 outliers final: 2 residues processed: 894 average time/residue: 1.2520 time to fit residues: 1439.7505 Evaluate side-chains 734 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 732 time to evaluate : 4.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain u residue 133 ILE Chi-restraints excluded: chain AG residue 133 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 506 optimal weight: 4.9990 chunk 454 optimal weight: 0.8980 chunk 252 optimal weight: 0.4980 chunk 155 optimal weight: 2.9990 chunk 306 optimal weight: 40.0000 chunk 242 optimal weight: 1.9990 chunk 470 optimal weight: 3.9990 chunk 181 optimal weight: 0.3980 chunk 285 optimal weight: 4.9990 chunk 350 optimal weight: 8.9990 chunk 544 optimal weight: 0.0670 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN B 73 ASN D 73 ASN F 39 GLN F 73 ASN H 73 ASN J 73 ASN L 73 ASN ** N 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 73 ASN P 29 ASN P 73 ASN S 73 ASN U 39 GLN U 73 ASN W 73 ASN Y 29 ASN Y 39 GLN Y 57 GLN Y 73 ASN 0 73 ASN 2 73 ASN 4 29 ASN 4 39 GLN 4 73 ASN 6 29 ASN 6 39 GLN 6 73 ASN ** 8 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 73 ASN a 29 ASN a 33 ASN a 73 ASN c 29 ASN c 73 ASN e 29 ASN e 39 GLN e 73 ASN g 29 ASN g 33 ASN g 39 GLN g 73 ASN g 101 ASN i 73 ASN k 39 GLN k 57 GLN k 73 ASN m 29 ASN m 73 ASN o 29 ASN o 73 ASN q 33 ASN q 73 ASN s 73 ASN u 33 ASN u 73 ASN u 126 ASN w 29 ASN w 73 ASN y 29 ASN y 73 ASN AA 29 ASN AA 73 ASN AA 126 ASN AC 29 ASN AC 73 ASN AE 73 ASN AG 73 ASN AI 29 ASN AI 73 ASN AI 126 ASN AK 33 ASN AK 73 ASN AM 29 ASN AM 73 ASN AO 29 ASN AO 73 ASN AQ 29 ASN AQ 73 ASN AQ 127 ASN Total number of N/Q/H flips: 78 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.253 52320 Z= 0.478 Angle : 1.408 43.608 72000 Z= 0.739 Chirality : 0.071 0.862 8520 Planarity : 0.017 0.441 8920 Dihedral : 11.427 79.497 8324 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.48 % Allowed : 5.12 % Favored : 94.40 % Rotamer: Outliers : 2.91 % Allowed : 7.15 % Favored : 89.94 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.09), residues: 6040 helix: -1.20 (0.08), residues: 3440 sheet: None (None), residues: 0 loop : -1.75 (0.11), residues: 2600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.117 0.010 TRP u 17 PHE 0.124 0.008 PHEAC 10 TYR 0.180 0.010 TYR H 139 ARG 0.092 0.003 ARG 2 112 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1005 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 848 time to evaluate : 4.426 Fit side-chains REVERT: F 53 LYS cc_start: 0.8326 (mmtm) cc_final: 0.8122 (mptt) REVERT: 2 79 LEU cc_start: 0.8567 (mt) cc_final: 0.8313 (mt) REVERT: 6 146 SER cc_start: 0.8078 (OUTLIER) cc_final: 0.7761 (p) REVERT: 8 128 LEU cc_start: 0.8159 (tp) cc_final: 0.7786 (mt) REVERT: i 128 LEU cc_start: 0.8262 (tp) cc_final: 0.7855 (mp) REVERT: q 77 ASP cc_start: 0.7916 (OUTLIER) cc_final: 0.7654 (t0) REVERT: q 84 LEU cc_start: 0.8854 (mt) cc_final: 0.8652 (mt) REVERT: y 132 LEU cc_start: 0.8613 (mt) cc_final: 0.8331 (mm) outliers start: 157 outliers final: 46 residues processed: 921 average time/residue: 1.2572 time to fit residues: 1487.0635 Evaluate side-chains 799 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 751 time to evaluate : 4.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain F residue 146 SER Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 138 SER Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 142 SER Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain U residue 129 ILE Chi-restraints excluded: chain 0 residue 58 VAL Chi-restraints excluded: chain 0 residue 77 ASP Chi-restraints excluded: chain 0 residue 146 SER Chi-restraints excluded: chain 2 residue 6 THR Chi-restraints excluded: chain 2 residue 93 ILE Chi-restraints excluded: chain 4 residue 58 VAL Chi-restraints excluded: chain 4 residue 138 SER Chi-restraints excluded: chain 6 residue 133 ILE Chi-restraints excluded: chain 6 residue 146 SER Chi-restraints excluded: chain 8 residue 50 GLU Chi-restraints excluded: chain 8 residue 58 VAL Chi-restraints excluded: chain 8 residue 133 ILE Chi-restraints excluded: chain a residue 6 THR Chi-restraints excluded: chain c residue 58 VAL Chi-restraints excluded: chain g residue 133 ILE Chi-restraints excluded: chain g residue 142 SER Chi-restraints excluded: chain i residue 50 GLU Chi-restraints excluded: chain i residue 58 VAL Chi-restraints excluded: chain i residue 142 SER Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain q residue 77 ASP Chi-restraints excluded: chain q residue 129 ILE Chi-restraints excluded: chain q residue 138 SER Chi-restraints excluded: chain s residue 50 GLU Chi-restraints excluded: chain y residue 6 THR Chi-restraints excluded: chain y residue 68 LYS Chi-restraints excluded: chain y residue 142 SER Chi-restraints excluded: chain AC residue 57 GLN Chi-restraints excluded: chain AC residue 133 ILE Chi-restraints excluded: chain AG residue 6 THR Chi-restraints excluded: chain AG residue 21 ILE Chi-restraints excluded: chain AG residue 133 ILE Chi-restraints excluded: chain AK residue 81 THR Chi-restraints excluded: chain AQ residue 77 ASP Chi-restraints excluded: chain AQ residue 142 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 302 optimal weight: 9.9990 chunk 169 optimal weight: 20.0000 chunk 453 optimal weight: 0.2980 chunk 371 optimal weight: 8.9990 chunk 150 optimal weight: 30.0000 chunk 545 optimal weight: 7.9990 chunk 589 optimal weight: 9.9990 chunk 486 optimal weight: 9.9990 chunk 541 optimal weight: 6.9990 chunk 186 optimal weight: 10.0000 chunk 437 optimal weight: 6.9990 overall best weight: 6.