Starting phenix.real_space_refine on Wed Feb 14 08:51:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5j_20647/02_2024/6u5j_20647.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5j_20647/02_2024/6u5j_20647.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5j_20647/02_2024/6u5j_20647.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5j_20647/02_2024/6u5j_20647.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5j_20647/02_2024/6u5j_20647.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5j_20647/02_2024/6u5j_20647.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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 168 5.16 5 C 37602 2.51 5 N 10416 2.21 5 O 11430 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 92": "NH1" <-> "NH2" Residue "A ARG 107": "NH1" <-> "NH2" Residue "a PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 92": "NH1" <-> "NH2" Residue "B ARG 107": "NH1" <-> "NH2" Residue "C ARG 92": "NH1" <-> "NH2" Residue "C ARG 107": "NH1" <-> "NH2" Residue "D ARG 92": "NH1" <-> "NH2" Residue "D ARG 107": "NH1" <-> "NH2" Residue "E ARG 92": "NH1" <-> "NH2" Residue "E ARG 107": "NH1" <-> "NH2" Residue "F ARG 92": "NH1" <-> "NH2" Residue "F ARG 107": "NH1" <-> "NH2" Residue "b PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 59616 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1284 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 16, 'TRANS': 147} Chain: "a" Number of atoms: 2884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2884 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 16, 'TRANS': 366} Chain: "B" Number of atoms: 1284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1284 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 16, 'TRANS': 147} Chain: "C" Number of atoms: 1284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1284 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 16, 'TRANS': 147} Chain: "D" Number of atoms: 1284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1284 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 16, 'TRANS': 147} Chain: "E" Number of atoms: 1284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1284 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 16, 'TRANS': 147} Chain: "F" Number of atoms: 1284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1284 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 16, 'TRANS': 147} Chain: "b" Number of atoms: 2884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2884 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 16, 'TRANS': 366} Chain: "c" Number of atoms: 2884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2884 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 16, 'TRANS': 366} Chain: "d" Number of atoms: 2884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2884 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 16, 'TRANS': 366} Chain: "e" Number of atoms: 2884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2884 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 16, 'TRANS': 366} Chain: "f" Number of atoms: 2884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2884 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 16, 'TRANS': 366} Chain: "g" Number of atoms: 2884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2884 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 16, 'TRANS': 366} Chain: "h" Number of atoms: 2884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2884 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 16, 'TRANS': 366} Chain: "l" Number of atoms: 2884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2884 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 16, 'TRANS': 366} Chain: "k" Number of atoms: 2884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2884 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 16, 'TRANS': 366} Chain: "j" Number of atoms: 2884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2884 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 16, 'TRANS': 366} Chain: "i" Number of atoms: 2884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2884 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 16, 'TRANS': 366} Chain: "m" Number of atoms: 2884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2884 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 16, 'TRANS': 366} Chain: "n" Number of atoms: 2884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2884 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 16, 'TRANS': 366} Chain: "r" Number of atoms: 2884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2884 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 16, 'TRANS': 366} Chain: "q" Number of atoms: 2884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2884 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 16, 'TRANS': 366} Chain: "p" Number of atoms: 2884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2884 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 16, 'TRANS': 366} Chain: "o" Number of atoms: 2884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2884 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 16, 'TRANS': 366} Time building chain proxies: 22.84, per 1000 atoms: 0.38 Number of scatterers: 59616 At special positions: 0 Unit cell: (238.389, 240.471, 117.633, 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 168 16.00 O 11430 8.00 N 10416 7.00 C 37602 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 17.79 Conformation dependent library (CDL) restraints added in 8.7 seconds 15660 Ramachandran restraints generated. 7830 Oldfield, 0 Emsley, 7830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14568 Finding SS restraints... Secondary structure from input PDB file: 264 helices and 95 sheets defined 35.3% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.94 Creating SS restraints... Processing helix chain 'A' and resid 7 through 23 removed outlier: 3.555A pdb=" N ALA A 13 " --> pdb=" O GLU A 9 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU A 16 " --> pdb=" O TYR A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 91 removed outlier: 3.520A pdb=" N VAL A 81 " --> pdb=" O ASP A 77 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE A 83 " --> pdb=" O GLN A 79 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE A 87 " --> pdb=" O ILE A 83 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR A 90 " --> pdb=" O GLY A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 156 removed outlier: 3.849A pdb=" N GLN A 155 " --> pdb=" O PHE A 152 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N THR A 156 " --> pdb=" O ASP A 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 152 through 156' Processing helix chain 'a' and resid 51 through 60 Processing helix chain 'a' and resid 65 through 74 Processing helix chain 'a' and resid 90 through 100 removed outlier: 4.008A pdb=" N ALA a 95 " --> pdb=" O PRO a 91 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N SER a 96 " --> pdb=" O GLU a 92 " (cutoff:3.500A) Processing helix chain 'a' and resid 110 through 116 Processing helix chain 'a' and resid 117 through 122 Processing helix chain 'a' and resid 136 through 151 removed outlier: 3.647A pdb=" N ALA a 142 " --> pdb=" O ALA a 138 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU a 148 " --> pdb=" O ASP a 144 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS a 149 " --> pdb=" O GLY a 145 " (cutoff:3.500A) Processing helix chain 'a' and resid 162 through 171 removed outlier: 3.709A pdb=" N ALA a 168 " --> pdb=" O GLU a 164 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR a 169 " --> pdb=" O ALA a 165 " (cutoff:3.500A) Processing helix chain 'a' and resid 201 through 215 removed outlier: 3.541A pdb=" N ALA a 205 " --> pdb=" O SER a 201 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA a 213 " --> pdb=" O ALA a 209 " (cutoff:3.500A) Processing helix chain 'a' and resid 247 through 252 Processing helix chain 'a' and resid 280 through 296 removed outlier: 3.611A pdb=" N ASP a 292 " --> pdb=" O ASP a 288 " (cutoff:3.500A) Processing helix chain 'a' and resid 307 through 309 No H-bonds generated for 'chain 'a' and resid 307 through 309' Processing helix chain 'a' and resid 310 through 328 removed outlier: 3.683A pdb=" N GLU a 316 " --> pdb=" O LYS a 312 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY a 317 " --> pdb=" O ASP a 313 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA a 320 " --> pdb=" O GLU a 316 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE a 321 " --> pdb=" O GLY a 317 " (cutoff:3.500A) Processing helix chain 'a' and resid 344 through 349 removed outlier: 3.867A pdb=" N ALA a 349 " --> pdb=" O ALA a 345 " (cutoff:3.500A) Processing helix chain 'a' and resid 377 through 382 removed outlier: 4.352A pdb=" N THR a 380 " --> pdb=" O GLN a 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 23 removed outlier: 3.555A pdb=" N ALA B 13 " --> pdb=" O GLU B 9 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU B 16 " --> pdb=" O TYR B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 91 removed outlier: 3.521A pdb=" N VAL B 81 " --> pdb=" O ASP B 77 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE B 83 " --> pdb=" O GLN B 79 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE B 87 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR B 90 " --> pdb=" O GLY B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 156 removed outlier: 3.849A pdb=" N GLN B 155 " --> pdb=" O PHE B 152 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR B 156 " --> pdb=" O ASP B 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 152 through 156' Processing helix chain 'C' and resid 7 through 23 removed outlier: 3.556A pdb=" N ALA C 13 " --> pdb=" O GLU C 9 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU C 16 " --> pdb=" O TYR C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 91 removed outlier: 3.521A pdb=" N VAL C 81 " --> pdb=" O ASP C 77 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE C 83 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLY C 86 " --> pdb=" O SER C 82 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE C 87 " --> pdb=" O ILE C 83 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR C 90 " --> pdb=" O GLY C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 156 removed outlier: 3.848A pdb=" N GLN C 155 " --> pdb=" O PHE C 152 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N THR C 156 " --> pdb=" O ASP C 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 152 through 156' Processing helix chain 'D' and resid 7 through 23 removed outlier: 3.556A pdb=" N ALA D 13 " --> pdb=" O GLU D 9 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU D 16 " --> pdb=" O TYR D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 91 removed outlier: 3.521A pdb=" N VAL D 81 " --> pdb=" O ASP D 77 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE D 83 " --> pdb=" O GLN D 79 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE D 87 " --> pdb=" O ILE D 83 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR D 90 " --> pdb=" O GLY D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 156 removed outlier: 3.849A pdb=" N GLN D 155 " --> pdb=" O PHE D 152 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N THR D 156 " --> pdb=" O ASP D 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 152 through 156' Processing helix chain 'E' and resid 7 through 23 removed outlier: 3.556A pdb=" N ALA E 13 " --> pdb=" O GLU E 9 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU E 16 " --> pdb=" O TYR E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 91 removed outlier: 3.521A pdb=" N VAL E 81 " --> pdb=" O ASP E 77 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE E 83 " --> pdb=" O GLN E 79 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY E 86 " --> pdb=" O SER E 82 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE E 87 " --> pdb=" O ILE E 83 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR E 90 " --> pdb=" O GLY E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 156 removed outlier: 3.849A pdb=" N GLN E 155 " --> pdb=" O PHE E 152 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N THR E 156 " --> pdb=" O ASP E 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 152 through 156' Processing helix chain 'F' and resid 7 through 23 removed outlier: 3.555A pdb=" N ALA F 13 " --> pdb=" O GLU F 9 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU F 16 " --> pdb=" O TYR F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 91 removed outlier: 3.522A pdb=" N VAL F 81 " --> pdb=" O ASP F 77 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE F 83 " --> pdb=" O GLN F 79 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLY F 86 " --> pdb=" O SER F 82 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE F 87 " --> pdb=" O ILE F 83 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR F 90 " --> pdb=" O GLY F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 156 removed outlier: 3.849A pdb=" N GLN F 155 " --> pdb=" O PHE F 152 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR F 156 " --> pdb=" O ASP F 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 152 through 156' Processing helix chain 'b' and resid 51 through 60 Processing helix chain 'b' and resid 65 through 74 Processing helix chain 'b' and resid 90 through 100 removed outlier: 4.008A pdb=" N ALA b 95 " --> pdb=" O PRO b 91 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N SER b 96 " --> pdb=" O GLU b 92 " (cutoff:3.500A) Processing helix chain 'b' and resid 110 through 116 Processing helix chain 'b' and resid 117 through 122 Processing helix chain 'b' and resid 136 through 151 removed outlier: 3.647A pdb=" N ALA b 142 " --> pdb=" O ALA b 138 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU b 148 " --> pdb=" O ASP b 144 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS b 149 " --> pdb=" O GLY b 145 " (cutoff:3.500A) Processing helix chain 'b' and resid 162 through 171 removed outlier: 3.710A pdb=" N ALA b 168 " --> pdb=" O GLU b 164 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR b 169 " --> pdb=" O ALA b 165 " (cutoff:3.500A) Processing helix chain 'b' and resid 201 through 215 removed outlier: 3.541A pdb=" N ALA b 205 " --> pdb=" O SER b 201 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA b 213 " --> pdb=" O ALA b 209 " (cutoff:3.500A) Processing helix chain 'b' and resid 247 through 252 Processing helix chain 'b' and resid 280 through 296 removed outlier: 3.611A pdb=" N ASP b 292 " --> pdb=" O ASP b 288 " (cutoff:3.500A) Processing helix chain 'b' and resid 307 through 309 No H-bonds generated for 'chain 'b' and resid 307 through 309' Processing helix chain 'b' and resid 310 through 328 removed outlier: 3.683A pdb=" N GLU b 316 " --> pdb=" O LYS b 312 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY b 317 " --> pdb=" O ASP b 313 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA b 320 " --> pdb=" O GLU b 316 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE b 321 " --> pdb=" O GLY b 317 " (cutoff:3.500A) Processing helix chain 'b' and resid 344 through 349 removed outlier: 3.867A pdb=" N ALA b 349 " --> pdb=" O ALA b 345 " (cutoff:3.500A) Processing helix chain 'b' and resid 377 through 382 removed outlier: 4.352A pdb=" N THR b 380 " --> pdb=" O GLN b 377 " (cutoff:3.500A) Processing helix chain 'c' and resid 51 through 60 Processing helix chain 'c' and resid 65 through 74 Processing helix chain 'c' and resid 90 through 100 removed outlier: 4.008A pdb=" N ALA c 95 " --> pdb=" O PRO c 91 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N SER c 96 " --> pdb=" O GLU c 92 " (cutoff:3.500A) Processing helix chain 'c' and resid 110 through 116 Processing helix chain 'c' and resid 117 through 122 Processing helix chain 'c' and resid 136 through 151 removed outlier: 3.647A pdb=" N ALA c 142 " --> pdb=" O ALA c 138 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU c 148 " --> pdb=" O ASP c 144 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS c 149 " --> pdb=" O GLY c 145 " (cutoff:3.500A) Processing helix chain 'c' and resid 162 through 171 removed outlier: 3.709A pdb=" N ALA c 168 " --> pdb=" O GLU c 164 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR c 169 " --> pdb=" O ALA c 165 " (cutoff:3.500A) Processing helix chain 'c' and resid 201 through 215 removed outlier: 3.541A pdb=" N ALA c 205 " --> pdb=" O SER c 201 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA c 213 " --> pdb=" O ALA c 209 " (cutoff:3.500A) Processing helix chain 'c' and resid 247 through 252 Processing helix chain 'c' and resid 280 through 296 removed outlier: 3.611A pdb=" N ASP c 292 " --> pdb=" O ASP c 288 " (cutoff:3.500A) Processing helix chain 'c' and resid 307 through 309 No H-bonds generated for 'chain 'c' and resid 307 through 309' Processing helix chain 'c' and resid 310 through 328 removed outlier: 3.683A pdb=" N GLU c 316 " --> pdb=" O LYS c 312 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY c 317 " --> pdb=" O ASP c 313 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA c 320 " --> pdb=" O GLU c 316 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE c 321 " --> pdb=" O GLY c 317 " (cutoff:3.500A) Processing helix chain 'c' and resid 344 through 349 removed outlier: 3.867A pdb=" N ALA c 349 " --> pdb=" O ALA c 345 " (cutoff:3.500A) Processing helix chain 'c' and resid 377 through 382 removed outlier: 4.352A pdb=" N THR c 380 " --> pdb=" O GLN c 377 " (cutoff:3.500A) Processing helix chain 'd' and resid 51 through 60 Processing helix chain 'd' and resid 65 through 74 Processing helix chain 'd' and resid 90 through 100 removed outlier: 4.008A pdb=" N ALA d 95 " --> pdb=" O PRO d 91 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N SER d 96 " --> pdb=" O GLU d 92 " (cutoff:3.500A) Processing helix chain 'd' and resid 110 through 116 Processing helix chain 'd' and resid 117 through 122 Processing helix chain 'd' and resid 136 through 151 removed outlier: 3.648A pdb=" N ALA d 142 " --> pdb=" O ALA d 138 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU d 148 " --> pdb=" O ASP d 144 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS d 149 " --> pdb=" O GLY d 145 " (cutoff:3.500A) Processing helix chain 'd' and resid 162 through 171 removed outlier: 3.710A pdb=" N ALA d 168 " --> pdb=" O GLU d 164 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR d 169 " --> pdb=" O ALA d 165 " (cutoff:3.500A) Processing helix chain 'd' and resid 201 through 215 removed outlier: 3.542A pdb=" N ALA d 205 " --> pdb=" O SER d 201 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA d 213 " --> pdb=" O ALA d 209 " (cutoff:3.500A) Processing helix chain 'd' and resid 247 through 252 Processing helix chain 'd' and resid 280 through 296 removed outlier: 3.611A pdb=" N ASP d 292 " --> pdb=" O ASP d 288 " (cutoff:3.500A) Processing helix chain 'd' and resid 307 through 309 No H-bonds generated for 'chain 'd' and resid 307 through 309' Processing helix chain 'd' and resid 310 through 328 removed outlier: 3.683A pdb=" N GLU d 316 " --> pdb=" O LYS d 312 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY d 317 " --> pdb=" O ASP d 313 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA d 320 " --> pdb=" O GLU d 316 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE d 321 " --> pdb=" O GLY d 317 " (cutoff:3.500A) Processing helix chain 'd' and resid 344 through 349 removed outlier: 3.868A pdb=" N ALA d 349 " --> pdb=" O ALA d 345 " (cutoff:3.500A) Processing helix chain 'd' and resid 377 through 382 removed outlier: 4.352A pdb=" N THR d 380 " --> pdb=" O GLN d 377 " (cutoff:3.500A) Processing helix chain 'e' and resid 51 through 60 Processing helix chain 'e' and resid 65 through 74 Processing helix chain 'e' and resid 90 through 100 removed outlier: 4.008A pdb=" N ALA e 95 " --> pdb=" O PRO e 91 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N SER e 96 " --> pdb=" O GLU e 92 " (cutoff:3.500A) Processing helix chain 'e' and resid 110 through 116 Processing helix chain 'e' and resid 117 through 122 Processing helix chain 'e' and resid 136 through 151 removed outlier: 3.648A pdb=" N ALA e 142 " --> pdb=" O ALA e 138 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU e 148 " --> pdb=" O ASP e 144 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS e 149 " --> pdb=" O GLY e 145 " (cutoff:3.500A) Processing helix chain 'e' and resid 162 through 171 removed outlier: 3.709A pdb=" N ALA e 168 " --> pdb=" O GLU e 164 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR e 169 " --> pdb=" O ALA e 165 " (cutoff:3.500A) Processing helix chain 'e' and resid 201 through 215 removed outlier: 3.541A pdb=" N ALA e 205 " --> pdb=" O SER e 201 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA e 213 " --> pdb=" O ALA e 209 " (cutoff:3.500A) Processing helix chain 'e' and resid 247 through 252 Processing helix chain 'e' and resid 280 through 296 removed outlier: 3.611A pdb=" N ASP e 292 " --> pdb=" O ASP e 288 " (cutoff:3.500A) Processing helix chain 'e' and resid 307 through 309 No H-bonds generated for 'chain 'e' and resid 307 through 309' Processing helix chain 'e' and resid 310 through 328 removed outlier: 3.683A pdb=" N GLU e 316 " --> pdb=" O LYS e 312 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY e 317 " --> pdb=" O ASP e 313 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA e 320 " --> pdb=" O GLU e 316 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE e 321 " --> pdb=" O GLY e 317 " (cutoff:3.500A) Processing helix chain 'e' and resid 344 through 349 removed outlier: 3.867A pdb=" N ALA e 349 " --> pdb=" O ALA e 345 " (cutoff:3.500A) Processing helix chain 'e' and resid 377 through 382 removed outlier: 4.352A pdb=" N THR e 380 " --> pdb=" O GLN e 377 " (cutoff:3.500A) Processing helix chain 'f' and resid 51 through 60 Processing helix chain 'f' and resid 65 through 74 Processing helix chain 'f' and resid 90 through 100 removed outlier: 4.008A pdb=" N ALA f 95 " --> pdb=" O PRO f 91 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N SER f 96 " --> pdb=" O GLU f 92 " (cutoff:3.500A) Processing helix chain 'f' and resid 110 through 116 Processing helix chain 'f' and resid 117 through 122 Processing helix chain 'f' and resid 136 through 151 removed outlier: 3.647A pdb=" N ALA f 142 " --> pdb=" O ALA f 138 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU f 148 " --> pdb=" O ASP f 144 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS f 149 " --> pdb=" O GLY f 145 " (cutoff:3.500A) Processing helix chain 'f' and resid 162 through 171 removed outlier: 3.710A pdb=" N ALA f 168 " --> pdb=" O GLU f 164 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR f 169 " --> pdb=" O ALA f 165 " (cutoff:3.500A) Processing helix chain 'f' and resid 201 through 215 removed outlier: 3.541A pdb=" N ALA f 205 " --> pdb=" O SER f 201 