Starting phenix.real_space_refine on Tue Sep 24 02:55:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ueg_26474/09_2024/7ueg_26474.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ueg_26474/09_2024/7ueg_26474.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ueg_26474/09_2024/7ueg_26474.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ueg_26474/09_2024/7ueg_26474.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ueg_26474/09_2024/7ueg_26474.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ueg_26474/09_2024/7ueg_26474.cif" } resolution = 4.0 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 ------------------------------------------------------------------------------- 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= 0.004 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 32040 2.51 5 N 7848 2.21 5 O 9972 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 102 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 49968 Number of models: 1 Model: "" Number of chains: 36 Chain: "G" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "H" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "I" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "J" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "K" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "L" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "M" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "N" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "O" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "P" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "Q" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "R" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "S" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "T" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "U" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "V" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "W" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "X" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "A" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "E" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "B" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "C" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "D" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "F" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "Y" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "Z" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "0" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "1" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "2" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "3" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "4" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "5" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "6" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "7" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "8" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "9" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1388 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Time building chain proxies: 22.23, per 1000 atoms: 0.44 Number of scatterers: 49968 At special positions: 0 Unit cell: (168.48, 169.56, 322.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 9972 8.00 N 7848 7.00 C 32040 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS G 101 " - pdb=" SG CYS G 167 " distance=2.04 Simple disulfide: pdb=" SG CYS H 101 " - pdb=" SG CYS H 167 " distance=2.03 Simple disulfide: pdb=" SG CYS I 101 " - pdb=" SG CYS I 167 " distance=2.03 Simple disulfide: pdb=" SG CYS J 101 " - pdb=" SG CYS J 167 " distance=2.04 Simple disulfide: pdb=" SG CYS K 101 " - pdb=" SG CYS K 167 " distance=2.04 Simple disulfide: pdb=" SG CYS L 101 " - pdb=" SG CYS L 167 " distance=2.03 Simple disulfide: pdb=" SG CYS M 101 " - pdb=" SG CYS M 167 " distance=2.04 Simple disulfide: pdb=" SG CYS N 101 " - pdb=" SG CYS N 167 " distance=2.03 Simple disulfide: pdb=" SG CYS O 101 " - pdb=" SG CYS O 167 " distance=2.03 Simple disulfide: pdb=" SG CYS P 101 " - pdb=" SG CYS P 167 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 101 " - pdb=" SG CYS Q 167 " distance=2.04 Simple disulfide: pdb=" SG CYS R 101 " - pdb=" SG CYS R 167 " distance=2.03 Simple disulfide: pdb=" SG CYS S 101 " - pdb=" SG CYS S 167 " distance=2.04 Simple disulfide: pdb=" SG CYS T 101 " - pdb=" SG CYS T 167 " distance=2.03 Simple disulfide: pdb=" SG CYS U 101 " - pdb=" SG CYS U 167 " distance=2.03 Simple disulfide: pdb=" SG CYS V 101 " - pdb=" SG CYS V 167 " distance=2.04 Simple disulfide: pdb=" SG CYS W 101 " - pdb=" SG CYS W 167 " distance=2.04 Simple disulfide: pdb=" SG CYS X 101 " - pdb=" SG CYS X 167 " distance=2.03 Simple disulfide: pdb=" SG CYS A 101 " - pdb=" SG CYS A 167 " distance=2.04 Simple disulfide: pdb=" SG CYS E 101 " - pdb=" SG CYS E 167 " distance=2.03 Simple disulfide: pdb=" SG CYS B 101 " - pdb=" SG CYS B 167 " distance=2.03 Simple disulfide: pdb=" SG CYS C 101 " - pdb=" SG CYS C 167 " distance=2.04 Simple disulfide: pdb=" SG CYS D 101 " - pdb=" SG CYS D 167 " distance=2.04 Simple disulfide: pdb=" SG CYS F 101 " - pdb=" SG CYS F 167 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 101 " - pdb=" SG CYS Y 167 " distance=2.04 Simple disulfide: pdb=" SG CYS Z 101 " - pdb=" SG CYS Z 167 " distance=2.03 Simple disulfide: pdb=" SG CYS 0 101 " - pdb=" SG CYS 0 167 " distance=2.03 Simple disulfide: pdb=" SG CYS 1 101 " - pdb=" SG CYS 1 167 " distance=2.04 Simple disulfide: pdb=" SG CYS 2 101 " - pdb=" SG CYS 2 167 " distance=2.04 Simple disulfide: pdb=" SG CYS 3 101 " - pdb=" SG CYS 3 167 " distance=2.03 Simple disulfide: pdb=" SG CYS 4 101 " - pdb=" SG CYS 4 167 " distance=2.03 Simple disulfide: pdb=" SG CYS 5 101 " - pdb=" SG CYS 5 167 " distance=2.03 Simple disulfide: pdb=" SG CYS 6 101 " - pdb=" SG CYS 6 167 " distance=2.03 Simple disulfide: pdb=" SG CYS 7 101 " - pdb=" SG CYS 7 167 " distance=2.04 Simple disulfide: pdb=" SG CYS 8 101 " - pdb=" SG CYS 8 167 " distance=2.04 Simple disulfide: pdb=" SG CYS 9 101 " - pdb=" SG CYS 9 167 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.51 Conformation dependent library (CDL) restraints added in 5.1 seconds 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11952 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 132 sheets defined 8.1% alpha, 29.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.38 Creating SS restraints... Processing helix chain 'A' and resid 49 through 53 Processing helix chain 'A' and resid 124 through 126 No H-bonds generated for 'chain 'A' and resid 124 through 126' Processing helix chain 'A' and resid 181 through 185 Processing helix chain 'E' and resid 49 through 53 removed outlier: 3.761A pdb=" N ILE E 53 " --> pdb=" O ASP E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 126 No H-bonds generated for 'chain 'E' and resid 124 through 126' Processing helix chain 'E' and resid 181 through 185 Processing helix chain 'B' and resid 49 through 53 removed outlier: 4.028A pdb=" N ILE B 53 " --> pdb=" O ASP B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 126 No H-bonds generated for 'chain 'B' and resid 124 through 126' Processing helix chain 'B' and resid 181 through 185 Processing helix chain 'C' and resid 49 through 54 removed outlier: 4.492A pdb=" N THR C 54 " --> pdb=" O THR C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 128 Processing helix chain 'C' and resid 181 through 185 Processing helix chain 'D' and resid 49 through 53 Processing helix chain 'D' and resid 124 through 126 No H-bonds generated for 'chain 'D' and resid 124 through 126' Processing helix chain 'D' and resid 181 through 187 removed outlier: 4.319A pdb=" N ASP D 186 " --> pdb=" O SER D 183 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY D 187 " --> pdb=" O ALA D 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 54 removed outlier: 3.780A pdb=" N THR F 51 " --> pdb=" O GLY F 48 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE F 53 " --> pdb=" O ASP F 50 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR F 54 " --> pdb=" O THR F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 126 No H-bonds generated for 'chain 'F' and resid 124 through 126' Processing helix chain 'F' and resid 181 through 187 removed outlier: 3.936A pdb=" N ASP F 186 " --> pdb=" O SER F 183 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLY F 187 " --> pdb=" O ALA F 184 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 53 Processing helix chain 'G' and resid 124 through 126 No H-bonds generated for 'chain 'G' and resid 124 through 126' Processing helix chain 'G' and resid 181 through 185 Processing helix chain 'H' and resid 49 through 53 removed outlier: 3.761A pdb=" N ILE H 53 " --> pdb=" O ASP H 50 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 126 No H-bonds generated for 'chain 'H' and resid 124 through 126' Processing helix chain 'H' and resid 181 through 185 Processing helix chain 'I' and resid 49 through 53 removed outlier: 4.028A pdb=" N ILE I 53 " --> pdb=" O ASP I 50 " (cutoff:3.500A) Processing helix chain 'I' and resid 124 through 126 No H-bonds generated for 'chain 'I' and resid 124 through 126' Processing helix chain 'I' and resid 181 through 185 Processing helix chain 'J' and resid 49 through 54 removed outlier: 4.492A pdb=" N THR J 54 " --> pdb=" O THR J 51 " (cutoff:3.500A) Processing helix chain 'J' and resid 124 through 128 Processing helix chain 'J' and resid 181 through 185 Processing helix chain 'K' and resid 49 through 53 Processing helix chain 'K' and resid 124 through 126 No H-bonds generated for 'chain 'K' and resid 124 through 126' Processing helix chain 'K' and resid 181 through 187 removed outlier: 4.319A pdb=" N ASP K 186 " --> pdb=" O SER K 183 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY K 187 " --> pdb=" O ALA K 184 " (cutoff:3.500A) Processing helix chain 'L' and resid 48 through 54 removed outlier: 3.780A pdb=" N THR L 51 " --> pdb=" O GLY L 48 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE L 53 " --> pdb=" O ASP L 50 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR L 54 " --> pdb=" O THR L 51 " (cutoff:3.500A) Processing helix chain 'L' and resid 124 through 126 No H-bonds generated for 'chain 'L' and resid 124 through 126' Processing helix chain 'L' and resid 181 through 187 removed outlier: 3.936A pdb=" N ASP L 186 " --> pdb=" O SER L 183 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLY L 187 " --> pdb=" O ALA L 184 " (cutoff:3.500A) Processing helix chain 'M' and resid 49 through 53 Processing helix chain 'M' and resid 124 through 126 No H-bonds generated for 'chain 'M' and resid 124 through 126' Processing helix chain 'M' and resid 181 through 185 Processing helix chain 'N' and resid 49 through 53 removed outlier: 3.761A pdb=" N ILE N 53 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 124 through 126 No H-bonds generated for 'chain 'N' and resid 124 through 126' Processing helix chain 'N' and resid 181 through 185 Processing helix chain 'O' and resid 49 through 53 removed outlier: 4.029A pdb=" N ILE O 53 " --> pdb=" O ASP O 50 " (cutoff:3.500A) Processing helix chain 'O' and resid 124 through 126 No H-bonds generated for 'chain 'O' and resid 124 through 126' Processing helix chain 'O' and resid 181 through 185 Processing helix chain 'P' and resid 49 through 54 removed outlier: 4.492A pdb=" N THR P 54 " --> pdb=" O THR P 51 " (cutoff:3.500A) Processing helix chain 'P' and resid 124 through 128 Processing helix chain 'P' and resid 181 through 185 Processing helix chain 'Q' and resid 49 through 53 Processing helix chain 'Q' and resid 124 through 126 No H-bonds generated for 'chain 'Q' and resid 124 through 126' Processing helix chain 'Q' and resid 181 through 187 removed outlier: 4.320A pdb=" N ASP Q 186 " --> pdb=" O SER Q 183 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY Q 187 " --> pdb=" O ALA Q 184 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 54 removed outlier: 3.780A pdb=" N THR R 51 " --> pdb=" O GLY R 48 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE R 53 " --> pdb=" O ASP R 50 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR R 54 " --> pdb=" O THR R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 124 through 126 No H-bonds generated for 'chain 'R' and resid 124 through 126' Processing helix chain 'R' and resid 181 through 187 removed outlier: 3.936A pdb=" N ASP R 186 " --> pdb=" O SER R 183 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLY R 187 " --> pdb=" O ALA R 184 " (cutoff:3.500A) Processing helix chain 'S' and resid 49 through 53 Processing helix chain 'S' and resid 124 through 126 No H-bonds generated for 'chain 'S' and resid 124 through 126' Processing helix chain 'S' and resid 181 through 185 Processing helix chain 'T' and resid 49 through 53 removed outlier: 3.761A pdb=" N ILE T 53 " --> pdb=" O ASP T 50 " (cutoff:3.500A) Processing helix chain 'T' and resid 124 through 126 No H-bonds generated for 'chain 'T' and resid 124 through 126' Processing helix chain 'T' and resid 181 through 185 Processing helix chain 'U' and resid 49 through 53 removed outlier: 4.028A pdb=" N ILE U 53 " --> pdb=" O ASP U 50 " (cutoff:3.500A) Processing helix chain 'U' and resid 124 through 126 No H-bonds generated for 'chain 'U' and resid 124 through 126' Processing helix chain 'U' and resid 181 through 185 Processing helix chain 'V' and resid 49 through 54 removed outlier: 4.492A pdb=" N THR V 54 " --> pdb=" O THR V 51 " (cutoff:3.500A) Processing helix chain 'V' and resid 124 through 128 Processing helix chain 'V' and resid 181 through 185 Processing helix chain 'W' and resid 49 through 53 Processing helix chain 'W' and resid 124 through 126 No H-bonds generated for 'chain 'W' and resid 124 through 126' Processing helix chain 'W' and resid 181 through 187 removed outlier: 4.320A pdb=" N ASP W 186 " --> pdb=" O SER W 183 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY W 187 " --> pdb=" O ALA W 184 " (cutoff:3.500A) Processing helix chain 'X' and resid 48 through 54 removed outlier: 3.780A pdb=" N THR X 51 " --> pdb=" O GLY X 48 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE X 53 " --> pdb=" O ASP X 50 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR X 54 " --> pdb=" O THR X 51 " (cutoff:3.500A) Processing helix chain 'X' and resid 124 through 126 No H-bonds generated for 'chain 'X' and resid 124 through 126' Processing helix chain 'X' and resid 181 through 187 removed outlier: 3.936A pdb=" N ASP X 186 " --> pdb=" O SER X 183 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLY X 187 " --> pdb=" O ALA X 184 " (cutoff:3.500A) Processing helix chain 'Y' and resid 49 through 53 Processing helix chain 'Y' and resid 124 through 126 No H-bonds generated for 'chain 'Y' and resid 124 through 126' Processing helix chain 'Y' and resid 181 through 185 Processing helix chain 'Z' and resid 49 through 53 removed outlier: 3.761A pdb=" N ILE Z 53 " --> pdb=" O ASP Z 50 " (cutoff:3.500A) Processing helix chain 'Z' and resid 124 through 126 No H-bonds generated for 'chain 'Z' and resid 124 through 126' Processing helix chain 'Z' and resid 181 through 185 Processing