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 29 ASN L 29 ASN N 29 ASN P 29 ASN S 29 ASN S 33 ASN U 29 ASN W 29 ASN 0 29 ASN 4 29 ASN 8 29 ASN a 29 ASN c 29 ASN e 29 ASN g 29 ASN g 33 ASN i 29 ASN k 29 ASN k 57 GLN m 29 ASN s 29 ASN u 29 ASN u 57 GLN w 29 ASN y 29 ASN AC 29 ASN AC 126 ASN AO 29 ASN AQ 29 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 52320 Z= 0.261 Angle : 0.661 6.654 72000 Z= 0.355 Chirality : 0.043 0.211 8520 Planarity : 0.007 0.077 8920 Dihedral : 10.966 64.009 8322 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.89 % Allowed : 7.57 % Favored : 90.54 % 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: 0.29 (0.10), residues: 6040 helix: 0.86 (0.08), residues: 3440 sheet: None (None), residues: 0 loop : -0.65 (0.12), residues: 2600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 52 PHE 0.020 0.002 PHE W 67 TYR 0.027 0.002 TYRAA 72 ARG 0.010 0.001 ARG c 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 886 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 784 time to evaluate : 4.557 Fit side-chains REVERT: B 68 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8633 (mttm) REVERT: D 50 GLU cc_start: 0.8111 (tt0) cc_final: 0.7906 (mt-10) REVERT: 2 79 LEU cc_start: 0.8621 (mt) cc_final: 0.8416 (mt) REVERT: s 57 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7566 (mt0) REVERT: u 68 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8228 (mmpt) REVERT: AA 53 LYS cc_start: 0.8166 (mmtt) cc_final: 0.7936 (mptt) outliers start: 102 outliers final: 44 residues processed: 821 average time/residue: 1.3464 time to fit residues: 1403.6268 Evaluate side-chains 785 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 738 time to evaluate : 4.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain F residue 146 SER Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain J residue 142 SER Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain S residue 133 ILE Chi-restraints excluded: chain S residue 142 SER Chi-restraints excluded: chain U residue 21 ILE Chi-restraints excluded: chain U residue 129 ILE Chi-restraints excluded: chain 0 residue 58 VAL Chi-restraints excluded: chain 4 residue 6 THR Chi-restraints excluded: chain 4 residue 21 ILE Chi-restraints excluded: chain 4 residue 129 ILE Chi-restraints excluded: chain 6 residue 93 ILE Chi-restraints excluded: chain 8 residue 129 ILE Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 138 SER Chi-restraints excluded: chain e residue 58 VAL Chi-restraints excluded: chain g residue 142 SER Chi-restraints excluded: chain i residue 142 SER Chi-restraints excluded: chain m residue 6 THR Chi-restraints excluded: chain m residue 68 LYS Chi-restraints excluded: chain o residue 6 THR Chi-restraints excluded: chain q residue 6 THR Chi-restraints excluded: chain q residue 129 ILE Chi-restraints excluded: chain s residue 6 THR Chi-restraints excluded: chain s residue 57 GLN Chi-restraints excluded: chain s residue 128 LEU Chi-restraints excluded: chain s residue 130 VAL Chi-restraints excluded: chain s residue 142 SER Chi-restraints excluded: chain u residue 68 LYS Chi-restraints excluded: chain u residue 133 ILE Chi-restraints excluded: chain y residue 142 SER Chi-restraints excluded: chain AA residue 129 ILE Chi-restraints excluded: chain AC residue 58 VAL Chi-restraints excluded: chain AC residue 133 ILE Chi-restraints excluded: chain AG residue 6 THR Chi-restraints excluded: chain AG residue 130 VAL Chi-restraints excluded: chain AK residue 6 THR Chi-restraints excluded: chain AM residue 129 ILE Chi-restraints excluded: chain AQ residue 133 ILE Chi-restraints excluded: chain AQ residue 142 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 539 optimal weight: 7.9990 chunk 410 optimal weight: 0.3980 chunk 283 optimal weight: 4.9990 chunk 60 optimal weight: 30.0000 chunk 260 optimal weight: 9.9990 chunk 366 optimal weight: 9.9990 chunk 547 optimal weight: 0.8980 chunk 579 optimal weight: 6.9990 chunk 286 optimal weight: 20.0000 chunk 519 optimal weight: 0.0970 chunk 156 optimal weight: 9.9990 overall best weight: 2.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 29 ASN H 29 ASN N 29 ASN P 29 ASN Y 29 ASN 0 29 ASN 4 29 ASN 6 29 ASN 8 29 ASN a 29 ASN e 29 ASN g 29 ASN g 101 ASN i 29 ASN k 29 ASN k 57 GLN m 29 ASN o 29 ASN o 57 GLN q 29 ASN u 29 ASN u 57 GLN w 29 ASN y 29 ASN AI 29 ASN AM 29 ASN AQ 29 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 52320 Z= 0.159 Angle : 0.538 6.579 72000 Z= 0.285 Chirality : 0.038 0.221 8520 Planarity : 0.005 0.045 8920 Dihedral : 10.581 63.860 8320 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.39 % Allowed : 9.02 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.11), residues: 6040 helix: 1.63 (0.09), residues: 3440 sheet: None (None), residues: 0 loop : -0.17 (0.12), residues: 2600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 52 PHE 0.012 0.001 PHE W 67 TYR 0.020 0.002 TYRAA 72 ARG 0.007 0.000 ARGAI 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 859 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 784 time to evaluate : 4.576 Fit side-chains REVERT: 2 79 LEU cc_start: 0.8622 (mt) cc_final: 0.8414 (mt) REVERT: s 57 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7604 (mt0) REVERT: w 6 THR cc_start: 0.8283 (OUTLIER) cc_final: 0.7950 (p) REVERT: AA 53 LYS cc_start: 0.7997 (mmtt) cc_final: 0.7727 (mptt) outliers start: 75 outliers final: 37 residues processed: 807 average time/residue: 1.3805 time to fit residues: 1409.8701 Evaluate side-chains 780 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 741 time to evaluate : 4.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain J residue 142 SER Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 142 SER Chi-restraints excluded: chain S residue 21 ILE Chi-restraints excluded: chain S residue 133 ILE Chi-restraints excluded: chain S residue 142 SER Chi-restraints excluded: chain U residue 129 ILE Chi-restraints excluded: chain 4 residue 6 THR Chi-restraints excluded: chain 4 residue 129 ILE Chi-restraints excluded: chain 4 residue 142 SER Chi-restraints excluded: chain a residue 138 SER Chi-restraints excluded: chain c residue 129 ILE Chi-restraints excluded: chain g residue 133 ILE Chi-restraints excluded: chain g residue 142 SER Chi-restraints excluded: chain i residue 142 SER Chi-restraints excluded: chain m residue 6 THR Chi-restraints excluded: chain m residue 68 LYS Chi-restraints excluded: chain o residue 6 THR Chi-restraints excluded: chain q residue 129 ILE Chi-restraints excluded: chain s residue 6 THR Chi-restraints excluded: chain s residue 57 GLN Chi-restraints excluded: chain s residue 130 VAL Chi-restraints excluded: chain s residue 142 SER Chi-restraints excluded: chain u residue 129 ILE Chi-restraints excluded: chain u residue 133 ILE Chi-restraints excluded: chain w residue 6 THR Chi-restraints excluded: chain w residue 94 ILE Chi-restraints excluded: chain y residue 142 SER Chi-restraints excluded: chain AA residue 6 THR Chi-restraints excluded: chain AC residue 58 VAL Chi-restraints excluded: chain AG residue 6 THR Chi-restraints excluded: chain AG residue 130 VAL Chi-restraints excluded: chain AK residue 6 THR Chi-restraints excluded: chain AK residue 94 ILE Chi-restraints excluded: chain AO residue 6 THR Chi-restraints excluded: chain AQ residue 133 ILE Chi-restraints excluded: chain AQ residue 142 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 483 optimal weight: 6.9990 chunk 329 optimal weight: 30.0000 chunk 8 optimal weight: 20.0000 chunk 431 optimal weight: 5.9990 chunk 239 optimal weight: 20.0000 chunk 494 optimal weight: 4.9990 chunk 400 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 296 optimal weight: 30.0000 chunk 520 optimal weight: 9.9990 chunk 146 optimal weight: 30.