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA f 213 " --> pdb=" O ALA f 209 " (cutoff:3.500A) Processing helix chain 'f' and resid 247 through 252 Processing helix chain 'f' and resid 280 through 296 removed outlier: 3.611A pdb=" N ASP f 292 " --> pdb=" O ASP f 288 " (cutoff:3.500A) Processing helix chain 'f' and resid 307 through 309 No H-bonds generated for 'chain 'f' and resid 307 through 309' Processing helix chain 'f' and resid 310 through 328 removed outlier: 3.682A pdb=" N GLU f 316 " --> pdb=" O LYS f 312 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY f 317 " --> pdb=" O ASP f 313 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA f 320 " --> pdb=" O GLU f 316 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE f 321 " --> pdb=" O GLY f 317 " (cutoff:3.500A) Processing helix chain 'f' and resid 344 through 349 removed outlier: 3.868A pdb=" N ALA f 349 " --> pdb=" O ALA f 345 " (cutoff:3.500A) Processing helix chain 'f' and resid 377 through 382 removed outlier: 4.352A pdb=" N THR f 380 " --> pdb=" O GLN f 377 " (cutoff:3.500A) Processing helix chain 'g' and resid 51 through 60 Processing helix chain 'g' and resid 65 through 74 Processing helix chain 'g' and resid 90 through 100 removed outlier: 3.935A pdb=" N ALA g 95 " --> pdb=" O PRO g 91 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N SER g 96 " --> pdb=" O GLU g 92 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA g 97 " --> pdb=" O ALA g 93 " (cutoff:3.500A) Processing helix chain 'g' and resid 110 through 115 Processing helix chain 'g' and resid 116 through 122 Processing helix chain 'g' and resid 136 through 151 removed outlier: 3.728A pdb=" N LYS g 149 " --> pdb=" O GLY g 145 " (cutoff:3.500A) Processing helix chain 'g' and resid 162 through 171 removed outlier: 3.582A pdb=" N ALA g 166 " --> pdb=" O THR g 162 " (cutoff:3.500A) Processing helix chain 'g' and resid 201 through 215 removed outlier: 3.995A pdb=" N ALA g 213 " --> pdb=" O ALA g 209 " (cutoff:3.500A) Processing helix chain 'g' and resid 245 through 252 removed outlier: 3.747A pdb=" N LEU g 250 " --> pdb=" O ARG g 246 " (cutoff:3.500A) Processing helix chain 'g' and resid 280 through 296 removed outlier: 3.868A pdb=" N ILE g 294 " --> pdb=" O VAL g 290 " (cutoff:3.500A) Processing helix chain 'g' and resid 307 through 327 removed outlier: 3.623A pdb=" N VAL g 311 " --> pdb=" O THR g 307 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLY g 317 " --> pdb=" O ASP g 313 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA g 320 " --> pdb=" O GLU g 316 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE g 321 " --> pdb=" O GLY g 317 " (cutoff:3.500A) Processing helix chain 'g' and resid 344 through 350 removed outlier: 3.612A pdb=" N ALA g 349 " --> pdb=" O ALA g 345 " (cutoff:3.500A) Processing helix chain 'g' and resid 377 through 382 removed outlier: 4.520A pdb=" N THR g 380 " --> pdb=" O GLN g 377 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL g 382 " --> pdb=" O LEU g 379 " (cutoff:3.500A) Processing helix chain 'h' and resid 51 through 60 Processing helix chain 'h' and resid 65 through 74 Processing helix chain 'h' and resid 90 through 100 removed outlier: 3.934A pdb=" N ALA h 95 " --> pdb=" O PRO h 91 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N SER h 96 " --> pdb=" O GLU h 92 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA h 97 " --> pdb=" O ALA h 93 " (cutoff:3.500A) Processing helix chain 'h' and resid 110 through 115 Processing helix chain 'h' and resid 116 through 122 Processing helix chain 'h' and resid 136 through 151 removed outlier: 3.728A pdb=" N LYS h 149 " --> pdb=" O GLY h 145 " (cutoff:3.500A) Processing helix chain 'h' and resid 162 through 171 removed outlier: 3.582A pdb=" N ALA h 166 " --> pdb=" O THR h 162 " (cutoff:3.500A) Processing helix chain 'h' and resid 201 through 215 removed outlier: 3.996A pdb=" N ALA h 213 " --> pdb=" O ALA h 209 " (cutoff:3.500A) Processing helix chain 'h' and resid 245 through 252 removed outlier: 3.747A pdb=" N LEU h 250 " --> pdb=" O ARG h 246 " (cutoff:3.500A) Processing helix chain 'h' and resid 280 through 296 removed outlier: 3.868A pdb=" N ILE h 294 " --> pdb=" O VAL h 290 " (cutoff:3.500A) Processing helix chain 'h' and resid 307 through 327 removed outlier: 3.623A pdb=" N VAL h 311 " --> pdb=" O THR h 307 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLY h 317 " --> pdb=" O ASP h 313 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA h 320 " --> pdb=" O GLU h 316 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE h 321 " --> pdb=" O GLY h 317 " (cutoff:3.500A) Processing helix chain 'h' and resid 344 through 350 removed outlier: 3.613A pdb=" N ALA h 349 " --> pdb=" O ALA h 345 " (cutoff:3.500A) Processing helix chain 'h' and resid 377 through 382 removed outlier: 4.520A pdb=" N THR h 380 " --> pdb=" O GLN h 377 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL h 382 " --> pdb=" O LEU h 379 " (cutoff:3.500A) Processing helix chain 'l' and resid 51 through 60 Processing helix chain 'l' and resid 65 through 74 Processing helix chain 'l' and resid 90 through 100 removed outlier: 3.935A pdb=" N ALA l 95 " --> pdb=" O PRO l 91 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N SER l 96 " --> pdb=" O GLU l 92 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA l 97 " --> pdb=" O ALA l 93 " (cutoff:3.500A) Processing helix chain 'l' and resid 110 through 115 Processing helix chain 'l' and resid 116 through 122 Processing helix chain 'l' and resid 136 through 151 removed outlier: 3.727A pdb=" N LYS l 149 " --> pdb=" O GLY l 145 " (cutoff:3.500A) Processing helix chain 'l' and resid 162 through 171 removed outlier: 3.581A pdb=" N ALA l 166 " --> pdb=" O THR l 162 " (cutoff:3.500A) Processing helix chain 'l' and resid 201 through 215 removed outlier: 3.996A pdb=" N ALA l 213 " --> pdb=" O ALA l 209 " (cutoff:3.500A) Processing helix chain 'l' and resid 245 through 252 removed outlier: 3.747A pdb=" N LEU l 250 " --> pdb=" O ARG l 246 " (cutoff:3.500A) Processing helix chain 'l' and resid 280 through 296 removed outlier: 3.868A pdb=" N ILE l 294 " --> pdb=" O VAL l 290 " (cutoff:3.500A) Processing helix chain 'l' and resid 307 through 327 removed outlier: 3.623A pdb=" N VAL l 311 " --> pdb=" O THR l 307 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLY l 317 " --> pdb=" O ASP l 313 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA l 320 " --> pdb=" O GLU l 316 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE l 321 " --> pdb=" O GLY l 317 " (cutoff:3.500A) Processing helix chain 'l' and resid 344 through 350 removed outlier: 3.612A pdb=" N ALA l 349 " --> pdb=" O ALA l 345 " (cutoff:3.500A) Processing helix chain 'l' and resid 377 through 382 removed outlier: 4.519A pdb=" N THR l 380 " --> pdb=" O GLN l 377 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL l 382 " --> pdb=" O LEU l 379 " (cutoff:3.500A) Processing helix chain 'k' and resid 51 through 60 Processing helix chain 'k' and resid 65 through 74 Processing helix chain 'k' and resid 90 through 100 removed outlier: 3.936A pdb=" N ALA k 95 " --> pdb=" O PRO k 91 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N SER k 96 " --> pdb=" O GLU k 92 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA k 97 " --> pdb=" O ALA k 93 " (cutoff:3.500A) Processing helix chain 'k' and resid 110 through 115 Processing helix chain 'k' and resid 116 through 122 Processing helix chain 'k' and resid 136 through 151 removed outlier: 3.728A pdb=" N LYS k 149 " --> pdb=" O GLY k 145 " (cutoff:3.500A) Processing helix chain 'k' and resid 162 through 171 removed outlier: 3.582A pdb=" N ALA k 166 " --> pdb=" O THR k 162 " (cutoff:3.500A) Processing helix chain 'k' and resid 201 through 215 removed outlier: 3.996A pdb=" N ALA k 213 " --> pdb=" O ALA k 209 " (cutoff:3.500A) Processing helix chain 'k' and resid 245 through 252 removed outlier: 3.748A pdb=" N LEU k 250 " --> pdb=" O ARG k 246 " (cutoff:3.500A) Processing helix chain 'k' and resid 280 through 296 removed outlier: 3.868A pdb=" N ILE k 294 " --> pdb=" O VAL k 290 " (cutoff:3.500A) Processing helix chain 'k' and resid 307 through 327 removed outlier: 3.623A pdb=" N VAL k 311 " --> pdb=" O THR k 307 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLY k 317 " --> pdb=" O ASP k 313 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA k 320 " --> pdb=" O GLU k 316 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE k 321 " --> pdb=" O GLY k 317 " (cutoff:3.500A) Processing helix chain 'k' and resid 344 through 350 removed outlier: 3.611A pdb=" N ALA k 349 " --> pdb=" O ALA k 345 " (cutoff:3.500A) Processing helix chain 'k' and resid 377 through 382 removed outlier: 4.519A pdb=" N THR k 380 " --> pdb=" O GLN k 377 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL k 382 " --> pdb=" O LEU k 379 " (cutoff:3.500A) Processing helix chain 'j' and resid 51 through 60 Processing helix chain 'j' and resid 65 through 74 Processing helix chain 'j' and resid 90 through 100 removed outlier: 3.935A pdb=" N ALA j 95 " --> pdb=" O PRO j 91 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N SER j 96 " --> pdb=" O GLU j 92 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA j 97 " --> pdb=" O ALA j 93 " (cutoff:3.500A) Processing helix chain 'j' and resid 110 through 115 Processing helix chain 'j' and resid 116 through 122 Processing helix chain 'j' and resid 136 through 151 removed outlier: 3.728A pdb=" N LYS j 149 " --> pdb=" O GLY j 145 " (cutoff:3.500A) Processing helix chain 'j' and resid 162 through 171 removed outlier: 3.582A pdb=" N ALA j 166 " --> pdb=" O THR j 162 " (cutoff:3.500A) Processing helix chain 'j' and resid 201 through 215 removed outlier: 3.995A pdb=" N ALA j 213 " --> pdb=" O ALA j 209 " (cutoff:3.500A) Processing helix chain 'j' and resid 245 through 252 removed outlier: 3.748A pdb=" N LEU j 250 " --> pdb=" O ARG j 246 " (cutoff:3.500A) Processing helix chain 'j' and resid 280 through 296 removed outlier: 3.867A pdb=" N ILE j 294 " --> pdb=" O VAL j 290 " (cutoff:3.500A) Processing helix chain 'j' and resid 307 through 327 removed outlier: 3.623A pdb=" N VAL j 311 " --> pdb=" O THR j 307 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY j 317 " --> pdb=" O ASP j 313 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA j 320 " --> pdb=" O GLU j 316 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE j 321 " --> pdb=" O GLY j 317 " (cutoff:3.500A) Processing helix chain 'j' and resid 344 through 350 removed outlier: 3.612A pdb=" N ALA j 349 " --> pdb=" O ALA j 345 " (cutoff:3.500A) Processing helix chain 'j' and resid 377 through 382 removed outlier: 4.520A pdb=" N THR j 380 " --> pdb=" O GLN j 377 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL j 382 " --> pdb=" O LEU j 379 " (cutoff:3.500A) Processing helix chain 'i' and resid 51 through 60 Processing helix chain 'i' and resid 65 through 74 Processing helix chain 'i' and resid 90 through 100 removed outlier: 3.936A pdb=" N ALA i 95 " --> pdb=" O PRO i 91 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N SER i 96 " --> pdb=" O GLU i 92 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA i 97 " --> pdb=" O ALA i 93 " (cutoff:3.500A) Processing helix chain 'i' and resid 110 through 115 Processing helix chain 'i' and resid 116 through 122 Processing helix chain 'i' and resid 136 through 151 removed outlier: 3.728A pdb=" N LYS i 149 " --> pdb=" O GLY i 145 " (cutoff:3.500A) Processing helix chain 'i' and resid 162 through 171 removed outlier: 3.582A pdb=" N ALA i 166 " --> pdb=" O THR i 162 " (cutoff:3.500A) Processing helix chain 'i' and resid 201 through 215 removed outlier: 3.995A pdb=" N ALA i 213 " --> pdb=" O ALA i 209 " (cutoff:3.500A) Processing helix chain 'i' and resid 245 through 252 removed outlier: 3.747A pdb=" N LEU i 250 " --> pdb=" O ARG i 246 " (cutoff:3.500A) Processing helix chain 'i' and resid 280 through 296 removed outlier: 3.868A pdb=" N ILE i 294 " --> pdb=" O VAL i 290 " (cutoff:3.500A) Processing helix chain 'i' and resid 307 through 327 removed outlier: 3.623A pdb=" N VAL i 311 " --> pdb=" O THR i 307 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY i 317 " --> pdb=" O ASP i 313 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA i 320 " --> pdb=" O GLU i 316 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE i 321 " --> pdb=" O GLY i 317 " (cutoff:3.500A) Processing helix chain 'i' and resid 344 through 350 removed outlier: 3.611A pdb=" N ALA i 349 " --> pdb=" O ALA i 345 " (cutoff:3.500A) Processing helix chain 'i' and resid 377 through 382 removed outlier: 4.520A pdb=" N THR i 380 " --> pdb=" O GLN i 377 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL i 382 " --> pdb=" O LEU i 379 " (cutoff:3.500A) Processing helix chain 'm' and resid 51 through 60 Processing helix chain 'm' and resid 65 through 74 Processing helix chain 'm' and resid 90 through 100 removed outlier: 3.716A pdb=" N ALA m 95 " --> pdb=" O PRO m 91 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER m 96 " --> pdb=" O GLU m 92 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA m 97 " --> pdb=" O ALA m 93 " (cutoff:3.500A) Processing helix chain 'm' and resid 110 through 115 removed outlier: 3.533A pdb=" N ALA m 113 " --> pdb=" O GLY m 110 " (cutoff:3.500A) Processing helix chain 'm' and resid 116 through 122 Processing helix chain 'm' and resid 132 through 135 removed outlier: 3.770A pdb=" N ALA m 135 " --> pdb=" O GLY m 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 132 through 135' Processing helix chain 'm' and resid 136 through 150 removed outlier: 3.511A pdb=" N THR m 141 " --> pdb=" O GLN m 137 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY m 145 " --> pdb=" O THR m 141 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU m 148 " --> pdb=" O ASP m 144 " (cutoff:3.500A) Processing helix chain 'm' and resid 163 through 171 removed outlier: 3.733A pdb=" N TYR m 169 " --> pdb=" O ALA m 165 " (cutoff:3.500A) Processing helix chain 'm' and resid 201 through 215 removed outlier: 3.790A pdb=" N ASP m 212 " --> pdb=" O PHE m 208 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA m 213 " --> pdb=" O ALA m 209 " (cutoff:3.500A) Processing helix chain 'm' and resid 247 through 252 Processing helix chain 'm' and resid 280 through 291 removed outlier: 3.546A pdb=" N VAL m 284 " --> pdb=" O PHE m 280 " (cutoff:3.500A) Processing helix chain 'm' and resid 307 through 327 removed outlier: 3.844A pdb=" N ALA m 320 " --> pdb=" O GLU m 316 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE m 321 " --> pdb=" O GLY m 317 " (cutoff:3.500A) Processing helix chain 'm' and resid 344 through 350 removed outlier: 3.507A pdb=" N ALA m 349 " --> pdb=" O ALA m 345 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN m 350 " --> pdb=" O SER m 346 " (cutoff:3.500A) Processing helix chain 'm' and resid 377 through 382 removed outlier: 4.329A pdb=" N THR m 380 " --> pdb=" O GLN m 377 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL m 382 " --> pdb=" O LEU m 379 " (cutoff:3.500A) Processing helix chain 'n' and resid 51 through 60 Processing helix chain 'n' and resid 65 through 74 Processing helix chain 'n' and resid 90 through 100 removed outlier: 3.716A pdb=" N ALA n 95 " --> pdb=" O PRO n 91 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER n 96 " --> pdb=" O GLU n 92 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA n 97 " --> pdb=" O ALA n 93 " (cutoff:3.500A) Processing helix chain 'n' and resid 110 through 115 removed outlier: 3.532A pdb=" N ALA n 113 " --> pdb=" O GLY n 110 " (cutoff:3.500A) Processing helix chain 'n' and resid 116 through 122 Processing helix chain 'n' and resid 132 through 135 removed outlier: 3.770A pdb=" N ALA n 135 " --> pdb=" O GLY n 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 132 through 135' Processing helix chain 'n' and resid 136 through 150 removed outlier: 3.512A pdb=" N THR n 141 " --> pdb=" O GLN n 137 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY n 145 " --> pdb=" O THR n 141 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU n 148 " --> pdb=" O ASP n 144 " (cutoff:3.500A) Processing helix chain 'n' and resid 163 through 171 removed outlier: 3.733A pdb=" N TYR n 169 " --> pdb=" O ALA n 165 " (cutoff:3.500A) Processing helix chain 'n' and resid 201 through 215 removed outlier: 3.791A pdb=" N ASP n 212 " --> pdb=" O PHE n 208 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA n 213 " --> pdb=" O ALA n 209 " (cutoff:3.500A) Processing helix chain 'n' and resid 247 through 252 Processing helix chain 'n' and resid 280 through 291 removed outlier: 3.545A pdb=" N VAL n 284 " --> pdb=" O PHE n 280 " (cutoff:3.500A) Processing helix chain 'n' and resid 307 through 327 removed outlier: 3.845A pdb=" N ALA n 320 " --> pdb=" O GLU n 316 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE n 321 " --> pdb=" O GLY n 317 " (cutoff:3.500A) Processing helix chain 'n' and resid 344 through 350 removed outlier: 3.507A pdb=" N ALA n 349 " --> pdb=" O ALA n 345 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN n 350 " --> pdb=" O SER n 346 " (cutoff:3.500A) Processing helix chain 'n' and resid 377 through 382 removed outlier: 4.329A pdb=" N THR n 380 " --> pdb=" O GLN n 377 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL n 382 " --> pdb=" O LEU n 379 " (cutoff:3.500A) Processing helix chain 'r' and resid 51 through 60 Processing helix chain 'r' and resid 65 through 74 Processing helix chain 'r' and resid 90 through 100 removed outlier: 3.716A pdb=" N ALA r 95 " --> pdb=" O PRO r 91 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER r 96 " --> pdb=" O GLU r 92 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA r 97 " --> pdb=" O ALA r 93 " (cutoff:3.500A) Processing helix chain 'r' and resid 110 through 115 removed outlier: 3.533A pdb=" N ALA r 113 " --> pdb=" O GLY r 110 " (cutoff:3.500A) Processing helix chain 'r' and resid 116 through 122 Processing helix chain 'r' and resid 132 through 135 removed outlier: 3.770A pdb=" N ALA r 135 " --> pdb=" O GLY r 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 132 through 135' Processing helix chain 'r' and resid 136 through 150 removed outlier: 3.512A pdb=" N THR r 141 " --> pdb=" O GLN r 137 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY r 145 " --> pdb=" O THR r 141 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU r 148 " --> pdb=" O ASP r 144 " (cutoff:3.500A) Processing helix chain 'r' and resid 163 through 171 removed outlier: 3.732A pdb=" N TYR r 169 " --> pdb=" O ALA r 165 " (cutoff:3.500A) Processing helix chain 'r' and resid 201 through 215 removed outlier: 3.790A pdb=" N ASP r 212 " --> pdb=" O PHE r 208 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA r 213 " --> pdb=" O ALA r 209 " (cutoff:3.500A) Processing helix chain 'r' and resid 247 through 252 Processing helix chain 'r' and resid 280 through 291 removed outlier: 3.546A pdb=" N VAL r 284 " --> pdb=" O PHE r 280 " (cutoff:3.500A) Processing helix chain 'r' and resid 307 through 327 removed outlier: 3.844A pdb=" N ALA r 320 " --> pdb=" O GLU r 316 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE r 321 " --> pdb=" O GLY r 317 " (cutoff:3.500A) Processing helix chain 'r' and resid 344 through 350 removed outlier: 3.507A pdb=" N ALA r 349 " --> pdb=" O ALA r 345 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN r 350 " --> pdb=" O SER r 346 " (cutoff:3.500A) Processing helix chain 'r' and resid 377 through 382 removed outlier: 4.329A pdb=" N THR r 380 " --> pdb=" O GLN r 377 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL r 382 " --> pdb=" O LEU r 379 " (cutoff:3.500A) Processing helix chain 'q' and resid 51 through 60 Processing helix chain 'q' and resid 65 through 74 Processing helix chain 'q' and resid 90 through 100 removed outlier: 3.715A pdb=" N ALA q 95 " --> pdb=" O PRO q 91 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER q 96 " --> pdb=" O GLU q 92 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA q 97 " --> pdb=" O ALA q 93 " (cutoff:3.500A) Processing helix chain 'q' and resid 110 through 115 removed outlier: 3.533A pdb=" N ALA q 113 " --> pdb=" O GLY q 110 " (cutoff:3.500A) Processing helix chain 'q' and resid 116 through 122 Processing helix chain 'q' and resid 132 through 135 removed outlier: 3.771A pdb=" N ALA q 135 " --> pdb=" O GLY q 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 132 through 135' Processing helix chain 'q' and resid 136 through 150 removed outlier: 3.511A pdb=" N THR q 141 " --> pdb=" O GLN q 137 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY q 145 " --> pdb=" O THR q 141 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU q 148 " --> pdb=" O ASP q 144 " (cutoff:3.500A) Processing helix chain 'q' and resid 163 through 171 removed outlier: 3.733A pdb=" N TYR q 169 " --> pdb=" O ALA q 165 " (cutoff:3.500A) Processing helix chain 'q' and resid 201 through 215 removed outlier: 3.790A pdb=" N ASP q 212 " --> pdb=" O PHE q 208 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA q 213 " --> pdb=" O ALA q 209 " (cutoff:3.500A) Processing helix chain 'q' and resid 247 through 252 Processing helix chain 'q' and resid 280 through 291 removed outlier: 3.545A pdb=" N VAL q 284 " --> pdb=" O PHE q 280 " (cutoff:3.500A) Processing helix chain 'q' and resid 307 through 327 removed outlier: 3.844A pdb=" N ALA q 320 " --> pdb=" O GLU q 316 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE q 321 " --> pdb=" O GLY q 317 " (cutoff:3.500A) Processing helix chain 'q' and resid 344 through 350 removed outlier: 3.507A pdb=" N ALA q 349 " --> pdb=" O ALA q 345 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN q 350 " --> pdb=" O SER q 346 " (cutoff:3.500A) Processing helix chain 'q' and resid 377 through 382 removed outlier: 4.329A pdb=" N THR q 380 " --> pdb=" O GLN q 377 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL q 382 " --> pdb=" O LEU q 379 " (cutoff:3.500A) Processing helix chain 'p' and resid 51 through 60 Processing helix chain 'p' and resid 65 through 74 Processing helix chain 'p' and resid 90 through 100 removed outlier: 3.716A pdb=" N ALA p 95 " --> pdb=" O PRO p 91 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER p 96 " --> pdb=" O GLU p 92 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA p 97 " --> pdb=" O ALA p 93 " (cutoff:3.500A) Processing helix chain 'p' and resid 110 through 115 removed outlier: 3.532A pdb=" N ALA p 113 " --> pdb=" O GLY p 110 " (cutoff:3.500A) Processing helix chain 'p' and resid 116 through 122 Processing helix chain 'p' and resid 132 through 135 removed outlier: 3.770A pdb=" N ALA p 135 " --> pdb=" O GLY p 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 132 through 135' Processing helix chain 'p' and resid 136 through 150 removed outlier: 3.512A pdb=" N THR p 141 " --> pdb=" O GLN p 137 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY p 145 " --> pdb=" O THR p 141 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU p 148 " --> pdb=" O ASP p 144 " (cutoff:3.500A) Processing helix chain 'p' and resid 163 through 171 removed outlier: 3.732A pdb=" N TYR p 169 " --> pdb=" O ALA p 165 " (cutoff:3.500A) Processing helix chain 'p' and resid 201 through 215 removed outlier: 3.791A pdb=" N ASP p 212 " --> pdb=" O PHE p 208 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA p 213 " --> pdb=" O ALA p 209 " (cutoff:3.500A) Processing helix chain 'p' and resid 247 through 252 Processing helix chain 'p' and resid 280 through 291 removed outlier: 3.546A pdb=" N VAL p 284 " --> pdb=" O PHE p 280 " (cutoff:3.500A) Processing helix chain 'p' and resid 307 through 327 removed outlier: 3.845A pdb=" N ALA p 320 " --> pdb=" O GLU p 316 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE p 321 " --> pdb=" O GLY p 317 " (cutoff:3.500A) Processing helix chain 'p' and resid 344 through 350 removed outlier: 3.508A pdb=" N ALA p 349 " --> pdb=" O ALA p 345 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN p 350 " --> pdb=" O SER p 346 " (cutoff:3.500A) Processing helix chain 'p' and resid 377 through 382 removed outlier: 4.330A pdb=" N THR p 380 " --> pdb=" O GLN p 377 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL p 382 " --> pdb=" O LEU p 379 " (cutoff:3.500A) Processing helix chain 'o' and resid 51 through 60 Processing helix chain 'o' and resid 65 through 74 Processing helix chain 'o' and resid 90 through 100 removed outlier: 3.715A pdb=" N ALA o 95 " --> pdb=" O PRO o 91 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER o 96 " --> pdb=" O GLU o 92 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA o 97 " --> pdb=" O ALA o 93 " (cutoff:3.500A) Processing helix chain 'o' and resid 110 through 115 removed outlier: 3.533A pdb=" N ALA o 113 " --> pdb=" O GLY o 110 " (cutoff:3.500A) Processing helix chain 'o' and resid 116 through 122 Processing helix chain 'o' and resid 132 through 135 removed outlier: 3.770A pdb=" N ALA o 135 " --> pdb=" O GLY o 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 132 through 135' Processing helix chain 'o' and resid 136 through 150 removed outlier: 3.512A pdb=" N THR o 141 " --> pdb=" O GLN o 137 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY o 145 " --> pdb=" O THR o 141 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU o 148 " --> pdb=" O ASP o 144 " (cutoff:3.500A) Processing helix chain 'o' and resid 163 through 171 removed outlier: 3.733A pdb=" N TYR o 169 " --> pdb=" O ALA o 165 " (cutoff:3.500A) Processing helix chain 'o' and resid 201 through 215 removed outlier: 3.790A pdb=" N ASP o 212 " --> pdb=" O PHE o 208 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA o 213 " --> pdb=" O ALA o 209 " (cutoff:3.500A) Processing helix chain 'o' and resid 247 through 252 Processing helix chain 'o' and resid 280 through 291 removed outlier: 3.545A pdb=" N VAL o 284 " --> pdb=" O PHE o 280 " (cutoff:3.500A) Processing helix chain 'o' and resid 307 through 327 removed outlier: 3.844A pdb=" N ALA o 320 " --> pdb=" O GLU o 316 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N PHE o 321 " --> pdb=" O GLY o 317 " (cutoff:3.500A) Processing helix chain 'o' and resid 344 through 350 removed outlier: 3.507A pdb=" N ALA o 349 " --> pdb=" O ALA o 345 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN o 350 " --> pdb=" O SER o 346 " (cutoff:3.500A) Processing helix chain 'o' and resid 377 through 382 removed outlier: 4.329A pdb=" N THR o 380 " --> pdb=" O GLN o 377 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL o 382 " --> pdb=" O LEU o 379 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 29 through 30 removed outlier: 6.943A pdb=" N GLY B 30 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N ILE B 46 " --> pdb=" O GLY B 30 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N VAL B 42 " --> pdb=" O MET B 71 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N MET B 71 " --> pdb=" O VAL B 42 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N LEU B 44 " --> pdb=" O ARG B 69 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ARG B 69 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ILE B 46 " --> pdb=" O GLN B 67 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N GLN B 67 " --> pdb=" O ILE B 46 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU B 48 " --> pdb=" O ARG B 65 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N CYS B 64 " --> pdb=" O GLN B 129 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLN B 129 " --> pdb=" O CYS B 64 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N VAL B 122 " --> pdb=" O VAL B 110 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL B 110 " --> pdb=" O VAL B 122 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU B 124 " --> pdb=" O SER B 108 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N SER B 108 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N GLU B 126 " --> pdb=" O VAL B 106 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N VAL B 106 " --> pdb=" O PRO C 51 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL B 110 " --> pdb=" O ALA C 47 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ALA C 47 " --> pdb=" O VAL B 110 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N GLY C 30 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N ILE C 46 " --> pdb=" O GLY C 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 29 through 30 removed outlier: 6.944A pdb=" N GLY D 30 " --> pdb=" O LEU D 44 " (cutoff:3.500A) removed outlier: 8.721A pdb=" N ILE D 46 " --> pdb=" O GLY D 30 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ALA D 47 " --> pdb=" O VAL C 110 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL C 110 " --> pdb=" O ALA D 47 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N VAL C 106 " --> pdb=" O PRO D 51 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N GLU C 126 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N SER C 108 " --> pdb=" O LEU C 124 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU C 124 " --> pdb=" O SER C 108 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL C 110 " --> pdb=" O VAL C 122 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N VAL C 122 " --> pdb=" O VAL C 110 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLN C 129 " --> pdb=" O CYS C 64 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N CYS C 64 " --> pdb=" O GLN C 129 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLU C 48 " --> pdb=" O ARG C 65 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N GLN C 67 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ILE C 46 " --> pdb=" O GLN C 67 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ARG C 69 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N LEU C 44 " --> pdb=" O ARG C 69 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N MET C 71 " --> pdb=" O VAL C 42 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N VAL C 42 " --> pdb=" O MET C 71 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N GLY C 30 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N ILE C 46 " --> pdb=" O GLY C 30 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 29 through 30 removed outlier: 6.943A pdb=" N GLY B 30 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N ILE B 46 " --> pdb=" O GLY B 30 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N ALA B 47 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL A 110 " --> pdb=" O ALA B 47 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER A 108 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N VAL A 106 " --> pdb=" O PRO B 51 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N GLU A 126 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N SER A 108 " --> pdb=" O LEU A 124 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU A 124 " --> pdb=" O SER A 108 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL A 110 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N VAL A 122 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLN A 129 " --> pdb=" O CYS A 64 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N CYS A 64 " --> pdb=" O GLN A 129 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU A 48 " --> pdb=" O ARG A 65 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N GLN A 67 " --> pdb=" O ILE A 46 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ILE A 46 " --> pdb=" O GLN A 67 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N ARG A 69 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N LEU A 44 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N MET A 71 " --> pdb=" O VAL A 42 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N VAL A 42 " --> pdb=" O MET A 71 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N ALA A 47 " --> pdb=" O VAL F 110 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL F 110 " --> pdb=" O ALA A 47 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N VAL F 106 " --> pdb=" O PRO A 51 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N GLU F 126 " --> pdb=" O VAL F 106 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N SER F 108 " --> pdb=" O LEU F 124 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU F 124 " --> pdb=" O SER F 108 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL F 110 " --> pdb=" O VAL F 122 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N VAL F 122 " --> pdb=" O VAL F 110 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLN F 129 " --> pdb=" O CYS F 64 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N CYS F 64 " --> pdb=" O GLN F 129 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU F 48 " --> pdb=" O ARG F 65 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N GLN F 67 " --> pdb=" O ILE F 46 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ILE F 46 " --> pdb=" O GLN F 67 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N ARG F 69 " --> pdb=" O LEU F 44 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N LEU F 44 " --> pdb=" O ARG F 69 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N MET F 71 " --> pdb=" O VAL F 42 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N VAL F 42 " --> pdb=" O MET F 71 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N GLY F 30 " --> pdb=" O LEU F 44 " (cutoff:3.500A) removed outlier: 8.721A pdb=" N ILE F 46 " --> pdb=" O GLY F 30 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 29 through 30 removed outlier: 6.943A pdb=" N GLY A 30 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 8.721A pdb=" N ILE A 46 " --> pdb=" O GLY A 30 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 41 through 51 current: chain 'F' and resid 61 through 72 removed outlier: 4.010A pdb=" N GLU F 48 " --> pdb=" O ARG F 65 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N GLN F 67 " --> pdb=" O ILE F 46 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ILE F 46 " --> pdb=" O GLN F 67 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N ARG F 69 " --> pdb=" O LEU F 44 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N LEU F 44 " --> pdb=" O ARG F 69 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N MET F 71 " --> pdb=" O VAL F 42 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N VAL F 42 " --> pdb=" O MET F 71 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ALA F 47 " --> pdb=" O VAL E 110 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL E 110 " --> pdb=" O ALA F 47 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N VAL E 106 " --> pdb=" O PRO F 51 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N GLU E 126 " --> pdb=" O VAL E 106 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N SER E 108 " --> pdb=" O LEU E 124 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU E 124 " --> pdb=" O SER E 108 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL E 110 " --> pdb=" O VAL E 122 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N VAL E 122 " --> pdb=" O VAL E 110 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLN E 129 " --> pdb=" O CYS E 64 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N CYS E 64 " --> pdb=" O GLN E 129 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLU E 48 " --> pdb=" O ARG E 65 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N GLN E 67 " --> pdb=" O ILE E 46 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ILE E 46 " --> pdb=" O GLN E 67 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N ARG E 69 " --> pdb=" O LEU E 44 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N LEU E 44 " --> pdb=" O ARG E 69 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N MET E 71 " --> pdb=" O VAL E 42 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N VAL E 42 " --> pdb=" O MET E 71 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N GLY E 30 " --> pdb=" O LEU E 44 " (cutoff:3.500A) removed outlier: 8.721A pdb=" N ILE E 46 " --> pdb=" O GLY E 30 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 29 through 30 removed outlier: 6.943A pdb=" N GLY E 30 " --> pdb=" O LEU E 44 " (cutoff:3.500A) removed outlier: 8.721A pdb=" N ILE E 46 " --> pdb=" O GLY E 30 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ALA E 47 " --> pdb=" O VAL D 110 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL D 110 " --> pdb=" O ALA E 47 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N VAL D 106 " --> pdb=" O PRO E 51 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N GLU D 126 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N SER D 108 " --> pdb=" O LEU D 124 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU D 124 " --> pdb=" O SER D 108 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL D 110 " --> pdb=" O VAL D 122 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N VAL D 122 " --> pdb=" O VAL D 110 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLN D 129 " --> pdb=" O CYS D 64 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N CYS D 64 " --> pdb=" O GLN D 129 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU D 48 " --> pdb=" O ARG D 65 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N GLN D 67 " --> pdb=" O ILE D 46 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ILE D 46 " --> pdb=" O GLN D 67 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ARG D 69 " --> pdb=" O LEU D 44 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N LEU D 44 " --> pdb=" O ARG D 69 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N MET D 71 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N VAL D 42 " --> pdb=" O MET D 71 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N GLY D 30 " --> pdb=" O LEU D 44 " (cutoff:3.500A) removed outlier: 8.721A pdb=" N ILE D 46 " --> pdb=" O GLY D 30 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 147 through 151 removed outlier: 6.223A pdb=" N SER A 147 " --> pdb=" O VAL a 353 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N TRP a 355 " --> pdb=" O SER A 147 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N MET A 149 " --> pdb=" O TRP a 355 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ILE a 357 " --> pdb=" O MET A 149 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLY A 151 " --> pdb=" O ILE a 357 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N PHE a 359 " --> pdb=" O GLY A 151 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN a 333 " --> pdb=" O THR a 360 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'a' and resid 8 through 11 removed outlier: 6.327A pdb=" N THR a 8 " --> pdb=" O PHE b 370 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N VAL b 372 " --> pdb=" O THR a 8 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N THR a 10 " --> pdb=" O VAL b 372 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N VAL b 374 " --> pdb=" O THR a 10 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N TYR h 354 " --> pdb=" O ALA h 338 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ALA h 338 " --> pdb=" O TYR h 354 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ASN h 356 " --> pdb=" O VAL h 336 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N VAL h 336 " --> pdb=" O ASN h 356 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ARG h 358 " --> pdb=" O PHE h 334 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N PHE h 334 " --> pdb=" O ARG h 358 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR h 360 " --> pdb=" O ILE h 332 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'a' and resid 47 through 49 removed outlier: 6.722A pdb=" N LEU a 128 " --> pdb=" O ILE a 155 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'a' and resid 101 through 102 Processing sheet with id=AB1, first strand: chain 'a' and resid 186 through 189 Processing sheet with id=AB2, first strand: chain 'a' and resid 257 through 258 Processing sheet with id=AB3, first strand: chain 'f' and resid 8 through 11 removed outlier: 3.676A pdb=" N THR f 8 " --> pdb=" O PRO a 368 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N TYR g 354 " --> pdb=" O ALA g 338 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ALA g 338 " --> pdb=" O TYR g 354 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ASN g 356 " --> pdb=" O VAL g 336 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL g 336 " --> pdb=" O ASN g 356 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ARG g 358 " --> pdb=" O PHE g 334 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N PHE g 334 " --> pdb=" O ARG g 358 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N THR g 360 " --> pdb=" O ILE g 332 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 147 through 151 removed outlier: 6.223A pdb=" N SER B 147 " --> pdb=" O VAL b 353 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N TRP b 355 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N MET B 149 " --> pdb=" O TRP b 355 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ILE b 357 " --> pdb=" O MET B 149 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLY B 151 " --> pdb=" O ILE b 357 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N PHE b 359 " --> pdb=" O GLY B 151 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN b 333 " --> pdb=" O THR b 360 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 147 through 151 removed outlier: 6.223A pdb=" N SER C 147 " --> pdb=" O VAL c 353 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N TRP c 355 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N MET C 149 " --> pdb=" O TRP c 355 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ILE c 357 " --> pdb=" O MET C 149 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLY C 151 " --> pdb=" O ILE c 357 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N PHE c 359 " --> pdb=" O GLY C 151 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASN c 333 " --> pdb=" O THR c 360 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 147 through 151 removed outlier: 6.224A pdb=" N SER D 147 " --> pdb=" O VAL d 353 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N TRP d 355 " --> pdb=" O SER D 147 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N MET D 149 " --> pdb=" O TRP d 355 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ILE d 357 " --> pdb=" O MET D 149 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLY D 151 " --> pdb=" O ILE d 357 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N PHE d 359 " --> pdb=" O GLY D 151 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN d 333 " --> pdb=" O THR d 360 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 147 through 151 removed outlier: 6.223A pdb=" N SER E 147 " --> pdb=" O VAL e 353 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N TRP e 355 " --> pdb=" O SER E 147 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N MET E 149 " --> pdb=" O TRP e 355 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ILE e 357 " --> pdb=" O MET E 149 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLY E 151 " --> pdb=" O ILE e 357 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N PHE e 359 " --> pdb=" O GLY E 151 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASN e 333 " --> pdb=" O THR e 360 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 147 through 151 removed outlier: 6.224A pdb=" N SER F 147 " --> pdb=" O VAL f 353 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N TRP f 355 " --> pdb=" O SER F 147 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N MET F 149 " --> pdb=" O TRP f 355 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N ILE f 357 " --> pdb=" O MET F 149 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLY F 151 " --> pdb=" O ILE f 357 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N PHE f 359 " --> pdb=" O GLY F 151 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASN f 333 " --> pdb=" O THR f 360 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'b' and resid 8 through 11 removed outlier: 6.338A pdb=" N THR b 8 " --> pdb=" O PHE c 370 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL c 372 " --> pdb=" O THR b 8 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N THR b 10 " --> pdb=" O VAL c 372 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N VAL c 374 " --> pdb=" O THR b 10 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N TYR i 354 " --> pdb=" O ALA i 338 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ALA i 338 " --> pdb=" O TYR i 354 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ASN i 356 " --> pdb=" O VAL i 336 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N VAL i 336 " --> pdb=" O ASN i 356 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ARG i 358 " --> pdb=" O PHE i 334 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N PHE i 334 " --> pdb=" O ARG i 358 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N THR i 360 " --> pdb=" O ILE i 332 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'b' and resid 47 through 49 removed outlier: 6.722A pdb=" N LEU b 128 " --> pdb=" O ILE b 155 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'b' and resid 101 through 102 Processing sheet with id=AC3, first strand: chain 'b' and resid 186 through 189 Processing sheet with id=AC4, first strand: chain 'b' and resid 257 through 258 Processing sheet with id=AC5, first strand: chain 'c' and resid 8 through 11 removed outlier: 6.344A pdb=" N THR c 8 " --> pdb=" O PHE d 370 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N VAL d 372 " --> pdb=" O THR c 8 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N THR c 10 " --> pdb=" O VAL d 372 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N VAL d 374 " --> pdb=" O THR c 10 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N TYR j 354 " --> pdb=" O ALA j 338 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ALA j 338 " --> pdb=" O TYR j 354 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ASN j 356 " --> pdb=" O VAL j 336 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N VAL j 336 " --> pdb=" O ASN j 356 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ARG j 358 " --> pdb=" O PHE j 334 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N PHE j 334 " --> pdb=" O ARG j 358 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N THR j 360 " --> pdb=" O ILE j 332 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'c' and resid 47 through 49 removed outlier: 6.722A pdb=" N LEU c 128 " --> pdb=" O ILE c 155 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'c' and resid 101 through 102 Processing sheet with id=AC8, first strand: chain 'c' and resid 186 through 189 Processing sheet with id=AC9, first strand: chain 'c' and resid 257 through 258 Processing sheet with id=AD1, first strand: chain 'd' and resid 8 through 11 removed outlier: 6.321A pdb=" N THR d 8 " --> pdb=" O PHE e 370 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N VAL e 372 " --> pdb=" O THR d 8 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N THR d 10 " --> pdb=" O VAL e 372 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N VAL e 374 " --> pdb=" O THR d 10 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N TYR k 354 " --> pdb=" O ALA k 338 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ALA k 338 " --> pdb=" O TYR k 354 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ASN k 356 " --> pdb=" O VAL k 336 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N VAL k 336 " --> pdb=" O ASN k 356 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ARG k 358 " --> pdb=" O PHE k 334 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N PHE k 334 " --> pdb=" O ARG k 358 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR k 360 " --> pdb=" O ILE k 332 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'd' and resid 47 through 49 removed outlier: 6.722A pdb=" N LEU d 128 " --> pdb=" O ILE d 155 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'd' and resid 101 through 102 Processing sheet with id=AD4, first strand: chain 'd' and resid 186 through 189 Processing sheet with id=AD5, first strand: chain 'd' and resid 257 through 258 Processing sheet with id=AD6, first strand: chain 'e' and resid 8 through 11 removed outlier: 6.308A pdb=" N THR e 8 " --> pdb=" O PHE f 370 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N VAL f 372 " --> pdb=" O THR e 8 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N THR e 10 " --> pdb=" O VAL f 372 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N VAL f 374 " --> pdb=" O THR e 10 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N TYR l 354 " --> pdb=" O ALA l 338 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ALA l 338 " --> pdb=" O TYR l 354 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ASN l 356 " --> pdb=" O VAL l 336 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N VAL l 336 " --> pdb=" O ASN l 356 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ARG l 358 " --> pdb=" O PHE l 334 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N PHE l 334 " --> pdb=" O ARG l 358 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N THR l 360 " --> pdb=" O ILE l 332 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'e' and resid 47 through 49 removed outlier: 6.722A pdb=" N LEU e 128 " --> pdb=" O ILE e 155 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'e' and resid 101 through 102 Processing sheet with id=AD9, first strand: chain 'e' and resid 186 through 189 Processing sheet with id=AE1, first strand: chain 'e' and resid 257 through 258 Processing sheet with id=AE2, first strand: chain 'f' and resid 47 through 49 removed outlier: 6.722A pdb=" N LEU f 128 " --> pdb=" O ILE f 155 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'f' and resid 101 through 102 Processing sheet with id=AE4, first strand: chain 'f' and resid 186 through 189 Processing sheet with id=AE5, first strand: chain 'f' and resid 257 through 258 Processing sheet with id=AE6, first strand: chain 'g' and resid 8 through 11 removed outlier: 4.395A pdb=" N ASP n 361 " --> pdb=" O THR h 375 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ASN n 333 " --> pdb=" O THR n 360 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'g' and resid 47 through 49 removed outlier: 6.385A pdb=" N LEU g 128 " --> pdb=" O ILE g 155 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'g' and resid 194 through 198 Processing sheet with id=AE9, first strand: chain 'g' and resid 257 through 258 Processing sheet with id=AF1, first strand: chain 'l' and resid 8 through 11 removed outlier: 7.570A pdb=" N THR l 10 " --> pdb=" O PRO g 368 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N PHE g 370 " --> pdb=" O THR l 10 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ASP m 361 " --> pdb=" O THR g 375 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ASN m 333 " --> pdb=" O THR m 360 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'h' and resid 8 through 11 removed outlier: 4.394A pdb=" N ASP o 361 " --> pdb=" O THR i 375 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ASN o 333 " --> pdb=" O THR o 360 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'h' and resid 47 through 49 removed outlier: 6.384A pdb=" N LEU h 128 " --> pdb=" O ILE h 155 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'h' and resid 194 through 198 Processing sheet with id=AF5, first strand: chain 'h' and resid 257 through 258 Processing sheet with id=AF6, first strand: chain 'l' and resid 47 through 49 removed outlier: 6.384A pdb=" N LEU l 128 " --> pdb=" O ILE l 155 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'l' and resid 194 through 198 Processing sheet with id=AF8, first strand: chain 'l' and resid 257 through 258 Processing sheet with id=AF9, first strand: chain 'k' and resid 8 through 11 removed outlier: 7.590A pdb=" N THR k 10 " --> pdb=" O PRO l 368 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N PHE l 370 " --> pdb=" O THR k 10 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ASP r 361 " --> pdb=" O THR l 375 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ASN r 333 " --> pdb=" O THR r 360 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'k' and resid 47 through 49 removed outlier: 6.385A pdb=" N LEU k 128 " --> pdb=" O ILE k 155 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'k' and resid 194 through 198 Processing sheet with id=AG3, first strand: chain 'k' and resid 257 through 258 Processing sheet with id=AG4, first strand: chain 'j' and resid 8 through 11 removed outlier: 7.602A pdb=" N THR j 10 " --> pdb=" O PRO k 368 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N PHE k 370 " --> pdb=" O THR j 10 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ASP q 361 " --> pdb=" O THR k 375 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ASN q 333 " --> pdb=" O THR q 360 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'j' and resid 47 through 49 removed outlier: 6.383A pdb=" N LEU j 128 " --> pdb=" O ILE j 155 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'j' and resid 194 through 198 Processing sheet with id=AG7, first strand: chain 'j' and resid 257 through 258 Processing sheet with id=AG8, first strand: chain 'i' and resid 8 through 11 removed outlier: 7.618A pdb=" N THR i 10 " --> pdb=" O PRO j 368 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N PHE j 370 " --> pdb=" O THR i 10 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ASP p 361 " --> pdb=" O THR j 375 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ASN p 333 " --> pdb=" O THR p 360 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'i' and resid 47 through 49 removed outlier: 6.384A pdb=" N LEU i 128 " --> pdb=" O ILE i 155 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'i' and resid 194 through 198 Processing sheet with id=AH2, first strand: chain 'i' and resid 257 through 258 Processing sheet with id=AH3, first strand: chain 'm' and resid 8 through 11 removed outlier: 6.516A pdb=" N THR m 8 " --> pdb=" O PHE n 370 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N VAL n 372 " --> pdb=" O THR m 8 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N THR m 10 " --> pdb=" O VAL n 372 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH3 Processing sheet with id=AH4, first strand: chain 'm' and resid 47 through 49 removed outlier: 6.380A pdb=" N ILE m 27 " --> pdb=" O VAL m 81 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LEU m 128 " --> pdb=" O ILE m 155 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'm' and resid 32 through 33 Processing sheet with id=AH6, first strand: chain 'm' and resid 185 through 189 Processing sheet with id=AH7, first strand: chain 'm' and resid 257 through 258 Processing sheet with id=AH8, first strand: chain 'm' and resid 369 through 372 Processing sheet with id=AH9, first strand: chain 'n' and resid 8 through 11 removed outlier: 6.490A pdb=" N THR n 8 " --> pdb=" O PHE o 370 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N VAL o 372 " --> pdb=" O THR n 8 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N THR n 10 " --> pdb=" O VAL o 372 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH9 Processing sheet with id=AI1, first strand: chain 'n' and resid 47 through 49 removed outlier: 6.379A pdb=" N ILE n 27 " --> pdb=" O VAL n 81 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU n 128 " --> pdb=" O ILE n 155 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'n' and resid 32 through 33 Processing sheet with id=AI3, first strand: chain 'n' and resid 185 through 189 Processing sheet with id=AI4, first strand: chain 'n' and resid 257 through 258 Processing sheet with id=AI5, first strand: chain 'r' and resid 47 through 49 removed outlier: 6.380A pdb=" N ILE r 27 " --> pdb=" O VAL r 81 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU r 128 " --> pdb=" O ILE r 155 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'r' and resid 32 through 33 Processing sheet with id=AI7, first strand: chain 'r' and resid 185 through 189 Processing sheet with id=AI8, first strand: chain 'r' and resid 257 through 258 Processing sheet with id=AI9, first strand: chain 'r' and resid 369 through 372 Processing sheet with id=AJ1, first strand: chain 'q' and resid 47 through 49 removed outlier: 6.380A pdb=" N ILE q 27 " --> pdb=" O VAL q 81 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU q 128 " --> pdb=" O ILE q 155 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'q' and resid 32 through 33 Processing sheet with id=AJ3, first strand: chain 'q' and resid 185 through 189 Processing sheet with id=AJ4, first strand: chain 'q' and resid 257 through 258 Processing sheet with id=AJ5, first strand: chain 'q' and resid 369 through 372 Processing sheet with id=AJ6, first strand: chain 'p' and resid 47 through 49 removed outlier: 6.380A pdb=" N ILE p 27 " --> pdb=" O VAL p 81 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU p 128 " --> pdb=" O ILE p 155 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'p' and resid 32 through 33 Processing sheet with id=AJ8, first strand: chain 'p' and resid 185 through 189 Processing sheet with id=AJ9, first strand: chain 'p' and resid 257 through 258 Processing sheet with id=AK1, first strand: chain 'p' and resid 369 through 372 Processing sheet with id=AK2, first strand: chain 'o' and resid 47 through 49 removed outlier: 6.380A pdb=" N ILE o 27 " --> pdb=" O VAL o 81 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU o 128 " --> pdb=" O ILE o 155 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'o' and resid 32 through 33 Processing sheet with id=AK4, first strand: chain 'o' and resid 185 through 189 Processing sheet with id=AK5, first strand: chain 'o' and resid 257 through 258 2079 hydrogen bonds defined for protein. 5673 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: 21.28 Time building geometry restraints manager: 19.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 19941 1.34 - 1.46: 11608 1.46 - 1.58: 29045 1.58 - 1.70: 0 1.70 - 1.81: 270 Bond restraints: 60864 Sorted by residual: bond pdb=" C THR E 39 " pdb=" N PRO E 40 " ideal model delta sigma weight residual 1.334 1.380 -0.046 2.34e-02 1.83e+03 3.81e+00 bond pdb=" C THR A 39 " pdb=" N PRO A 40 " ideal model delta sigma weight residual 1.334 1.379 -0.045 2.34e-02 1.83e+03 3.71e+00 bond pdb=" C THR D 39 " pdb=" N PRO D 40 " ideal model delta sigma weight residual 1.334 1.379 -0.045 2.34e-02 1.83e+03 3.71e+00 bond pdb=" C THR C 39 " pdb=" N PRO C 40 " ideal model delta sigma weight residual 1.334 1.379 -0.045 2.34e-02 1.83e+03 3.65e+00 bond pdb=" C THR B 39 " pdb=" N PRO B 40 " ideal model delta sigma weight residual 1.334 1.378 -0.044 2.34e-02 1.83e+03 3.57e+00 ... (remaining 60859 not shown) Histogram of bond angle deviations from ideal: 99.64 - 106.59: 1855 106.59 - 113.55: 33566 113.55 - 120.50: 23983 120.50 - 127.45: 22889 127.45 - 134.41: 705 Bond angle restraints: 82998 Sorted by residual: angle pdb=" N ILE r 65 " pdb=" CA ILE r 65 " pdb=" C ILE r 65 " ideal model delta sigma weight residual 112.96 108.26 4.70 1.00e+00 1.00e+00 2.21e+01 angle pdb=" N ILE p 65 " pdb=" CA ILE p 65 " pdb=" C ILE p 65 " ideal model delta sigma weight residual 112.96 108.27 4.69 1.00e+00 1.00e+00 2.20e+01 angle pdb=" N ILE o 65 " pdb=" CA ILE o 65 " pdb=" C ILE o 65 " ideal model delta sigma weight residual 112.96 108.28 4.68 1.00e+00 1.00e+00 2.19e+01 angle pdb=" N ILE m 65 " pdb=" CA ILE m 65 " pdb=" C ILE m 65 " ideal model delta sigma weight residual 112.96 108.28 4.68 1.00e+00 1.00e+00 2.19e+01 angle pdb=" N ILE q 65 " pdb=" CA ILE q 65 " pdb=" C ILE q 65 " ideal model delta sigma weight residual 112.96 108.29 4.67 1.00e+00 1.00e+00 2.18e+01 ... (remaining 82993 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.00: 32607 15.00 - 30.01: 2776 30.01 - 45.01: 629 45.01 - 60.02: 132 60.02 - 75.02: 48 Dihedral angle restraints: 36192 sinusoidal: 13596 harmonic: 22596 Sorted by residual: dihedral pdb=" CA ILE k 258 " pdb=" C ILE k 258 " pdb=" N ILE k 259 " pdb=" CA ILE k 259 " ideal model delta harmonic sigma weight residual 180.00 -151.84 -28.16 0 5.00e+00 4.00e-02 3.17e+01 dihedral pdb=" CA ILE h 258 " pdb=" C ILE h 258 " pdb=" N ILE h 259 " pdb=" CA ILE h 259 " ideal model delta harmonic sigma weight residual -180.00 -151.84 -28.16 0 5.00e+00 4.00e-02 3.17e+01 dihedral pdb=" CA ILE l 258 " pdb=" C ILE l 258 " pdb=" N ILE l 259 " pdb=" CA ILE l 259 " ideal model delta harmonic sigma weight residual -180.00 -151.85 -28.15 0 5.00e+00 4.00e-02 3.17e+01 ... (remaining 36189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 5583 0.036 - 0.072: 2567 0.072 - 0.109: 890 0.109 - 0.145: 348 0.145 - 0.181: 56 Chirality restraints: 9444 Sorted by residual: chirality pdb=" CA ASP p 182 " pdb=" N ASP p 182 " pdb=" C ASP p 182 " pdb=" CB ASP p 182 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.19e-01 chirality pdb=" CA ASP o 182 " pdb=" N ASP o 182 " pdb=" C ASP o 182 " pdb=" CB ASP o 182 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.05e-01 chirality pdb=" CA ASP r 182 " pdb=" N ASP r 182 " pdb=" C ASP r 182 " pdb=" CB ASP r 182 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.00e-01 ... (remaining 9441 not shown) Planarity restraints: 10908 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA k 198 " 0.036 5.00e-02 4.00e+02 5.37e-02 4.61e+00 pdb=" N PRO k 199 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO k 199 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO k 199 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA i 198 " -0.035 5.00e-02 4.00e+02 5.36e-02 4.60e+00 pdb=" N PRO i 199 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO i 199 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO i 199 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA j 198 " 0.035 5.00e-02 4.00e+02 5.36e-02 4.60e+00 pdb=" N PRO j 199 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO j 199 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO j 199 " 0.030 5.00e-02 4.00e+02 ... (remaining 10905 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 16024 2.79 - 3.32: 49514 3.32 - 3.85: 98431 3.85 - 4.37: 117880 4.37 - 4.90: 202419 Nonbonded interactions: 484268 Sorted by model distance: nonbonded pdb=" OG1 THR j 50 " pdb=" O THR q 244 " model vdw 2.267 2.440 nonbonded pdb=" OG SER c 222 " pdb=" OD1 ASN c 269 " model vdw 2.270 2.440 nonbonded pdb=" OG SER f 222 " pdb=" OD1 ASN f 269 " model vdw 2.271 2.440 nonbonded pdb=" OG SER a 222 " pdb=" OD1 ASN a 269 " model vdw 2.271 2.440 nonbonded pdb=" OG SER e 222 " pdb=" OD1 ASN e 269 " model vdw 2.271 2.440 ... (remaining 484263 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' } 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=0.00 max=1.00 mean=0.97 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: 4.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 17.060 Check model and map are aligned: 0.670 Set scattering table: 0.420 Process input model: 121.080 Find NCS groups from input model: 3.140 Set up NCS constraints: 0.430 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:2.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 150.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 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 : 0.005 0.046 60864 Z= 0.323 Angle : 0.712 9.406 82998 Z= 0.398 Chirality : 0.049 0.181 9444 Planarity : 0.005 0.054 10908 Dihedral : 12.516 75.022 21624 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 3.03 % Allowed : 9.44 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.32 (0.07), residues: 7830 helix: -4.84 (0.03), residues: 2742 sheet: -2.81 (0.15), residues: 918 loop : -2.74 (0.08), residues: 4170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 32 HIS 0.002 0.001 HIS d 133 PHE 0.017 0.002 PHE q 359 TYR 0.028 0.002 TYR e 264 ARG 0.005 0.001 ARG F 121 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15660 Ramachandran restraints generated. 7830 Oldfield, 0 Emsley, 7830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15660 Ramachandran restraints generated. 7830 Oldfield, 0 Emsley, 7830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1870 residues out of total 6144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 1684 time to evaluate : 4.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 121 PHE cc_start: 0.9112 (m-80) cc_final: 0.8816 (m-80) REVERT: a 246 ARG cc_start: 0.7513 (ptm160) cc_final: 0.7151 (ptt180) REVERT: a 259 ILE cc_start: 0.7890 (OUTLIER) cc_final: 0.7684 (pp) REVERT: a 328 GLN cc_start: 0.8258 (tt0) cc_final: 0.7738 (mt0) REVERT: a 331 VAL cc_start: 0.8909 (t) cc_final: 0.8692 (m) REVERT: a 332 ILE cc_start: 0.8908 (mt) cc_final: 0.8670 (mt) REVERT: a 354 TYR cc_start: 0.8088 (m-80) cc_final: 0.7807 (m-80) REVERT: B 77 ASP cc_start: 0.3044 (m-30) cc_final: 0.2563 (p0) REVERT: C 77 ASP cc_start: 0.3307 (m-30) cc_final: 0.2815 (p0) REVERT: D 149 MET cc_start: 0.8584 (mmm) cc_final: 0.8326 (mmm) REVERT: E 77 ASP cc_start: 0.3754 (m-30) cc_final: 0.2851 (p0) REVERT: b 121 PHE cc_start: 0.9094 (m-80) cc_final: 0.8812 (m-80) REVERT: b 246 ARG cc_start: 0.7604 (ptm160) cc_final: 0.7129 (ptm160) REVERT: b 259 ILE cc_start: 0.7681 (OUTLIER) cc_final: 0.7429 (pp) REVERT: c 128 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8870 (mm) REVERT: c 143 MET cc_start: 0.8938 (mmm) cc_final: 0.8688 (mtp) REVERT: c 246 ARG cc_start: 0.7512 (ptm160) cc_final: 0.7176 (ptm160) REVERT: c 259 ILE cc_start: 0.7693 (OUTLIER) cc_final: 0.7454 (pp) REVERT: d 121 PHE cc_start: 0.9115 (m-80) cc_final: 0.8892 (m-80) REVERT: d 143 MET cc_start: 0.8967 (mmm) cc_final: 0.8728 (mtp) REVERT: d 246 ARG cc_start: 0.7488 (ptm160) cc_final: 0.7102 (ptt180) REVERT: d 259 ILE cc_start: 0.7879 (OUTLIER) cc_final: 0.7666 (pp) REVERT: d 309 THR cc_start: 0.7595 (p) cc_final: 0.7351 (t) REVERT: d 312 LYS cc_start: 0.8194 (mttt) cc_final: 0.7921 (mttp) REVERT: d 328 GLN cc_start: 0.8104 (tt0) cc_final: 0.7796 (mt0) REVERT: d 332 ILE cc_start: 0.8862 (mt) cc_final: 0.8629 (mt) REVERT: d 354 TYR cc_start: 0.8066 (m-80) cc_final: 0.7790 (m-80) REVERT: e 143 MET cc_start: 0.8975 (mmm) cc_final: 0.8716 (mtp) REVERT: e 246 ARG cc_start: 0.7633 (ptm160) cc_final: 0.7112 (ptm160) REVERT: f 133 HIS cc_start: 0.7656 (OUTLIER) cc_final: 0.7265 (m-70) REVERT: f 246 ARG cc_start: 0.7583 (ptm160) cc_final: 0.7239 (ptm160) REVERT: g 227 LYS cc_start: 0.8321 (mmtt) cc_final: 0.7263 (mmmt) REVERT: g 287 MET cc_start: 0.8949 (tpt) cc_final: 0.8731 (tpt) REVERT: h 48 LEU cc_start: 0.9058 (tp) cc_final: 0.8722 (tp) REVERT: h 75 ARG cc_start: 0.9031 (OUTLIER) cc_final: 0.8808 (tpt170) REVERT: h 237 GLU cc_start: 0.7114 (tt0) cc_final: 0.6693 (tp30) REVERT: l 177 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.8237 (mtt90) REVERT: l 181 VAL cc_start: 0.8714 (t) cc_final: 0.8432 (m) REVERT: k 48 LEU cc_start: 0.9041 (tp) cc_final: 0.8672 (tp) REVERT: k 75 ARG cc_start: 0.9099 (OUTLIER) cc_final: 0.8882 (tpt170) REVERT: k 177 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.8199 (mtt90) REVERT: j 227 LYS cc_start: 0.8132 (mmtt) cc_final: 0.6986 (mmmt) REVERT: i 177 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.8209 (mtt90) REVERT: i 181 VAL cc_start: 0.8698 (t) cc_final: 0.8399 (m) REVERT: i 328 GLN cc_start: 0.8255 (tt0) cc_final: 0.8055 (tt0) REVERT: m 127 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9188 (mt) REVERT: m 339 ASP cc_start: 0.8296 (t0) cc_final: 0.7927 (t70) REVERT: m 343 ASN cc_start: 0.8743 (m-40) cc_final: 0.8497 (m110) REVERT: m 383 LEU cc_start: 0.8470 (tp) cc_final: 0.8171 (mp) REVERT: n 18 THR cc_start: 0.8741 (m) cc_final: 0.8500 (p) REVERT: n 75 ARG cc_start: 0.9067 (OUTLIER) cc_final: 0.8745 (tpt170) REVERT: n 127 LEU cc_start: 0.9521 (OUTLIER) cc_final: 0.9279 (mt) REVERT: r 25 SER cc_start: 0.8587 (m) cc_final: 0.8342 (p) REVERT: r 75 ARG cc_start: 0.9042 (OUTLIER) cc_final: 0.8828 (tpt170) REVERT: r 226 ILE cc_start: 0.8965 (mt) cc_final: 0.8703 (mt) REVERT: r 383 LEU cc_start: 0.8410 (tp) cc_final: 0.8121 (mp) REVERT: q 18 THR cc_start: 0.8790 (m) cc_final: 0.8441 (p) REVERT: q 25 SER cc_start: 0.8566 (m) cc_final: 0.8360 (t) REVERT: q 75 ARG cc_start: 0.9117 (OUTLIER) cc_final: 0.8894 (tpt170) REVERT: q 127 LEU cc_start: 0.9431 (OUTLIER) cc_final: 0.9158 (mt) REVERT: q 128 LEU cc_start: 0.9247 (mp) cc_final: 0.8990 (mt) REVERT: p 75 ARG cc_start: 0.9076 (OUTLIER) cc_final: 0.8576 (tpt170) REVERT: p 127 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9088 (mt) REVERT: p 339 ASP cc_start: 0.8341 (t0) cc_final: 0.7999 (t70) REVERT: o 25 SER cc_start: 0.8611 (m) cc_final: 0.8375 (p) REVERT: o 75 ARG cc_start: 0.9045 (OUTLIER) cc_final: 0.8831 (tpt170) REVERT: o 226 ILE cc_start: 0.8955 (mt) cc_final: 0.8677 (mt) REVERT: o 379 LEU cc_start: 0.8648 (tp) cc_final: 0.8366 (tp) outliers start: 186 outliers final: 49 residues processed: 1817 average time/residue: 0.6326 time to fit residues: 1876.4953 Evaluate side-chains 1008 residues out of total 6144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 939 time to evaluate : 4.