helix chain '0' and resid 49 through 53 removed outlier: 4.028A pdb=" N ILE 0 53 " --> pdb=" O ASP 0 50 " (cutoff:3.500A) Processing helix chain '0' and resid 124 through 126 No H-bonds generated for 'chain '0' and resid 124 through 126' Processing helix chain '0' and resid 181 through 185 Processing helix chain '1' and resid 49 through 54 removed outlier: 4.492A pdb=" N THR 1 54 " --> pdb=" O THR 1 51 " (cutoff:3.500A) Processing helix chain '1' and resid 124 through 128 Processing helix chain '1' and resid 181 through 185 Processing helix chain '2' and resid 49 through 53 Processing helix chain '2' and resid 124 through 126 No H-bonds generated for 'chain '2' and resid 124 through 126' Processing helix chain '2' and resid 181 through 187 removed outlier: 4.319A pdb=" N ASP 2 186 " --> pdb=" O SER 2 183 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY 2 187 " --> pdb=" O ALA 2 184 " (cutoff:3.500A) Processing helix chain '3' and resid 48 through 54 removed outlier: 3.781A pdb=" N THR 3 51 " --> pdb=" O GLY 3 48 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE 3 53 " --> pdb=" O ASP 3 50 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR 3 54 " --> pdb=" O THR 3 51 " (cutoff:3.500A) Processing helix chain '3' and resid 124 through 126 No H-bonds generated for 'chain '3' and resid 124 through 126' Processing helix chain '3' and resid 181 through 187 removed outlier: 3.935A pdb=" N ASP 3 186 " --> pdb=" O SER 3 183 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLY 3 187 " --> pdb=" O ALA 3 184 " (cutoff:3.500A) Processing helix chain '4' and resid 49 through 53 Processing helix chain '4' and resid 124 through 126 No H-bonds generated for 'chain '4' and resid 124 through 126' Processing helix chain '4' and resid 181 through 185 Processing helix chain '5' and resid 49 through 53 removed outlier: 3.762A pdb=" N ILE 5 53 " --> pdb=" O ASP 5 50 " (cutoff:3.500A) Processing helix chain '5' and resid 124 through 126 No H-bonds generated for 'chain '5' and resid 124 through 126' Processing helix chain '5' and resid 181 through 185 Processing helix chain '6' and resid 49 through 53 removed outlier: 4.028A pdb=" N ILE 6 53 " --> pdb=" O ASP 6 50 " (cutoff:3.500A) Processing helix chain '6' and resid 124 through 126 No H-bonds generated for 'chain '6' and resid 124 through 126' Processing helix chain '6' and resid 181 through 185 Processing helix chain '7' and resid 49 through 54 removed outlier: 4.492A pdb=" N THR 7 54 " --> pdb=" O THR 7 51 " (cutoff:3.500A) Processing helix chain '7' and resid 124 through 128 Processing helix chain '7' and resid 181 through 185 Processing helix chain '8' and resid 49 through 53 Processing helix chain '8' and resid 124 through 126 No H-bonds generated for 'chain '8' and resid 124 through 126' Processing helix chain '8' and resid 181 through 187 removed outlier: 4.319A pdb=" N ASP 8 186 " --> pdb=" O SER 8 183 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY 8 187 " --> pdb=" O ALA 8 184 " (cutoff:3.500A) Processing helix chain '9' and resid 48 through 54 removed outlier: 3.780A pdb=" N THR 9 51 " --> pdb=" O GLY 9 48 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE 9 53 " --> pdb=" O ASP 9 50 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR 9 54 " --> pdb=" O THR 9 51 " (cutoff:3.500A) Processing helix chain '9' and resid 124 through 126 No H-bonds generated for 'chain '9' and resid 124 through 126' Processing helix chain '9' and resid 181 through 187 removed outlier: 3.936A pdb=" N ASP 9 186 " --> pdb=" O SER 9 183 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLY 9 187 " --> pdb=" O ALA 9 184 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'A' and resid 65 through 71 removed outlier: 3.955A pdb=" N VAL A 79 " --> pdb=" O TYR A 70 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 92 through 100 removed outlier: 8.494A pdb=" N THR A 92 " --> pdb=" O VAL A 176 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N VAL A 176 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N TYR A 94 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N VAL A 174 " --> pdb=" O TYR A 94 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ASN A 96 " --> pdb=" O ALA A 172 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N ALA A 172 " --> pdb=" O ASN A 96 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP A 130 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLN A 146 " --> pdb=" O THR A 153 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 160 through 162 removed outlier: 5.739A pdb=" N ALA A 111 " --> pdb=" O SER A 201 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N SER A 201 " --> pdb=" O ALA A 111 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N LEU A 113 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VAL A 199 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ALA A 115 " --> pdb=" O ASN A 197 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ASN A 197 " --> pdb=" O ALA A 115 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLY A 117 " --> pdb=" O GLN A 195 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'E' and resid 65 through 67 Processing sheet with id=5, first strand: chain 'E' and resid 70 through 71 removed outlier: 3.767A pdb=" N VAL E 79 " --> pdb=" O TYR E 70 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'E' and resid 92 through 93 removed outlier: 3.855A pdb=" N ASP E 130 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE E 131 " --> pdb=" O PHE E 147 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'E' and resid 98 through 100 Processing sheet with id=8, first strand: chain 'E' and resid 160 through 162 removed outlier: 3.700A pdb=" N ILE E 162 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLN E 195 " --> pdb=" O VAL E 116 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'B' and resid 65 through 71 Processing sheet with id=10, first strand: chain 'B' and resid 92 through 100 removed outlier: 8.397A pdb=" N THR B 92 " --> pdb=" O VAL B 176 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N VAL B 176 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N TYR B 94 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N VAL B 174 " --> pdb=" O TYR B 94 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ASN B 96 " --> pdb=" O ALA B 172 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ALA B 172 " --> pdb=" O ASN B 96 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP B 130 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE B 131 " --> pdb=" O PHE B 147 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'B' and resid 160 through 162 removed outlier: 6.928A pdb=" N GLN B 195 " --> pdb=" O VAL B 116 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'C' and resid 65 through 71 Processing sheet with id=13, first strand: chain 'C' and resid 92 through 93 removed outlier: 3.625A pdb=" N LEU C 98 " --> pdb=" O VAL C 170 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'C' and resid 92 through 93 removed outlier: 3.742A pdb=" N ASP C 130 " --> pdb=" O LEU C 175 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE C 131 " --> pdb=" O PHE C 147 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'C' and resid 161 through 162 removed outlier: 3.656A pdb=" N VAL C 116 " --> pdb=" O GLN C 195 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N GLN C 195 " --> pdb=" O VAL C 116 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'D' and resid 65 through 71 removed outlier: 3.584A pdb=" N VAL D 79 " --> pdb=" O TYR D 70 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'D' and resid 92 through 93 Processing sheet with id=18, first strand: chain 'D' and resid 92 through 93 removed outlier: 3.652A pdb=" N TYR D 134 " --> pdb=" O GLY D 171 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL D 133 " --> pdb=" O VAL D 145 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'D' and resid 160 through 162 removed outlier: 6.754A pdb=" N GLN D 195 " --> pdb=" O VAL D 116 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'F' and resid 45 through 46 removed outlier: 3.743A pdb=" N TYR F 46 " --> pdb=" O GLN F 99 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN F 99 " --> pdb=" O TYR F 46 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ASN F 96 " --> pdb=" O VAL F 170 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL F 170 " --> pdb=" O ASN F 96 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU F 98 " --> pdb=" O ALA F 168 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA F 168 " --> pdb=" O LEU F 98 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ASP F 130 " --> pdb=" O LEU F 175 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL F 145 " --> pdb=" O VAL F 133 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'F' and resid 68 through 72 Processing sheet with id=22, first strand: chain 'F' and resid 160 through 162 removed outlier: 6.816A pdb=" N GLN F 195 " --> pdb=" O VAL F 116 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'G' and resid 65 through 71 removed outlier: 3.955A pdb=" N VAL G 79 " --> pdb=" O TYR G 70 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'G' and resid 92 through 100 removed outlier: 8.494A pdb=" N THR G 92 " --> pdb=" O VAL G 176 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N VAL G 176 " --> pdb=" O THR G 92 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N TYR G 94 " --> pdb=" O VAL G 174 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N VAL G 174 " --> pdb=" O TYR G 94 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASN G 96 " --> pdb=" O ALA G 172 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N ALA G 172 " --> pdb=" O ASN G 96 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP G 130 " --> pdb=" O LEU G 175 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N GLN G 146 " --> pdb=" O THR G 153 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'G' and resid 160 through 162 removed outlier: 5.739A pdb=" N ALA G 111 " --> pdb=" O SER G 201 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N SER G 201 " --> pdb=" O ALA G 111 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N LEU G 113 " --> pdb=" O VAL G 199 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VAL G 199 " --> pdb=" O LEU G 113 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ALA G 115 " --> pdb=" O ASN G 197 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ASN G 197 " --> pdb=" O ALA G 115 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLY G 117 " --> pdb=" O GLN G 195 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'H' and resid 65 through 67 Processing sheet with id=27, first strand: chain 'H' and resid 70 through 71 removed outlier: 3.767A pdb=" N VAL H 79 " --> pdb=" O TYR H 70 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'H' and resid 92 through 93 removed outlier: 3.855A pdb=" N ASP H 130 " --> pdb=" O LEU H 175 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE H 131 " --> pdb=" O PHE H 147 " (cutoff:3.500A) Processing sheet with id=29, first strand: chain 'H' and resid 98 through 100 Processing sheet with id=30, first strand: chain 'H' and resid 160 through 162 removed outlier: 3.701A pdb=" N ILE H 162 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N GLN H 195 " --> pdb=" O VAL H 116 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'I' and resid 65 through 71 Processing sheet with id=32, first strand: chain 'I' and resid 92 through 100 removed outlier: 8.397A pdb=" N THR I 92 " --> pdb=" O VAL I 176 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N VAL I 176 " --> pdb=" O THR I 92 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N TYR I 94 " --> pdb=" O VAL I 174 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N VAL I 174 " --> pdb=" O TYR I 94 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ASN I 96 " --> pdb=" O ALA I 172 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ALA I 172 " --> pdb=" O ASN I 96 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP I 130 " --> pdb=" O LEU I 175 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE I 131 " --> pdb=" O PHE I 147 " (cutoff:3.500A) Processing sheet with id=33, first strand: chain 'I' and resid 160 through 162 removed outlier: 6.928A pdb=" N GLN I 195 " --> pdb=" O VAL I 116 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain 'J' and resid 65 through 71 Processing sheet with id=35, first strand: chain 'J' and resid 92 through 93 removed outlier: 3.625A pdb=" N LEU J 98 " --> pdb=" O VAL J 170 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain 'J' and resid 92 through 93 removed outlier: 3.742A pdb=" N ASP J 130 " --> pdb=" O LEU J 175 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE J 131 " --> pdb=" O PHE J 147 " (cutoff:3.500A) Processing sheet with id=37, first strand: chain 'J' and resid 161 through 162 removed outlier: 3.656A pdb=" N VAL J 116 " --> pdb=" O GLN J 195 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N GLN J 195 " --> pdb=" O VAL J 116 " (cutoff:3.500A) Processing sheet with id=38, first strand: chain 'K' and resid 65 through 71 removed outlier: 3.584A pdb=" N VAL K 79 " --> pdb=" O TYR K 70 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'K' and resid 92 through 93 Processing sheet with id=40, first strand: chain 'K' and resid 92 through 93 removed outlier: 3.652A pdb=" N TYR K 134 " --> pdb=" O GLY K 171 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL K 133 " --> pdb=" O VAL K 145 " (cutoff:3.500A) Processing sheet with id=41, first strand: chain 'K' and resid 160 through 162 removed outlier: 6.755A pdb=" N GLN K 195 " --> pdb=" O VAL K 116 " (cutoff:3.500A) Processing sheet with id=42, first strand: chain 'L' and resid 45 through 46 removed outlier: 3.743A pdb=" N TYR L 46 " --> pdb=" O GLN L 99 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN L 99 " --> pdb=" O TYR L 46 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ASN L 96 " --> pdb=" O VAL L 170 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL L 170 " --> pdb=" O ASN L 96 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU L 98 " --> pdb=" O ALA L 168 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA L 168 " --> pdb=" O LEU L 98 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ASP L 130 " --> pdb=" O LEU L 175 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL L 145 " --> pdb=" O VAL L 133 " (cutoff:3.500A) Processing sheet with id=43, first strand: chain 'L' and resid 68 through 72 Processing sheet with id=44, first strand: chain 'L' and resid 160 through 162 removed outlier: 6.816A pdb=" N GLN L 195 " --> pdb=" O VAL L 116 " (cutoff:3.500A) Processing sheet with id=45, first strand: chain 'M' and resid 65 through 71 removed outlier: 3.954A pdb=" N VAL M 79 " --> pdb=" O TYR M 70 " (cutoff:3.500A) Processing sheet with id=46, first strand: chain 'M' and resid 92 through 100 removed outlier: 8.494A pdb=" N THR M 92 " --> pdb=" O VAL M 176 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N VAL M 176 " --> pdb=" O THR M 92 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N TYR M 94 " --> pdb=" O VAL M 174 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N VAL M 174 " --> pdb=" O