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 29 ASN N 29 ASN P 29 ASN U 33 ASN W 29 ASN 0 29 ASN 4 29 ASN 6 29 ASN 8 29 ASN a 29 ASN a 57 GLN c 29 ASN e 29 ASN g 29 ASN g 101 ASN i 29 ASN k 29 ASN k 57 GLN m 29 ASN o 29 ASN q 29 ASN u 29 ASN u 33 ASN u 57 GLN u 127 ASN w 29 ASN y 29 ASN AI 29 ASN AM 29 ASN AQ 29 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 52320 Z= 0.267 Angle : 0.644 6.184 72000 Z= 0.347 Chirality : 0.042 0.168 8520 Planarity : 0.006 0.063 8920 Dihedral : 10.912 63.992 8320 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.37 % Allowed : 8.56 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.10), residues: 6040 helix: 1.52 (0.08), residues: 3440 sheet: None (None), residues: 0 loop : -0.08 (0.12), residues: 2600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP S 52 PHE 0.016 0.002 PHEAM 35 TYR 0.027 0.002 TYR a 72 ARG 0.009 0.001 ARGAI 134 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 901 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 773 time to evaluate : 4.523 Fit side-chains REVERT: L 57 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.7627 (mt0) REVERT: P 46 ARG cc_start: 0.8702 (mtt180) cc_final: 0.8459 (mtt180) REVERT: S 68 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8630 (mttm) REVERT: 0 57 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.7726 (mt0) REVERT: g 57 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7720 (mt0) REVERT: s 57 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.7600 (mt0) REVERT: w 6 THR cc_start: 0.8402 (OUTLIER) cc_final: 0.8127 (p) REVERT: AA 53 LYS cc_start: 0.8148 (mmtt) cc_final: 0.7885 (mptt) REVERT: AA 97 GLU cc_start: 0.8100 (mp0) cc_final: 0.7720 (mp0) REVERT: AG 57 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7502 (mt0) REVERT: AO 57 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7535 (mt0) REVERT: AO 68 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8673 (mttp) outliers start: 128 outliers final: 64 residues processed: 825 average time/residue: 1.3504 time to fit residues: 1413.7616 Evaluate side-chains 823 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 750 time to evaluate : 4.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain F residue 146 SER Chi-restraints excluded: chain J residue 142 SER Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 57 GLN Chi-restraints excluded: chain L residue 142 SER Chi-restraints excluded: chain N residue 142 SER Chi-restraints excluded: chain P residue 108 LEU Chi-restraints excluded: chain S residue 21 ILE Chi-restraints excluded: chain S residue 68 LYS Chi-restraints excluded: chain S residue 133 ILE Chi-restraints excluded: chain S residue 142 SER Chi-restraints excluded: chain U residue 21 ILE Chi-restraints excluded: chain U residue 129 ILE Chi-restraints excluded: chain W residue 129 ILE Chi-restraints excluded: chain W residue 138 SER Chi-restraints excluded: chain 0 residue 57 GLN Chi-restraints excluded: chain 4 residue 6 THR Chi-restraints excluded: chain 4 residue 21 ILE Chi-restraints excluded: chain 4 residue 129 ILE Chi-restraints excluded: chain 4 residue 142 SER Chi-restraints excluded: chain 6 residue 93 ILE Chi-restraints excluded: chain 8 residue 129 ILE Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 138 SER Chi-restraints excluded: chain c residue 129 ILE Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain e residue 142 SER Chi-restraints excluded: chain g residue 57 GLN Chi-restraints excluded: chain g residue 142 SER Chi-restraints excluded: chain i residue 142 SER Chi-restraints excluded: chain k residue 93 ILE Chi-restraints excluded: chain k residue 142 SER Chi-restraints excluded: chain m residue 6 THR Chi-restraints excluded: chain m residue 21 ILE Chi-restraints excluded: chain m residue 68 LYS Chi-restraints excluded: chain o residue 6 THR Chi-restraints excluded: chain o residue 55 SER Chi-restraints excluded: chain q residue 6 THR Chi-restraints excluded: chain q residue 129 ILE Chi-restraints excluded: chain s residue 6 THR Chi-restraints excluded: chain s residue 57 GLN Chi-restraints excluded: chain s residue 130 VAL Chi-restraints excluded: chain s residue 142 SER Chi-restraints excluded: chain u residue 146 SER Chi-restraints excluded: chain w residue 6 THR Chi-restraints excluded: chain w residue 94 ILE Chi-restraints excluded: chain w residue 142 SER Chi-restraints excluded: chain y residue 129 ILE Chi-restraints excluded: chain y residue 142 SER Chi-restraints excluded: chain AA residue 6 THR Chi-restraints excluded: chain AA residue 129 ILE Chi-restraints excluded: chain AA residue 146 SER Chi-restraints excluded: chain AC residue 58 VAL Chi-restraints excluded: chain AC residue 133 ILE Chi-restraints excluded: chain AE residue 94 ILE Chi-restraints excluded: chain AG residue 6 THR Chi-restraints excluded: chain AG residue 57 GLN Chi-restraints excluded: chain AG residue 129 ILE Chi-restraints excluded: chain AG residue 130 VAL Chi-restraints excluded: chain AI residue 129 ILE Chi-restraints excluded: chain AK residue 6 THR Chi-restraints excluded: chain AK residue 94 ILE Chi-restraints excluded: chain AK residue 129 ILE Chi-restraints excluded: chain AM residue 108 LEU Chi-restraints excluded: chain AM residue 129 ILE Chi-restraints excluded: chain AO residue 6 THR Chi-restraints excluded: chain AO residue 57 GLN Chi-restraints excluded: chain AO residue 68 LYS Chi-restraints excluded: chain AQ residue 129 ILE Chi-restraints excluded: chain AQ residue 133 ILE Chi-restraints excluded: chain AQ residue 142 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 195 optimal weight: 30.0000 chunk 522 optimal weight: 10.0000 chunk 114 optimal weight: 5.9990 chunk 340 optimal weight: 9.9990 chunk 143 optimal weight: 20.0000 chunk 580 optimal weight: 0.0370 chunk 481 optimal weight: 10.0000 chunk 268 optimal weight: 6.9990 chunk 48 optimal weight: 7.9990 chunk 192 optimal weight: 0.9980 chunk 304 optimal weight: 9.9990 overall best weight: 4.