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 133 HIS Chi-restraints excluded: chain a residue 146 LEU Chi-restraints excluded: chain a residue 259 ILE Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain b residue 61 ILE Chi-restraints excluded: chain b residue 133 HIS Chi-restraints excluded: chain b residue 146 LEU Chi-restraints excluded: chain b residue 259 ILE Chi-restraints excluded: chain b residue 372 VAL Chi-restraints excluded: chain c residue 61 ILE Chi-restraints excluded: chain c residue 128 LEU Chi-restraints excluded: chain c residue 133 HIS Chi-restraints excluded: chain c residue 146 LEU Chi-restraints excluded: chain c residue 259 ILE Chi-restraints excluded: chain c residue 372 VAL Chi-restraints excluded: chain d residue 133 HIS Chi-restraints excluded: chain d residue 146 LEU Chi-restraints excluded: chain d residue 259 ILE Chi-restraints excluded: chain d residue 372 VAL Chi-restraints excluded: chain e residue 133 HIS Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain e residue 372 VAL Chi-restraints excluded: chain f residue 61 ILE Chi-restraints excluded: chain f residue 133 HIS Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain f residue 372 VAL Chi-restraints excluded: chain g residue 229 VAL Chi-restraints excluded: chain g residue 243 GLU Chi-restraints excluded: chain g residue 245 CYS Chi-restraints excluded: chain g residue 353 VAL Chi-restraints excluded: chain h residue 75 ARG Chi-restraints excluded: chain h residue 243 GLU Chi-restraints excluded: chain h residue 245 CYS Chi-restraints excluded: chain h residue 353 VAL Chi-restraints excluded: chain l residue 177 ARG Chi-restraints excluded: chain l residue 243 GLU Chi-restraints excluded: chain l residue 245 CYS Chi-restraints excluded: chain l residue 353 VAL Chi-restraints excluded: chain k residue 75 ARG Chi-restraints excluded: chain k residue 177 ARG Chi-restraints excluded: chain k residue 243 GLU Chi-restraints excluded: chain k residue 245 CYS Chi-restraints excluded: chain k residue 353 VAL Chi-restraints excluded: chain j residue 229 VAL Chi-restraints excluded: chain j residue 243 GLU Chi-restraints excluded: chain j residue 245 CYS Chi-restraints excluded: chain j residue 353 VAL Chi-restraints excluded: chain i residue 177 ARG Chi-restraints excluded: chain i residue 243 GLU Chi-restraints excluded: chain i residue 245 CYS Chi-restraints excluded: chain i residue 259 ILE Chi-restraints excluded: chain i residue 353 VAL Chi-restraints excluded: chain m residue 127 LEU Chi-restraints excluded: chain m residue 229 VAL Chi-restraints excluded: chain m residue 259 ILE Chi-restraints excluded: chain n residue 75 ARG Chi-restraints excluded: chain n residue 127 LEU Chi-restraints excluded: chain n residue 185 VAL Chi-restraints excluded: chain r residue 75 ARG Chi-restraints excluded: chain r residue 127 LEU Chi-restraints excluded: chain q residue 75 ARG Chi-restraints excluded: chain q residue 127 LEU Chi-restraints excluded: chain p residue 75 ARG Chi-restraints excluded: chain p residue 127 LEU Chi-restraints excluded: chain p residue 229 VAL Chi-restraints excluded: chain p residue 259 ILE Chi-restraints excluded: chain o residue 75 ARG Chi-restraints excluded: chain o residue 127 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 658 optimal weight: 9.9990 chunk 591 optimal weight: 10.0000 chunk 328 optimal weight: 7.9990 chunk 201 optimal weight: 5.9990 chunk 398 optimal weight: 3.9990 chunk 315 optimal weight: 7.9990 chunk 611 optimal weight: 0.9980 chunk 236 optimal weight: 0.9980 chunk 371 optimal weight: 20.0000 chunk 455 optimal weight: 10.0000 chunk 708 optimal weight: 10.0000 overall best weight: 3.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN A 38 ASN A 129 GLN a 5 HIS a 193 ASN a 223 ASN B 27 GLN B 38 ASN B 129 GLN C 27 GLN C 38 ASN C 129 GLN D 27 GLN D 38 ASN D 129 GLN E 27 GLN E 38 ASN E 129 GLN F 27 GLN F 38 ASN F 129 GLN b 5 HIS b 193 ASN b 223 ASN c 5 HIS c 74 ASN c 193 ASN c 223 ASN c 298 HIS d 5 HIS d 193 ASN d 223 ASN e 160 ASN e 193 ASN e 223 ASN f 74 ASN f 193 ASN f 223 ASN g 343 ASN g 367 ASN j 343 ASN i 77 GLN m 5 HIS m 172 ASN m 197 ASN m 369 ASN n 5 HIS n 172 ASN n 197 ASN n 343 ASN n 369 ASN r 5 HIS r 77 GLN r 172 ASN r 369 ASN q 5 HIS q 137 GLN q 172 ASN q 186 GLN q 197 ASN q 328 GLN q 343 ASN q 369 ASN p 5 HIS ** p 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 172 ASN p 197 ASN p 369 ASN o 5 HIS o 77 GLN o 172 ASN o 369 ASN Total number of N/Q/H flips: 71 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 60864 Z= 0.298 Angle : 0.619 9.855 82998 Z= 0.328 Chirality : 0.046 0.161 9444 Planarity : 0.005 0.045 10908 Dihedral : 6.670 52.862 8608 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 4.70 % Allowed : 14.50 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.86 (0.08), residues: 7830 helix: -2.96 (0.07), residues: 2694 sheet: -2.78 (0.15), residues: 954 loop : -2.19 (0.09), residues: 4182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP k 300 HIS 0.003 0.001 HIS a 133 PHE 0.016 0.002 PHE r 359 TYR 0.022 0.002 TYR c 264 ARG 0.010 0.001 ARG h 285 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15660 Ramachandran restraints generated. 7830 Oldfield, 0 Emsley, 7830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15660 Ramachandran restraints generated. 7830 Oldfield, 0 Emsley, 7830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1241 residues out of total 6144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 289 poor density : 952 time to evaluate : 4.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 ASP cc_start: -0.1571 (OUTLIER) cc_final: -0.2076 (t70) REVERT: a 73 TYR cc_start: 0.9278 (m-80) cc_final: 0.8954 (m-10) REVERT: a 246 ARG cc_start: 0.7513 (ptm160) cc_final: 0.7226 (ptm160) REVERT: a 282 THR cc_start: 0.9121 (m) cc_final: 0.8853 (p) REVERT: B 135 ASP cc_start: -0.2021 (OUTLIER) cc_final: -0.2533 (t70) REVERT: B 149 MET cc_start: 0.8567 (mmm) cc_final: 0.8320 (mmm) REVERT: C 135 ASP cc_start: -0.2098 (OUTLIER) cc_final: -0.2770 (t0) REVERT: D 135 ASP cc_start: -0.1808 (OUTLIER) cc_final: -0.2298 (t70) REVERT: D 149 MET cc_start: 0.8546 (mmm) cc_final: 0.8269 (mmm) REVERT: E 135 ASP cc_start: -0.2009 (OUTLIER) cc_final: -0.2476 (t70) REVERT: F 135 ASP cc_start: -0.1988 (OUTLIER) cc_final: -0.2399 (t70) REVERT: b 73 TYR cc_start: 0.9324 (m-80) cc_final: 0.9123 (m-80) REVERT: b 246 ARG cc_start: 0.7553 (ptm160) cc_final: 0.6971 (ptm160) REVERT: b 282 THR cc_start: 0.9113 (m) cc_final: 0.8804 (p) REVERT: c 133 HIS cc_start: 0.7714 (OUTLIER) cc_final: 0.7164 (m-70) REVERT: c 246 ARG cc_start: 0.7499 (ptm160) cc_final: 0.7129 (ptm160) REVERT: c 282 THR cc_start: 0.9228 (m) cc_final: 0.8877 (p) REVERT: d 73 TYR cc_start: 0.9275 (m-80) cc_final: 0.8977 (m-10) REVERT: d 246 ARG cc_start: 0.7502 (ptm160) cc_final: 0.7238 (ptm160) REVERT: d 282 THR cc_start: 0.9143 (m) cc_final: 0.8856 (p) REVERT: d 324 ASP cc_start: 0.7265 (m-30) cc_final: 0.6997 (m-30) REVERT: e 246 ARG cc_start: 0.7618 (ptm160) cc_final: 0.7099 (ptm160) REVERT: e 282 THR cc_start: 0.9092 (m) cc_final: 0.8721 (p) REVERT: e 361 ASP cc_start: 0.7334 (t70) cc_final: 0.7069 (t70) REVERT: f 133 HIS cc_start: 0.7913 (OUTLIER) cc_final: 0.7245 (m-70) REVERT: f 246 ARG cc_start: 0.7606 (ptm160) cc_final: 0.7163 (ptm160) REVERT: f 282 THR cc_start: 0.9186 (m) cc_final: 0.8847 (p) REVERT: g 48 LEU cc_start: 0.9057 (tp) cc_final: 0.8743 (tp) REVERT: g 127 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.9128 (mt) REVERT: g 287 MET cc_start: 0.9022 (tpt) cc_final: 0.8758 (tpt) REVERT: g 308 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8191 (mmtt) REVERT: g 312 LYS cc_start: 0.8323 (tptt) cc_final: 0.8068 (mmtt) REVERT: g 383 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.8088 (mp) REVERT: h 48 LEU cc_start: 0.9112 (tp) cc_final: 0.8748 (tp) REVERT: h 128 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8880 (mp) REVERT: l 234 ARG cc_start: 0.8249 (ttp80) cc_final: 0.7805 (ttp80) REVERT: k 48 LEU cc_start: 0.9086 (tp) cc_final: 0.8720 (tp) REVERT: k 308 LYS cc_start: 0.8738 (mmtm) cc_final: 0.8414 (mmtt) REVERT: k 312 LYS cc_start: 0.8349 (tptt) cc_final: 0.8104 (mmtt) REVERT: k 374 VAL cc_start: 0.8965 (m) cc_final: 0.8763 (t) REVERT: j 48 LEU cc_start: 0.9005 (tp) cc_final: 0.8702 (tp) REVERT: j 127 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9108 (mt) REVERT: j 383 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.8033 (mp) REVERT: i 234 ARG cc_start: 0.8224 (ttp80) cc_final: 0.7842 (ttp80) REVERT: m 127 LEU cc_start: 0.9460 (OUTLIER) cc_final: 0.9246 (mt) REVERT: m 282 THR cc_start: 0.9209 (OUTLIER) cc_final: 0.8701 (p) REVERT: m 383 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8135 (mp) REVERT: n 18 THR cc_start: 0.8805 (m) cc_final: 0.8565 (p) REVERT: n 75 ARG cc_start: 0.9145 (OUTLIER) cc_final: 0.8921 (tpt170) REVERT: n 127 LEU cc_start: 0.9530 (OUTLIER) cc_final: 0.9325 (mt) REVERT: n 322 MET cc_start: 0.8688 (mmt) cc_final: 0.8454 (mmp) REVERT: n 327 ASN cc_start: 0.8643 (OUTLIER) cc_final: 0.8034 (m-40) REVERT: r 75 ARG cc_start: 0.9096 (OUTLIER) cc_final: 0.8618 (tpt170) REVERT: r 96 SER cc_start: 0.8376 (m) cc_final: 0.7835 (p) REVERT: q 18 THR cc_start: 0.8771 (m) cc_final: 0.8537 (p) REVERT: q 75 ARG cc_start: 0.9148 (OUTLIER) cc_final: 0.8884 (tpt170) REVERT: q 96 SER cc_start: 0.8435 (m) cc_final: 0.7690 (p) REVERT: q 127 LEU cc_start: 0.9513 (OUTLIER) cc_final: 0.9288 (mt) REVERT: q 287 MET cc_start: 0.8377 (tpp) cc_final: 0.7913 (tpp) REVERT: q 327 ASN cc_start: 0.8576 (OUTLIER) cc_final: 0.8143 (m-40) REVERT: p 75 ARG cc_start: 0.9139 (OUTLIER) cc_final: 0.8917 (tpt90) REVERT: p 127 LEU cc_start: 0.9429 (OUTLIER) cc_final: 0.9166 (mt) REVERT: p 282 THR cc_start: 0.9196 (m) cc_final: 0.8757 (p) REVERT: p 383 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8218 (mp) REVERT: o 75 ARG cc_start: 0.9164 (OUTLIER) cc_final: 0.8938 (tpt170) REVERT: o 96 SER cc_start: 0.8458 (m) cc_final: 0.7918 (p) REVERT: o 383 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8164 (mp) outliers start: 289 outliers final: 196 residues processed: 1147 average time/residue: 0.5751 time to fit residues: 1118.4319 Evaluate side-chains 1063 residues out of total 6144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 838 time to evaluate : 4.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain a residue 32 VAL Chi-restraints excluded: chain a residue 34 THR Chi-restraints excluded: chain a residue 133 HIS Chi-restraints excluded: chain a residue 146 LEU Chi-restraints excluded: chain a residue 257 THR Chi-restraints excluded: chain a residue 258 ILE Chi-restraints excluded: chain a residue 318 LEU Chi-restraints excluded: chain a residue 335 GLU Chi-restraints excluded: chain a residue 372 VAL Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain C residue 135 ASP Chi-restraints excluded: chain D residue 135 ASP Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain F residue 71 MET Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 135 ASP Chi-restraints excluded: chain b residue 32 VAL Chi-restraints excluded: chain b residue 34 THR Chi-restraints excluded: chain b residue 61 ILE Chi-restraints excluded: chain b residue 133 HIS Chi-restraints excluded: chain b residue 146 LEU Chi-restraints excluded: chain b residue 161 SER Chi-restraints excluded: chain b residue 257 THR Chi-restraints excluded: chain b residue 372 VAL Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain c residue 34 THR Chi-restraints excluded: chain c residue 61 ILE Chi-restraints excluded: chain c residue 133 HIS Chi-restraints excluded: chain c residue 161 SER Chi-restraints excluded: chain c residue 257 THR Chi-restraints excluded: chain c residue 372 VAL Chi-restraints excluded: chain d residue 32 VAL Chi-restraints excluded: chain d residue 34 THR Chi-restraints excluded: chain d residue 133 HIS Chi-restraints excluded: chain d residue 146 LEU Chi-restraints excluded: chain d residue 257 THR Chi-restraints excluded: chain d residue 258 ILE Chi-restraints excluded: chain d residue 318 LEU Chi-restraints excluded: chain d residue 335 GLU Chi-restraints excluded: chain d residue 372 VAL Chi-restraints excluded: chain e residue 32 VAL Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 61 ILE Chi-restraints excluded: chain e residue 133 HIS Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain e residue 161 SER Chi-restraints excluded: chain e residue 257 THR Chi-restraints excluded: chain e residue 258 ILE Chi-restraints excluded: chain e residue 372 VAL Chi-restraints excluded: chain f residue 32 VAL Chi-restraints excluded: chain f residue 40 SER Chi-restraints excluded: chain f residue 61 ILE Chi-restraints excluded: chain f residue 133 HIS Chi-restraints excluded: chain f residue 146 LEU Chi-restraints excluded: chain f residue 161 SER Chi-restraints excluded: chain f residue 236 VAL Chi-restraints excluded: chain f residue 257 THR Chi-restraints excluded: chain f residue 372 VAL Chi-restraints excluded: chain g residue 64 SER Chi-restraints excluded: chain g residue 116 ASP Chi-restraints excluded: chain g residue 127 LEU Chi-restraints excluded: chain g residue 181 VAL Chi-restraints excluded: chain g residue 229 VAL Chi-restraints excluded: chain g residue 236 VAL Chi-restraints excluded: chain g residue 243 GLU Chi-restraints excluded: chain g residue 245 CYS Chi-restraints excluded: chain g residue 252 ASN Chi-restraints excluded: chain g residue 308 LYS Chi-restraints excluded: chain g residue 325 LEU Chi-restraints excluded: chain g residue 353 VAL Chi-restraints excluded: chain g residue 375 THR Chi-restraints excluded: chain g residue 379 LEU Chi-restraints excluded: chain g residue 383 LEU Chi-restraints excluded: chain h residue 64 SER Chi-restraints excluded: chain h residue 127 LEU Chi-restraints excluded: chain h residue 128 LEU Chi-restraints excluded: chain h residue 181 VAL Chi-restraints excluded: chain h residue 225 GLU Chi-restraints excluded: chain h residue 236 VAL Chi-restraints excluded: chain h residue 243 GLU Chi-restraints excluded: chain h residue 245 CYS Chi-restraints excluded: chain h residue 252 ASN Chi-restraints excluded: chain h residue 275 ASP Chi-restraints excluded: chain h residue 307 THR Chi-restraints excluded: chain h residue 353 VAL Chi-restraints excluded: chain h residue 362 VAL Chi-restraints excluded: chain h residue 379 LEU Chi-restraints excluded: chain l residue 64 SER Chi-restraints excluded: chain l residue 181 VAL Chi-restraints excluded: chain l residue 222 SER Chi-restraints excluded: chain l residue 243 GLU Chi-restraints excluded: chain l residue 252 ASN Chi-restraints excluded: chain l residue 275 ASP Chi-restraints excluded: chain l residue 289 LEU Chi-restraints excluded: chain l residue 325 LEU Chi-restraints excluded: chain l residue 353 VAL Chi-restraints excluded: chain l residue 362 VAL Chi-restraints excluded: chain l residue 376 ASP Chi-restraints excluded: chain k residue 64 SER Chi-restraints excluded: chain k residue 127 LEU Chi-restraints excluded: chain k residue 181 VAL Chi-restraints excluded: chain k residue 232 THR Chi-restraints excluded: chain k residue 243 GLU Chi-restraints excluded: chain k residue 245 CYS Chi-restraints excluded: chain k residue 252 ASN Chi-restraints excluded: chain k residue 275 ASP Chi-restraints excluded: chain k residue 307 THR Chi-restraints excluded: chain k residue 353 VAL Chi-restraints excluded: chain k residue 362 VAL Chi-restraints excluded: chain j residue 64 SER Chi-restraints excluded: chain j residue 116 ASP Chi-restraints excluded: chain j residue 127 LEU Chi-restraints excluded: chain j residue 181 VAL Chi-restraints excluded: chain j residue 236 VAL Chi-restraints excluded: chain j residue 243 GLU Chi-restraints excluded: chain j residue 245 CYS Chi-restraints excluded: chain j residue 252 ASN Chi-restraints excluded: chain j residue 275 ASP Chi-restraints excluded: chain j residue 302 VAL Chi-restraints excluded: chain j residue 325 LEU Chi-restraints excluded: chain j residue 353 VAL Chi-restraints excluded: chain j residue 375 THR Chi-restraints excluded: chain j residue 379 LEU Chi-restraints excluded: chain j residue 383 LEU Chi-restraints excluded: chain i residue 10 THR Chi-restraints excluded: chain i residue 64 SER Chi-restraints excluded: chain i residue 181 VAL Chi-restraints excluded: chain i residue 243 GLU Chi-restraints excluded: chain i residue 252 ASN Chi-restraints excluded: chain i residue 275 ASP Chi-restraints excluded: chain i residue 289 LEU Chi-restraints excluded: chain i residue 302 VAL Chi-restraints excluded: chain i residue 325 LEU Chi-restraints excluded: chain i residue 344 SER Chi-restraints excluded: chain i residue 353 VAL Chi-restraints excluded: chain i residue 362 VAL Chi-restraints excluded: chain i residue 376 ASP Chi-restraints excluded: chain m residue 10 THR Chi-restraints excluded: chain m residue 25 SER Chi-restraints excluded: chain m residue 61 ILE Chi-restraints excluded: chain m residue 127 LEU Chi-restraints excluded: chain m residue 197 ASN Chi-restraints excluded: chain m residue 229 VAL Chi-restraints excluded: chain m residue 230 THR Chi-restraints excluded: chain m residue 282 THR Chi-restraints excluded: chain m residue 344 SER Chi-restraints excluded: chain m residue 379 LEU Chi-restraints excluded: chain m residue 380 THR Chi-restraints excluded: chain m residue 382 VAL Chi-restraints excluded: chain m residue 383 LEU Chi-restraints excluded: chain n residue 10 THR Chi-restraints excluded: chain n residue 25 SER Chi-restraints excluded: chain n residue 75 ARG Chi-restraints excluded: chain n residue 127 LEU Chi-restraints excluded: chain n residue 185 VAL Chi-restraints excluded: chain n residue 197 ASN Chi-restraints excluded: chain n residue 222 SER Chi-restraints excluded: chain n residue 229 VAL Chi-restraints excluded: chain n residue 244 THR Chi-restraints excluded: chain n residue 282 THR Chi-restraints excluded: chain n residue 327 ASN Chi-restraints excluded: chain n residue 344 SER Chi-restraints excluded: chain n residue 379 LEU Chi-restraints excluded: chain n residue 383 LEU Chi-restraints excluded: chain r residue 10 THR Chi-restraints excluded: chain r residue 34 THR Chi-restraints excluded: chain r residue 75 ARG Chi-restraints excluded: chain r residue 127 LEU Chi-restraints excluded: chain r residue 162 THR Chi-restraints excluded: chain r residue 222 SER Chi-restraints excluded: chain r residue 230 THR Chi-restraints excluded: chain r residue 282 THR Chi-restraints excluded: chain r residue 307 THR Chi-restraints excluded: chain r residue 327 ASN Chi-restraints excluded: chain r residue 344 SER Chi-restraints excluded: chain r residue 382 VAL Chi-restraints excluded: chain q residue 10 THR Chi-restraints excluded: chain q residue 54 ASP Chi-restraints excluded: chain q residue 63 SER Chi-restraints excluded: chain q residue 75 ARG Chi-restraints excluded: chain q residue 127 LEU Chi-restraints excluded: chain q residue 162 THR Chi-restraints excluded: chain q residue 197 ASN Chi-restraints excluded: chain q residue 222 SER Chi-restraints excluded: chain q residue 229 VAL Chi-restraints excluded: chain q residue 257 THR Chi-restraints excluded: chain q residue 282 THR Chi-restraints excluded: chain q residue 327 ASN Chi-restraints excluded: chain q residue 344 SER Chi-restraints excluded: chain q residue 379 LEU Chi-restraints excluded: chain q residue 380 THR Chi-restraints excluded: chain q residue 382 VAL Chi-restraints excluded: chain q residue 383 LEU Chi-restraints excluded: chain p residue 10 THR Chi-restraints excluded: chain p residue 25 SER Chi-restraints excluded: chain p residue 34 THR Chi-restraints excluded: chain p residue 61 ILE Chi-restraints excluded: chain p residue 75 ARG Chi-restraints excluded: chain p residue 127 LEU Chi-restraints excluded: chain p residue 197 ASN Chi-restraints excluded: chain p residue 222 SER Chi-restraints excluded: chain p residue 229 VAL Chi-restraints excluded: chain p residue 230 THR Chi-restraints excluded: chain p residue 244 THR Chi-restraints excluded: chain p residue 344 SER Chi-restraints excluded: chain p residue 376 ASP Chi-restraints excluded: chain p residue 379 LEU Chi-restraints excluded: chain p residue 382 VAL Chi-restraints excluded: chain p residue 383 LEU Chi-restraints excluded: chain o residue 10 THR Chi-restraints excluded: chain o residue 18 THR Chi-restraints excluded: chain o residue 34 THR Chi-restraints excluded: chain o residue 75 ARG Chi-restraints excluded: chain o residue 127 LEU Chi-restraints excluded: chain o residue 143 MET Chi-restraints excluded: chain o residue 162 THR Chi-restraints excluded: chain o residue 222 SER Chi-restraints excluded: chain o residue 230 THR Chi-restraints excluded: chain o residue 282 THR Chi-restraints excluded: chain o residue 307 THR Chi-restraints excluded: chain o residue 327 ASN Chi-restraints excluded: chain o residue 344 SER Chi-restraints excluded: chain o residue 382 VAL Chi-restraints excluded: chain o residue 383 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 393 optimal weight: 0.9990 chunk 219 optimal weight: 4.9990 chunk 589 optimal weight: 8.9990 chunk 482 optimal weight: 7.9990 chunk 195 optimal weight: 0.0000 chunk 709 optimal weight: 8.9990 chunk 766 optimal weight: 9.9990 chunk 631 optimal weight: 3.9990 chunk 703 optimal weight: 1.9990 chunk 241 optimal weight: 9.9990 chunk 569 optimal weight: 10.0000 overall best weight: 2.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 74 ASN c 74 ASN e 5 HIS f 5 HIS f 74 ASN k 367 ASN j 367 ASN m 172 ASN m 343 ASN m 347 GLN n 197 ASN n 328 GLN r 77 GLN q 197 ASN q 343 ASN p 347 GLN o 77 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 60864 Z= 0.202 Angle : 0.542 9.322 82998 Z= 0.286 Chirality : 0.044 0.147 9444 Planarity : 0.004 0.042 10908 Dihedral : 6.016 51.000 8563 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 3.91 % Allowed : 16.21 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.09), residues: 7830 helix: -1.82 (0.09), residues: 2730 sheet: -2.60 (0.15), residues: 990 loop : -1.88 (0.09), residues: 4110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP g 218 HIS 0.002 0.001 HIS f 133 PHE 0.013 0.001 PHE A 31 TYR 0.020 0.001 TYR d 264 ARG 0.005 0.000 ARG l 151 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15660 Ramachandran restraints generated. 7830 Oldfield, 0 Emsley, 7830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15660 Ramachandran restraints generated. 7830 Oldfield, 0 Emsley, 7830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1157 residues out of total 6144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 917 time to evaluate : 5.