TYR M 94 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASN M 96 " --> pdb=" O ALA M 172 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N ALA M 172 " --> pdb=" O ASN M 96 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP M 130 " --> pdb=" O LEU M 175 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLN M 146 " --> pdb=" O THR M 153 " (cutoff:3.500A) Processing sheet with id=47, first strand: chain 'M' and resid 160 through 162 removed outlier: 5.740A pdb=" N ALA M 111 " --> pdb=" O SER M 201 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N SER M 201 " --> pdb=" O ALA M 111 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N LEU M 113 " --> pdb=" O VAL M 199 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VAL M 199 " --> pdb=" O LEU M 113 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ALA M 115 " --> pdb=" O ASN M 197 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ASN M 197 " --> pdb=" O ALA M 115 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLY M 117 " --> pdb=" O GLN M 195 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'N' and resid 65 through 67 Processing sheet with id=49, first strand: chain 'N' and resid 70 through 71 removed outlier: 3.766A pdb=" N VAL N 79 " --> pdb=" O TYR N 70 " (cutoff:3.500A) Processing sheet with id=50, first strand: chain 'N' and resid 92 through 93 removed outlier: 3.855A pdb=" N ASP N 130 " --> pdb=" O LEU N 175 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE N 131 " --> pdb=" O PHE N 147 " (cutoff:3.500A) Processing sheet with id=51, first strand: chain 'N' and resid 98 through 100 Processing sheet with id=52, first strand: chain 'N' and resid 160 through 162 removed outlier: 3.700A pdb=" N ILE N 162 " --> pdb=" O LEU N 109 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N GLN N 195 " --> pdb=" O VAL N 116 " (cutoff:3.500A) Processing sheet with id=53, first strand: chain 'O' and resid 65 through 71 Processing sheet with id=54, first strand: chain 'O' and resid 92 through 100 removed outlier: 8.397A pdb=" N THR O 92 " --> pdb=" O VAL O 176 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N VAL O 176 " --> pdb=" O THR O 92 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N TYR O 94 " --> pdb=" O VAL O 174 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N VAL O 174 " --> pdb=" O TYR O 94 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ASN O 96 " --> pdb=" O ALA O 172 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ALA O 172 " --> pdb=" O ASN O 96 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP O 130 " --> pdb=" O LEU O 175 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE O 131 " --> pdb=" O PHE O 147 " (cutoff:3.500A) Processing sheet with id=55, first strand: chain 'O' and resid 160 through 162 removed outlier: 6.928A pdb=" N GLN O 195 " --> pdb=" O VAL O 116 " (cutoff:3.500A) Processing sheet with id=56, first strand: chain 'P' and resid 65 through 71 Processing sheet with id=57, first strand: chain 'P' and resid 92 through 93 removed outlier: 3.625A pdb=" N LEU P 98 " --> pdb=" O VAL P 170 " (cutoff:3.500A) Processing sheet with id=58, first strand: chain 'P' and resid 92 through 93 removed outlier: 3.742A pdb=" N ASP P 130 " --> pdb=" O LEU P 175 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE P 131 " --> pdb=" O PHE P 147 " (cutoff:3.500A) Processing sheet with id=59, first strand: chain 'P' and resid 161 through 162 removed outlier: 3.655A pdb=" N VAL P 116 " --> pdb=" O GLN P 195 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N GLN P 195 " --> pdb=" O VAL P 116 " (cutoff:3.500A) Processing sheet with id=60, first strand: chain 'Q' and resid 65 through 71 removed outlier: 3.584A pdb=" N VAL Q 79 " --> pdb=" O TYR Q 70 " (cutoff:3.500A) Processing sheet with id=61, first strand: chain 'Q' and resid 92 through 93 Processing sheet with id=62, first strand: chain 'Q' and resid 92 through 93 removed outlier: 3.652A pdb=" N TYR Q 134 " --> pdb=" O GLY Q 171 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL Q 133 " --> pdb=" O VAL Q 145 " (cutoff:3.500A) Processing sheet with id=63, first strand: chain 'Q' and resid 160 through 162 removed outlier: 6.755A pdb=" N GLN Q 195 " --> pdb=" O VAL Q 116 " (cutoff:3.500A) Processing sheet with id=64, first strand: chain 'R' and resid 45 through 46 removed outlier: 3.744A pdb=" N TYR R 46 " --> pdb=" O GLN R 99 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN R 99 " --> pdb=" O TYR R 46 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ASN R 96 " --> pdb=" O VAL R 170 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL R 170 " --> pdb=" O ASN R 96 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU R 98 " --> pdb=" O ALA R 168 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA R 168 " --> pdb=" O LEU R 98 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ASP R 130 " --> pdb=" O LEU R 175 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL R 145 " --> pdb=" O VAL R 133 " (cutoff:3.500A) Processing sheet with id=65, first strand: chain 'R' and resid 68 through 72 Processing sheet with id=66, first strand: chain 'R' and resid 160 through 162 removed outlier: 6.816A pdb=" N GLN R 195 " --> pdb=" O VAL R 116 " (cutoff:3.500A) Processing sheet with id=67, first strand: chain 'S' and resid 65 through 71 removed outlier: 3.955A pdb=" N VAL S 79 " --> pdb=" O TYR S 70 " (cutoff:3.500A) Processing sheet with id=68, first strand: chain 'S' and resid 92 through 100 removed outlier: 8.495A pdb=" N THR S 92 " --> pdb=" O VAL S 176 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N VAL S 176 " --> pdb=" O THR S 92 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N TYR S 94 " --> pdb=" O VAL S 174 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N VAL S 174 " --> pdb=" O TYR S 94 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ASN S 96 " --> pdb=" O ALA S 172 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N ALA S 172 " --> pdb=" O ASN S 96 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP S 130 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLN S 146 " --> pdb=" O THR S 153 " (cutoff:3.500A) Processing sheet with id=69, first strand: chain 'S' and resid 160 through 162 removed outlier: 5.740A pdb=" N ALA S 111 " --> pdb=" O SER S 201 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N SER S 201 " --> pdb=" O ALA S 111 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N LEU S 113 " --> pdb=" O VAL S 199 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VAL S 199 " --> pdb=" O LEU S 113 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ALA S 115 " --> pdb=" O ASN S 197 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ASN S 197 " --> pdb=" O ALA S 115 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLY S 117 " --> pdb=" O GLN S 195 " (cutoff:3.500A) Processing sheet with id=70, first strand: chain 'T' and resid 65 through 67 Processing sheet with id=71, first strand: chain 'T' and resid 70 through 71 removed outlier: 3.766A pdb=" N VAL T 79 " --> pdb=" O TYR T 70 " (cutoff:3.500A) Processing sheet with id=72, first strand: chain 'T' and resid 92 through 93 removed outlier: 3.855A pdb=" N ASP T 130 " --> pdb=" O LEU T 175 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE T 131 " --> pdb=" O PHE T 147 " (cutoff:3.500A) Processing sheet with id=73, first strand: chain 'T' and resid 98 through 100 Processing sheet with id=74, first strand: chain 'T' and resid 160 through 162 removed outlier: 3.701A pdb=" N ILE T 162 " --> pdb=" O LEU T 109 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLN T 195 " --> pdb=" O VAL T 116 " (cutoff:3.500A) Processing sheet with id=75, first strand: chain 'U' and resid 65 through 71 Processing sheet with id=76, first strand: chain 'U' and resid 92 through 100 removed outlier: 8.396A pdb=" N THR U 92 " --> pdb=" O VAL U 176 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N VAL U 176 " --> pdb=" O THR U 92 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N TYR U 94 " --> pdb=" O VAL U 174 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N VAL U 174 " --> pdb=" O TYR U 94 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ASN U 96 " --> pdb=" O ALA U 172 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ALA U 172 " --> pdb=" O ASN U 96 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP U 130 " --> pdb=" O LEU U 175 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE U 131 " --> pdb=" O PHE U 147 " (cutoff:3.500A) Processing sheet with id=77, first strand: chain 'U' and resid 160 through 162 removed outlier: 6.928A pdb=" N GLN U 195 " --> pdb=" O VAL U 116 " (cutoff:3.500A) Processing sheet with id=78, first strand: chain 'V' and resid 65 through 71 Processing sheet with id=79, first strand: chain 'V' and resid 92 through 93 removed outlier: 3.625A pdb=" N LEU V 98 " --> pdb=" O VAL V 170 " (cutoff:3.500A) Processing sheet with id=80, first strand: chain 'V' and resid 92 through 93 removed outlier: 3.742A pdb=" N ASP V 130 " --> pdb=" O LEU V 175 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE V 131 " --> pdb=" O PHE V 147 " (cutoff:3.500A) Processing sheet with id=81, first strand: chain 'V' and resid 161 through 162 removed outlier: 3.656A pdb=" N VAL V 116 " --> pdb=" O GLN V 195 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N GLN V 195 " --> pdb=" O VAL V 116 " (cutoff:3.500A) Processing sheet with id=82, first strand: chain 'W' and resid 65 through 71 removed outlier: 3.584A pdb=" N VAL W 79 " --> pdb=" O TYR W 70 " (cutoff:3.500A) Processing sheet with id=83, first strand: chain 'W' and resid 92 through 93 Processing sheet with id=84, first strand: chain 'W' and resid 92 through 93 removed outlier: 3.653A pdb=" N TYR W 134 " --> pdb=" O GLY W 171 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL W 133 " --> pdb=" O VAL W 145 " (cutoff:3.500A) Processing sheet with id=85, first strand: chain 'W' and resid 160 through 162 removed outlier: 6.755A pdb=" N GLN W 195 " --> pdb=" O VAL W 116 " (cutoff:3.500A) Processing sheet with id=86, first strand: chain 'X' and resid 45 through 46 removed outlier: 3.743A pdb=" N TYR X 46 " --> pdb=" O GLN X 99 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN X 99 " --> pdb=" O TYR X 46 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ASN X 96 " --> pdb=" O VAL X 170 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL X 170 " --> pdb=" O ASN X 96 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU X 98 " --> pdb=" O ALA X 168 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA X 168 " --> pdb=" O LEU X 98 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ASP X 130 " --> pdb=" O LEU X 175 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL X 145 " --> pdb=" O VAL X 133 " (cutoff:3.500A) Processing sheet with id=87, first strand: chain 'X' and resid 68 through 72 Processing sheet with id=88, first strand: chain 'X' and resid 160 through 162 removed outlier: 6.817A pdb=" N GLN X 195 " --> pdb=" O VAL X 116 " (cutoff:3.500A) Processing sheet with id=89, first strand: chain 'Y' and resid 65 through 71 removed outlier: 3.955A pdb=" N VAL Y 79 " --> pdb=" O TYR Y 70 " (cutoff:3.500A) Processing sheet with id=90, first strand: chain 'Y' and resid 92 through 100 removed outlier: 8.494A pdb=" N THR Y 92 " --> pdb=" O VAL Y 176 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N VAL Y 176 " --> pdb=" O THR Y 92 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N TYR Y 94 " --> pdb=" O VAL Y 174 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N VAL Y 174 " --> pdb=" O TYR Y 94 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N ASN Y 96 " --> pdb=" O ALA Y 172 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N ALA Y 172 " --> pdb=" O ASN Y 96 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP Y 130 " --> pdb=" O LEU Y 175 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N GLN Y 146 " --> pdb=" O THR Y 153 " (cutoff:3.500A) Processing sheet with id=91, first strand: chain 'Y' and resid 160 through 162 removed outlier: 5.740A pdb=" N ALA Y 111 " --> pdb=" O SER Y 201 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N SER Y 201 " --> pdb=" O ALA Y 111 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N LEU Y 113 " --> pdb=" O VAL Y 199 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VAL Y 199 " --> pdb=" O LEU Y 113 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ALA Y 115 " --> pdb=" O ASN Y 197 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ASN Y 197 " --> pdb=" O ALA Y 115 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLY Y 117 " --> pdb=" O GLN Y 195 " (cutoff:3.500A) Processing sheet with id=92, first strand: chain 'Z' and resid 65 through 67 Processing sheet with id=93, first strand: chain 'Z' and resid 70 through 71 removed outlier: 3.766A pdb=" N VAL Z 79 " --> pdb=" O TYR Z 70 " (cutoff:3.500A) Processing sheet with id=94, first strand: chain 'Z' and resid 92 through 93 removed outlier: 3.855A pdb=" N ASP Z 130 " --> pdb=" O LEU Z 175 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE Z 131 " --> pdb=" O PHE Z 147 " (cutoff:3.500A) Processing sheet with id=95, first strand: chain 'Z' and resid 98 through 100 Processing sheet with id=96, first strand: chain 'Z' and resid 160 through 162 removed outlier: 3.701A pdb=" N ILE Z 162 " --> pdb=" O LEU Z 109 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N GLN Z 195 " --> pdb=" O VAL Z 116 " (cutoff:3.500A) Processing sheet with id=97, first strand: chain '0' and resid 65 through 71 Processing sheet with id=98, first strand: chain '0' and resid 92 through 100 removed outlier: 8.397A pdb=" N THR 0 92 " --> pdb=" O VAL 0 176 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N VAL 0 176 " --> pdb=" O THR 0 92 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N TYR 0 94 " --> pdb=" O VAL 0 174 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N VAL 0 174 " --> pdb=" O TYR 0 94 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ASN 0 96 " --> pdb=" O ALA 0 172 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ALA 0 172 " --> pdb=" O ASN 0 96 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP 0 130 " --> pdb=" O LEU 0 175 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE 0 131 " --> pdb=" O PHE 0 147 " (cutoff:3.500A) Processing sheet with id=99, first strand: chain '0' and resid 160 through 162 removed outlier: 6.928A pdb=" N GLN 0 195 " --> pdb=" O VAL 0 116 " (cutoff:3.500A) Processing sheet with id=100, first strand: chain '1' and resid 65 through 71 Processing sheet with id=101, first strand: chain '1' and resid 92 through 93 removed outlier: 3.625A pdb=" N LEU 1 98 " --> pdb=" O VAL 1 170 " (cutoff:3.500A) Processing sheet with id=102, first strand: chain '1' and resid 92 through 93 removed outlier: 3.742A pdb=" N ASP 1 130 " --> pdb=" O LEU 1 175 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE 1 131 " --> pdb=" O PHE 1 147 " (cutoff:3.500A) Processing sheet with id=103, first strand: chain '1' and resid 161 through 162 removed outlier: 3.655A pdb=" N VAL 1 116 " --> pdb=" O GLN 1 195 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N GLN 1 195 " --> pdb=" O VAL 1 116 " (cutoff:3.500A) Processing sheet with id=104, first strand: chain '2' and resid 65 through 71 removed outlier: 3.585A pdb=" N VAL 2 79 " --> pdb=" O TYR 2 70 " (cutoff:3.500A) Processing sheet with id=105, first strand: chain '2' and resid 92 through 93 Processing sheet with id=106, first strand: chain '2' and resid 92 through 93 removed outlier: 3.653A pdb=" N TYR 2 134 " --> pdb=" O GLY 2 171 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL 2 133 " --> pdb=" O VAL 2 145 " (cutoff:3.500A) Processing sheet with id=107, first strand: chain '2' and resid 160 through 162 removed outlier: 6.755A pdb=" N GLN 2 195 " --> pdb=" O VAL 2 116 " (cutoff:3.500A) Processing sheet with id=108, first strand: chain '3' and resid 45 through 46 removed outlier: 3.743A pdb=" N TYR 3 46 " --> pdb=" O GLN 3 99 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN 3 99 " --> pdb=" O TYR 3 46 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ASN 3 96 " --> pdb=" O VAL 3 170 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL 3 170 " --> pdb=" O ASN 3 96 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU 3 98 " --> pdb=" O ALA 3 168 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA 3 168 " --> pdb=" O LEU 3 98 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ASP 3 130 " --> pdb=" O LEU 3 175 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL 3 145 " --> pdb=" O VAL 3 133 " (cutoff:3.500A) Processing sheet with id=109, first strand: chain '3' and resid 68 through 72 Processing sheet with id=110, first strand: chain '3' and resid 160 through 162 removed outlier: 6.816A pdb=" N GLN 3 195 " --> pdb=" O VAL 3 116 " (cutoff:3.500A) Processing sheet with id=111, first strand: chain '4' and resid 65 through 71 removed outlier: 3.954A pdb=" N VAL 4 79 " --> pdb=" O TYR 4 70 " (cutoff:3.500A) Processing sheet with id=112, first strand: chain '4' and resid 92 through 100 removed outlier: 8.494A pdb=" N THR 4 92 " --> pdb=" O VAL 4 176 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N VAL 4 176 " --> pdb=" O THR 4 92 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N TYR 4 94 " --> pdb=" O VAL 4 174 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N VAL 4 174 " --> pdb=" O TYR 4 94 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ASN 4 96 " --> pdb=" O ALA 4 172 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N ALA 4 172 " --> pdb=" O ASN 4 96 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP 4 130 " --> pdb=" O LEU 4 175 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLN 4 146 " --> pdb=" O THR 4 153 " (cutoff:3.500A) Processing sheet with id=113, first strand: chain '4' and resid 160 through 162 removed outlier: 5.740A pdb=" N ALA 4 111 " --> pdb=" O SER 4 201 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N SER 4 201 " --> pdb=" O ALA 4 111 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N LEU 4 113 " --> pdb=" O VAL 4 199 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VAL 4 199 " --> pdb=" O LEU 4 113 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ALA 4 115 " --> pdb=" O ASN 4 197 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ASN 4 197 " --> pdb=" O ALA 4 115 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLY 4 117 " --> pdb=" O GLN 4 195 " (cutoff:3.500A) Processing sheet with id=114, first strand: chain '5' and resid 65 through 67 Processing sheet with id=115, first strand: chain '5' and resid 70 through 71 removed outlier: 3.767A pdb=" N VAL 5 79 " --> pdb=" O TYR 5 70 " (cutoff:3.500A) Processing sheet with id=116, first strand: chain '5' and resid 92 through 93 removed outlier: 3.855A pdb=" N ASP 5 130 " --> pdb=" O LEU 5 175 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE 5 131 " --> pdb=" O PHE 5 147 " (cutoff:3.500A) Processing sheet with id=117, first strand: chain '5' and resid 98 through 100 Processing sheet with id=118, first strand: chain '5' and resid 160 through 162 removed outlier: 3.701A pdb=" N ILE 5 162 " --> pdb=" O LEU 5 109 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLN 5 195 " --> pdb=" O VAL 5 116 " (cutoff:3.500A) Processing sheet with id=119, first strand: chain '6' and resid 65 through 71 Processing sheet with id=120, first strand: chain '6' and resid 92 through 100 removed outlier: 8.397A pdb=" N THR 6 92 " --> pdb=" O VAL 6 176 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N VAL 6 176 " --> pdb=" O THR 6 92 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N TYR 6 94 " --> pdb=" O VAL 6 174 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N VAL 6 174 " --> pdb=" O TYR 6 94 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ASN 6 96 " --> pdb=" O ALA 6 172 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ALA 6 172 " --> pdb=" O ASN 6 96 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP 6 130 " --> pdb=" O LEU 6 175 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE 6 131 " --> pdb=" O PHE 6 147 " (cutoff:3.500A) Processing sheet with id=121, first strand: chain '6' and resid 160 through 162 removed outlier: 6.928A pdb=" N GLN 6 195 " --> pdb=" O VAL 6 116 " (cutoff:3.500A) Processing sheet with id=122, first strand: chain '7' and resid 65 through 71 Processing sheet with id=123, first strand: chain '7' and resid 92 through 93 removed outlier: 3.625A pdb=" N LEU 7 98 " --> pdb=" O VAL 7 170 " (cutoff:3.500A) Processing sheet with id=124, first strand: chain '7' and resid 92 through 93 removed outlier: 3.741A pdb=" N ASP 7 130 " --> pdb=" O LEU 7 175 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE 7 131 " --> pdb=" O PHE 7 147 " (cutoff:3.500A) Processing sheet with id=125, first strand: chain '7' and resid 161 through 162 removed outlier: 3.655A pdb=" N VAL 7 116 " --> pdb=" O GLN 7 195 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N GLN 7 195 " --> pdb=" O VAL 7 116 " (cutoff:3.500A) Processing sheet with id=126, first strand: chain '8' and resid 65 through 71 removed outlier: 3.584A pdb=" N VAL 8 79 " --> pdb=" O TYR 8 70 " (cutoff:3.500A) Processing sheet with id=127, first strand: chain '8' and resid 92 through 93 Processing sheet with id=128, first strand: chain '8' and resid 92 through 93 removed outlier: 3.652A pdb=" N TYR 8 134 " --> pdb=" O GLY 8 171 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL 8 133 " --> pdb=" O VAL 8 145 " (cutoff:3.500A) Processing sheet with id=129, first strand: chain '8' and resid 160 through 162 removed outlier: 6.754A pdb=" N GLN 8 195 " --> pdb=" O VAL 8 116 " (cutoff:3.500A) Processing sheet with id=130, first strand: chain '9' and resid 45 through 46 removed outlier: 3.744A pdb=" N TYR 9 46 " --> pdb=" O GLN 9 99 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN 9 99 " --> pdb=" O TYR 9 46 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ASN 9 96 " --> pdb=" O VAL 9 170 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL 9 170 " --> pdb=" O ASN 9 96 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU 9 98 " --> pdb=" O ALA 9 168 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA 9 168 " --> pdb=" O LEU 9 98 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ASP 9 130 " --> pdb=" O LEU 9 175 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL 9 145 " --> pdb=" O VAL 9 133 " (cutoff:3.500A) Processing sheet with id=131, first strand: chain '9' and resid 68 through 72 Processing sheet with id=132, first strand: chain '9' and resid 160 through 162 removed outlier: 6.816A pdb=" N GLN 9 195 " --> pdb=" O VAL 9 116 " (cutoff:3.500A) 1182 hydrogen bonds defined for protein. 2448 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: 18.66 Time building geometry restraints manager: 11.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.51: 31654 1.51 - 1.79: 19431 1.79 - 2.07: 155 2.07 - 2.35: 48 2.35 - 2.63: 12 Bond restraints: 51300 Sorted by residual: bond pdb=" CA PHE 5 28 " pdb=" CB PHE 5 28 " ideal model delta sigma weight residual 1.530 2.251 -0.721 1.43e-02 4.89e+03 2.55e+03 bond pdb=" CA PHE E 28 " pdb=" CB PHE E 28 " ideal model delta sigma weight residual 1.530 2.251 -0.721 1.43e-02 4.89e+03 2.54e+03 bond pdb=" CA PHE Z 28 " pdb=" CB PHE Z 28 " ideal model delta sigma weight residual 1.530 2.251 -0.721 1.43e-02 4.89e+03 2.54e+03 bond pdb=" CA PHE H 28 " pdb=" CB PHE H 28 " ideal model delta sigma weight residual 1.530 2.251 -0.721 1.43e-02 4.89e+03 2.54e+03 bond pdb=" CA PHE N 28 " pdb=" CB PHE N 28 " ideal model delta sigma weight residual 1.530 2.251 -0.721 1.43e-02 4.89e+03 2.54e+03 ... (remaining 51295 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.08: 69936 3.08 - 6.16: 558 6.16 - 9.24: 60 9.24 - 12.32: 12 12.32 - 15.40: 30 Bond angle restraints: 70596 Sorted by residual: angle pdb=" CA PHE T 28 " pdb=" CB PHE T 28 " pdb=" CG PHE T 28 " ideal model delta sigma weight residual 113.80 129.12 -15.32 1.00e+00 1.00e+00 2.35e+02 angle pdb=" CA PHE H 28 " pdb=" CB PHE H 28 " pdb=" CG PHE H 28 " ideal model delta sigma weight residual 113.80 129.11 -15.31 1.00e+00 1.00e+00 2.35e+02 angle pdb=" CA PHE N 28 " pdb=" CB PHE N 28 " pdb=" CG PHE N 28 " ideal model delta sigma weight residual 113.80 129.10 -15.30 1.00e+00 1.00e+00 2.34e+02 angle pdb=" CA PHE Z 28 " pdb=" CB PHE Z 28 " pdb=" CG PHE Z 28 " ideal model delta sigma weight residual 113.80 129.10 -15.30 1.00e+00 1.00e+00 2.34e+02 angle pdb=" CA PHE E 28 " pdb=" CB PHE E 28 " pdb=" CG PHE E 28 " ideal model delta sigma weight residual 113.80 129.10 -15.30 1.00e+00 1.00e+00 2.34e+02 ... (remaining 70591 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.73: 26671 14.73 - 29.46: 2290 29.46 - 44.19: 577 44.19 - 58.92: 78 58.92 - 73.65: 48 Dihedral angle restraints: 29664 sinusoidal: 10584 harmonic: 19080 Sorted by residual: dihedral pdb=" CA THR Y 141 " pdb=" C THR Y 141 " pdb=" N PRO Y 142 " pdb=" CA PRO Y 142 " ideal model delta harmonic sigma weight residual -180.00 -130.92 -49.08 0 5.00e+00 4.00e-02 9.63e+01 dihedral pdb=" CA THR 4 141 " pdb=" C THR 4 141 " pdb=" N PRO 4 142 " pdb=" CA PRO 4 142 " ideal model delta harmonic sigma weight residual 180.00 -130.94 -49.06 0 5.00e+00 4.00e-02 9.63e+01 dihedral pdb=" CA THR M 141 " pdb=" C THR M 141 " pdb=" N PRO M 142 " pdb=" CA PRO M 142 " ideal model delta harmonic sigma weight residual -180.00 -130.96 -49.04 0 5.00e+00 4.00e-02 9.62e+01 ... (remaining 29661 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 8224 0.121 - 0.242: 122 0.242 - 0.363: 0 0.363 - 0.484: 0 0.484 - 0.605: 6 Chirality restraints: 8352 Sorted by residual: chirality pdb=" CA PHE E 28 " pdb=" N PHE E 28 " pdb=" C PHE E 28 " pdb=" CB PHE E 28 " both_signs ideal model delta sigma weight residual False 2.51 3.12 -0.61 2.00e-01 2.50e+01 9.15e+00 chirality pdb=" CA PHE N 28 " pdb=" N PHE N 28 " pdb=" C PHE N 28 " pdb=" CB PHE N 28 " both_signs ideal model delta sigma weight residual False 2.51 3.12 -0.60 2.00e-01 2.50e+01 9.15e+00 chirality pdb=" CA PHE H 28 " pdb=" N PHE H 28 " pdb=" C PHE H 28 " pdb=" CB PHE H 28 " both_signs ideal model delta sigma weight residual False 2.51 3.11 -0.60 2.00e-01 2.50e+01 9.14e+00 ... (remaining 8349 not shown) Planarity restraints: 8856 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP 3 34 " 0.007 2.00e-02 2.50e+03 3.03e-02 2.30e+01 pdb=" CG TRP 3 34 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP 3 34 " -0.060 2.00e-02 2.50e+03 pdb=" CD2 TRP 3 34 " 0.018 2.00e-02 2.50e+03 pdb=" NE1 TRP 3 34 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP 3 34 " 0.015 2.00e-02 2.50e+03 pdb=" CE3 TRP 3 34 " -0.037 2.00e-02 2.50e+03 pdb=" CZ2 TRP 3 34 " -0.014 2.00e-02 2.50e+03 pdb=" CZ3 TRP 3 34 " -0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP 3 34 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP L 34 " -0.007 2.00e-02 2.50e+03 3.03e-02 2.30e+01 pdb=" CG TRP L 34 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP L 34 " 0.060 2.00e-02 2.50e+03 pdb=" CD2 TRP L 34 " -0.018 2.00e-02 2.50e+03 pdb=" NE1 TRP L 34 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP L 34 " -0.015 2.00e-02 2.50e+03 pdb=" CE3 TRP L 34 " 0.038 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 34 " 0.014 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 34 " 0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP L 34 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP X 34 " -0.007 2.00e-02 2.50e+03 3.03e-02 2.30e+01 pdb=" CG TRP X 34 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP X 34 " 0.060 2.00e-02 2.50e+03 pdb=" CD2 TRP X 34 " -0.018 2.00e-02 2.50e+03 pdb=" NE1 TRP X 34 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP X 34 " -0.015 2.00e-02 2.50e+03 pdb=" CE3 TRP X 34 " 0.037 2.00e-02 2.50e+03 pdb=" CZ2 TRP X 34 " 0.014 2.00e-02 2.50e+03 pdb=" CZ3 TRP X 34 " 0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP X 34 " -0.023 2.00e-02 2.50e+03 ... (remaining 8853 not shown) Histogram of nonbonded interaction distances: 0.44 - 1.33: 44 1.33 - 2.22: 270 2.22 - 3.11: 40911 3.11 - 4.01: 124146 4.01 - 4.90: 224206 Warning: very small nonbonded interaction distances. Nonbonded interactions: 389577 Sorted by model distance: nonbonded pdb=" CZ2 TRP R 34 " pdb=" O THR C 193 " model vdw 0.436 3.340 nonbonded pdb=" CZ2 TRP F 34 " pdb=" O THR 7 193 " model vdw 0.436 3.340 nonbonded pdb=" CZ2 TRP L 34 " pdb=" O THR V 193 " model vdw 0.437 3.340 nonbonded pdb=" CZ2 TRP X 34 " pdb=" O THR 1 193 " model vdw 0.437 3.340 nonbonded pdb=" NH2 ARG R 55 " pdb=" OH TYR U 105 " model vdw 0.782 3.120 ... (remaining 389572 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 '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain '9' selection = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.400 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: 0.060 Extract box with map and model: 1.650 Check model and map are aligned: 0.310 Set scattering table: 0.410 Process input model: 91.430 Find NCS groups from input model: 1.520 Set up NCS constraints: 0.360 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 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 : 0.034 1.132 51300 Z= 2.253 Angle : 0.786 15.397 70596 Z= 0.487 Chirality : 0.050 0.605 8352 Planarity : 0.007 0.078 8856 Dihedral : 12.164 73.655 17604 Min Nonbonded Distance : 0.436 Molprobity Statistics. All-atom Clashscore : 24.88 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.96 % Favored : 90.86 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.09 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.10), residues: 6408 helix: -4.50 (0.08), residues: 438 sheet: -0.81 (0.11), residues: 2346 loop : -2.27 (0.10), residues: 3624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.005 TRP R 34 PHE 0.033 0.003 PHE W 28 TYR 0.023 0.001 TYR 5 105 ARG 0.008 0.001 ARG X 55 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 482 time to evaluate : 4.