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 29 ASN L 29 ASN N 29 ASN S 29 ASN W 29 ASN 4 29 ASN 6 29 ASN 8 29 ASN a 29 ASN c 29 ASN e 29 ASN g 29 ASN g 101 ASN i 29 ASN k 29 ASN k 57 GLN m 29 ASN o 29 ASN q 29 ASN u 29 ASN u 57 GLN w 29 ASN y 29 ASN AM 29 ASN AQ 29 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 52320 Z= 0.199 Angle : 0.579 6.353 72000 Z= 0.310 Chirality : 0.040 0.187 8520 Planarity : 0.005 0.049 8920 Dihedral : 10.765 63.900 8320 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.39 % Allowed : 8.41 % Favored : 89.20 % 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: 1.43 (0.11), residues: 6040 helix: 1.68 (0.09), residues: 3440 sheet: None (None), residues: 0 loop : 0.03 (0.12), residues: 2600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 52 PHE 0.012 0.001 PHEAI 35 TYR 0.022 0.002 TYR a 72 ARG 0.007 0.001 ARGAI 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 886 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 757 time to evaluate : 4.445 Fit side-chains REVERT: L 57 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.7568 (mt0) REVERT: S 68 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8602 (mttm) REVERT: Y 57 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.7588 (mt0) REVERT: 0 57 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7695 (mt0) REVERT: g 57 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7674 (mt0) REVERT: s 57 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.7557 (mt0) REVERT: w 6 THR cc_start: 0.8374 (OUTLIER) cc_final: 0.8100 (p) REVERT: AG 57 GLN cc_start: 0.8130 (OUTLIER) cc_final: 0.7472 (mt0) REVERT: AO 57 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7497 (mt0) REVERT: AO 68 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8630 (mttp) outliers start: 129 outliers final: 66 residues processed: 815 average time/residue: 1.3566 time to fit residues: 1409.3255 Evaluate side-chains 823 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 747 time to evaluate : 4.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain F residue 146 SER Chi-restraints excluded: chain J residue 142 SER Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 50 GLU Chi-restraints excluded: chain L residue 57 GLN Chi-restraints excluded: chain L residue 142 SER Chi-restraints excluded: chain S residue 68 LYS Chi-restraints excluded: chain S residue 129 ILE Chi-restraints excluded: chain S residue 133 ILE Chi-restraints excluded: chain S residue 142 SER Chi-restraints excluded: chain U residue 129 ILE Chi-restraints excluded: chain W residue 129 ILE Chi-restraints excluded: chain W residue 138 SER Chi-restraints excluded: chain W residue 142 SER Chi-restraints excluded: chain Y residue 57 GLN Chi-restraints excluded: chain Y residue 142 SER Chi-restraints excluded: chain Y residue 146 SER Chi-restraints excluded: chain 0 residue 57 GLN Chi-restraints excluded: chain 4 residue 6 THR Chi-restraints excluded: chain 4 residue 21 ILE Chi-restraints excluded: chain 4 residue 129 ILE Chi-restraints excluded: chain 4 residue 142 SER Chi-restraints excluded: chain 6 residue 93 ILE Chi-restraints excluded: chain 8 residue 129 ILE Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 138 SER Chi-restraints excluded: chain c residue 129 ILE Chi-restraints excluded: chain e residue 58 VAL Chi-restraints excluded: chain e residue 142 SER Chi-restraints excluded: chain g residue 57 GLN Chi-restraints excluded: chain g residue 142 SER Chi-restraints excluded: chain i residue 142 SER Chi-restraints excluded: chain k residue 93 ILE Chi-restraints excluded: chain k residue 142 SER Chi-restraints excluded: chain m residue 6 THR Chi-restraints excluded: chain m residue 21 ILE Chi-restraints excluded: chain m residue 68 LYS Chi-restraints excluded: chain o residue 6 THR Chi-restraints excluded: chain q residue 6 THR Chi-restraints excluded: chain q residue 129 ILE Chi-restraints excluded: chain s residue 6 THR Chi-restraints excluded: chain s residue 57 GLN Chi-restraints excluded: chain s residue 130 VAL Chi-restraints excluded: chain s residue 142 SER Chi-restraints excluded: chain u residue 133 ILE Chi-restraints excluded: chain u residue 146 SER Chi-restraints excluded: chain w residue 6 THR Chi-restraints excluded: chain w residue 94 ILE Chi-restraints excluded: chain w residue 142 SER Chi-restraints excluded: chain y residue 129 ILE Chi-restraints excluded: chain y residue 142 SER Chi-restraints excluded: chain AA residue 6 THR Chi-restraints excluded: chain AA residue 129 ILE Chi-restraints excluded: chain AC residue 58 VAL Chi-restraints excluded: chain AC residue 129 ILE Chi-restraints excluded: chain AC residue 133 ILE Chi-restraints excluded: chain AG residue 57 GLN Chi-restraints excluded: chain AG residue 129 ILE Chi-restraints excluded: chain AG residue 130 VAL Chi-restraints excluded: chain AI residue 129 ILE Chi-restraints excluded: chain AK residue 6 THR Chi-restraints excluded: chain AK residue 94 ILE Chi-restraints excluded: chain AK residue 129 ILE Chi-restraints excluded: chain AM residue 129 ILE Chi-restraints excluded: chain AO residue 6 THR Chi-restraints excluded: chain AO residue 57 GLN Chi-restraints excluded: chain AO residue 68 LYS Chi-restraints excluded: chain AQ residue 6 THR Chi-restraints excluded: chain AQ residue 129 ILE Chi-restraints excluded: chain AQ residue 133 ILE Chi-restraints excluded: chain AQ residue 142 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 559 optimal weight: 5.9990 chunk 65 optimal weight: 8.9990 chunk 330 optimal weight: 4.9990 chunk 423 optimal weight: 7.9990 chunk 328 optimal weight: 0.9990 chunk 488 optimal weight: 20.0000 chunk 324 optimal weight: 7.9990 chunk 578 optimal weight: 30.0000 chunk 361 optimal weight: 20.0000 chunk 352 optimal weight: 2.9990 chunk 266 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 29 ASN N 29 ASN S 