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 ASP cc_start: -0.1402 (OUTLIER) cc_final: -0.1880 (t70) REVERT: a 73 TYR cc_start: 0.9242 (m-80) cc_final: 0.8882 (m-10) REVERT: a 246 ARG cc_start: 0.7428 (ptm160) cc_final: 0.6989 (ptm-80) REVERT: a 282 THR cc_start: 0.9125 (m) cc_final: 0.8920 (p) REVERT: a 312 LYS cc_start: 0.8461 (mttp) cc_final: 0.7971 (tptp) REVERT: B 135 ASP cc_start: -0.1994 (OUTLIER) cc_final: -0.2516 (t70) REVERT: C 135 ASP cc_start: -0.2019 (OUTLIER) cc_final: -0.2733 (t0) REVERT: D 135 ASP cc_start: -0.1630 (OUTLIER) cc_final: -0.2149 (t70) REVERT: D 149 MET cc_start: 0.8606 (mmm) cc_final: 0.8365 (mmm) REVERT: E 135 ASP cc_start: -0.1893 (OUTLIER) cc_final: -0.2369 (t70) REVERT: F 135 ASP cc_start: -0.2076 (OUTLIER) cc_final: -0.2432 (t70) REVERT: b 73 TYR cc_start: 0.9268 (m-80) cc_final: 0.9040 (m-80) REVERT: b 246 ARG cc_start: 0.7528 (ptm160) cc_final: 0.7271 (ptm-80) REVERT: b 282 THR cc_start: 0.9094 (m) cc_final: 0.8836 (p) REVERT: b 312 LYS cc_start: 0.8089 (tptp) cc_final: 0.7657 (mttp) REVERT: c 133 HIS cc_start: 0.7630 (OUTLIER) cc_final: 0.7020 (m-70) REVERT: c 246 ARG cc_start: 0.7462 (ptm160) cc_final: 0.7070 (ptm160) REVERT: c 282 THR cc_start: 0.9200 (m) cc_final: 0.8948 (p) REVERT: d 73 TYR cc_start: 0.9243 (m-80) cc_final: 0.8923 (m-10) REVERT: d 246 ARG cc_start: 0.7478 (ptm160) cc_final: 0.7000 (ptm-80) REVERT: d 332 ILE cc_start: 0.8734 (mt) cc_final: 0.8445 (mt) REVERT: e 246 ARG cc_start: 0.7536 (ptm160) cc_final: 0.6978 (mtm180) REVERT: e 282 THR cc_start: 0.9093 (m) cc_final: 0.8807 (p) REVERT: f 133 HIS cc_start: 0.7767 (OUTLIER) cc_final: 0.7081 (m-70) REVERT: f 180 MET cc_start: 0.8561 (tpp) cc_final: 0.8286 (ttm) REVERT: f 246 ARG cc_start: 0.7471 (ptm160) cc_final: 0.7031 (ptm-80) REVERT: f 258 ILE cc_start: 0.8481 (mt) cc_final: 0.8269 (mt) REVERT: f 282 THR cc_start: 0.9164 (m) cc_final: 0.8906 (p) REVERT: g 48 LEU cc_start: 0.9053 (tp) cc_final: 0.8720 (tp) REVERT: g 287 MET cc_start: 0.8982 (tpt) cc_final: 0.8623 (tpt) REVERT: h 48 LEU cc_start: 0.9069 (tp) cc_final: 0.8702 (tp) REVERT: k 48 LEU cc_start: 0.9054 (tp) cc_final: 0.8679 (tp) REVERT: k 308 LYS cc_start: 0.8733 (mmtm) cc_final: 0.8495 (mmtt) REVERT: j 48 LEU cc_start: 0.8997 (tp) cc_final: 0.8672 (tp) REVERT: j 127 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.9099 (mt) REVERT: m 14 ILE cc_start: 0.8395 (pt) cc_final: 0.8083 (pt) REVERT: m 282 THR cc_start: 0.9214 (OUTLIER) cc_final: 0.8688 (p) REVERT: m 383 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8167 (mp) REVERT: n 18 THR cc_start: 0.8808 (OUTLIER) cc_final: 0.8603 (p) REVERT: n 75 ARG cc_start: 0.9172 (OUTLIER) cc_final: 0.8868 (tpt170) REVERT: n 96 SER cc_start: 0.8606 (m) cc_final: 0.7827 (p) REVERT: n 99 ILE cc_start: 0.9396 (mt) cc_final: 0.9120 (mt) REVERT: n 327 ASN cc_start: 0.8466 (p0) cc_final: 0.8022 (m-40) REVERT: r 75 ARG cc_start: 0.9152 (OUTLIER) cc_final: 0.8532 (tpt170) REVERT: r 96 SER cc_start: 0.8363 (m) cc_final: 0.7802 (p) REVERT: q 75 ARG cc_start: 0.9184 (OUTLIER) cc_final: 0.8872 (tpt170) REVERT: q 96 SER cc_start: 0.8395 (m) cc_final: 0.7599 (p) REVERT: q 327 ASN cc_start: 0.8445 (p0) cc_final: 0.8168 (m-40) REVERT: p 75 ARG cc_start: 0.9137 (OUTLIER) cc_final: 0.8838 (tpt90) REVERT: p 282 THR cc_start: 0.9179 (OUTLIER) cc_final: 0.8721 (p) REVERT: p 327 ASN cc_start: 0.8574 (p0) cc_final: 0.8179 (m110) REVERT: p 383 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8170 (mp) REVERT: o 75 ARG cc_start: 0.9134 (OUTLIER) cc_final: 0.8860 (tpt170) REVERT: o 96 SER cc_start: 0.8455 (m) cc_final: 0.7886 (p) REVERT: o 127 LEU cc_start: 0.9459 (OUTLIER) cc_final: 0.9258 (mt) REVERT: o 327 ASN cc_start: 0.8415 (p0) cc_final: 0.8053 (m-40) outliers start: 240 outliers final: 159 residues processed: 1076 average time/residue: 0.6015 time to fit residues: 1107.5402 Evaluate side-chains 1000 residues out of total 6144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 821 time to evaluate : 4.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain a residue 133 HIS Chi-restraints excluded: chain a residue 146 LEU Chi-restraints excluded: chain a residue 257 THR Chi-restraints excluded: chain a residue 258 ILE Chi-restraints excluded: chain a residue 335 GLU Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain C residue 135 ASP Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 135 ASP Chi-restraints excluded: chain E residue 71 MET Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain F residue 71 MET Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 135 ASP Chi-restraints excluded: chain b residue 10 THR Chi-restraints excluded: chain b residue 34 THR Chi-restraints excluded: chain b residue 133 HIS Chi-restraints excluded: chain b residue 146 LEU Chi-restraints excluded: chain b residue 257 THR Chi-restraints excluded: chain b residue 335 GLU Chi-restraints excluded: chain b residue 372 VAL Chi-restraints excluded: chain c residue 34 THR Chi-restraints excluded: chain c residue 61 ILE Chi-restraints excluded: chain c residue 133 HIS Chi-restraints excluded: chain c residue 257 THR Chi-restraints excluded: chain c residue 335 GLU Chi-restraints excluded: chain c residue 369 ASN Chi-restraints excluded: chain c residue 372 VAL Chi-restraints excluded: chain d residue 133 HIS Chi-restraints excluded: chain d residue 146 LEU Chi-restraints excluded: chain d residue 258 ILE Chi-restraints excluded: chain d residue 335 GLU Chi-restraints excluded: chain d residue 372 VAL Chi-restraints excluded: chain e residue 32 VAL Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 133 HIS Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain e residue 257 THR Chi-restraints excluded: chain e residue 372 VAL Chi-restraints excluded: chain f residue 10 THR Chi-restraints excluded: chain f residue 32 VAL Chi-restraints excluded: chain f residue 61 ILE Chi-restraints excluded: chain f residue 133 HIS Chi-restraints excluded: chain f residue 161 SER Chi-restraints excluded: chain f residue 164 GLU Chi-restraints excluded: chain f residue 257 THR Chi-restraints excluded: chain f residue 372 VAL Chi-restraints excluded: chain g residue 116 ASP Chi-restraints excluded: chain g residue 181 VAL Chi-restraints excluded: chain g residue 236 VAL Chi-restraints excluded: chain g residue 243 GLU Chi-restraints excluded: chain g residue 252 ASN Chi-restraints excluded: chain g residue 325 LEU Chi-restraints excluded: chain g residue 353 VAL Chi-restraints excluded: chain g residue 375 THR Chi-restraints excluded: chain h residue 127 LEU Chi-restraints excluded: chain h residue 181 VAL Chi-restraints excluded: chain h residue 211 THR Chi-restraints excluded: chain h residue 225 GLU Chi-restraints excluded: chain h residue 232 THR Chi-restraints excluded: chain h residue 243 GLU Chi-restraints excluded: chain h residue 252 ASN Chi-restraints excluded: chain h residue 302 VAL Chi-restraints excluded: chain h residue 307 THR Chi-restraints excluded: chain h residue 353 VAL Chi-restraints excluded: chain h residue 362 VAL Chi-restraints excluded: chain l residue 116 ASP Chi-restraints excluded: chain l residue 181 VAL Chi-restraints excluded: chain l residue 243 GLU Chi-restraints excluded: chain l residue 245 CYS Chi-restraints excluded: chain l residue 252 ASN Chi-restraints excluded: chain l residue 275 ASP Chi-restraints excluded: chain l residue 302 VAL Chi-restraints excluded: chain l residue 325 LEU Chi-restraints excluded: chain l residue 344 SER Chi-restraints excluded: chain l residue 353 VAL Chi-restraints excluded: chain l residue 362 VAL Chi-restraints excluded: chain l residue 376 ASP Chi-restraints excluded: chain k residue 127 LEU Chi-restraints excluded: chain k residue 181 VAL Chi-restraints excluded: chain k residue 211 THR Chi-restraints excluded: chain k residue 243 GLU Chi-restraints excluded: chain k residue 252 ASN Chi-restraints excluded: chain k residue 275 ASP Chi-restraints excluded: chain k residue 302 VAL Chi-restraints excluded: chain k residue 307 THR Chi-restraints excluded: chain k residue 353 VAL Chi-restraints excluded: chain k residue 362 VAL Chi-restraints excluded: chain k residue 374 VAL Chi-restraints excluded: chain j residue 116 ASP Chi-restraints excluded: chain j residue 127 LEU Chi-restraints excluded: chain j residue 181 VAL Chi-restraints excluded: chain j residue 222 SER Chi-restraints excluded: chain j residue 236 VAL Chi-restraints excluded: chain j residue 243 GLU Chi-restraints excluded: chain j residue 252 ASN Chi-restraints excluded: chain j residue 275 ASP Chi-restraints excluded: chain j residue 325 LEU Chi-restraints excluded: chain j residue 353 VAL Chi-restraints excluded: chain j residue 375 THR Chi-restraints excluded: chain i residue 10 THR Chi-restraints excluded: chain i residue 181 VAL Chi-restraints excluded: chain i residue 243 GLU Chi-restraints excluded: chain i residue 245 CYS Chi-restraints excluded: chain i residue 252 ASN Chi-restraints excluded: chain i residue 275 ASP Chi-restraints excluded: chain i residue 302 VAL Chi-restraints excluded: chain i residue 325 LEU Chi-restraints excluded: chain i residue 344 SER Chi-restraints excluded: chain i residue 353 VAL Chi-restraints excluded: chain i residue 362 VAL Chi-restraints excluded: chain i residue 376 ASP Chi-restraints excluded: chain m residue 10 THR Chi-restraints excluded: chain m residue 25 SER Chi-restraints excluded: chain m residue 34 THR Chi-restraints excluded: chain m residue 222 SER Chi-restraints excluded: chain m residue 229 VAL Chi-restraints excluded: chain m residue 243 GLU Chi-restraints excluded: chain m residue 282 THR Chi-restraints excluded: chain m residue 307 THR Chi-restraints excluded: chain m residue 344 SER Chi-restraints excluded: chain m residue 379 LEU Chi-restraints excluded: chain m residue 380 THR Chi-restraints excluded: chain m residue 382 VAL Chi-restraints excluded: chain m residue 383 LEU Chi-restraints excluded: chain n residue 10 THR Chi-restraints excluded: chain n residue 12 VAL Chi-restraints excluded: chain n residue 18 THR Chi-restraints excluded: chain n residue 75 ARG Chi-restraints excluded: chain n residue 197 ASN Chi-restraints excluded: chain n residue 229 VAL Chi-restraints excluded: chain n residue 282 THR Chi-restraints excluded: chain n residue 307 THR Chi-restraints excluded: chain n residue 344 SER Chi-restraints excluded: chain n residue 379 LEU Chi-restraints excluded: chain r residue 10 THR Chi-restraints excluded: chain r residue 75 ARG Chi-restraints excluded: chain r residue 282 THR Chi-restraints excluded: chain r residue 307 THR Chi-restraints excluded: chain r residue 344 SER Chi-restraints excluded: chain r residue 382 VAL Chi-restraints excluded: chain q residue 10 THR Chi-restraints excluded: chain q residue 12 VAL Chi-restraints excluded: chain q residue 54 ASP Chi-restraints excluded: chain q residue 63 SER Chi-restraints excluded: chain q residue 75 ARG Chi-restraints excluded: chain q residue 92 GLU Chi-restraints excluded: chain q residue 197 ASN Chi-restraints excluded: chain q residue 229 VAL Chi-restraints excluded: chain q residue 282 THR Chi-restraints excluded: chain q residue 307 THR Chi-restraints excluded: chain q residue 344 SER Chi-restraints excluded: chain q residue 379 LEU Chi-restraints excluded: chain q residue 380 THR Chi-restraints excluded: chain q residue 383 LEU Chi-restraints excluded: chain p residue 10 THR Chi-restraints excluded: chain p residue 12 VAL Chi-restraints excluded: chain p residue 25 SER Chi-restraints excluded: chain p residue 75 ARG Chi-restraints excluded: chain p residue 222 SER Chi-restraints excluded: chain p residue 229 VAL Chi-restraints excluded: chain p residue 244 THR Chi-restraints excluded: chain p residue 282 THR Chi-restraints excluded: chain p residue 307 THR Chi-restraints excluded: chain p residue 344 SER Chi-restraints excluded: chain p residue 376 ASP Chi-restraints excluded: chain p residue 379 LEU Chi-restraints excluded: chain p residue 382 VAL Chi-restraints excluded: chain p residue 383 LEU Chi-restraints excluded: chain o residue 10 THR Chi-restraints excluded: chain o residue 75 ARG Chi-restraints excluded: chain o residue 127 LEU Chi-restraints excluded: chain o residue 143 MET Chi-restraints excluded: chain o residue 244 THR Chi-restraints excluded: chain o residue 282 THR Chi-restraints excluded: chain o residue 307 THR Chi-restraints excluded: chain o residue 344 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 701 optimal weight: 8.9990 chunk 533 optimal weight: 6.9990 chunk 368 optimal weight: 10.0000 chunk 78 optimal weight: 20.0000 chunk 338 optimal weight: 1.9990 chunk 476 optimal weight: 9.9990 chunk 712 optimal weight: 3.9990 chunk 753 optimal weight: 5.9990 chunk 372 optimal weight: 9.9990 chunk 674 optimal weight: 4.9990 chunk 203 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 298 HIS E 67 GLN b 74 ASN c 74 ASN d 298 HIS e 298 HIS f 74 ASN f 298 HIS m 172 ASN m 197 ASN m 343 ASN m 347 GLN ** n 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 197 ASN r 77 GLN r 172 ASN r 197 ASN q 172 ASN q 197 ASN q 343 ASN p 197 ASN p 347 GLN o 77 GLN ** o 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 197 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 60864 Z= 0.289 Angle : 0.569 8.795 82998 Z= 0.299 Chirality : 0.045 0.230 9444 Planarity : 0.004 0.048 10908 Dihedral : 5.867 48.809 8543 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 4.83 % Allowed : 16.86 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.09), residues: 7830 helix: -1.27 (0.09), residues: 2742 sheet: -2.60 (0.14), residues: 1116 loop : -1.81 (0.10), residues: 3972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP g 218 HIS 0.003 0.001 HIS f 133 PHE 0.015 0.002 PHE o 359 TYR 0.021 0.002 TYR b 264 ARG 0.005 0.000 ARG k 265 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15660 Ramachandran restraints generated. 7830 Oldfield, 0 Emsley, 7830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15660 Ramachandran restraints generated. 7830 Oldfield, 0 Emsley, 7830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1134 residues out of total 6144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 297 poor density : 837 time to evaluate : 6.114 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 ASP cc_start: -0.1307 (OUTLIER) cc_final: -0.1810 (t70) REVERT: a 61 ILE cc_start: 0.8390 (OUTLIER) cc_final: 0.8175 (mp) REVERT: a 73 TYR cc_start: 0.9261 (m-80) cc_final: 0.8850 (m-10) REVERT: a 180 MET cc_start: 0.8661 (tpp) cc_final: 0.8216 (ttm) REVERT: a 246 ARG cc_start: 0.7546 (ptm160) cc_final: 0.7117 (ptm-80) REVERT: a 287 MET cc_start: 0.8618 (tpp) cc_final: 0.8391 (tpp) REVERT: B 135 ASP cc_start: -0.1808 (OUTLIER) cc_final: -0.2118 (t70) REVERT: C 135 ASP cc_start: -0.2034 (OUTLIER) cc_final: -0.2728 (t0) REVERT: D 135 ASP cc_start: -0.1586 (OUTLIER) cc_final: -0.2220 (t70) REVERT: D 149 MET cc_start: 0.8618 (mmm) cc_final: 0.8371 (mmm) REVERT: E 135 ASP cc_start: -0.1854 (OUTLIER) cc_final: -0.2360 (t70) REVERT: E 149 MET cc_start: 0.8607 (mmm) cc_final: 0.8378 (mmm) REVERT: F 135 ASP cc_start: -0.1757 (OUTLIER) cc_final: -0.2183 (t70) REVERT: b 102 ILE cc_start: 0.8750 (mp) cc_final: 0.8491 (mp) REVERT: b 246 ARG cc_start: 0.7485 (ptm160) cc_final: 0.6964 (ptm160) REVERT: b 282 THR cc_start: 0.9148 (m) cc_final: 0.8867 (p) REVERT: b 312 LYS cc_start: 0.8146 (tptp) cc_final: 0.7699 (mttp) REVERT: c 133 HIS cc_start: 0.7680 (OUTLIER) cc_final: 0.7027 (m-70) REVERT: c 246 ARG cc_start: 0.7442 (ptm160) cc_final: 0.7011 (ptm-80) REVERT: c 282 THR cc_start: 0.9219 (m) cc_final: 0.8952 (p) REVERT: d 61 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.8169 (mp) REVERT: d 73 TYR cc_start: 0.9271 (m-80) cc_final: 0.8949 (m-10) REVERT: d 180 MET cc_start: 0.8641 (tpp) cc_final: 0.8208 (ttm) REVERT: d 246 ARG cc_start: 0.7628 (ptm160) cc_final: 0.7316 (ptm-80) REVERT: d 381 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7452 (tt0) REVERT: e 143 MET cc_start: 0.8903 (mtp) cc_final: 0.8682 (ttm) REVERT: e 246 ARG cc_start: 0.7376 (ptm160) cc_final: 0.7063 (ptm160) REVERT: e 282 THR cc_start: 0.9131 (m) cc_final: 0.8836 (p) REVERT: e 312 LYS cc_start: 0.8228 (tptt) cc_final: 0.7769 (mttp) REVERT: f 133 HIS cc_start: 0.7808 (OUTLIER) cc_final: 0.7041 (m-70) REVERT: f 180 MET cc_start: 0.8612 (tpp) cc_final: 0.8378 (ttm) REVERT: f 246 ARG cc_start: 0.7424 (ptm160) cc_final: 0.6992 (ptm-80) REVERT: f 258 ILE cc_start: 0.8600 (mt) cc_final: 0.8365 (mt) REVERT: f 282 THR cc_start: 0.9223 (m) cc_final: 0.8962 (p) REVERT: f 367 ASN cc_start: 0.8826 (OUTLIER) cc_final: 0.8369 (t0) REVERT: g 127 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9102 (mt) REVERT: g 287 MET cc_start: 0.9067 (tpt) cc_final: 0.8805 (tpt) REVERT: g 383 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.8020 (mp) REVERT: h 48 LEU cc_start: 0.9127 (tp) cc_final: 0.8800 (tp) REVERT: l 177 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.8260 (mtt90) REVERT: k 48 LEU cc_start: 0.9103 (tp) cc_final: 0.8759 (tp) REVERT: k 308 LYS cc_start: 0.8749 (mmtm) cc_final: 0.8515 (mmtt) REVERT: j 127 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.9105 (mt) REVERT: j 383 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.8013 (mp) REVERT: i 177 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.8281 (mtt90) REVERT: m 14 ILE cc_start: 0.8454 (pt) cc_final: 0.8138 (pt) REVERT: m 127 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.9149 (mt) REVERT: m 282 THR cc_start: 0.9224 (OUTLIER) cc_final: 0.8795 (p) REVERT: m 383 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8148 (mp) REVERT: n 75 ARG cc_start: 0.9243 (OUTLIER) cc_final: 0.8973 (tpt170) REVERT: n 96 SER cc_start: 0.8726 (m) cc_final: 0.7943 (p) REVERT: n 99 ILE cc_start: 0.9400 (mt) cc_final: 0.9120 (mt) REVERT: n 327 ASN cc_start: 0.8525 (p0) cc_final: 0.8086 (m-40) REVERT: r 75 ARG cc_start: 0.9162 (OUTLIER) cc_final: 0.8583 (tpt170) REVERT: r 96 SER cc_start: 0.8496 (m) cc_final: 0.7955 (p) REVERT: q 75 ARG cc_start: 0.9229 (OUTLIER) cc_final: 0.8938 (tpt170) REVERT: q 96 SER cc_start: 0.8421 (m) cc_final: 0.7727 (p) REVERT: q 327 ASN cc_start: 0.8565 (p0) cc_final: 0.8239 (m-40) REVERT: p 75 ARG cc_start: 0.9155 (OUTLIER) cc_final: 0.8869 (tpt90) REVERT: p 96 SER cc_start: 0.8574 (m) cc_final: 0.7911 (p) REVERT: p 127 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.9114 (mt) REVERT: p 282 THR cc_start: 0.9191 (OUTLIER) cc_final: 0.8729 (p) REVERT: p 383 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8205 (mp) REVERT: o 75 ARG cc_start: 0.9201 (OUTLIER) cc_final: 0.8940 (tpt170) REVERT: o 96 SER cc_start: 0.8522 (m) cc_final: 0.8020 (p) REVERT: o 143 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.8129 (ttp) outliers start: 297 outliers final: 215 residues processed: 1047 average time/residue: 0.5520 time to fit residues: 985.1962 Evaluate side-chains 1049 residues out of total 6144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 245 poor density : 804 time to evaluate : 4.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain a residue 32 VAL Chi-restraints excluded: chain a residue 61 ILE Chi-restraints excluded: chain a residue 133 HIS Chi-restraints excluded: chain a residue 146 LEU Chi-restraints excluded: chain a residue 230 THR Chi-restraints excluded: chain a residue 257 THR Chi-restraints excluded: chain a residue 258 ILE Chi-restraints excluded: chain a residue 318 LEU Chi-restraints excluded: chain a residue 335 GLU Chi-restraints excluded: chain a residue 372 VAL Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain C residue 135 ASP Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 135 ASP Chi-restraints excluded: chain E residue 71 MET Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain F residue 71 MET Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 135 ASP Chi-restraints excluded: chain b residue 10 THR Chi-restraints excluded: chain b residue 32 VAL Chi-restraints excluded: chain b residue 34 THR Chi-restraints excluded: chain b residue 133 HIS Chi-restraints excluded: chain b residue 146 LEU Chi-restraints excluded: chain b residue 161 SER Chi-restraints excluded: chain b residue 257 THR Chi-restraints excluded: chain b residue 326 LYS Chi-restraints excluded: chain b residue 335 GLU Chi-restraints excluded: chain b residue 369 ASN Chi-restraints excluded: chain b residue 372 VAL Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain c residue 34 THR Chi-restraints excluded: chain c residue 61 ILE Chi-restraints excluded: chain c residue 133 HIS Chi-restraints excluded: chain c residue 146 LEU Chi-restraints excluded: chain c residue 161 SER Chi-restraints excluded: chain c residue 257 THR Chi-restraints excluded: chain c residue 369 ASN Chi-restraints excluded: chain c residue 372 VAL Chi-restraints excluded: chain d residue 32 VAL Chi-restraints excluded: chain d residue 61 ILE Chi-restraints excluded: chain d residue 133 HIS Chi-restraints excluded: chain d residue 146 LEU Chi-restraints excluded: chain d residue 257 THR Chi-restraints excluded: chain d residue 258 ILE Chi-restraints excluded: chain d residue 282 THR Chi-restraints excluded: chain d residue 318 LEU Chi-restraints excluded: chain d residue 335 GLU Chi-restraints excluded: chain d residue 362 VAL Chi-restraints excluded: chain d residue 369 ASN Chi-restraints excluded: chain d residue 372 VAL Chi-restraints excluded: chain d residue 381 GLU Chi-restraints excluded: chain e residue 32 VAL Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 133 HIS Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain e residue 161 SER Chi-restraints excluded: chain e residue 257 THR Chi-restraints excluded: chain e residue 289 LEU Chi-restraints excluded: chain e residue 372 VAL Chi-restraints excluded: chain f residue 10 THR Chi-restraints excluded: chain f residue 32 VAL Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 133 HIS Chi-restraints excluded: chain f residue 161 SER Chi-restraints excluded: chain f residue 164 GLU Chi-restraints excluded: chain f residue 236 VAL Chi-restraints excluded: chain f residue 257 THR Chi-restraints excluded: chain f residue 367 ASN Chi-restraints excluded: chain f residue 372 VAL Chi-restraints excluded: chain g residue 64 SER Chi-restraints excluded: chain g residue 116 ASP Chi-restraints excluded: chain g residue 127 LEU Chi-restraints excluded: chain g residue 181 VAL Chi-restraints excluded: chain g residue 236 VAL Chi-restraints excluded: chain g residue 243 GLU Chi-restraints excluded: chain g residue 282 THR Chi-restraints excluded: chain g residue 325 LEU Chi-restraints excluded: chain g residue 344 SER Chi-restraints excluded: chain g residue 353 VAL Chi-restraints excluded: chain g residue 375 THR Chi-restraints excluded: chain g residue 379 LEU Chi-restraints excluded: chain g residue 383 LEU Chi-restraints excluded: chain h residue 64 SER Chi-restraints excluded: chain h residue 127 LEU Chi-restraints excluded: chain h residue 181 VAL Chi-restraints excluded: chain h residue 211 THR Chi-restraints excluded: chain h residue 225 GLU Chi-restraints excluded: chain h residue 236 VAL Chi-restraints excluded: chain h residue 243 GLU Chi-restraints excluded: chain h residue 275 ASP Chi-restraints excluded: chain h residue 302 VAL Chi-restraints excluded: chain h residue 307 THR Chi-restraints excluded: chain h residue 325 LEU Chi-restraints excluded: chain h residue 353 VAL Chi-restraints excluded: chain h residue 362 VAL Chi-restraints excluded: chain l residue 64 SER Chi-restraints excluded: chain l residue 116 ASP Chi-restraints excluded: chain l residue 177 ARG Chi-restraints excluded: chain l residue 181 VAL Chi-restraints excluded: chain l residue 245 CYS Chi-restraints excluded: chain l residue 252 ASN Chi-restraints excluded: chain l residue 275 ASP Chi-restraints excluded: chain l residue 302 VAL Chi-restraints excluded: chain l residue 325 LEU Chi-restraints excluded: chain l residue 344 SER Chi-restraints excluded: chain l residue 353 VAL Chi-restraints excluded: chain l residue 362 VAL Chi-restraints excluded: chain k residue 64 SER Chi-restraints excluded: chain k residue 127 LEU Chi-restraints excluded: chain k residue 181 VAL Chi-restraints excluded: chain k residue 211 THR Chi-restraints excluded: chain k residue 232 THR Chi-restraints excluded: chain k residue 243 GLU Chi-restraints excluded: chain k residue 275 ASP Chi-restraints excluded: chain k residue 302 VAL Chi-restraints excluded: chain k residue 307 THR Chi-restraints excluded: chain k residue 325 LEU Chi-restraints excluded: chain k residue 353 VAL Chi-restraints excluded: chain k residue 362 VAL Chi-restraints excluded: chain k residue 376 ASP Chi-restraints excluded: chain j residue 64 SER Chi-restraints excluded: chain j residue 116 ASP Chi-restraints excluded: chain j residue 127 LEU Chi-restraints excluded: chain j residue 181 VAL Chi-restraints excluded: chain j residue 236 VAL Chi-restraints excluded: chain j residue 243 GLU Chi-restraints excluded: chain j residue 275 ASP Chi-restraints excluded: chain j residue 302 VAL Chi-restraints excluded: chain j residue 325 LEU Chi-restraints excluded: chain j residue 344 SER Chi-restraints excluded: chain j residue 353 VAL Chi-restraints excluded: chain j residue 375 THR Chi-restraints excluded: chain j residue 379 LEU Chi-restraints excluded: chain j residue 383 LEU Chi-restraints excluded: chain i residue 10 THR Chi-restraints excluded: chain i residue 64 SER Chi-restraints excluded: chain i residue 177 ARG Chi-restraints excluded: chain i residue 181 VAL Chi-restraints excluded: chain i residue 245 CYS Chi-restraints excluded: chain i residue 252 ASN Chi-restraints excluded: chain i residue 275 ASP Chi-restraints excluded: chain i residue 282 THR Chi-restraints excluded: chain i residue 302 VAL Chi-restraints excluded: chain i residue 325 LEU Chi-restraints excluded: chain i residue 344 SER Chi-restraints excluded: chain i residue 353 VAL Chi-restraints excluded: chain i residue 362 VAL Chi-restraints excluded: chain m residue 10 THR Chi-restraints excluded: chain m residue 12 VAL Chi-restraints excluded: chain m residue 25 SER Chi-restraints excluded: chain m residue 127 LEU Chi-restraints excluded: chain m residue 197 ASN Chi-restraints excluded: chain m residue 222 SER Chi-restraints excluded: chain m residue 229 VAL Chi-restraints excluded: chain m residue 230 THR Chi-restraints excluded: chain m residue 282 THR Chi-restraints excluded: chain m residue 307 THR Chi-restraints excluded: chain m residue 344 SER Chi-restraints excluded: chain m residue 379 LEU Chi-restraints excluded: chain m residue 380 THR Chi-restraints excluded: chain m residue 382 VAL Chi-restraints excluded: chain m residue 383 LEU Chi-restraints excluded: chain n residue 10 THR Chi-restraints excluded: chain n residue 12 VAL Chi-restraints excluded: chain n residue 25 SER Chi-restraints excluded: chain n residue 54 ASP Chi-restraints excluded: chain n residue 75 ARG Chi-restraints excluded: chain n residue 185 VAL Chi-restraints excluded: chain n residue 229 VAL Chi-restraints excluded: chain n residue 244 THR Chi-restraints excluded: chain n residue 257 THR Chi-restraints excluded: chain n residue 282 THR Chi-restraints excluded: chain n residue 307 THR Chi-restraints excluded: chain n residue 344 SER Chi-restraints excluded: chain n residue 379 LEU Chi-restraints excluded: chain n residue 383 LEU Chi-restraints excluded: chain r residue 10 THR Chi-restraints excluded: chain r residue 25 SER Chi-restraints excluded: chain r residue 70 GLU Chi-restraints excluded: chain r residue 75 ARG Chi-restraints excluded: chain r residue 92 GLU Chi-restraints excluded: chain r residue 222 SER Chi-restraints excluded: chain r residue 230 THR Chi-restraints excluded: chain r residue 282 THR Chi-restraints excluded: chain r residue 291 MET Chi-restraints excluded: chain r residue 307 THR Chi-restraints excluded: chain r residue 344 SER Chi-restraints excluded: chain r residue 382 VAL Chi-restraints excluded: chain q residue 10 THR Chi-restraints excluded: chain q residue 12 VAL Chi-restraints excluded: chain q residue 25 SER Chi-restraints excluded: chain q residue 54 ASP Chi-restraints excluded: chain q residue 63 SER Chi-restraints excluded: chain q residue 75 ARG Chi-restraints excluded: chain q residue 92 GLU Chi-restraints excluded: chain q residue 162 THR Chi-restraints excluded: chain q residue 222 SER Chi-restraints excluded: chain q residue 229 VAL Chi-restraints excluded: chain q residue 244 THR Chi-restraints excluded: chain q residue 257 THR Chi-restraints excluded: chain q residue 282 THR Chi-restraints excluded: chain q residue 307 THR Chi-restraints excluded: chain q residue 344 SER Chi-restraints excluded: chain q residue 379 LEU Chi-restraints excluded: chain q residue 380 THR Chi-restraints excluded: chain q residue 383 LEU Chi-restraints excluded: chain p residue 10 THR Chi-restraints excluded: chain p residue 12 VAL Chi-restraints excluded: chain p residue 25 SER Chi-restraints excluded: chain p residue 75 ARG Chi-restraints excluded: chain p residue 127 LEU Chi-restraints excluded: chain p residue 197 ASN Chi-restraints excluded: chain p residue 222 SER Chi-restraints excluded: chain p residue 229 VAL Chi-restraints excluded: chain p residue 230 THR Chi-restraints excluded: chain p residue 244 THR Chi-restraints excluded: chain p residue 282 THR Chi-restraints excluded: chain p residue 307 THR Chi-restraints excluded: chain p residue 344 SER Chi-restraints excluded: chain p residue 376 ASP Chi-restraints excluded: chain p residue 379 LEU Chi-restraints excluded: chain p residue 382 VAL Chi-restraints excluded: chain p residue 383 LEU Chi-restraints excluded: chain o residue 10 THR Chi-restraints excluded: chain o residue 25 SER Chi-restraints excluded: chain o residue 75 ARG Chi-restraints excluded: chain o residue 92 GLU Chi-restraints excluded: chain o residue 127 LEU Chi-restraints excluded: chain o residue 143 MET Chi-restraints excluded: chain o residue 162 THR Chi-restraints excluded: chain o residue 222 SER Chi-restraints excluded: chain o residue 230 THR Chi-restraints excluded: chain o residue 244 THR Chi-restraints excluded: chain o residue 282 THR Chi-restraints excluded: chain o residue 307 THR Chi-restraints excluded: chain o residue 344 SER Chi-restraints excluded: chain o residue 376 ASP Chi-restraints excluded: chain o residue 383 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 627 optimal weight: 5.9990 chunk 427 optimal weight: 6.9990 chunk 10 optimal weight: 20.0000 chunk 561 optimal weight: 5.9990 chunk 311 optimal weight: 1.9990 chunk 643 optimal weight: 6.9990 chunk 521 optimal weight: 7.9990 chunk 0 optimal weight: 40.0000 chunk 384 optimal weight: 0.4980 chunk 676 optimal weight: 20.0000 chunk 190 optimal weight: 0.8980 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 67 GLN c 74 ASN f 74 ASN g 343 ASN j 343 ASN m 197 ASN r 77 GLN q 172 ASN q 252 ASN p 197 ASN p 327 ASN o 77 GLN o 137 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 60864 Z= 0.235 Angle : 0.541 8.979 82998 Z= 0.285 Chirality : 0.044 0.176 9444 Planarity : 0.004 0.054 10908 Dihedral : 5.715 47.935 8535 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 4.82 % Allowed : 17.14 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.09), residues: 7830 helix: -0.92 (0.10), residues: 2724 sheet: -2.56 (0.15), residues: 1038 loop : -1.68 (0.10), residues: 4068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP g 218 HIS 0.003 0.001 HIS e 133 PHE 0.014 0.001 PHE i 238 TYR 0.021 0.002 TYR d 264 ARG 0.005 0.000 ARG l 234 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15660 Ramachandran restraints generated. 7830 Oldfield, 0 Emsley, 7830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15660 Ramachandran restraints generated. 7830 Oldfield, 0 Emsley, 7830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1140 residues out of total 6144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 296 poor density : 844 time to evaluate : 4.960 Fit side-chains revert: symmetry clash REVERT: A 135 ASP cc_start: -0.1265 (OUTLIER) cc_final: -0.1947 (t70) REVERT: a 61 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.8147 (mp) REVERT: a 180 MET cc_start: 0.8643 (tpp) cc_final: 0.8191 (ttm) REVERT: a 219 SER cc_start: 0.9118 (t) cc_final: 0.8906 (p) REVERT: a 246 ARG cc_start: 0.7584 (ptm160) cc_final: 0.7178 (ptm-80) REVERT: B 135 ASP cc_start: -0.1829 (OUTLIER) cc_final: -0.2134 (t70) REVERT: C 135 ASP cc_start: -0.1315 (OUTLIER) cc_final: -0.1910 (t70) REVERT: D 135 ASP cc_start: -0.1602 (OUTLIER) cc_final: -0.2228 (t70) REVERT: D 149 MET cc_start: 0.8636 (mmm) cc_final: 0.8405 (mmm) REVERT: E 135 ASP cc_start: -0.1886 (OUTLIER) cc_final: -0.2394 (t70) REVERT: F 135 ASP cc_start: -0.1756 (OUTLIER) cc_final: -0.2190 (t70) REVERT: b 102 ILE cc_start: 0.8680 (mp) cc_final: 0.8466 (mp) REVERT: b 246 ARG cc_start: 0.7469 (ptm160) cc_final: 0.7039 (ptm160) REVERT: b 259 ILE cc_start: 0.7923 (OUTLIER) cc_final: 0.7612 (pp) REVERT: b 282 THR cc_start: 0.9118 (m) cc_final: 0.8865 (p) REVERT: b 312 LYS cc_start: 0.8234 (tptp) cc_final: 0.7753 (mttp) REVERT: b 367 ASN cc_start: 0.8774 (OUTLIER) cc_final: 0.8479 (t0) REVERT: c 133 HIS cc_start: 0.7752 (OUTLIER) cc_final: 0.7060 (m-70) REVERT: c 215 TYR cc_start: 0.8485 (m-10) cc_final: 0.8260 (m-80) REVERT: c 246 ARG cc_start: 0.7413 (ptm160) cc_final: 0.7002 (ptm-80) REVERT: c 282 THR cc_start: 0.9199 (m) cc_final: 0.8960 (p) REVERT: c 367 ASN cc_start: 0.8785 (OUTLIER) cc_final: 0.8340 (t0) REVERT: d 61 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.8144 (mp) REVERT: d 180 MET cc_start: 0.8645 (tpp) cc_final: 0.8194 (ttm) REVERT: d 246 ARG cc_start: 0.7656 (ptm160) cc_final: 0.7300 (ptm-80) REVERT: e 246 ARG cc_start: 0.7385 (ptm160) cc_final: 0.7068 (mtp180) REVERT: e 282 THR cc_start: 0.9143 (m) cc_final: 0.8883 (p) REVERT: e 312 LYS cc_start: 0.8222 (tptt) cc_final: 0.7613 (mttp) REVERT: e 367 ASN cc_start: 0.8794 (OUTLIER) cc_final: 0.8503 (t0) REVERT: f 133 HIS cc_start: 0.7775 (OUTLIER) cc_final: 0.7025 (m-70) REVERT: f 246 ARG cc_start: 0.7421 (ptm160) cc_final: 0.7011 (ptm-80) REVERT: f 258 ILE cc_start: 0.8569 (mt) cc_final: 0.8336 (mt) REVERT: f 282 THR cc_start: 0.9206 (m) cc_final: 0.8940 (p) REVERT: f 367 ASN cc_start: 0.8789 (OUTLIER) cc_final: 0.8335 (t0) REVERT: g 127 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.9097 (mt) REVERT: g 287 MET cc_start: 0.9090 (tpt) cc_final: 0.8849 (tpt) REVERT: h 48 LEU cc_start: 0.9077 (tp) cc_final: 0.8753 (tp) REVERT: l 177 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.8215 (mtt90) REVERT: k 48 LEU cc_start: 0.9086 (tp) cc_final: 0.8767 (tp) REVERT: k 177 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.8006 (mtt90) REVERT: k 257 THR cc_start: 0.9174 (OUTLIER) cc_final: 0.8893 (p) REVERT: k 308 LYS cc_start: 0.8714 (mmtm) cc_final: 0.8504 (mmtt) REVERT: j 127 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9117 (mt) REVERT: i 177 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.8231 (mtt90) REVERT: m 14 ILE cc_start: 0.8446 (pt) cc_final: 0.8142 (pt) REVERT: m 96 SER cc_start: 0.8527 (m) cc_final: 0.7910 (p) REVERT: m 127 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.9134 (mt) REVERT: m 282 THR cc_start: 0.9207 (OUTLIER) cc_final: 0.8773 (p) REVERT: m 383 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8143 (mp) REVERT: n 75 ARG cc_start: 0.9199 (OUTLIER) cc_final: 0.8898 (tpt170) REVERT: n 96 SER cc_start: 0.8589 (m) cc_final: 0.7857 (p) REVERT: n 99 ILE cc_start: 0.9401 (mt) cc_final: 0.9126 (mt) REVERT: n 327 ASN cc_start: 0.8522 (p0) cc_final: 0.8167 (m-40) REVERT: r 96 SER cc_start: 0.8462 (m) cc_final: 0.7925 (p) REVERT: q 75 ARG cc_start: 0.9222 (OUTLIER) cc_final: 0.8905 (tpt170) REVERT: q 96 SER cc_start: 0.8360 (m) cc_final: 0.7663 (p) REVERT: q 151 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7702 (mtt90) REVERT: q 327 ASN cc_start: 0.8497 (p0) cc_final: 0.8242 (m-40) REVERT: p 75 ARG cc_start: 0.9152 (OUTLIER) cc_final: 0.8840 (tpt90) REVERT: p 96 SER cc_start: 0.8664 (m) cc_final: 0.8082 (p) REVERT: p 282 THR cc_start: 0.9176 (OUTLIER) cc_final: 0.8689 (p) REVERT: p 383 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8192 (mp) REVERT: o 75 ARG cc_start: 0.9163 (OUTLIER) cc_final: 0.8877 (tpt170) REVERT: o 96 SER cc_start: 0.8480 (m) cc_final: 0.8005 (p) REVERT: o 327 ASN cc_start: 0.8460 (p0) cc_final: 0.8113 (m-40) outliers start: 296 outliers final: 222 residues processed: 1051 average time/residue: 0.5486 time to fit residues: 983.2331 Evaluate side-chains 1055 residues out of total 6144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 253 poor density : 802 time to evaluate : 4.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain a residue 32 VAL Chi-restraints excluded: chain a residue 61 ILE Chi-restraints excluded: chain a residue 133 HIS Chi-restraints excluded: chain a residue 146 LEU Chi-restraints excluded: chain a residue 257 THR Chi-restraints excluded: chain a residue 258 ILE Chi-restraints excluded: chain a residue 282 THR Chi-restraints excluded: chain a residue 335 GLU Chi-restraints excluded: chain a residue 372 VAL Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 135 ASP Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 135 ASP Chi-restraints excluded: chain E residue 71 MET Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain F residue 71 MET Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 135 ASP Chi-restraints excluded: chain b residue 10 THR Chi-restraints excluded: chain b residue 34 THR Chi-restraints excluded: chain b residue 133 HIS Chi-restraints excluded: chain b residue 161 SER Chi-restraints excluded: chain b residue 257 THR Chi-restraints excluded: chain b residue 259 ILE Chi-restraints excluded: chain b residue 289 LEU Chi-restraints excluded: chain b residue 326 LYS Chi-restraints excluded: chain b residue 335 GLU Chi-restraints excluded: chain b residue 367 ASN Chi-restraints excluded: chain b residue 369 ASN Chi-restraints excluded: chain b residue 372 VAL Chi-restraints excluded: chain c residue 34 THR Chi-restraints excluded: chain c residue 61 ILE Chi-restraints excluded: chain c residue 133 HIS Chi-restraints excluded: chain c residue 146 LEU Chi-restraints excluded: chain c residue 161 SER Chi-restraints excluded: chain c residue 257 THR Chi-restraints excluded: chain c residue 289 LEU Chi-restraints excluded: chain c residue 335 GLU Chi-restraints excluded: chain c residue 367 ASN Chi-restraints excluded: chain c residue 372 VAL Chi-restraints excluded: chain d residue 32 VAL Chi-restraints excluded: chain d residue 61 ILE Chi-restraints excluded: chain d residue 133 HIS Chi-restraints excluded: chain d residue 146 LEU Chi-restraints excluded: chain d residue 257 THR Chi-restraints excluded: chain d residue 258 ILE Chi-restraints excluded: chain d residue 282 THR Chi-restraints excluded: chain d residue 335 GLU Chi-restraints excluded: chain d residue 362 VAL Chi-restraints excluded: chain d residue 372 VAL Chi-restraints excluded: chain e residue 32 VAL Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 133 HIS Chi-restraints excluded: chain e residue 161 SER Chi-restraints excluded: chain e residue 257 THR Chi-restraints excluded: chain e residue 289 LEU Chi-restraints excluded: chain e residue 367 ASN Chi-restraints excluded: chain e residue 372 VAL Chi-restraints excluded: chain f residue 10 THR Chi-restraints excluded: chain f residue 32 VAL Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 133 HIS Chi-restraints excluded: chain f residue 164 GLU Chi-restraints excluded: chain f residue 236 VAL Chi-restraints excluded: chain f residue 257 THR Chi-restraints excluded: chain f residue 289 LEU Chi-restraints excluded: chain f residue 367 ASN Chi-restraints excluded: chain f residue 372 VAL Chi-restraints excluded: chain g residue 64 SER Chi-restraints excluded: chain g residue 116 ASP Chi-restraints excluded: chain g residue 127 LEU Chi-restraints excluded: chain g residue 181 VAL Chi-restraints excluded: chain g residue 236 VAL Chi-restraints excluded: chain g residue 243 GLU Chi-restraints excluded: chain g residue 252 ASN Chi-restraints excluded: chain g residue 275 ASP Chi-restraints excluded: chain g residue 302 VAL Chi-restraints excluded: chain g residue 309 THR Chi-restraints excluded: chain g residue 325 LEU Chi-restraints excluded: chain g residue 344 SER Chi-restraints excluded: chain g residue 353 VAL Chi-restraints excluded: chain g residue 375 THR Chi-restraints excluded: chain g residue 379 LEU Chi-restraints excluded: chain h residue 64 SER Chi-restraints excluded: chain h residue 127 LEU Chi-restraints excluded: chain h residue 181 VAL Chi-restraints excluded: chain h residue 211 THR Chi-restraints excluded: chain h residue 232 THR Chi-restraints excluded: chain h residue 236 VAL Chi-restraints excluded: chain h residue 243 GLU Chi-restraints excluded: chain h residue 245 CYS Chi-restraints excluded: chain h residue 252 ASN Chi-restraints excluded: chain h residue 275 ASP Chi-restraints excluded: chain h residue 282 THR Chi-restraints excluded: chain h residue 302 VAL Chi-restraints excluded: chain h residue 307 THR Chi-restraints excluded: chain h residue 325 LEU Chi-restraints excluded: chain h residue 353 VAL Chi-restraints excluded: chain h residue 362 VAL Chi-restraints excluded: chain l residue 64 SER Chi-restraints excluded: chain l residue 116 ASP Chi-restraints excluded: chain l residue 177 ARG Chi-restraints excluded: chain l residue 181 VAL Chi-restraints excluded: chain l residue 229 VAL Chi-restraints excluded: chain l residue 275 ASP Chi-restraints excluded: chain l residue 282 THR Chi-restraints excluded: chain l residue 302 VAL Chi-restraints excluded: chain l residue 307 THR Chi-restraints excluded: chain l residue 325 LEU Chi-restraints excluded: chain l residue 344 SER Chi-restraints excluded: chain l residue 353 VAL Chi-restraints excluded: chain l residue 362 VAL Chi-restraints excluded: chain k residue 64 SER Chi-restraints excluded: chain k residue 127 LEU Chi-restraints excluded: chain k residue 177 ARG Chi-restraints excluded: chain k residue 181 VAL Chi-restraints excluded: chain k residue 211 THR Chi-restraints excluded: chain k residue 232 THR Chi-restraints excluded: chain k residue 243 GLU Chi-restraints excluded: chain k residue 245 CYS Chi-restraints excluded: chain k residue 252 ASN Chi-restraints excluded: chain k residue 257 THR Chi-restraints excluded: chain k residue 275 ASP Chi-restraints excluded: chain k residue 282 THR Chi-restraints excluded: chain k residue 302 VAL Chi-restraints excluded: chain k residue 307 THR Chi-restraints excluded: chain k residue 325 LEU Chi-restraints excluded: chain k residue 353 VAL Chi-restraints excluded: chain k residue 362 VAL Chi-restraints excluded: chain k residue 376 ASP Chi-restraints excluded: chain k residue 379 LEU Chi-restraints excluded: chain j residue 64 SER Chi-restraints excluded: chain j residue 116 ASP Chi-restraints excluded: chain j residue 127 LEU Chi-restraints excluded: chain j residue 181 VAL Chi-restraints excluded: chain j residue 236 VAL Chi-restraints excluded: chain j residue 243 GLU Chi-restraints excluded: chain j residue 252 ASN Chi-restraints excluded: chain j residue 275 ASP Chi-restraints excluded: chain j residue 282 THR Chi-restraints excluded: chain j residue 302 VAL Chi-restraints excluded: chain j residue 325 LEU Chi-restraints excluded: chain j residue 344 SER Chi-restraints excluded: chain j residue 353 VAL Chi-restraints excluded: chain j residue 375 THR Chi-restraints excluded: chain j residue 379 LEU Chi-restraints excluded: chain i residue 10 THR Chi-restraints excluded: chain i residue 64 SER Chi-restraints excluded: chain i residue 177 ARG Chi-restraints excluded: chain i residue 180 MET Chi-restraints excluded: chain i residue 181 VAL Chi-restraints excluded: chain i residue 245 CYS Chi-restraints excluded: chain i residue 275 ASP Chi-restraints excluded: chain i residue 302 VAL Chi-restraints excluded: chain i residue 307 THR Chi-restraints excluded: chain i residue 325 LEU Chi-restraints excluded: chain i residue 344 SER Chi-restraints excluded: chain i residue 353 VAL Chi-restraints excluded: chain i residue 362 VAL Chi-restraints excluded: chain m residue 10 THR Chi-restraints excluded: chain m residue 25 SER Chi-restraints excluded: chain m residue 127 LEU Chi-restraints excluded: chain m residue 222 SER Chi-restraints excluded: chain m residue 229 VAL Chi-restraints excluded: chain m residue 230 THR Chi-restraints excluded: chain m residue 244 THR Chi-restraints excluded: chain m residue 282 THR Chi-restraints excluded: chain m residue 307 THR Chi-restraints excluded: chain m residue 325 LEU Chi-restraints excluded: chain m residue 344 SER Chi-restraints excluded: chain m residue 379 LEU Chi-restraints excluded: chain m residue 380 THR Chi-restraints excluded: chain m residue 382 VAL Chi-restraints excluded: chain m residue 383 LEU Chi-restraints excluded: chain n residue 10 THR Chi-restraints excluded: chain n residue 12 VAL Chi-restraints excluded: chain n residue 25 SER Chi-restraints excluded: chain n residue 54 ASP Chi-restraints excluded: chain n residue 75 ARG Chi-restraints excluded: chain n residue 222 SER Chi-restraints excluded: chain n residue 229 VAL Chi-restraints excluded: chain n residue 257 THR Chi-restraints excluded: chain n residue 282 THR Chi-restraints excluded: chain n residue 307 THR Chi-restraints excluded: chain n residue 344 SER Chi-restraints excluded: chain n residue 379 LEU Chi-restraints excluded: chain n residue 383 LEU Chi-restraints excluded: chain r residue 10 THR Chi-restraints excluded: chain r residue 25 SER Chi-restraints excluded: chain r residue 70 GLU Chi-restraints excluded: chain r residue 162 THR Chi-restraints excluded: chain r residue 222 SER Chi-restraints excluded: chain r residue 230 THR Chi-restraints excluded: chain r residue 243 GLU Chi-restraints excluded: chain r residue 282 THR Chi-restraints excluded: chain r residue 291 MET Chi-restraints excluded: chain r residue 307 THR Chi-restraints excluded: chain r residue 344 SER Chi-restraints excluded: chain q residue 10 THR Chi-restraints excluded: chain q residue 12 VAL Chi-restraints excluded: chain q residue 25 SER Chi-restraints excluded: chain q residue 54 ASP Chi-restraints excluded: chain q residue 63 SER Chi-restraints excluded: chain q residue 70 GLU Chi-restraints excluded: chain q residue 75 ARG Chi-restraints excluded: chain q residue 151 ARG Chi-restraints excluded: chain q residue 222 SER Chi-restraints excluded: chain q residue 229 VAL Chi-restraints excluded: chain q residue 252 ASN Chi-restraints excluded: chain q residue 257 THR Chi-restraints excluded: chain q residue 282 THR Chi-restraints excluded: chain q residue 307 THR Chi-restraints excluded: chain q residue 344 SER Chi-restraints excluded: chain q residue 379 LEU Chi-restraints excluded: chain q residue 380 THR Chi-restraints excluded: chain q residue 383 LEU Chi-restraints excluded: chain p residue 10 THR Chi-restraints excluded: chain p residue 12 VAL Chi-restraints excluded: chain p residue 25 SER Chi-restraints excluded: chain p residue 75 ARG Chi-restraints excluded: chain p residue 222 SER Chi-restraints excluded: chain p residue 229 VAL Chi-restraints excluded: chain p residue 230 THR Chi-restraints excluded: chain p residue 244 THR Chi-restraints excluded: chain p residue 282 THR Chi-restraints excluded: chain p residue 307 THR Chi-restraints excluded: chain p residue 327 ASN Chi-restraints excluded: chain p residue 344 SER Chi-restraints excluded: chain p residue 372 VAL Chi-restraints excluded: chain p residue 376 ASP Chi-restraints excluded: chain p residue 379 LEU Chi-restraints excluded: chain p residue 382 VAL Chi-restraints excluded: chain p residue 383 LEU Chi-restraints excluded: chain o residue 10 THR Chi-restraints excluded: chain o residue 25 SER Chi-restraints excluded: chain o residue 75 ARG Chi-restraints excluded: chain o residue 127 LEU Chi-restraints excluded: chain o residue 222 SER Chi-restraints excluded: chain o residue 282 THR Chi-restraints excluded: chain o residue 291 MET Chi-restraints excluded: chain o residue 307 THR Chi-restraints excluded: chain o residue 344 SER Chi-restraints excluded: chain o residue 376 ASP Chi-restraints excluded: chain o residue 383 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 253 optimal weight: 7.9990 chunk 678 optimal weight: 0.8980 chunk 149 optimal weight: 3.9990 chunk 442 optimal weight: 5.9990 chunk 186 optimal weight: 9.9990 chunk 754 optimal weight: 9.9990 chunk 626 optimal weight: 2.9990 chunk 349 optimal weight: 9.9990 chunk 62 optimal weight: 20.0000 chunk 249 optimal weight: 0.8980 chunk 396 optimal weight: 1.