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 185 ARG cc_start: 0.6863 (tpp-160) cc_final: 0.6125 (tpt90) REVERT: H 186 ASP cc_start: 0.9045 (p0) cc_final: 0.8585 (p0) REVERT: I 191 ILE cc_start: 0.8987 (pt) cc_final: 0.8716 (tt) REVERT: L 57 ASP cc_start: 0.7580 (p0) cc_final: 0.7370 (p0) REVERT: N 44 MET cc_start: 0.5900 (mtp) cc_final: 0.5313 (mtp) REVERT: O 57 ASP cc_start: 0.8128 (p0) cc_final: 0.7732 (p0) REVERT: U 84 ILE cc_start: 0.8934 (mm) cc_final: 0.8705 (mt) REVERT: W 185 ARG cc_start: 0.7784 (mmm160) cc_final: 0.7438 (mmm160) REVERT: X 57 ASP cc_start: 0.7167 (p0) cc_final: 0.6557 (p0) REVERT: E 186 ASP cc_start: 0.9284 (p0) cc_final: 0.8790 (p0) REVERT: B 35 LEU cc_start: 0.8950 (mp) cc_final: 0.8660 (pp) REVERT: Z 44 MET cc_start: 0.6739 (mtp) cc_final: 0.6400 (mtp) REVERT: 0 44 MET cc_start: 0.2764 (tpt) cc_final: 0.2422 (tpt) REVERT: 0 186 ASP cc_start: 0.8615 (p0) cc_final: 0.8257 (p0) REVERT: 6 57 ASP cc_start: 0.8141 (p0) cc_final: 0.7917 (p0) REVERT: 9 57 ASP cc_start: 0.7435 (p0) cc_final: 0.6562 (m-30) outliers start: 0 outliers final: 0 residues processed: 482 average time/residue: 0.5205 time to fit residues: 421.6033 Evaluate side-chains 237 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 4.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 547 optimal weight: 3.9990 chunk 491 optimal weight: 20.0000 chunk 272 optimal weight: 20.0000 chunk 167 optimal weight: 20.0000 chunk 331 optimal weight: 3.9990 chunk 262 optimal weight: 5.9990 chunk 507 optimal weight: 3.9990 chunk 196 optimal weight: 20.0000 chunk 308 optimal weight: 9.9990 chunk 378 optimal weight: 10.0000 chunk 588 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 195 GLN ** H 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 ASN ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 93 ASN L 102 ASN L 143 ASN ** M 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 195 GLN O 123 ASN O 195 GLN ** P 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 93 ASN R 143 ASN ** S 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 195 GLN U 195 GLN V 37 ASN ** W 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 93 ASN X 143 ASN ** X 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 ASN F 143 ASN ** Y 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 102 ASN 1 37 ASN ** 1 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 143 ASN ** 4 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 30 ASN 6 195 GLN 7 30 ASN ** 7 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 102 ASN 9 143 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.032 1.151 51300 Z= 2.159 Angle : 0.918 39.178 70596 Z= 0.524 Chirality : 0.052 0.360 8352 Planarity : 0.007 0.080 8856 Dihedral : 6.247 54.236 7308 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 21.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.74 % Favored : 89.19 % Rotamer: Outliers : 0.69 % Allowed : 7.98 % Favored : 91.33 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.09 % Twisted General : 0.05 % 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: -3.05 (0.10), residues: 6408 helix: -4.50 (0.08), residues: 402 sheet: -1.00 (0.10), residues: 2424 loop : -2.53 (0.10), residues: 3582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP L 34 PHE 0.108 0.005 PHE U 200 TYR 0.041 0.002 TYR V 194 ARG 0.011 0.001 ARG X 55 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 278 time to evaluate : 4.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 26 LEU cc_start: 0.8387 (tp) cc_final: 0.7943 (tt) REVERT: G 55 ARG cc_start: 0.7722 (mtp180) cc_final: 0.7503 (mtm180) REVERT: H 186 ASP cc_start: 0.8972 (p0) cc_final: 0.8611 (p0) REVERT: I 191 ILE cc_start: 0.9108 (pt) cc_final: 0.8806 (tt) REVERT: N 44 MET cc_start: 0.5892 (mtp) cc_final: 0.5366 (mtp) REVERT: N 84 ILE cc_start: 0.9358 (mm) cc_final: 0.9109 (mt) REVERT: O 57 ASP cc_start: 0.8215 (p0) cc_final: 0.7721 (p0) REVERT: O 186 ASP cc_start: 0.8999 (p0) cc_final: 0.8765 (p0) REVERT: P 90 ASP cc_start: 0.7558 (t0) cc_final: 0.7339 (t0) REVERT: R 55 ARG cc_start: 0.6277 (ptt180) cc_final: 0.5927 (ptt-90) REVERT: R 177 ASP cc_start: 0.9200 (t0) cc_final: 0.8973 (t0) REVERT: S 55 ARG cc_start: 0.7334 (mtm110) cc_final: 0.6742 (mmm-85) REVERT: T 55 ARG cc_start: 0.7026 (ptm160) cc_final: 0.6376 (mtm180) REVERT: U 90 ASP cc_start: 0.7384 (OUTLIER) cc_final: 0.7088 (m-30) REVERT: X 57 ASP cc_start: 0.7424 (p0) cc_final: 0.6804 (p0) REVERT: E 55 ARG cc_start: 0.6580 (ptm160) cc_final: 0.6227 (mtm180) REVERT: B 35 LEU cc_start: 0.9224 (mp) cc_final: 0.8693 (pp) REVERT: D 175 LEU cc_start: 0.8711 (tt) cc_final: 0.8303 (tp) REVERT: Z 44 MET cc_start: 0.6860 (mtp) cc_final: 0.6477 (mtp) REVERT: 0 35 LEU cc_start: 0.9204 (mp) cc_final: 0.8806 (pp) REVERT: 0 186 ASP cc_start: 0.8758 (p0) cc_final: 0.8463 (p0) REVERT: 6 57 ASP cc_start: 0.8271 (p0) cc_final: 0.8053 (p0) REVERT: 7 188 LYS cc_start: 0.6171 (mmmt) cc_final: 0.5955 (mmmt) REVERT: 8 90 ASP cc_start: 0.7465 (t0) cc_final: 0.6938 (t0) REVERT: 8 175 LEU cc_start: 0.9311 (tt) cc_final: 0.9037 (tp) REVERT: 9 57 ASP cc_start: 0.7473 (p0) cc_final: 0.6735 (m-30) outliers start: 39 outliers final: 22 residues processed: 310 average time/residue: 0.5053 time to fit residues: 265.9336 Evaluate side-chains 241 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 218 time to evaluate : 4.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 123 ASN Chi-restraints excluded: chain H residue 191 ILE Chi-restraints excluded: chain I residue 112 LYS Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain K residue 123 ASN Chi-restraints excluded: chain L residue 123 ASN Chi-restraints excluded: chain N residue 190 VAL Chi-restraints excluded: chain O residue 98 LEU Chi-restraints excluded: chain O residue 191 ILE Chi-restraints excluded: chain P residue 182 THR Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain W residue 100 LEU Chi-restraints excluded: chain E residue 123 ASN Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain D residue 123 ASN Chi-restraints excluded: chain Y residue 95 THR Chi-restraints excluded: chain 2 residue 99 GLN Chi-restraints excluded: chain 3 residue 123 ASN Chi-restraints excluded: chain 4 residue 95 THR Chi-restraints excluded: chain 6 residue 36 ILE Chi-restraints excluded: chain 7 residue 26 LEU Chi-restraints excluded: chain 9 residue 84 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 327 optimal weight: 0.0070 chunk 182 optimal weight: 4.9990 chunk 489 optimal weight: 20.0000 chunk 400 optimal weight: 9.9990 chunk 162 optimal weight: 10.0000 chunk 589 optimal weight: 10.0000 chunk 636 optimal weight: 9.9990 chunk 525 optimal weight: 9.9990 chunk 584 optimal weight: 5.9990 chunk 200 optimal weight: 4.9990 chunk 472 optimal weight: 4.9990 overall best weight: 4.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 30 ASN ** H 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 30 ASN L 37 ASN ** M 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 195 GLN R 37 ASN R 102 ASN ** S 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 30 ASN V 30 ASN ** W 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 37 ASN ** X 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 GLN C 30 ASN ** Z 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 30 ASN 3 93 ASN ** 4 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 30 ASN 9 93 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.032 1.135 51300 Z= 2.131 Angle : 0.855 40.086 70596 Z= 0.488 Chirality : 0.051 0.383 8352 Planarity : 0.006 0.080 8856 Dihedral : 6.109 54.991 7308 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 20.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.28 % Favored : 89.62 % Rotamer: Outliers : 1.13 % Allowed : 11.41 % Favored : 87.46 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.09 % Twisted General : 0.03 % 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: -3.04 (0.10), residues: 6408 helix: -4.59 (0.07), residues: 396 sheet: -1.04 (0.10), residues: 2424 loop : -2.48 (0.10), residues: 3588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP L 34 PHE 0.060 0.004 PHE T 200 TYR 0.023 0.001 TYR Y 105 ARG 0.008 0.001 ARG F 55 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 242 time to evaluate : 4.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 26 LEU cc_start: 0.8362 (tp) cc_final: 0.8075 (tp) REVERT: G 40 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.8917 (mp) REVERT: H 186 ASP cc_start: 0.8953 (p0) cc_final: 0.8743 (p0) REVERT: L 57 ASP cc_start: 0.7620 (p0) cc_final: 0.7419 (p0) REVERT: N 44 MET cc_start: 0.6604 (mtp) cc_final: 0.6090 (mtp) REVERT: O 57 ASP cc_start: 0.8173 (p0) cc_final: 0.7707 (p0) REVERT: P 90 ASP cc_start: 0.7567 (t0) cc_final: 0.7323 (t0) REVERT: R 55 ARG cc_start: 0.6001 (ptt180) cc_final: 0.5710 (ptt-90) REVERT: R 177 ASP cc_start: 0.9086 (t0) cc_final: 0.8762 (t0) REVERT: U 90 ASP cc_start: 0.7228 (OUTLIER) cc_final: 0.7025 (m-30) REVERT: X 57 ASP cc_start: 0.7419 (p0) cc_final: 0.6949 (p0) REVERT: E 55 ARG cc_start: 0.6903 (ptm160) cc_final: 0.6560 (mtm110) REVERT: B 35 LEU cc_start: 0.9254 (mp) cc_final: 0.8711 (pp) REVERT: Y 195 GLN cc_start: 0.9010 (OUTLIER) cc_final: 0.7915 (tp40) REVERT: Z 44 MET cc_start: 0.6873 (mtp) cc_final: 0.6580 (mtp) REVERT: 0 35 LEU cc_start: 0.9241 (mp) cc_final: 0.8832 (pp) REVERT: 0 186 ASP cc_start: 0.8824 (p0) cc_final: 0.8572 (p0) REVERT: 6 57 ASP cc_start: 0.8224 (p0) cc_final: 0.8000 (p0) REVERT: 8 90 ASP cc_start: 0.7853 (t0) cc_final: 0.6869 (t0) REVERT: 8 175 LEU cc_start: 0.9254 (tt) cc_final: 0.9000 (tp) REVERT: 9 57 ASP cc_start: 0.7435 (p0) cc_final: 0.6802 (m-30) REVERT: 9 98 LEU cc_start: 0.9279 (mt) cc_final: 0.8912 (tp) outliers start: 64 outliers final: 36 residues processed: 301 average time/residue: 0.4680 time to fit residues: 242.3833 Evaluate side-chains 253 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 214 time to evaluate : 4.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain I residue 112 LYS Chi-restraints excluded: chain J residue 30 ASN Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 123 ASN Chi-restraints excluded: chain N residue 190 VAL Chi-restraints excluded: chain O residue 98 LEU Chi-restraints excluded: chain O residue 191 ILE Chi-restraints excluded: chain P residue 145 VAL Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 37 ASN Chi-restraints excluded: chain S residue 88 THR Chi-restraints excluded: chain S residue 157 THR Chi-restraints excluded: chain T residue 198 VAL Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain U residue 191 ILE Chi-restraints excluded: chain V residue 30 ASN Chi-restraints excluded: chain W residue 100 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain Y residue 157 THR Chi-restraints excluded: chain Y residue 195 GLN Chi-restraints excluded: chain Z residue 198 VAL Chi-restraints excluded: chain 1 residue 26 LEU Chi-restraints excluded: chain 1 residue 30 ASN Chi-restraints excluded: chain 1 residue 145 VAL Chi-restraints excluded: chain 2 residue 99 GLN Chi-restraints excluded: chain 3 residue 123 ASN Chi-restraints excluded: chain 3 residue 198 VAL Chi-restraints excluded: chain 4 residue 88 THR Chi-restraints excluded: chain 4 residue 157 THR Chi-restraints excluded: chain 6 residue 35 LEU Chi-restraints excluded: chain 7 residue 26 LEU Chi-restraints excluded: chain 7 residue 145 VAL Chi-restraints excluded: chain 9 residue 84 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 582 optimal weight: 5.9990 chunk 443 optimal weight: 4.9990 chunk 305 optimal weight: 6.9990 chunk 65 optimal weight: 7.9990 chunk 281 optimal weight: 5.9990 chunk 395 optimal weight: 10.0000 chunk 591 optimal weight: 0.6980 chunk 626 optimal weight: 5.9990 chunk 309 optimal weight: 20.0000 chunk 560 optimal weight: 3.9990 chunk 168 optimal weight: 9.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 30 ASN ** H 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 37 ASN ** R 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 195 GLN ** X 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN ** Z 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 195 GLN ** 4 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.032 1.130 51300 Z= 2.131 Angle : 0.860 40.356 70596 Z= 0.488 Chirality : 0.051 0.360 8352 Planarity : 0.006 0.141 8856 Dihedral : 6.113 56.508 7308 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 20.58 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.72 % Favored : 89.17 % Rotamer: Outliers : 1.63 % Allowed : 13.31 % Favored : 85.07 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.09 % Twisted General : 0.03 % 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: -3.02 (0.10), residues: 6408 helix: -4.57 (0.07), residues: 396 sheet: -1.00 (0.10), residues: 2394 loop : -2.48 (0.10), residues: 3618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP L 34 PHE 0.059 0.004 PHE T 200 TYR 0.025 0.001 TYR S 105 ARG 0.009 0.001 ARG 5 55 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 238 time to evaluate : 4.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 26 LEU cc_start: 0.8363 (tp) cc_final: 0.7847 (tt) REVERT: H 55 ARG cc_start: 0.3171 (ttt180) cc_final: 0.2675 (ttt-90) REVERT: H 186 ASP cc_start: 0.8949 (p0) cc_final: 0.8732 (p0) REVERT: J 130 ASP cc_start: 0.8433 (m-30) cc_final: 0.7553 (t0) REVERT: N 44 MET cc_start: 0.7246 (mtp) cc_final: 0.6656 (mtp) REVERT: O 57 ASP cc_start: 0.8222 (p0) cc_final: 0.7727 (p0) REVERT: P 90 ASP cc_start: 0.7687 (t0) cc_final: 0.7411 (t0) REVERT: Q 129 LYS cc_start: 0.8881 (tttt) cc_final: 0.8579 (ttpt) REVERT: R 177 ASP cc_start: 0.9098 (t0) cc_final: 0.8751 (t0) REVERT: U 90 ASP cc_start: 0.7251 (OUTLIER) cc_final: 0.7028 (m-30) REVERT: V 30 ASN cc_start: 0.9118 (OUTLIER) cc_final: 0.8906 (t0) REVERT: W 31 LEU cc_start: 0.9127 (tp) cc_final: 0.8895 (tp) REVERT: X 57 ASP cc_start: 0.7603 (p0) cc_final: 0.7195 (p0) REVERT: B 35 LEU cc_start: 0.9269 (mp) cc_final: 0.8733 (pp) REVERT: B 90 ASP cc_start: 0.8764 (OUTLIER) cc_final: 0.8556 (m-30) REVERT: D 175 LEU cc_start: 0.8768 (tt) cc_final: 0.8301 (tp) REVERT: Y 195 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.7997 (tp40) REVERT: Z 44 MET cc_start: 0.6825 (mtp) cc_final: 0.6590 (mtp) REVERT: 0 35 LEU cc_start: 0.9263 (mp) cc_final: 0.8908 (pp) REVERT: 2 175 LEU cc_start: 0.9233 (tt) cc_final: 0.8778 (tp) REVERT: 6 46 TYR cc_start: 0.6693 (m-10) cc_final: 0.6491 (m-10) REVERT: 6 57 ASP cc_start: 0.8196 (p0) cc_final: 0.7976 (p0) REVERT: 8 90 ASP cc_start: 0.7801 (t0) cc_final: 0.6964 (t0) REVERT: 8 92 THR cc_start: 0.8610 (OUTLIER) cc_final: 0.7385 (m) REVERT: 8 175 LEU cc_start: 0.9249 (tt) cc_final: 0.8992 (tp) REVERT: 9 57 ASP cc_start: 0.7522 (p0) cc_final: 0.6964 (m-30) REVERT: 9 98 LEU cc_start: 0.9319 (mt) cc_final: 0.8916 (tp) outliers start: 92 outliers final: 51 residues processed: 320 average time/residue: 0.4642 time to fit residues: 255.4778 Evaluate side-chains 270 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 214 time to evaluate : 4.