29 ASN W 29 ASN 4 29 ASN 6 29 ASN 8 29 ASN a 29 ASN c 29 ASN e 29 ASN g 29 ASN g 101 ASN i 29 ASN k 29 ASN k 57 GLN m 29 ASN o 29 ASN q 29 ASN u 29 ASN u 57 GLN w 29 ASN y 29 ASN AM 29 ASN AQ 29 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 52320 Z= 0.205 Angle : 0.590 6.588 72000 Z= 0.316 Chirality : 0.040 0.202 8520 Planarity : 0.005 0.049 8920 Dihedral : 10.799 63.910 8320 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.28 % Allowed : 8.48 % Favored : 89.24 % 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: 1.47 (0.11), residues: 6040 helix: 1.69 (0.09), residues: 3440 sheet: None (None), residues: 0 loop : 0.09 (0.12), residues: 2600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP S 52 PHE 0.012 0.001 PHE W 67 TYR 0.023 0.002 TYR a 72 ARG 0.007 0.001 ARGAI 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 874 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 751 time to evaluate : 4.524 Fit side-chains REVERT: B 68 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8588 (mttm) REVERT: F 94 ILE cc_start: 0.8442 (tt) cc_final: 0.8156 (pp) REVERT: L 57 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.7552 (mt0) REVERT: S 68 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8600 (mttm) REVERT: Y 57 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7610 (mt0) REVERT: 0 57 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7704 (mt0) REVERT: 8 57 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7823 (mt0) REVERT: g 57 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7685 (mt0) REVERT: q 68 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8484 (mttm) REVERT: s 57 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.7575 (mt0) REVERT: w 6 THR cc_start: 0.8396 (OUTLIER) cc_final: 0.8118 (p) REVERT: AA 97 GLU cc_start: 0.8056 (mp0) cc_final: 0.7691 (mp0) REVERT: AC 57 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7730 (mt0) REVERT: AG 57 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7481 (mt0) REVERT: AO 57 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7502 (mt0) REVERT: AO 68 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8669 (mttp) outliers start: 123 outliers final: 76 residues processed: 802 average time/residue: 1.3456 time to fit residues: 1369.0641 Evaluate side-chains 833 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 743 time to evaluate : 4.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain F residue 146 SER Chi-restraints excluded: chain J residue 142 SER Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 50 GLU Chi-restraints excluded: chain L residue 57 GLN Chi-restraints excluded: chain L residue 142 SER Chi-restraints excluded: chain P residue 108 LEU Chi-restraints excluded: chain S residue 68 LYS Chi-restraints excluded: chain S residue 129 ILE Chi-restraints excluded: chain S residue 133 ILE Chi-restraints excluded: chain S residue 142 SER Chi-restraints excluded: chain U residue 129 ILE Chi-restraints excluded: chain W residue 129 ILE Chi-restraints excluded: chain W residue 138 SER Chi-restraints excluded: chain W residue 142 SER Chi-restraints excluded: chain Y residue 57 GLN Chi-restraints excluded: chain Y residue 142 SER Chi-restraints excluded: chain Y residue 146 SER Chi-restraints excluded: chain 0 residue 57 GLN Chi-restraints excluded: chain 4 residue 6 THR Chi-restraints excluded: chain 4 residue 21 ILE Chi-restraints excluded: chain 4 residue 129 ILE Chi-restraints excluded: chain 4 residue 142 SER Chi-restraints excluded: chain 6 residue 93 ILE Chi-restraints excluded: chain 8 residue 57 GLN Chi-restraints excluded: chain 8 residue 129 ILE Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 138 SER Chi-restraints excluded: chain c residue 129 ILE Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain e residue 58 VAL Chi-restraints excluded: chain e residue 142 SER Chi-restraints excluded: chain g residue 57 GLN Chi-restraints excluded: chain g residue 142 SER Chi-restraints excluded: chain i residue 142 SER Chi-restraints excluded: chain k residue 93 ILE Chi-restraints excluded: chain k residue 142 SER Chi-restraints excluded: chain m residue 6 THR Chi-restraints excluded: chain m residue 21 ILE Chi-restraints excluded: chain m residue 68 LYS Chi-restraints excluded: chain o residue 6 THR Chi-restraints excluded: chain q residue 6 THR Chi-restraints excluded: chain q residue 68 LYS Chi-restraints excluded: chain q residue 129 ILE Chi-restraints excluded: chain s residue 6 THR Chi-restraints excluded: chain s residue 57 GLN Chi-restraints excluded: chain s residue 130 VAL Chi-restraints excluded: chain s residue 142 SER Chi-restraints excluded: chain u residue 50 GLU Chi-restraints excluded: chain u residue 129 ILE Chi-restraints excluded: chain u residue 133 ILE Chi-restraints excluded: chain u residue 146 SER Chi-restraints excluded: chain w residue 6 THR Chi-restraints excluded: chain w residue 94 ILE Chi-restraints excluded: chain w residue 142 SER Chi-restraints excluded: chain y residue 6 THR Chi-restraints excluded: chain y residue 129 ILE Chi-restraints excluded: chain y residue 142 SER Chi-restraints excluded: chain AA residue 6 THR Chi-restraints excluded: chain AA residue 129 ILE Chi-restraints excluded: chain AA residue 146 SER Chi-restraints excluded: chain AC residue 57 GLN Chi-restraints excluded: chain AC residue 58 VAL Chi-restraints excluded: chain AC residue 129 ILE Chi-restraints excluded: chain AC residue 133 ILE Chi-restraints excluded: chain AG residue 57 GLN Chi-restraints excluded: chain AG residue 129 ILE Chi-restraints excluded: chain AG residue 130 VAL Chi-restraints excluded: chain AI residue 21 ILE Chi-restraints excluded: chain AI residue 129 ILE Chi-restraints excluded: chain AK residue 6 THR Chi-restraints excluded: chain AK residue 94 ILE Chi-restraints excluded: chain AK residue 129 ILE Chi-restraints excluded: chain AK residue 142 SER Chi-restraints excluded: chain AM residue 129 ILE Chi-restraints excluded: chain AO residue 6 THR Chi-restraints excluded: chain AO residue 57 GLN Chi-restraints excluded: chain AO residue 68 LYS Chi-restraints excluded: chain AQ residue 6 THR Chi-restraints excluded: chain AQ residue 68 LYS Chi-restraints excluded: chain AQ residue 129 ILE Chi-restraints excluded: chain AQ residue 142 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 357 optimal weight: 10.0000 chunk 230 optimal weight: 4.9990 chunk 345 optimal weight: 0.0980 chunk 174 optimal weight: 20.0000 chunk 113 optimal weight: 20.0000 chunk 112 optimal weight: 3.9990 chunk 367 optimal weight: 8.9990 chunk 393 optimal weight: 6.9990 chunk 285 optimal weight: 0.5980 chunk 53 optimal weight: 20.0000 chunk 454 optimal weight: 20.0000 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 29 ASN J 29 ASN L 29 ASN N 29 ASN S 29 ASN W 29 ASN 4 29 ASN 6 29 ASN 8 29 ASN a 29 ASN c 29 ASN e 29 ASN g 29 ASN g 101 ASN i 29 ASN k 29 ASN k 57 GLN m 29 ASN o 29 ASN q 29 ASN u 29 ASN u 57 GLN w 29 ASN y 29 ASN AM 29 ASN AQ 29 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 52320 Z= 0.172 Angle : 0.554 6.596 72000 Z= 0.294 Chirality : 0.039 0.188 8520 Planarity : 0.005 0.043 8920 Dihedral : 10.651 63.873 8320 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.80 % Allowed : 8.91 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.11), residues: 6040 helix: 1.85 (0.09), residues: 3440 sheet: None (None), residues: 0 loop : 0.17 (0.12), residues: 2600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 52 PHE 0.011 0.001 PHEAC 10 TYR 0.018 0.002 TYR F 72 ARG 0.007 0.000 ARGAI 134 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 851 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 754 time to evaluate : 4.490 Fit side-chains REVERT: F 94 ILE cc_start: 0.8386 (tt) cc_final: 0.8148 (pp) REVERT: H 57 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7624 (mt0) REVERT: S 68 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8566 (mttm) REVERT: Y 57 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7548 (mt0) REVERT: s 57 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.7504 (mt0) REVERT: w 6 THR cc_start: 0.8353 (OUTLIER) cc_final: 0.8078 (p) REVERT: AO 68 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8624 (mttp) outliers start: 97 outliers final: 62 residues processed: 794 average time/residue: 1.3724 time to fit residues: 1377.7411 Evaluate side-chains 816 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 748 time to evaluate : 4.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain F residue 146 SER Chi-restraints excluded: chain H residue 57 GLN Chi-restraints excluded: chain J residue 142 SER Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 50 GLU Chi-restraints excluded: chain L residue 142 SER Chi-restraints excluded: chain N residue 138 SER Chi-restraints excluded: chain S residue 68 LYS Chi-restraints excluded: chain S residue 133 ILE Chi-restraints excluded: chain U residue 21 ILE Chi-restraints excluded: chain U residue 129 ILE Chi-restraints excluded: chain W residue 129 ILE Chi-restraints excluded: chain W residue 138 SER Chi-restraints excluded: chain W residue 142 SER Chi-restraints excluded: chain Y residue 57 GLN Chi-restraints excluded: chain 4 residue 6 THR Chi-restraints excluded: chain 4 residue 21 ILE Chi-restraints excluded: chain 4 residue 129 ILE Chi-restraints excluded: chain 4 residue 142 SER Chi-restraints excluded: chain 8 residue 129 ILE Chi-restraints excluded: chain a residue 138 SER Chi-restraints excluded: chain c residue 129 ILE Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain e residue 142 SER Chi-restraints excluded: chain i residue 142 SER Chi-restraints excluded: chain m residue 6 THR Chi-restraints excluded: chain m residue 68 LYS Chi-restraints excluded: chain o residue 6 THR Chi-restraints excluded: chain q residue 6 THR Chi-restraints excluded: chain q residue 129 ILE Chi-restraints excluded: chain s residue 6 THR Chi-restraints excluded: chain s residue 57 GLN Chi-restraints excluded: chain s residue 130 VAL Chi-restraints excluded: chain s residue 142 SER Chi-restraints excluded: chain u residue 50 GLU Chi-restraints excluded: chain u residue 133 ILE Chi-restraints excluded: chain u residue 146 SER Chi-restraints excluded: chain w residue 6 THR Chi-restraints excluded: chain w residue 142 SER Chi-restraints excluded: chain y residue 6 THR Chi-restraints excluded: chain y residue 129 ILE Chi-restraints excluded: chain y residue 142 SER Chi-restraints excluded: chain AA residue 6 THR Chi-restraints excluded: chain AA residue 129 ILE Chi-restraints excluded: chain AA residue 142 SER Chi-restraints excluded: chain AA residue 146 SER Chi-restraints excluded: chain AC residue 58 VAL Chi-restraints excluded: chain AC residue 129 ILE Chi-restraints excluded: chain AC residue 133 ILE Chi-restraints excluded: chain AG residue 6 THR Chi-restraints excluded: chain AG residue 129 ILE Chi-restraints excluded: chain AG residue 130 VAL Chi-restraints excluded: chain AK residue 6 THR Chi-restraints excluded: chain AK residue 94 ILE Chi-restraints excluded: chain AK residue 129 ILE Chi-restraints excluded: chain AK residue 142 SER Chi-restraints excluded: chain AM residue 21 ILE Chi-restraints excluded: chain AM residue 129 ILE Chi-restraints excluded: chain AO residue 6 THR Chi-restraints excluded: chain AO residue 68 LYS Chi-restraints excluded: chain AQ residue 6 THR Chi-restraints excluded: chain AQ residue 129 ILE Chi-restraints excluded: chain AQ residue 142 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 526 optimal weight: 20.0000 chunk 554 optimal weight: 8.9990 chunk 505 optimal weight: 5.9990 chunk 538 optimal weight: 10.0000 chunk 553 optimal weight: 7.9990 chunk 324 optimal weight: 7.9990 chunk 234 optimal weight: 4.9990 chunk 423 optimal weight: 5.9990 chunk 165 optimal weight: 30.0000 chunk 486 optimal weight: 10.0000 chunk 509 optimal weight: 30.