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 191 ILE Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 123 ASN Chi-restraints excluded: chain L residue 137 ASN Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 101 CYS Chi-restraints excluded: chain M residue 157 THR Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 190 VAL Chi-restraints excluded: chain O residue 98 LEU Chi-restraints excluded: chain O residue 191 ILE Chi-restraints excluded: chain P residue 182 THR Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain S residue 88 THR Chi-restraints excluded: chain S residue 157 THR Chi-restraints excluded: chain T residue 198 VAL Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain V residue 30 ASN Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 137 ASN Chi-restraints excluded: chain Y residue 88 THR Chi-restraints excluded: chain Y residue 95 THR Chi-restraints excluded: chain Y residue 157 THR Chi-restraints excluded: chain Y residue 195 GLN Chi-restraints excluded: chain Z residue 198 VAL Chi-restraints excluded: chain 0 residue 72 ASP Chi-restraints excluded: chain 0 residue 191 ILE Chi-restraints excluded: chain 1 residue 26 LEU Chi-restraints excluded: chain 2 residue 53 ILE Chi-restraints excluded: chain 2 residue 99 GLN Chi-restraints excluded: chain 3 residue 123 ASN Chi-restraints excluded: chain 3 residue 137 ASN Chi-restraints excluded: chain 3 residue 198 VAL Chi-restraints excluded: chain 4 residue 40 LEU Chi-restraints excluded: chain 4 residue 88 THR Chi-restraints excluded: chain 4 residue 95 THR Chi-restraints excluded: chain 4 residue 157 THR Chi-restraints excluded: chain 6 residue 35 LEU Chi-restraints excluded: chain 7 residue 26 LEU Chi-restraints excluded: chain 7 residue 145 VAL Chi-restraints excluded: chain 8 residue 92 THR Chi-restraints excluded: chain 9 residue 137 ASN Chi-restraints excluded: chain 9 residue 175 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 521 optimal weight: 6.9990 chunk 355 optimal weight: 8.9990 chunk 9 optimal weight: 7.9990 chunk 466 optimal weight: 10.0000 chunk 258 optimal weight: 8.9990 chunk 534 optimal weight: 10.0000 chunk 432 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 319 optimal weight: 30.0000 chunk 562 optimal weight: 5.9990 chunk 158 optimal weight: 7.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 ASN ** M 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 30 ASN X 102 ASN ** X 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN C 37 ASN F 93 ASN ** Z 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 30 ASN ** 4 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.032 1.126 51300 Z= 2.152 Angle : 0.906 40.598 70596 Z= 0.509 Chirality : 0.052 0.344 8352 Planarity : 0.007 0.144 8856 Dihedral : 6.361 58.742 7308 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 22.03 Ramachandran Plot: Outliers : 0.19 % Allowed : 11.67 % Favored : 88.14 % Rotamer: Outliers : 2.30 % Allowed : 14.95 % Favored : 82.75 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.09 % Twisted General : 0.03 % 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: -3.21 (0.10), residues: 6408 helix: -4.59 (0.07), residues: 432 sheet: -1.19 (0.10), residues: 2568 loop : -2.59 (0.10), residues: 3408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP L 34 PHE 0.056 0.004 PHE T 200 TYR 0.026 0.002 TYR 2 105 ARG 0.031 0.001 ARG 5 55 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 223 time to evaluate : 4.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 26 LEU cc_start: 0.8220 (tp) cc_final: 0.7729 (tt) REVERT: H 55 ARG cc_start: 0.3277 (ttt180) cc_final: 0.2767 (ttt-90) REVERT: H 145 VAL cc_start: 0.9396 (OUTLIER) cc_final: 0.9037 (p) REVERT: H 185 ARG cc_start: 0.7162 (tpp-160) cc_final: 0.6046 (tpt90) REVERT: I 191 ILE cc_start: 0.8327 (OUTLIER) cc_final: 0.7980 (mp) REVERT: N 44 MET cc_start: 0.7261 (mtp) cc_final: 0.6722 (mtp) REVERT: O 35 LEU cc_start: 0.9183 (mp) cc_final: 0.8898 (mt) REVERT: O 46 TYR cc_start: 0.5152 (m-10) cc_final: 0.4950 (m-80) REVERT: O 57 ASP cc_start: 0.8147 (p0) cc_final: 0.7671 (p0) REVERT: P 90 ASP cc_start: 0.7900 (t0) cc_final: 0.7592 (t0) REVERT: Q 129 LYS cc_start: 0.8902 (tttt) cc_final: 0.8620 (ttpt) REVERT: R 55 ARG cc_start: 0.6581 (ptt180) cc_final: 0.6324 (ptt-90) REVERT: R 57 ASP cc_start: 0.7620 (p0) cc_final: 0.7309 (p0) REVERT: R 65 VAL cc_start: 0.8908 (OUTLIER) cc_final: 0.8635 (p) REVERT: R 177 ASP cc_start: 0.9130 (t0) cc_final: 0.8750 (t0) REVERT: S 44 MET cc_start: 0.6487 (OUTLIER) cc_final: 0.6269 (mmm) REVERT: U 90 ASP cc_start: 0.7381 (OUTLIER) cc_final: 0.7096 (m-30) REVERT: W 31 LEU cc_start: 0.9189 (tp) cc_final: 0.8930 (tp) REVERT: W 146 GLN cc_start: 0.6909 (OUTLIER) cc_final: 0.6519 (tp40) REVERT: X 46 TYR cc_start: 0.6654 (m-10) cc_final: 0.6364 (m-10) REVERT: X 57 ASP cc_start: 0.7858 (p0) cc_final: 0.7585 (p0) REVERT: E 44 MET cc_start: 0.6826 (mtp) cc_final: 0.6384 (mtp) REVERT: B 35 LEU cc_start: 0.9301 (mp) cc_final: 0.8776 (pp) REVERT: B 90 ASP cc_start: 0.8803 (OUTLIER) cc_final: 0.8592 (m-30) REVERT: B 186 ASP cc_start: 0.8085 (p0) cc_final: 0.7850 (p0) REVERT: D 130 ASP cc_start: 0.9138 (t0) cc_final: 0.8923 (t0) REVERT: D 175 LEU cc_start: 0.8826 (tt) cc_final: 0.8358 (tp) REVERT: F 65 VAL cc_start: 0.8155 (OUTLIER) cc_final: 0.7694 (p) REVERT: 0 35 LEU cc_start: 0.9202 (mp) cc_final: 0.8988 (pp) REVERT: 0 109 LEU cc_start: 0.9079 (mt) cc_final: 0.8649 (mt) REVERT: 0 121 THR cc_start: 0.9225 (OUTLIER) cc_final: 0.8931 (p) REVERT: 0 186 ASP cc_start: 0.8624 (p0) cc_final: 0.8417 (p0) REVERT: 5 145 VAL cc_start: 0.9227 (OUTLIER) cc_final: 0.9018 (p) REVERT: 6 46 TYR cc_start: 0.6953 (m-10) cc_final: 0.6714 (m-80) REVERT: 6 57 ASP cc_start: 0.8175 (p0) cc_final: 0.7953 (p0) REVERT: 6 69 TYR cc_start: 0.6998 (OUTLIER) cc_final: 0.6186 (p90) REVERT: 8 90 ASP cc_start: 0.7775 (t0) cc_final: 0.7133 (t0) REVERT: 8 175 LEU cc_start: 0.9261 (tt) cc_final: 0.8978 (tp) REVERT: 9 57 ASP cc_start: 0.7618 (p0) cc_final: 0.7162 (m-30) REVERT: 9 98 LEU cc_start: 0.9415 (mt) cc_final: 0.9005 (tp) outliers start: 130 outliers final: 76 residues processed: 343 average time/residue: 0.4796 time to fit residues: 283.0257 Evaluate side-chains 288 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 201 time to evaluate : 4.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain H residue 95 THR Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain I residue 72 ASP Chi-restraints excluded: chain I residue 112 LYS Chi-restraints excluded: chain I residue 145 VAL Chi-restraints excluded: chain I residue 191 ILE Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 191 ILE Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain L residue 123 ASN Chi-restraints excluded: chain L residue 137 ASN Chi-restraints excluded: chain M residue 101 CYS Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 157 THR Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 101 CYS Chi-restraints excluded: chain N residue 190 VAL Chi-restraints excluded: chain O residue 72 ASP Chi-restraints excluded: chain O residue 98 LEU Chi-restraints excluded: chain O residue 191 ILE Chi-restraints excluded: chain P residue 33 TYR Chi-restraints excluded: chain P residue 145 VAL Chi-restraints excluded: chain P residue 182 THR Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain S residue 44 MET Chi-restraints excluded: chain S residue 88 THR Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain S residue 157 THR Chi-restraints excluded: chain T residue 198 VAL Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain U residue 95 THR Chi-restraints excluded: chain U residue 191 ILE Chi-restraints excluded: chain W residue 146 GLN Chi-restraints excluded: chain W residue 198 VAL Chi-restraints excluded: chain X residue 30 ASN Chi-restraints excluded: chain X residue 137 ASN Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain F residue 28 PHE Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 93 ASN Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 137 ASN Chi-restraints excluded: chain Y residue 95 THR Chi-restraints excluded: chain Y residue 157 THR Chi-restraints excluded: chain Z residue 34 TRP Chi-restraints excluded: chain Z residue 198 VAL Chi-restraints excluded: chain 0 residue 72 ASP Chi-restraints excluded: chain 0 residue 121 THR Chi-restraints excluded: chain 0 residue 191 ILE Chi-restraints excluded: chain 1 residue 26 LEU Chi-restraints excluded: chain 1 residue 145 VAL Chi-restraints excluded: chain 2 residue 53 ILE Chi-restraints excluded: chain 2 residue 99 GLN Chi-restraints excluded: chain 3 residue 123 ASN Chi-restraints excluded: chain 3 residue 137 ASN Chi-restraints excluded: chain 3 residue 198 VAL Chi-restraints excluded: chain 4 residue 40 LEU Chi-restraints excluded: chain 4 residue 88 THR Chi-restraints excluded: chain 4 residue 95 THR Chi-restraints excluded: chain 4 residue 157 THR Chi-restraints excluded: chain 5 residue 98 LEU Chi-restraints excluded: chain 5 residue 101 CYS Chi-restraints excluded: chain 5 residue 145 VAL Chi-restraints excluded: chain 6 residue 35 LEU Chi-restraints excluded: chain 6 residue 69 TYR Chi-restraints excluded: chain 7 residue 26 LEU Chi-restraints excluded: chain 7 residue 145 VAL Chi-restraints excluded: chain 9 residue 137 ASN Chi-restraints excluded: chain 9 residue 175 LEU Chi-restraints excluded: chain 9 residue 198 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 210 optimal weight: 2.9990 chunk 564 optimal weight: 5.9990 chunk 123 optimal weight: 0.9990 chunk 367 optimal weight: 2.9990 chunk 154 optimal weight: 0.9990 chunk 626 optimal weight: 10.0000 chunk 520 optimal weight: 20.0000 chunk 290 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 207 optimal weight: 30.0000 chunk 329 optimal weight: 0.0370 overall best weight: 1.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 148 GLN ** T 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN F 93 ASN F 102 ASN ** Z 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 30 ASN 2 146 GLN 2 148 GLN ** 7 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.031 1.140 51300 Z= 2.112 Angle : 0.820 40.844 70596 Z= 0.466 Chirality : 0.050 0.367 8352 Planarity : 0.006 0.080 8856 Dihedral : 5.978 55.983 7308 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 18.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.88 % Favored : 90.03 % Rotamer: Outliers : 1.38 % Allowed : 16.45 % Favored : 82.17 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.09 % Twisted General : 0.02 % 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: -2.88 (0.10), residues: 6408 helix: -4.51 (0.08), residues: 396 sheet: -1.00 (0.10), residues: 2448 loop : -2.32 (0.10), residues: 3564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP R 34 PHE 0.052 0.003 PHE T 200 TYR 0.022 0.001 TYR A 105 ARG 0.011 0.000 ARG A 55 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 241 time to evaluate : 4.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 26 LEU cc_start: 0.8148 (tp) cc_final: 0.7620 (tt) REVERT: H 55 ARG cc_start: 0.3152 (ttt180) cc_final: 0.2705 (ttt-90) REVERT: H 185 ARG cc_start: 0.7095 (tpp-160) cc_final: 0.5807 (tpt170) REVERT: J 32 THR cc_start: 0.7613 (OUTLIER) cc_final: 0.7389 (p) REVERT: J 130 ASP cc_start: 0.8374 (m-30) cc_final: 0.7563 (t0) REVERT: K 28 PHE cc_start: 0.7635 (OUTLIER) cc_final: 0.6990 (m-80) REVERT: L 177 ASP cc_start: 0.9212 (t0) cc_final: 0.8943 (t0) REVERT: N 44 MET cc_start: 0.7488 (mtp) cc_final: 0.6983 (mtp) REVERT: O 35 LEU cc_start: 0.9191 (mp) cc_final: 0.8937 (mt) REVERT: O 57 ASP cc_start: 0.8239 (p0) cc_final: 0.7757 (p0) REVERT: P 90 ASP cc_start: 0.7832 (t0) cc_final: 0.7546 (t0) REVERT: P 130 ASP cc_start: 0.8704 (m-30) cc_final: 0.7641 (t0) REVERT: Q 129 LYS cc_start: 0.8914 (tttt) cc_final: 0.8626 (ttpt) REVERT: R 57 ASP cc_start: 0.7435 (p0) cc_final: 0.7136 (p0) REVERT: R 167 CYS cc_start: 0.7919 (OUTLIER) cc_final: 0.7686 (t) REVERT: R 177 ASP cc_start: 0.9166 (t0) cc_final: 0.8820 (t0) REVERT: S 44 MET cc_start: 0.6426 (OUTLIER) cc_final: 0.5443 (mmm) REVERT: U 90 ASP cc_start: 0.7186 (OUTLIER) cc_final: 0.6851 (m-30) REVERT: X 57 ASP cc_start: 0.7662 (p0) cc_final: 0.7421 (p0) REVERT: E 44 MET cc_start: 0.6647 (mtp) cc_final: 0.6197 (mtp) REVERT: E 95 THR cc_start: 0.8731 (OUTLIER) cc_final: 0.8409 (t) REVERT: B 35 LEU cc_start: 0.9277 (mp) cc_final: 0.8785 (pp) REVERT: B 90 ASP cc_start: 0.8733 (OUTLIER) cc_final: 0.8454 (m-30) REVERT: D 130 ASP cc_start: 0.9142 (t0) cc_final: 0.8887 (t0) REVERT: D 175 LEU cc_start: 0.8769 (tt) cc_final: 0.8295 (tp) REVERT: F 65 VAL cc_start: 0.8194 (OUTLIER) cc_final: 0.7769 (p) REVERT: 0 109 LEU cc_start: 0.9035 (mt) cc_final: 0.8598 (mt) REVERT: 0 186 ASP cc_start: 0.8621 (p0) cc_final: 0.8386 (p0) REVERT: 1 44 MET cc_start: 0.2292 (tpt) cc_final: 0.1374 (tpt) REVERT: 4 44 MET cc_start: 0.4725 (OUTLIER) cc_final: 0.3831 (mmt) REVERT: 5 145 VAL cc_start: 0.9169 (OUTLIER) cc_final: 0.8888 (p) REVERT: 6 46 TYR cc_start: 0.6607 (m-10) cc_final: 0.6317 (m-80) REVERT: 8 90 ASP cc_start: 0.7682 (t0) cc_final: 0.7139 (t0) REVERT: 8 175 LEU cc_start: 0.9188 (tt) cc_final: 0.8899 (tp) REVERT: 9 57 ASP cc_start: 0.7546 (p0) cc_final: 0.7120 (m-30) REVERT: 9 98 LEU cc_start: 0.9409 (mt) cc_final: 0.9006 (tp) outliers start: 78 outliers final: 50 residues processed: 316 average time/residue: 0.5255 time to fit residues: 287.7267 Evaluate side-chains 271 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 211 time to evaluate : 4.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 101 CYS Chi-restraints excluded: chain I residue 112 LYS Chi-restraints excluded: chain I residue 145 VAL Chi-restraints excluded: chain I residue 198 VAL Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain K residue 28 PHE Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 123 ASN Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 101 CYS Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 157 THR Chi-restraints excluded: chain N residue 29 THR Chi-restraints excluded: chain N residue 101 CYS Chi-restraints excluded: chain N residue 190 VAL Chi-restraints excluded: chain O residue 72 ASP Chi-restraints excluded: chain P residue 33 TYR Chi-restraints excluded: chain P residue 145 VAL Chi-restraints excluded: chain P residue 182 THR Chi-restraints excluded: chain Q residue 160 VAL Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 167 CYS Chi-restraints excluded: chain S residue 44 MET Chi-restraints excluded: chain S residue 157 THR Chi-restraints excluded: chain T residue 198 VAL Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain U residue 128 ILE Chi-restraints excluded: chain V residue 122 THR Chi-restraints excluded: chain X residue 30 ASN Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain Z residue 186 ASP Chi-restraints excluded: chain 1 residue 26 LEU Chi-restraints excluded: chain 1 residue 30 ASN Chi-restraints excluded: chain 1 residue 145 VAL Chi-restraints excluded: chain 2 residue 28 PHE Chi-restraints excluded: chain 3 residue 123 ASN Chi-restraints excluded: chain 3 residue 198 VAL Chi-restraints excluded: chain 4 residue 40 LEU Chi-restraints excluded: chain 4 residue 44 MET Chi-restraints excluded: chain 5 residue 40 LEU Chi-restraints excluded: chain 5 residue 145 VAL Chi-restraints excluded: chain 5 residue 160 VAL Chi-restraints excluded: chain 5 residue 196 VAL Chi-restraints excluded: chain 6 residue 35 LEU Chi-restraints excluded: chain 6 residue 72 ASP Chi-restraints excluded: chain 7 residue 26 LEU Chi-restraints excluded: chain 7 residue 145 VAL Chi-restraints excluded: chain 8 residue 122 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 604 optimal weight: 1.9990 chunk 70 optimal weight: 20.0000 chunk 357 optimal weight: 3.9990 chunk 457 optimal weight: 5.9990 chunk 354 optimal weight: 4.9990 chunk 527 optimal weight: 30.0000 chunk 350 optimal weight: 10.0000 chunk 624 optimal weight: 5.9990 chunk 390 optimal weight: 0.0970 chunk 380 optimal weight: 10.0000 chunk 288 optimal weight: 20.0000 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 148 GLN ** S 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 30 ASN ** V 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 30 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.032 1.131 51300 Z= 2.120 Angle : 0.844 40.888 70596 Z= 0.475 Chirality : 0.050 0.361 8352 Planarity : 0.006 0.090 8856 Dihedral : 5.937 55.920 7308 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 19.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.74 % Favored : 89.17 % Rotamer: Outliers : 2.00 % Allowed : 16.72 % Favored : 81.28 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.34 % Twisted General : 0.03 % 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: -2.98 (0.10), residues: 6408 helix: -4.52 (0.08), residues: 432 sheet: -1.02 (0.10), residues: 2448 loop : -2.39 (0.10), residues: 3528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP L 34 PHE 0.052 0.003 PHE Z 200 TYR 0.047 0.001 TYR U 105 ARG 0.030 0.001 ARG N 55 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 213 time to evaluate : 4.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 26 LEU cc_start: 0.8145 (tp) cc_final: 0.7608 (tt) REVERT: H 55 ARG cc_start: 0.3219 (ttt180) cc_final: 0.2799 (ttt-90) REVERT: H 145 VAL cc_start: 0.9374 (OUTLIER) cc_final: 0.9017 (p) REVERT: H 185 ARG cc_start: 0.7159 (tpp-160) cc_final: 0.5924 (tpt170) REVERT: J 32 THR cc_start: 0.7616 (OUTLIER) cc_final: 0.7378 (p) REVERT: J 130 ASP cc_start: 0.8359 (m-30) cc_final: 0.7523 (t0) REVERT: K 28 PHE cc_start: 0.7666 (OUTLIER) cc_final: 0.6978 (m-80) REVERT: N 44 MET cc_start: 0.7168 (mtp) cc_final: 0.6654 (mtp) REVERT: O 35 LEU cc_start: 0.9178 (mp) cc_final: 0.8934 (mt) REVERT: O 57 ASP cc_start: 0.8196 (p0) cc_final: 0.7728 (p0) REVERT: P 90 ASP cc_start: 0.7880 (t0) cc_final: 0.7593 (t0) REVERT: P 130 ASP cc_start: 0.8720 (m-30) cc_final: 0.7642 (t0) REVERT: Q 129 LYS cc_start: 0.8951 (tttt) cc_final: 0.8682 (ttpt) REVERT: R 57 ASP cc_start: 0.7798 (p0) cc_final: 0.7452 (p0) REVERT: R 167 CYS cc_start: 0.7693 (OUTLIER) cc_final: 0.7465 (t) REVERT: R 177 ASP cc_start: 0.9177 (t0) cc_final: 0.8811 (t0) REVERT: S 44 MET cc_start: 0.6588 (OUTLIER) cc_final: 0.6322 (mmm) REVERT: U 90 ASP cc_start: 0.7283 (OUTLIER) cc_final: 0.6935 (m-30) REVERT: X 57 ASP cc_start: 0.7780 (p0) cc_final: 0.7514 (p0) REVERT: E 44 MET cc_start: 0.6599 (mtp) cc_final: 0.6155 (mtp) REVERT: E 95 THR cc_start: 0.8741 (OUTLIER) cc_final: 0.8445 (t) REVERT: B 35 LEU cc_start: 0.9276 (mp) cc_final: 0.8832 (pp) REVERT: B 90 ASP cc_start: 0.8727 (OUTLIER) cc_final: 0.8457 (m-30) REVERT: D 130 ASP cc_start: 0.9193 (t0) cc_final: 0.8943 (t0) REVERT: D 175 LEU cc_start: 0.8800 (tt) cc_final: 0.8323 (tp) REVERT: F 65 VAL cc_start: 0.8185 (OUTLIER) cc_final: 0.7712 (p) REVERT: 0 109 LEU cc_start: 0.9059 (mt) cc_final: 0.8572 (mt) REVERT: 0 186 ASP cc_start: 0.8667 (p0) cc_final: 0.8382 (p0) REVERT: 1 44 MET cc_start: 0.2410 (tpt) cc_final: 0.1308 (tpt) REVERT: 2 175 LEU cc_start: 0.9159 (tt) cc_final: 0.8704 (tp) REVERT: 4 44 MET cc_start: 0.4641 (OUTLIER) cc_final: 0.3622 (mmt) REVERT: 5 55 ARG cc_start: 0.6817 (OUTLIER) cc_final: 0.6536 (mtp180) REVERT: 5 145 VAL cc_start: 0.9178 (OUTLIER) cc_final: 0.8902 (p) REVERT: 6 46 TYR cc_start: 0.6795 (m-10) cc_final: 0.6405 (m-80) REVERT: 8 90 ASP cc_start: 0.7727 (t0) cc_final: 0.7259 (t0) REVERT: 8 175 LEU cc_start: 0.9189 (tt) cc_final: 0.8891 (tp) REVERT: 9 57 ASP cc_start: 0.7591 (p0) cc_final: 0.7163 (m-30) REVERT: 9 98 LEU cc_start: 0.9429 (mt) cc_final: 0.9040 (tp) outliers start: 113 outliers final: 80 residues processed: 317 average time/residue: 0.4730 time to fit residues: 260.9984 Evaluate side-chains 297 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 205 time to evaluate : 4.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 44 MET Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 95 THR Chi-restraints excluded: chain H residue 101 CYS Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 191 ILE Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain I residue 145 VAL Chi-restraints excluded: chain I residue 198 VAL Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain K residue 28 PHE Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 123 ASN Chi-restraints excluded: chain L residue 137 ASN Chi-restraints excluded: chain L residue 162 ILE Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 51 THR Chi-restraints excluded: chain M residue 101 CYS Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 157 THR Chi-restraints excluded: chain N residue 29 THR Chi-restraints excluded: chain N residue 101 CYS Chi-restraints excluded: chain N residue 190 VAL Chi-restraints excluded: chain N residue 198 VAL Chi-restraints excluded: chain O residue 72 ASP Chi-restraints excluded: chain O residue 98 LEU Chi-restraints excluded: chain O residue 128 ILE Chi-restraints excluded: chain O residue 191 ILE Chi-restraints excluded: chain P residue 33 TYR Chi-restraints excluded: chain P residue 145 VAL Chi-restraints excluded: chain P residue 182 THR Chi-restraints excluded: chain Q residue 101 CYS Chi-restraints excluded: chain Q residue 160 VAL Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 162 ILE Chi-restraints excluded: chain R residue 167 CYS Chi-restraints excluded: chain S residue 44 MET Chi-restraints excluded: chain S residue 157 THR Chi-restraints excluded: chain T residue 198 VAL Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain U residue 128 ILE Chi-restraints excluded: chain V residue 122 THR Chi-restraints excluded: chain W residue 198 VAL Chi-restraints excluded: chain X residue 30 ASN Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain F residue 28 PHE Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain Z residue 95 THR Chi-restraints excluded: chain Z residue 186 ASP Chi-restraints excluded: chain Z residue 198 VAL Chi-restraints excluded: chain 0 residue 35 LEU Chi-restraints excluded: chain 0 residue 72 ASP Chi-restraints excluded: chain 1 residue 26 LEU Chi-restraints excluded: chain 1 residue 145 VAL Chi-restraints excluded: chain 2 residue 28 PHE Chi-restraints excluded: chain 2 residue 53 ILE Chi-restraints excluded: chain 2 residue 99 GLN Chi-restraints excluded: chain 2 residue 198 VAL Chi-restraints excluded: chain 3 residue 123 ASN Chi-restraints excluded: chain 3 residue 137 ASN Chi-restraints excluded: chain 3 residue 198 VAL Chi-restraints excluded: chain 4 residue 27 THR Chi-restraints excluded: chain 4 residue 40 LEU Chi-restraints excluded: chain 4 residue 44 MET Chi-restraints excluded: chain 4 residue 157 THR Chi-restraints excluded: chain 5 residue 55 ARG Chi-restraints excluded: chain 5 residue 101 CYS Chi-restraints excluded: chain 5 residue 145 VAL Chi-restraints excluded: chain 5 residue 160 VAL Chi-restraints excluded: chain 5 residue 196 VAL Chi-restraints excluded: chain 6 residue 35 LEU Chi-restraints excluded: chain 6 residue 72 ASP Chi-restraints excluded: chain 7 residue 26 LEU Chi-restraints excluded: chain 7 residue 145 VAL Chi-restraints excluded: chain 8 residue 122 THR Chi-restraints excluded: chain 8 residue 198 VAL Chi-restraints excluded: chain 9 residue 137 ASN Chi-restraints excluded: chain 9 residue 175 LEU Chi-restraints excluded: chain 9 residue 198 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 386 optimal weight: 20.0000 chunk 249 optimal weight: 3.9990 chunk 373 optimal weight: 4.9990 chunk 188 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 397 optimal weight: 1.9990 chunk 425 optimal weight: 2.9990 chunk 308 optimal weight: 0.9990 chunk 58 optimal weight: 20.0000 chunk 490 optimal weight: 7.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 30 ASN ** V 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.031 1.135 51300 Z= 2.113 Angle : 0.824 40.961 70596 Z= 0.466 Chirality : 0.050 0.377 8352 Planarity : 0.006 0.079 8856 Dihedral : 5.841 55.087 7308 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 18.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.02 % Favored : 89.89 % Rotamer: Outliers : 1.77 % Allowed : 17.36 % Favored : 80.87 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.34 % Twisted General : 0.02 % 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: -2.98 (0.10), residues: 6408 helix: -4.40 (0.08), residues: 474 sheet: -1.02 (0.10), residues: 2460 loop : -2.38 (0.10), residues: 3474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP R 34 PHE 0.057 0.003 PHE T 200 TYR 0.034 0.001 TYR U 105 ARG 0.027 0.001 ARG N 55 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 225 time to evaluate : 4.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 26 LEU cc_start: 0.8130 (tp) cc_final: 0.7608 (tt) REVERT: H 55 ARG cc_start: 0.3160 (ttt180) cc_final: 0.2800 (ttt-90) REVERT: H 145 VAL cc_start: 0.9337 (OUTLIER) cc_final: 0.8953 (p) REVERT: H 185 ARG cc_start: 0.7132 (tpp-160) cc_final: 0.5962 (tpt170) REVERT: J 32 THR cc_start: 0.7506 (OUTLIER) cc_final: 0.7256 (p) REVERT: J 130 ASP cc_start: 0.8283 (m-30) cc_final: 0.7502 (t0) REVERT: K 28 PHE cc_start: 0.7635 (OUTLIER) cc_final: 0.7005 (m-80) REVERT: K 195 GLN cc_start: 0.4605 (OUTLIER) cc_final: 0.4284 (mp10) REVERT: N 44 MET cc_start: 0.7681 (mtp) cc_final: 0.7177 (mtp) REVERT: O 35 LEU cc_start: 0.9186 (mp) cc_final: 0.8949 (mt) REVERT: O 44 MET cc_start: 0.3676 (tpt) cc_final: 0.3391 (tpt) REVERT: O 57 ASP cc_start: 0.8219 (p0) cc_final: 0.7743 (p0) REVERT: P 130 ASP cc_start: 0.8671 (m-30) cc_final: 0.7663 (t0) REVERT: Q 129 LYS cc_start: 0.8952 (tttt) cc_final: 0.8683 (ttpt) REVERT: R 57 ASP cc_start: 0.7807 (p0) cc_final: 0.7469 (p0) REVERT: R 167 CYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7749 (t) REVERT: R 177 ASP cc_start: 0.9211 (t0) cc_final: 0.8840 (t0) REVERT: U 90 ASP cc_start: 0.7233 (OUTLIER) cc_final: 0.6894 (m-30) REVERT: X 57 ASP cc_start: 0.7766 (p0) cc_final: 0.7529 (p0) REVERT: E 44 MET cc_start: 0.6928 (mtp) cc_final: 0.6332 (mtp) REVERT: E 95 THR cc_start: 0.8722 (OUTLIER) cc_final: 0.8408 (t) REVERT: B 35 LEU cc_start: 0.9244 (mp) cc_final: 0.8818 (pp) REVERT: B 90 ASP cc_start: 0.8711 (OUTLIER) cc_final: 0.8451 (m-30) REVERT: C 44 MET cc_start: 0.2149 (tpt) cc_final: 0.1838 (tpt) REVERT: D 130 ASP cc_start: 0.9203 (t0) cc_final: 0.8982 (t0) REVERT: D 175 LEU cc_start: 0.8836 (tt) cc_final: 0.8387 (tp) REVERT: F 65 VAL cc_start: 0.8195 (OUTLIER) cc_final: 0.7714 (p) REVERT: 0 109 LEU cc_start: 0.9064 (mt) cc_final: 0.8587 (mt) REVERT: 0 186 ASP cc_start: 0.8671 (p0) cc_final: 0.8373 (p0) REVERT: 1 44 MET cc_start: 0.2133 (tpt) cc_final: 0.1153 (tpt) REVERT: 2 175 LEU cc_start: 0.9147 (tt) cc_final: 0.8713 (tp) REVERT: 4 44 MET cc_start: 0.4352 (OUTLIER) cc_final: 0.3309 (mmt) REVERT: 5 63 ARG cc_start: 0.8287 (mmm-85) cc_final: 0.7884 (mmm-85) REVERT: 6 46 TYR cc_start: 0.6753 (m-10) cc_final: 0.6364 (m-80) REVERT: 9 57 ASP cc_start: 0.7591 (p0) cc_final: 0.7218 (m-30) REVERT: 9 98 LEU cc_start: 0.9415 (mt) cc_final: 0.9029 (tp) outliers start: 100 outliers final: 76 residues processed: 317 average time/residue: 0.5011 time to fit residues: 275.3693 Evaluate side-chains 292 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 206 time to evaluate : 4.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 44 MET Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 101 CYS Chi-restraints excluded: chain H residue 105 TYR Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain I residue 72 ASP Chi-restraints excluded: chain I residue 112 LYS Chi-restraints excluded: chain I residue 145 VAL Chi-restraints excluded: chain I residue 198 VAL Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain K residue 28 PHE Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain K residue 195 GLN Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 123 ASN Chi-restraints excluded: chain L residue 162 ILE Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 101 CYS Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 157 THR Chi-restraints excluded: chain N residue 29 THR Chi-restraints excluded: chain N residue 101 CYS Chi-restraints excluded: chain N residue 160 VAL Chi-restraints excluded: chain N residue 198 VAL Chi-restraints excluded: chain O residue 72 ASP Chi-restraints excluded: chain O residue 98 LEU Chi-restraints excluded: chain O residue 128 ILE Chi-restraints excluded: chain P residue 33 TYR Chi-restraints excluded: chain P residue 145 VAL Chi-restraints excluded: chain P residue 182 THR Chi-restraints excluded: chain Q residue 101 CYS Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain Q residue 160 VAL Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 162 ILE Chi-restraints excluded: chain R residue 167 CYS Chi-restraints excluded: chain S residue 157 THR Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain U residue 128 ILE Chi-restraints excluded: chain V residue 122 THR Chi-restraints excluded: chain W residue 122 THR Chi-restraints excluded: chain X residue 30 ASN Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain F residue 28 PHE Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain Y residue 88 THR Chi-restraints excluded: chain Z residue 186 ASP Chi-restraints excluded: chain Z residue 198 VAL Chi-restraints excluded: chain 0 residue 72 ASP Chi-restraints excluded: chain 1 residue 26 LEU Chi-restraints excluded: chain 1 residue 145 VAL Chi-restraints excluded: chain 2 residue 28 PHE Chi-restraints excluded: chain 2 residue 198 VAL Chi-restraints excluded: chain 3 residue 198 VAL Chi-restraints excluded: chain 4 residue 27 THR Chi-restraints excluded: chain 4 residue 40 LEU Chi-restraints excluded: chain 4 residue 44 MET Chi-restraints excluded: chain 4 residue 95 THR Chi-restraints excluded: chain 4 residue 157 THR Chi-restraints excluded: chain 5 residue 40 LEU Chi-restraints excluded: chain 5 residue 101 CYS Chi-restraints excluded: chain 5 residue 160 VAL Chi-restraints excluded: chain 5 residue 196 VAL Chi-restraints excluded: chain 6 residue 35 LEU Chi-restraints excluded: chain 6 residue 36 ILE Chi-restraints excluded: chain 6 residue 72 ASP Chi-restraints excluded: chain 7 residue 26 LEU Chi-restraints excluded: chain 7 residue 122 THR Chi-restraints excluded: chain 7 residue 145 VAL Chi-restraints excluded: chain 8 residue 122 THR Chi-restraints excluded: chain 8 residue 198 VAL Chi-restraints excluded: chain 9 residue 175 LEU Chi-restraints excluded: chain 9 residue 198 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 568 optimal weight: 8.9990 chunk 598 optimal weight: 9.9990 chunk 545 optimal weight: 2.9990 chunk 582 optimal weight: 6.9990 chunk 350 optimal weight: 5.9990 chunk 253 optimal weight: 0.9980 chunk 457 optimal weight: 0.9990 chunk 178 optimal weight: 0.3980 chunk 525 optimal weight: 20.0000 chunk 550 optimal weight: 0.9980 chunk 579 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 143 ASN ** N 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 148 GLN T 30 ASN ** V 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN Z 102 ASN ** 2 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 102 ASN 3 143 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.031 1.138 51300 Z= 2.108 Angle : 0.810 40.894 70596 Z= 0.458 Chirality : 0.049 0.391 8352 Planarity : 0.005 0.075 8856 Dihedral : 5.595 52.683 7308 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.24 % Favored : 90.71 % Rotamer: Outliers : 1.49 % Allowed : 17.76 % Favored : 80.75 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.09 % Twisted General : 0.02 % 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: -2.84 (0.10), residues: 6408 helix: -4.35 (0.09), residues: 474 sheet: -0.89 (0.10), residues: 2460 loop : -2.31 (0.10), residues: 3474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP R 34 PHE 0.100 0.003 PHE T 200 TYR 0.033 0.001 TYR U 105 ARG 0.017 0.001 ARG N 55 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 230 time to evaluate : 4.