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 29 ASN N 29 ASN S 29 ASN W 29 ASN 4 29 ASN 6 29 ASN 8 29 ASN a 29 ASN c 29 ASN e 29 ASN g 29 ASN g 101 ASN i 29 ASN k 29 ASN k 57 GLN m 29 ASN o 29 ASN q 29 ASN u 29 ASN w 29 ASN y 29 ASN AM 29 ASN AQ 29 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 52320 Z= 0.259 Angle : 0.641 7.131 72000 Z= 0.345 Chirality : 0.042 0.205 8520 Planarity : 0.006 0.060 8920 Dihedral : 10.913 63.988 8320 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.89 % Allowed : 8.74 % Favored : 89.37 % 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: 1.41 (0.10), residues: 6040 helix: 1.60 (0.08), residues: 3440 sheet: None (None), residues: 0 loop : 0.13 (0.12), residues: 2600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 52 PHE 0.015 0.002 PHEAC 10 TYR 0.026 0.002 TYR a 72 ARG 0.010 0.001 ARG o 134 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 864 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 762 time to evaluate : 4.526 Fit side-chains REVERT: B 57 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7849 (mm110) REVERT: F 94 ILE cc_start: 0.8508 (tt) cc_final: 0.8210 (pp) REVERT: H 57 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7668 (mt0) REVERT: S 68 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8636 (mttm) REVERT: Y 57 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7662 (mt0) REVERT: s 57 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.7593 (mt0) REVERT: w 6 THR cc_start: 0.8437 (OUTLIER) cc_final: 0.8152 (p) REVERT: AA 97 GLU cc_start: 0.8104 (mp0) cc_final: 0.7754 (mp0) REVERT: AC 57 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.7757 (mt0) REVERT: AM 68 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8449 (mttp) REVERT: AO 68 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8705 (mttp) outliers start: 102 outliers final: 70 residues processed: 800 average time/residue: 1.4118 time to fit residues: 1427.1701 Evaluate side-chains 828 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 749 time to evaluate : 4.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain B residue 57 GLN Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain F residue 146 SER Chi-restraints excluded: chain H residue 57 GLN Chi-restraints excluded: chain J residue 142 SER Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 50 GLU Chi-restraints excluded: chain L residue 142 SER Chi-restraints excluded: chain N residue 138 SER Chi-restraints excluded: chain P residue 108 LEU Chi-restraints excluded: chain P residue 147 SER Chi-restraints excluded: chain S residue 68 LYS Chi-restraints excluded: chain S residue 133 ILE Chi-restraints excluded: chain U residue 21 ILE Chi-restraints excluded: chain U residue 129 ILE Chi-restraints excluded: chain W residue 129 ILE Chi-restraints excluded: chain W residue 138 SER Chi-restraints excluded: chain W residue 142 SER Chi-restraints excluded: chain Y residue 57 GLN Chi-restraints excluded: chain 4 residue 6 THR Chi-restraints excluded: chain 4 residue 21 ILE Chi-restraints excluded: chain 4 residue 129 ILE Chi-restraints excluded: chain 4 residue 142 SER Chi-restraints excluded: chain 8 residue 129 ILE Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 138 SER Chi-restraints excluded: chain c residue 129 ILE Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain e residue 58 VAL Chi-restraints excluded: chain e residue 142 SER Chi-restraints excluded: chain g residue 142 SER Chi-restraints excluded: chain i residue 142 SER Chi-restraints excluded: chain k residue 93 ILE Chi-restraints excluded: chain k residue 142 SER Chi-restraints excluded: chain m residue 6 THR Chi-restraints excluded: chain m residue 68 LYS Chi-restraints excluded: chain o residue 6 THR Chi-restraints excluded: chain q residue 6 THR Chi-restraints excluded: chain q residue 129 ILE Chi-restraints excluded: chain s residue 6 THR Chi-restraints excluded: chain s residue 57 GLN Chi-restraints excluded: chain s residue 130 VAL Chi-restraints excluded: chain s residue 142 SER Chi-restraints excluded: chain u residue 50 GLU Chi-restraints excluded: chain u residue 108 LEU Chi-restraints excluded: chain u residue 146 SER Chi-restraints excluded: chain w residue 6 THR Chi-restraints excluded: chain w residue 142 SER Chi-restraints excluded: chain y residue 6 THR Chi-restraints excluded: chain y residue 129 ILE Chi-restraints excluded: chain y residue 142 SER Chi-restraints excluded: chain AA residue 6 THR Chi-restraints excluded: chain AA residue 129 ILE Chi-restraints excluded: chain AA residue 142 SER Chi-restraints excluded: chain AA residue 146 SER Chi-restraints excluded: chain AC residue 57 GLN Chi-restraints excluded: chain AC residue 58 VAL Chi-restraints excluded: chain AC residue 133 ILE Chi-restraints excluded: chain AE residue 94 ILE Chi-restraints excluded: chain AE residue 108 LEU Chi-restraints excluded: chain AG residue 6 THR Chi-restraints excluded: chain AG residue 129 ILE Chi-restraints excluded: chain AG residue 130 VAL Chi-restraints excluded: chain AK residue 6 THR Chi-restraints excluded: chain AK residue 94 ILE Chi-restraints excluded: chain AK residue 129 ILE Chi-restraints excluded: chain AK residue 142 SER Chi-restraints excluded: chain AM residue 68 LYS Chi-restraints excluded: chain AM residue 129 ILE Chi-restraints excluded: chain AO residue 6 THR Chi-restraints excluded: chain AO residue 68 LYS Chi-restraints excluded: chain AQ residue 6 THR Chi-restraints excluded: chain AQ residue 68 LYS Chi-restraints excluded: chain AQ residue 129 ILE Chi-restraints excluded: chain AQ residue 142 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 537 optimal weight: 20.0000 chunk 353 optimal weight: 30.0000 chunk 569 optimal weight: 30.0000 chunk 347 optimal weight: 0.0870 chunk 270 optimal weight: 6.9990 chunk 396 optimal weight: 10.0000 chunk 597 optimal weight: 20.0000 chunk 550 optimal weight: 20.0000 chunk 475 optimal weight: 20.0000 chunk 49 optimal weight: 20.0000 chunk 367 optimal weight: 7.9990 overall best weight: 9.0170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 29 ASN L 29 ASN N 29 ASN S 29 ASN W 29 ASN 4 29 ASN 6 29 ASN 8 29 ASN a 29 ASN c 29 ASN e 29 ASN g 29 ASN i 29 ASN k 29 ASN k 57 GLN m 29 ASN o 29 ASN q 29 ASN u 29 ASN w 29 ASN y 29 ASN AM 29 ASN AQ 29 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 52320 Z= 0.327 Angle : 0.699 6.815 72000 Z= 0.378 Chirality : 0.045 0.214 8520 Planarity : 0.007 0.069 8920 Dihedral : 11.012 64.047 8320 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.78 % Allowed : 8.78 % Favored : 89.44 % 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: 1.20 (0.10), residues: 6040 helix: 1.42 (0.08), residues: 3440 sheet: None (None), residues: 0 loop : 0.05 (0.12), residues: 2600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP e 52 PHE 0.017 0.002 PHEAC 10 TYR 0.027 0.003 TYR a 72 ARG 0.015 0.001 ARG o 134 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 864 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 768 time to evaluate : 4.700 Fit side-chains REVERT: B 57 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7850 (mm110) REVERT: H 57 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7688 (mt0) REVERT: Y 57 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7676 (mt0) REVERT: i 128 LEU cc_start: 0.8581 (tp) cc_final: 0.8103 (mt) REVERT: s 57 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.7625 (mt0) REVERT: AA 97 GLU cc_start: 0.8133 (mp0) cc_final: 0.7788 (mp0) REVERT: AM 68 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8463 (mttp) REVERT: AO 68 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8705 (mttp) outliers start: 96 outliers final: 77 residues processed: 806 average time/residue: 1.3955 time to fit residues: 1423.3608 Evaluate side-chains 841 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 758 time to evaluate : 4.