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 26 LEU cc_start: 0.8114 (tp) cc_final: 0.7613 (tt) REVERT: H 55 ARG cc_start: 0.3289 (ttt180) cc_final: 0.2706 (ttp80) REVERT: H 145 VAL cc_start: 0.9284 (OUTLIER) cc_final: 0.8880 (p) REVERT: H 185 ARG cc_start: 0.7064 (tpp-160) cc_final: 0.5830 (tpt170) REVERT: I 44 MET cc_start: 0.2626 (tpt) cc_final: 0.1268 (tpt) REVERT: J 32 THR cc_start: 0.7380 (OUTLIER) cc_final: 0.7146 (p) REVERT: J 130 ASP cc_start: 0.8189 (m-30) cc_final: 0.7542 (t0) REVERT: K 28 PHE cc_start: 0.7484 (OUTLIER) cc_final: 0.6897 (m-80) REVERT: L 177 ASP cc_start: 0.9217 (t0) cc_final: 0.8954 (t0) REVERT: N 44 MET cc_start: 0.7288 (mtp) cc_final: 0.6796 (mtp) REVERT: N 55 ARG cc_start: 0.5361 (ttp80) cc_final: 0.5125 (ptm160) REVERT: O 44 MET cc_start: 0.2919 (tpt) cc_final: 0.2633 (tpt) REVERT: O 57 ASP cc_start: 0.8216 (p0) cc_final: 0.7741 (p0) REVERT: P 130 ASP cc_start: 0.8699 (m-30) cc_final: 0.7788 (t0) REVERT: Q 129 LYS cc_start: 0.8935 (tttt) cc_final: 0.8665 (ttpt) REVERT: R 57 ASP cc_start: 0.7715 (p0) cc_final: 0.7455 (p0) REVERT: R 167 CYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7841 (t) REVERT: R 177 ASP cc_start: 0.9201 (t0) cc_final: 0.8843 (t0) REVERT: U 90 ASP cc_start: 0.7146 (OUTLIER) cc_final: 0.6854 (m-30) REVERT: X 57 ASP cc_start: 0.7748 (p0) cc_final: 0.7533 (p0) REVERT: E 44 MET cc_start: 0.6897 (mtp) cc_final: 0.6302 (mtp) REVERT: E 95 THR cc_start: 0.8674 (OUTLIER) cc_final: 0.8289 (t) REVERT: E 186 ASP cc_start: 0.9306 (p0) cc_final: 0.8646 (p0) REVERT: B 35 LEU cc_start: 0.9244 (mp) cc_final: 0.8876 (pp) REVERT: B 90 ASP cc_start: 0.8626 (OUTLIER) cc_final: 0.8299 (m-30) REVERT: D 130 ASP cc_start: 0.9135 (t0) cc_final: 0.8922 (t0) REVERT: D 175 LEU cc_start: 0.8841 (tt) cc_final: 0.8396 (tp) REVERT: F 65 VAL cc_start: 0.8113 (OUTLIER) cc_final: 0.7606 (p) REVERT: 0 109 LEU cc_start: 0.9050 (mt) cc_final: 0.8604 (mt) REVERT: 0 186 ASP cc_start: 0.8669 (p0) cc_final: 0.8367 (p0) REVERT: 1 44 MET cc_start: 0.2325 (tpt) cc_final: 0.1369 (tpt) REVERT: 2 175 LEU cc_start: 0.9062 (tt) cc_final: 0.8604 (tp) REVERT: 4 44 MET cc_start: 0.4275 (OUTLIER) cc_final: 0.3221 (mmt) REVERT: 5 63 ARG cc_start: 0.8306 (mmm-85) cc_final: 0.8077 (mmm-85) REVERT: 6 46 TYR cc_start: 0.6558 (m-10) cc_final: 0.6249 (m-80) REVERT: 8 90 ASP cc_start: 0.7970 (t70) cc_final: 0.7746 (t0) REVERT: 8 175 LEU cc_start: 0.8905 (tt) cc_final: 0.8350 (tp) REVERT: 9 57 ASP cc_start: 0.7549 (p0) cc_final: 0.7189 (m-30) REVERT: 9 98 LEU cc_start: 0.9351 (mt) cc_final: 0.9023 (tp) outliers start: 84 outliers final: 65 residues processed: 311 average time/residue: 0.4776 time to fit residues: 256.5713 Evaluate side-chains 285 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 211 time to evaluate : 4.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 44 MET Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 101 CYS Chi-restraints excluded: chain H residue 105 TYR Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain I residue 145 VAL Chi-restraints excluded: chain I residue 198 VAL Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain K residue 28 PHE Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 101 CYS Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 157 THR Chi-restraints excluded: chain N residue 29 THR Chi-restraints excluded: chain N residue 101 CYS Chi-restraints excluded: chain N residue 160 VAL Chi-restraints excluded: chain N residue 198 VAL Chi-restraints excluded: chain O residue 72 ASP Chi-restraints excluded: chain P residue 33 TYR Chi-restraints excluded: chain P residue 145 VAL Chi-restraints excluded: chain Q residue 101 CYS Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain Q residue 160 VAL Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 162 ILE Chi-restraints excluded: chain R residue 167 CYS Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 157 THR Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain V residue 122 THR Chi-restraints excluded: chain W residue 198 VAL Chi-restraints excluded: chain X residue 30 ASN Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 105 TYR Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain F residue 28 PHE Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain Y residue 88 THR Chi-restraints excluded: chain Y residue 95 THR Chi-restraints excluded: chain Z residue 95 THR Chi-restraints excluded: chain Z residue 186 ASP Chi-restraints excluded: chain Z residue 198 VAL Chi-restraints excluded: chain 1 residue 26 LEU Chi-restraints excluded: chain 1 residue 145 VAL Chi-restraints excluded: chain 2 residue 28 PHE Chi-restraints excluded: chain 2 residue 198 VAL Chi-restraints excluded: chain 3 residue 198 VAL Chi-restraints excluded: chain 4 residue 27 THR Chi-restraints excluded: chain 4 residue 40 LEU Chi-restraints excluded: chain 4 residue 44 MET Chi-restraints excluded: chain 4 residue 157 THR Chi-restraints excluded: chain 5 residue 40 LEU Chi-restraints excluded: chain 5 residue 101 CYS Chi-restraints excluded: chain 5 residue 160 VAL Chi-restraints excluded: chain 5 residue 196 VAL Chi-restraints excluded: chain 6 residue 72 ASP Chi-restraints excluded: chain 7 residue 26 LEU Chi-restraints excluded: chain 7 residue 122 THR Chi-restraints excluded: chain 7 residue 145 VAL Chi-restraints excluded: chain 8 residue 122 THR Chi-restraints excluded: chain 8 residue 198 VAL Chi-restraints excluded: chain 9 residue 198 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 382 optimal weight: 20.0000 chunk 615 optimal weight: 10.0000 chunk 375 optimal weight: 0.7980 chunk 291 optimal weight: 30.0000 chunk 427 optimal weight: 10.0000 chunk 645 optimal weight: 8.9990 chunk 594 optimal weight: 9.9990 chunk 514 optimal weight: 8.9990 chunk 53 optimal weight: 6.9990 chunk 397 optimal weight: 2.9990 chunk 315 optimal weight: 30.0000 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 143 ASN ** M 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 148 GLN ** S 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 30 ASN ** V 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN ** 2 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 143 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.032 1.124 51300 Z= 2.145 Angle : 0.905 40.970 70596 Z= 0.505 Chirality : 0.052 0.358 8352 Planarity : 0.006 0.117 8856 Dihedral : 6.068 57.448 7308 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 21.03 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.39 % Favored : 88.47 % Rotamer: Outliers : 1.75 % Allowed : 17.96 % Favored : 80.29 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.59 % Twisted General : 0.03 % 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: -3.08 (0.10), residues: 6408 helix: -4.40 (0.08), residues: 474 sheet: -1.16 (0.10), residues: 2490 loop : -2.40 (0.10), residues: 3444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP V 34 PHE 0.087 0.004 PHE T 200 TYR 0.042 0.002 TYR M 105 ARG 0.027 0.001 ARG N 55 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 206 time to evaluate : 4.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 26 LEU cc_start: 0.7942 (tp) cc_final: 0.7401 (tt) REVERT: H 55 ARG cc_start: 0.3222 (ttt180) cc_final: 0.2625 (ttp80) REVERT: H 145 VAL cc_start: 0.9414 (OUTLIER) cc_final: 0.9064 (p) REVERT: H 185 ARG cc_start: 0.7344 (tpp-160) cc_final: 0.6141 (tpt170) REVERT: I 44 MET cc_start: 0.2621 (tpt) cc_final: 0.1702 (tpt) REVERT: J 32 THR cc_start: 0.7709 (OUTLIER) cc_final: 0.7487 (p) REVERT: J 130 ASP cc_start: 0.8142 (m-30) cc_final: 0.7433 (t0) REVERT: N 44 MET cc_start: 0.7632 (mtp) cc_final: 0.7024 (mtp) REVERT: O 57 ASP cc_start: 0.8153 (p0) cc_final: 0.7671 (p0) REVERT: P 130 ASP cc_start: 0.8719 (m-30) cc_final: 0.7622 (t0) REVERT: Q 129 LYS cc_start: 0.8966 (tttt) cc_final: 0.8680 (ttpt) REVERT: R 55 ARG cc_start: 0.6358 (ptt-90) cc_final: 0.6043 (ttt-90) REVERT: R 57 ASP cc_start: 0.8184 (p0) cc_final: 0.7856 (p0) REVERT: R 65 VAL cc_start: 0.9024 (OUTLIER) cc_final: 0.8716 (p) REVERT: R 177 ASP cc_start: 0.9201 (t0) cc_final: 0.8826 (t0) REVERT: T 44 MET cc_start: 0.4674 (OUTLIER) cc_final: 0.3591 (mtp) REVERT: E 44 MET cc_start: 0.6907 (mtp) cc_final: 0.6344 (mtp) REVERT: E 95 THR cc_start: 0.8772 (OUTLIER) cc_final: 0.8494 (t) REVERT: B 35 LEU cc_start: 0.9243 (mp) cc_final: 0.8845 (pp) REVERT: C 30 ASN cc_start: 0.8561 (OUTLIER) cc_final: 0.8354 (m110) REVERT: D 175 LEU cc_start: 0.8828 (tt) cc_final: 0.8358 (tp) REVERT: 0 109 LEU cc_start: 0.9035 (mt) cc_final: 0.8575 (mt) REVERT: 0 186 ASP cc_start: 0.8735 (p0) cc_final: 0.8456 (p0) REVERT: 1 44 MET cc_start: 0.2360 (tpt) cc_final: 0.1435 (tpt) REVERT: 2 175 LEU cc_start: 0.9177 (tt) cc_final: 0.8733 (tp) REVERT: 4 44 MET cc_start: 0.4459 (OUTLIER) cc_final: 0.3129 (mmt) REVERT: 6 46 TYR cc_start: 0.6922 (m-10) cc_final: 0.6414 (m-80) REVERT: 8 90 ASP cc_start: 0.7943 (t70) cc_final: 0.7714 (t0) REVERT: 9 57 ASP cc_start: 0.7896 (p0) cc_final: 0.7537 (m-30) REVERT: 9 98 LEU cc_start: 0.9415 (mt) cc_final: 0.9038 (tp) outliers start: 99 outliers final: 79 residues processed: 298 average time/residue: 0.4767 time to fit residues: 245.2862 Evaluate side-chains 283 residues out of total 5652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 197 time to evaluate : 4.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 95 THR Chi-restraints excluded: chain H residue 101 CYS Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain I residue 72 ASP Chi-restraints excluded: chain I residue 145 VAL Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain K residue 28 PHE Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 162 ILE Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 51 THR Chi-restraints excluded: chain M residue 101 CYS Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 157 THR Chi-restraints excluded: chain N residue 101 CYS Chi-restraints excluded: chain N residue 160 VAL Chi-restraints excluded: chain N residue 198 VAL Chi-restraints excluded: chain O residue 72 ASP Chi-restraints excluded: chain O residue 128 ILE Chi-restraints excluded: chain O residue 191 ILE Chi-restraints excluded: chain P residue 33 TYR Chi-restraints excluded: chain Q residue 101 CYS Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain Q residue 160 VAL Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 162 ILE Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain S residue 157 THR Chi-restraints excluded: chain T residue 44 MET Chi-restraints excluded: chain U residue 128 ILE Chi-restraints excluded: chain V residue 109 LEU Chi-restraints excluded: chain V residue 122 THR Chi-restraints excluded: chain W residue 198 VAL Chi-restraints excluded: chain X residue 30 ASN Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain F residue 28 PHE Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain Y residue 95 THR Chi-restraints excluded: chain Z residue 34 TRP Chi-restraints excluded: chain Z residue 84 ILE Chi-restraints excluded: chain Z residue 95 THR Chi-restraints excluded: chain Z residue 186 ASP Chi-restraints excluded: chain Z residue 198 VAL Chi-restraints excluded: chain 0 residue 72 ASP Chi-restraints excluded: chain 0 residue 191 ILE Chi-restraints excluded: chain 1 residue 26 LEU Chi-restraints excluded: chain 1 residue 145 VAL Chi-restraints excluded: chain 2 residue 28 PHE Chi-restraints excluded: chain 2 residue 53 ILE Chi-restraints excluded: chain 2 residue 198 VAL Chi-restraints excluded: chain 3 residue 198 VAL Chi-restraints excluded: chain 4 residue 27 THR Chi-restraints excluded: chain 4 residue 40 LEU Chi-restraints excluded: chain 4 residue 44 MET Chi-restraints excluded: chain 4 residue 157 THR Chi-restraints excluded: chain 5 residue 101 CYS Chi-restraints excluded: chain 5 residue 160 VAL Chi-restraints excluded: chain 5 residue 196 VAL Chi-restraints excluded: chain 6 residue 36 ILE Chi-restraints excluded: chain 6 residue 72 ASP Chi-restraints excluded: chain 7 residue 26 LEU Chi-restraints excluded: chain 7 residue 122 THR Chi-restraints excluded: chain 7 residue 145 VAL Chi-restraints excluded: chain 8 residue 122 THR Chi-restraints excluded: chain 8 residue 198 VAL Chi-restraints excluded: chain 9 residue 137 ASN Chi-restraints excluded: chain 9 residue 175 LEU Chi-restraints excluded: chain 9 residue 198 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 408 optimal weight: 10.0000 chunk 547 optimal weight: 0.6980 chunk 157 optimal weight: 9.9990 chunk 474 optimal weight: 5.9990 chunk 75 optimal weight: 30.0000 chunk 142 optimal weight: 0.6980 chunk 514 optimal weight: 10.0000 chunk 215 optimal weight: 20.0000 chunk 528 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 94 optimal weight: 10.0000 overall best weight: 2.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 30 ASN ** V 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.075431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.054101 restraints weight = 275974.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.054585 restraints weight = 158122.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.054428 restraints weight = 110123.391| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.032 1.125 51300 Z= 2.141 Angle : 0.946 59.200 70596 Z= 0.534 Chirality : 0.052 1.001 8352 Planarity : 0.007 0.105 8856 Dihedral : 6.079 57.437 7308 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 21.95 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.31 % Favored : 88.48 % Rotamer: Outliers : 1.66 % Allowed : 18.06 % Favored : 80.27 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.59 % Twisted General : 0.03 % 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: -3.08 (0.10), residues: 6408 helix: -4.40 (0.08), residues: 474 sheet: -1.19 (0.10), residues: 2640 loop : -2.41 (0.11), residues: 3294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP R 34 PHE 0.068 0.004 PHE T 200 TYR 0.068 0.002 TYR Y 105 ARG 0.023 0.001 ARG N 55 =============================================================================== Job complete usr+sys time: 7007.77 seconds wall clock time: 127 minutes 28.96 seconds (7648.96 seconds total)