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain B residue 57 GLN Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain F residue 146 SER Chi-restraints excluded: chain H residue 57 GLN Chi-restraints excluded: chain J residue 142 SER Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 50 GLU Chi-restraints excluded: chain L residue 142 SER Chi-restraints excluded: chain N residue 138 SER Chi-restraints excluded: chain P residue 108 LEU Chi-restraints excluded: chain P residue 147 SER Chi-restraints excluded: chain S residue 129 ILE Chi-restraints excluded: chain S residue 133 ILE Chi-restraints excluded: chain U residue 21 ILE Chi-restraints excluded: chain U residue 129 ILE Chi-restraints excluded: chain W residue 129 ILE Chi-restraints excluded: chain W residue 138 SER Chi-restraints excluded: chain W residue 142 SER Chi-restraints excluded: chain Y residue 57 GLN Chi-restraints excluded: chain Y residue 146 SER Chi-restraints excluded: chain 4 residue 6 THR Chi-restraints excluded: chain 4 residue 21 ILE Chi-restraints excluded: chain 4 residue 129 ILE Chi-restraints excluded: chain 4 residue 142 SER Chi-restraints excluded: chain 6 residue 93 ILE Chi-restraints excluded: chain 8 residue 129 ILE Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain c residue 129 ILE Chi-restraints excluded: chain c residue 133 ILE Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain e residue 58 VAL Chi-restraints excluded: chain e residue 142 SER Chi-restraints excluded: chain g residue 142 SER Chi-restraints excluded: chain i residue 142 SER Chi-restraints excluded: chain k residue 6 THR Chi-restraints excluded: chain k residue 93 ILE Chi-restraints excluded: chain k residue 142 SER Chi-restraints excluded: chain m residue 6 THR Chi-restraints excluded: chain m residue 68 LYS Chi-restraints excluded: chain o residue 6 THR Chi-restraints excluded: chain o residue 93 ILE Chi-restraints excluded: chain q residue 6 THR Chi-restraints excluded: chain q residue 129 ILE Chi-restraints excluded: chain s residue 6 THR Chi-restraints excluded: chain s residue 57 GLN Chi-restraints excluded: chain s residue 130 VAL Chi-restraints excluded: chain s residue 142 SER Chi-restraints excluded: chain u residue 50 GLU Chi-restraints excluded: chain u residue 146 SER Chi-restraints excluded: chain w residue 6 THR Chi-restraints excluded: chain w residue 142 SER Chi-restraints excluded: chain y residue 6 THR Chi-restraints excluded: chain y residue 129 ILE Chi-restraints excluded: chain y residue 142 SER Chi-restraints excluded: chain AA residue 129 ILE Chi-restraints excluded: chain AA residue 142 SER Chi-restraints excluded: chain AA residue 146 SER Chi-restraints excluded: chain AC residue 58 VAL Chi-restraints excluded: chain AC residue 133 ILE Chi-restraints excluded: chain AE residue 94 ILE Chi-restraints excluded: chain AE residue 108 LEU Chi-restraints excluded: chain AG residue 6 THR Chi-restraints excluded: chain AG residue 129 ILE Chi-restraints excluded: chain AG residue 130 VAL Chi-restraints excluded: chain AI residue 129 ILE Chi-restraints excluded: chain AK residue 6 THR Chi-restraints excluded: chain AK residue 94 ILE Chi-restraints excluded: chain AK residue 129 ILE Chi-restraints excluded: chain AK residue 142 SER Chi-restraints excluded: chain AM residue 68 LYS Chi-restraints excluded: chain AM residue 129 ILE Chi-restraints excluded: chain AO residue 6 THR Chi-restraints excluded: chain AO residue 68 LYS Chi-restraints excluded: chain AQ residue 6 THR Chi-restraints excluded: chain AQ residue 68 LYS Chi-restraints excluded: chain AQ residue 129 ILE Chi-restraints excluded: chain AQ residue 142 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 291 optimal weight: 9.9990 chunk 378 optimal weight: 4.9990 chunk 507 optimal weight: 0.9990 chunk 145 optimal weight: 7.9990 chunk 438 optimal weight: 9.9990 chunk 70 optimal weight: 8.9990 chunk 132 optimal weight: 1.9990 chunk 476 optimal weight: 5.9990 chunk 199 optimal weight: 20.0000 chunk 489 optimal weight: 1.9990 chunk 60 optimal weight: 30.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 29 ASN N 29 ASN S 29 ASN W 29 ASN 4 29 ASN 6 29 ASN 8 29 ASN a 29 ASN c 29 ASN e 29 ASN g 29 ASN g 101 ASN i 29 ASN k 29 ASN k 57 GLN m 29 ASN o 29 ASN q 29 ASN u 29 ASN w 29 ASN y 29 ASN AM 29 ASN AQ 29 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.144369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.119771 restraints weight = 40219.627| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 0.75 r_work: 0.3182 rms_B_bonded: 1.15 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 1.90 restraints_weight: 0.2500 r_work: 0.2900 rms_B_bonded: 4.85 restraints_weight: 0.1250 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 52320 Z= 0.170 Angle : 0.556 7.137 72000 Z= 0.296 Chirality : 0.039 0.186 8520 Planarity : 0.005 0.042 8920 Dihedral : 10.672 63.865 8320 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.54 % Allowed : 9.13 % Favored : 89.33 % 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: 1.62 (0.11), residues: 6040 helix: 1.80 (0.09), residues: 3440 sheet: None (None), residues: 0 loop : 0.18 (0.12), residues: 2600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP e 52 PHE 0.012 0.001 PHEAC 10 TYR 0.018 0.002 TYR a 72 ARG 0.008 0.000 ARGAI 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21494.82 seconds wall clock time: 367 minutes 44.57 seconds (22064.57 seconds total)