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 74 ASN f 74 ASN m 197 ASN m 343 ASN r 77 GLN q 172 ASN q 252 ASN p 197 ASN o 77 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 60864 Z= 0.189 Angle : 0.518 9.486 82998 Z= 0.273 Chirality : 0.044 0.168 9444 Planarity : 0.004 0.062 10908 Dihedral : 5.477 46.540 8527 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 4.51 % Allowed : 17.66 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.09), residues: 7830 helix: -0.65 (0.10), residues: 2736 sheet: -2.50 (0.15), residues: 1044 loop : -1.57 (0.10), residues: 4050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP r 210 HIS 0.002 0.001 HIS e 133 PHE 0.015 0.001 PHE i 238 TYR 0.020 0.001 TYR d 264 ARG 0.007 0.000 ARG c 283 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15660 Ramachandran restraints generated. 7830 Oldfield, 0 Emsley, 7830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15660 Ramachandran restraints generated. 7830 Oldfield, 0 Emsley, 7830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1123 residues out of total 6144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 277 poor density : 846 time to evaluate : 5.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 ASP cc_start: -0.1475 (OUTLIER) cc_final: -0.2120 (t70) REVERT: a 61 ILE cc_start: 0.8299 (OUTLIER) cc_final: 0.8073 (mp) REVERT: a 180 MET cc_start: 0.8658 (tpp) cc_final: 0.8341 (ttt) REVERT: a 381 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7366 (tt0) REVERT: B 135 ASP cc_start: -0.1799 (OUTLIER) cc_final: -0.2272 (t70) REVERT: C 135 ASP cc_start: -0.1549 (OUTLIER) cc_final: -0.2084 (t70) REVERT: D 135 ASP cc_start: -0.1329 (OUTLIER) cc_final: -0.1881 (t70) REVERT: D 149 MET cc_start: 0.8689 (mmm) cc_final: 0.8463 (mmm) REVERT: E 135 ASP cc_start: -0.1852 (OUTLIER) cc_final: -0.2443 (t70) REVERT: F 135 ASP cc_start: -0.1812 (OUTLIER) cc_final: -0.2324 (t70) REVERT: b 246 ARG cc_start: 0.7486 (ptm160) cc_final: 0.6916 (mtp180) REVERT: b 259 ILE cc_start: 0.7949 (OUTLIER) cc_final: 0.7718 (pp) REVERT: b 282 THR cc_start: 0.9091 (m) cc_final: 0.8848 (p) REVERT: b 312 LYS cc_start: 0.8136 (tptp) cc_final: 0.7624 (mttp) REVERT: b 367 ASN cc_start: 0.8748 (OUTLIER) cc_final: 0.8487 (t0) REVERT: c 133 HIS cc_start: 0.7552 (OUTLIER) cc_final: 0.6818 (m-70) REVERT: c 246 ARG cc_start: 0.7438 (ptm160) cc_final: 0.7026 (ptm-80) REVERT: c 259 ILE cc_start: 0.7702 (OUTLIER) cc_final: 0.7444 (pp) REVERT: c 282 THR cc_start: 0.9186 (m) cc_final: 0.8968 (p) REVERT: c 367 ASN cc_start: 0.8762 (OUTLIER) cc_final: 0.8325 (t0) REVERT: d 61 ILE cc_start: 0.8331 (OUTLIER) cc_final: 0.8086 (mp) REVERT: d 246 ARG cc_start: 0.7623 (ptm160) cc_final: 0.7281 (ptm-80) REVERT: d 312 LYS cc_start: 0.8339 (tptp) cc_final: 0.7685 (mttp) REVERT: e 143 MET cc_start: 0.8903 (mtp) cc_final: 0.8693 (ttm) REVERT: e 246 ARG cc_start: 0.7373 (ptm160) cc_final: 0.6891 (mtp180) REVERT: e 282 THR cc_start: 0.9117 (m) cc_final: 0.8875 (p) REVERT: e 312 LYS cc_start: 0.8235 (tptt) cc_final: 0.7552 (mttp) REVERT: e 367 ASN cc_start: 0.8739 (OUTLIER) cc_final: 0.8480 (t0) REVERT: f 133 HIS cc_start: 0.7713 (OUTLIER) cc_final: 0.6958 (m-70) REVERT: f 246 ARG cc_start: 0.7411 (ptm160) cc_final: 0.7007 (ptm-80) REVERT: f 258 ILE cc_start: 0.8593 (mt) cc_final: 0.8347 (mt) REVERT: f 282 THR cc_start: 0.9178 (m) cc_final: 0.8957 (p) REVERT: f 367 ASN cc_start: 0.8768 (OUTLIER) cc_final: 0.8332 (t0) REVERT: g 287 MET cc_start: 0.9053 (tpt) cc_final: 0.8819 (tpt) REVERT: h 48 LEU cc_start: 0.9088 (tp) cc_final: 0.8752 (tp) REVERT: l 177 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8170 (mtt90) REVERT: k 48 LEU cc_start: 0.9064 (tp) cc_final: 0.8734 (tp) REVERT: k 177 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.8015 (mtt90) REVERT: k 257 THR cc_start: 0.9194 (OUTLIER) cc_final: 0.8895 (p) REVERT: j 127 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.9110 (mt) REVERT: j 287 MET cc_start: 0.8887 (tpt) cc_final: 0.8507 (tpt) REVERT: i 177 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.8195 (mtt90) REVERT: i 287 MET cc_start: 0.8973 (tpt) cc_final: 0.8645 (tpt) REVERT: m 14 ILE cc_start: 0.8436 (pt) cc_final: 0.8133 (pt) REVERT: m 96 SER cc_start: 0.8618 (m) cc_final: 0.8072 (p) REVERT: m 282 THR cc_start: 0.9182 (OUTLIER) cc_final: 0.8737 (p) REVERT: m 383 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8151 (mp) REVERT: n 75 ARG cc_start: 0.9174 (OUTLIER) cc_final: 0.8947 (tpt170) REVERT: n 96 SER cc_start: 0.8659 (m) cc_final: 0.7808 (p) REVERT: n 151 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7668 (mtt90) REVERT: n 260 ARG cc_start: 0.7534 (mtp85) cc_final: 0.6869 (mtp85) REVERT: n 327 ASN cc_start: 0.8449 (p0) cc_final: 0.8200 (m-40) REVERT: r 96 SER cc_start: 0.8431 (m) cc_final: 0.7873 (p) REVERT: r 327 ASN cc_start: 0.8370 (p0) cc_final: 0.8090 (m-40) REVERT: q 75 ARG cc_start: 0.9199 (OUTLIER) cc_final: 0.8835 (tpt90) REVERT: q 96 SER cc_start: 0.8298 (m) cc_final: 0.7603 (p) REVERT: q 151 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7686 (mtt90) REVERT: q 328 GLN cc_start: 0.8564 (tt0) cc_final: 0.8332 (tt0) REVERT: p 75 ARG cc_start: 0.9109 (OUTLIER) cc_final: 0.8760 (tpt90) REVERT: p 96 SER cc_start: 0.8779 (m) cc_final: 0.8195 (p) REVERT: p 127 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.9124 (mt) REVERT: p 282 THR cc_start: 0.9164 (OUTLIER) cc_final: 0.8600 (p) REVERT: p 383 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8168 (mp) REVERT: o 75 ARG cc_start: 0.9151 (OUTLIER) cc_final: 0.8837 (tpt170) REVERT: o 96 SER cc_start: 0.8450 (m) cc_final: 0.7773 (p) REVERT: o 327 ASN cc_start: 0.8376 (p0) cc_final: 0.8108 (m-40) outliers start: 277 outliers final: 195 residues processed: 1041 average time/residue: 0.5503 time to fit residues: 971.6113 Evaluate side-chains 1035 residues out of total 6144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 807 time to evaluate : 4.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain a residue 61 ILE Chi-restraints excluded: chain a residue 133 HIS Chi-restraints excluded: chain a residue 230 THR Chi-restraints excluded: chain a residue 236 VAL Chi-restraints excluded: chain a residue 257 THR Chi-restraints excluded: chain a residue 258 ILE Chi-restraints excluded: chain a residue 282 THR Chi-restraints excluded: chain a residue 335 GLU Chi-restraints excluded: chain a residue 367 ASN Chi-restraints excluded: chain a residue 372 VAL Chi-restraints excluded: chain a residue 381 GLU Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 135 ASP Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 135 ASP Chi-restraints excluded: chain E residue 71 MET Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 135 ASP Chi-restraints excluded: chain b residue 10 THR Chi-restraints excluded: chain b residue 34 THR Chi-restraints excluded: chain b residue 133 HIS Chi-restraints excluded: chain b residue 161 SER Chi-restraints excluded: chain b residue 207 LEU Chi-restraints excluded: chain b residue 257 THR Chi-restraints excluded: chain b residue 259 ILE Chi-restraints excluded: chain b residue 289 LEU Chi-restraints excluded: chain b residue 326 LYS Chi-restraints excluded: chain b residue 335 GLU Chi-restraints excluded: chain b residue 367 ASN Chi-restraints excluded: chain b residue 372 VAL Chi-restraints excluded: chain c residue 10 THR Chi-restraints excluded: chain c residue 34 THR Chi-restraints excluded: chain c residue 133 HIS Chi-restraints excluded: chain c residue 146 LEU Chi-restraints excluded: chain c residue 161 SER Chi-restraints excluded: chain c residue 257 THR Chi-restraints excluded: chain c residue 259 ILE Chi-restraints excluded: chain c residue 298 HIS Chi-restraints excluded: chain c residue 367 ASN Chi-restraints excluded: chain c residue 372 VAL Chi-restraints excluded: chain d residue 61 ILE Chi-restraints excluded: chain d residue 133 HIS Chi-restraints excluded: chain d residue 236 VAL Chi-restraints excluded: chain d residue 257 THR Chi-restraints excluded: chain d residue 258 ILE Chi-restraints excluded: chain d residue 282 THR Chi-restraints excluded: chain d residue 335 GLU Chi-restraints excluded: chain d residue 362 VAL Chi-restraints excluded: chain d residue 367 ASN Chi-restraints excluded: chain d residue 372 VAL Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 133 HIS Chi-restraints excluded: chain e residue 257 THR Chi-restraints excluded: chain e residue 367 ASN Chi-restraints excluded: chain e residue 372 VAL Chi-restraints excluded: chain f residue 10 THR Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 133 HIS Chi-restraints excluded: chain f residue 164 GLU Chi-restraints excluded: chain f residue 236 VAL Chi-restraints excluded: chain f residue 257 THR Chi-restraints excluded: chain f residue 289 LEU Chi-restraints excluded: chain f residue 367 ASN Chi-restraints excluded: chain f residue 372 VAL Chi-restraints excluded: chain g residue 116 ASP Chi-restraints excluded: chain g residue 181 VAL Chi-restraints excluded: chain g residue 211 THR Chi-restraints excluded: chain g residue 252 ASN Chi-restraints excluded: chain g residue 275 ASP Chi-restraints excluded: chain g residue 282 THR Chi-restraints excluded: chain g residue 302 VAL Chi-restraints excluded: chain g residue 309 THR Chi-restraints excluded: chain g residue 325 LEU Chi-restraints excluded: chain g residue 353 VAL Chi-restraints excluded: chain g residue 375 THR Chi-restraints excluded: chain h residue 64 SER Chi-restraints excluded: chain h residue 127 LEU Chi-restraints excluded: chain h residue 181 VAL Chi-restraints excluded: chain h residue 232 THR Chi-restraints excluded: chain h residue 236 VAL Chi-restraints excluded: chain h residue 243 GLU Chi-restraints excluded: chain h residue 245 CYS Chi-restraints excluded: chain h residue 252 ASN Chi-restraints excluded: chain h residue 275 ASP Chi-restraints excluded: chain h residue 282 THR Chi-restraints excluded: chain h residue 302 VAL Chi-restraints excluded: chain h residue 307 THR Chi-restraints excluded: chain h residue 309 THR Chi-restraints excluded: chain h residue 325 LEU Chi-restraints excluded: chain h residue 353 VAL Chi-restraints excluded: chain h residue 362 VAL Chi-restraints excluded: chain l residue 64 SER Chi-restraints excluded: chain l residue 177 ARG Chi-restraints excluded: chain l residue 181 VAL Chi-restraints excluded: chain l residue 245 CYS Chi-restraints excluded: chain l residue 252 ASN Chi-restraints excluded: chain l residue 275 ASP Chi-restraints excluded: chain l residue 302 VAL Chi-restraints excluded: chain l residue 307 THR Chi-restraints excluded: chain l residue 325 LEU Chi-restraints excluded: chain l residue 344 SER Chi-restraints excluded: chain l residue 353 VAL Chi-restraints excluded: chain l residue 362 VAL Chi-restraints excluded: chain l residue 376 ASP Chi-restraints excluded: chain k residue 64 SER Chi-restraints excluded: chain k residue 127 LEU Chi-restraints excluded: chain k residue 177 ARG Chi-restraints excluded: chain k residue 181 VAL Chi-restraints excluded: chain k residue 232 THR Chi-restraints excluded: chain k residue 257 THR Chi-restraints excluded: chain k residue 282 THR Chi-restraints excluded: chain k residue 302 VAL Chi-restraints excluded: chain k residue 307 THR Chi-restraints excluded: chain k residue 309 THR Chi-restraints excluded: chain k residue 325 LEU Chi-restraints excluded: chain k residue 353 VAL Chi-restraints excluded: chain k residue 362 VAL Chi-restraints excluded: chain k residue 376 ASP Chi-restraints excluded: chain j residue 116 ASP Chi-restraints excluded: chain j residue 127 LEU Chi-restraints excluded: chain j residue 181 VAL Chi-restraints excluded: chain j residue 252 ASN Chi-restraints excluded: chain j residue 275 ASP Chi-restraints excluded: chain j residue 282 THR Chi-restraints excluded: chain j residue 309 THR Chi-restraints excluded: chain j residue 325 LEU Chi-restraints excluded: chain j residue 344 SER Chi-restraints excluded: chain j residue 353 VAL Chi-restraints excluded: chain j residue 375 THR Chi-restraints excluded: chain i residue 10 THR Chi-restraints excluded: chain i residue 177 ARG Chi-restraints excluded: chain i residue 181 VAL Chi-restraints excluded: chain i residue 245 CYS Chi-restraints excluded: chain i residue 275 ASP Chi-restraints excluded: chain i residue 302 VAL Chi-restraints excluded: chain i residue 307 THR Chi-restraints excluded: chain i residue 325 LEU Chi-restraints excluded: chain i residue 344 SER Chi-restraints excluded: chain i residue 353 VAL Chi-restraints excluded: chain i residue 362 VAL Chi-restraints excluded: chain i residue 376 ASP Chi-restraints excluded: chain m residue 10 THR Chi-restraints excluded: chain m residue 18 THR Chi-restraints excluded: chain m residue 25 SER Chi-restraints excluded: chain m residue 148 GLU Chi-restraints excluded: chain m residue 222 SER Chi-restraints excluded: chain m residue 229 VAL Chi-restraints excluded: chain m residue 230 THR Chi-restraints excluded: chain m residue 282 THR Chi-restraints excluded: chain m residue 307 THR Chi-restraints excluded: chain m residue 325 LEU Chi-restraints excluded: chain m residue 344 SER Chi-restraints excluded: chain m residue 379 LEU Chi-restraints excluded: chain m residue 380 THR Chi-restraints excluded: chain m residue 382 VAL Chi-restraints excluded: chain m residue 383 LEU Chi-restraints excluded: chain n residue 10 THR Chi-restraints excluded: chain n residue 12 VAL Chi-restraints excluded: chain n residue 25 SER Chi-restraints excluded: chain n residue 54 ASP Chi-restraints excluded: chain n residue 75 ARG Chi-restraints excluded: chain n residue 151 ARG Chi-restraints excluded: chain n residue 222 SER Chi-restraints excluded: chain n residue 229 VAL Chi-restraints excluded: chain n residue 233 SER Chi-restraints excluded: chain n residue 257 THR Chi-restraints excluded: chain n residue 282 THR Chi-restraints excluded: chain n residue 344 SER Chi-restraints excluded: chain r residue 10 THR Chi-restraints excluded: chain r residue 34 THR Chi-restraints excluded: chain r residue 70 GLU Chi-restraints excluded: chain r residue 92 GLU Chi-restraints excluded: chain r residue 148 GLU Chi-restraints excluded: chain r residue 162 THR Chi-restraints excluded: chain r residue 243 GLU Chi-restraints excluded: chain r residue 282 THR Chi-restraints excluded: chain r residue 307 THR Chi-restraints excluded: chain r residue 344 SER Chi-restraints excluded: chain q residue 10 THR Chi-restraints excluded: chain q residue 54 ASP Chi-restraints excluded: chain q residue 75 ARG Chi-restraints excluded: chain q residue 92 GLU Chi-restraints excluded: chain q residue 151 ARG Chi-restraints excluded: chain q residue 162 THR Chi-restraints excluded: chain q residue 229 VAL Chi-restraints excluded: chain q residue 257 THR Chi-restraints excluded: chain q residue 282 THR Chi-restraints excluded: chain q residue 344 SER Chi-restraints excluded: chain q residue 379 LEU Chi-restraints excluded: chain q residue 380 THR Chi-restraints excluded: chain p residue 10 THR Chi-restraints excluded: chain p residue 12 VAL Chi-restraints excluded: chain p residue 18 THR Chi-restraints excluded: chain p residue 25 SER Chi-restraints excluded: chain p residue 75 ARG Chi-restraints excluded: chain p residue 127 LEU Chi-restraints excluded: chain p residue 222 SER Chi-restraints excluded: chain p residue 229 VAL Chi-restraints excluded: chain p residue 230 THR Chi-restraints excluded: chain p residue 282 THR Chi-restraints excluded: chain p residue 307 THR Chi-restraints excluded: chain p residue 344 SER Chi-restraints excluded: chain p residue 376 ASP Chi-restraints excluded: chain p residue 379 LEU Chi-restraints excluded: chain p residue 382 VAL Chi-restraints excluded: chain p residue 383 LEU Chi-restraints excluded: chain o residue 10 THR Chi-restraints excluded: chain o residue 34 THR Chi-restraints excluded: chain o residue 70 GLU Chi-restraints excluded: chain o residue 75 ARG Chi-restraints excluded: chain o residue 162 THR Chi-restraints excluded: chain o residue 230 THR Chi-restraints excluded: chain o residue 282 THR Chi-restraints excluded: chain o residue 291 MET Chi-restraints excluded: chain o residue 307 THR Chi-restraints excluded: chain o residue 344 SER Chi-restraints excluded: chain o residue 383 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 727 optimal weight: 20.0000 chunk 85 optimal weight: 0.7980 chunk 429 optimal weight: 0.8980 chunk 551 optimal weight: 3.9990 chunk 427 optimal weight: 6.9990 chunk 635 optimal weight: 3.9990 chunk 421 optimal weight: 5.9990 chunk 751 optimal weight: 0.9990 chunk 470 optimal weight: 6.9990 chunk 458 optimal weight: 3.9990 chunk 347 optimal weight: 7.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 67 GLN c 74 ASN f 74 ASN m 197 ASN m 343 ASN r 77 GLN q 172 ASN q 327 ASN p 197 ASN p 327 ASN o 77 GLN o 112 GLN ** o 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 60864 Z= 0.188 Angle : 0.514 10.150 82998 Z= 0.270 Chirality : 0.043 0.178 9444 Planarity : 0.004 0.066 10908 Dihedral : 5.271 44.715 8510 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 4.64 % Allowed : 17.76 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.09), residues: 7830 helix: -0.43 (0.10), residues: 2736 sheet: -2.45 (0.15), residues: 1044 loop : -1.49 (0.10), residues: 4050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP r 210 HIS 0.003 0.001 HIS b 133 PHE 0.018 0.001 PHE i 238 TYR 0.019 0.001 TYR B 12 ARG 0.008 0.000 ARG l 285 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15660 Ramachandran restraints generated. 7830 Oldfield, 0 Emsley, 7830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15660 Ramachandran restraints generated. 7830 Oldfield, 0 Emsley, 7830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1127 residues out of total 6144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 285 poor density : 842 time to evaluate : 5.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 ASP cc_start: -0.1503 (OUTLIER) cc_final: -0.2173 (t70) REVERT: a 180 MET cc_start: 0.8664 (tpp) cc_final: 0.8348 (ttt) REVERT: a 381 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7329 (tt0) REVERT: B 135 ASP cc_start: -0.1776 (OUTLIER) cc_final: -0.2312 (t70) REVERT: C 135 ASP cc_start: -0.1655 (OUTLIER) cc_final: -0.2291 (t70) REVERT: D 135 ASP cc_start: -0.1335 (OUTLIER) cc_final: -0.1910 (t70) REVERT: D 149 MET cc_start: 0.8688 (mmm) cc_final: 0.8456 (mmm) REVERT: E 135 ASP cc_start: -0.2047 (OUTLIER) cc_final: -0.2583 (t70) REVERT: F 135 ASP cc_start: -0.2053 (OUTLIER) cc_final: -0.2388 (t70) REVERT: b 180 MET cc_start: 0.8569 (tpp) cc_final: 0.7977 (ttt) REVERT: b 246 ARG cc_start: 0.7484 (ptm160) cc_final: 0.6961 (mtp180) REVERT: b 259 ILE cc_start: 0.7911 (OUTLIER) cc_final: 0.7645 (pp) REVERT: b 282 THR cc_start: 0.9092 (m) cc_final: 0.8857 (p) REVERT: b 312 LYS cc_start: 0.8207 (tptp) cc_final: 0.7618 (mttp) REVERT: b 367 ASN cc_start: 0.8743 (OUTLIER) cc_final: 0.8474 (t0) REVERT: c 133 HIS cc_start: 0.7519 (OUTLIER) cc_final: 0.6837 (m-70) REVERT: c 259 ILE cc_start: 0.7638 (OUTLIER) cc_final: 0.7401 (pp) REVERT: c 367 ASN cc_start: 0.8746 (OUTLIER) cc_final: 0.8288 (t0) REVERT: d 61 ILE cc_start: 0.8345 (OUTLIER) cc_final: 0.8093 (mp) REVERT: d 246 ARG cc_start: 0.7625 (ptm160) cc_final: 0.7280 (ptm-80) REVERT: d 259 ILE cc_start: 0.7871 (OUTLIER) cc_final: 0.7569 (pp) REVERT: d 312 LYS cc_start: 0.8329 (tptp) cc_final: 0.7580 (mttp) REVERT: e 246 ARG cc_start: 0.7324 (ptm160) cc_final: 0.6823 (mtp180) REVERT: e 282 THR cc_start: 0.9130 (m) cc_final: 0.8882 (p) REVERT: e 312 LYS cc_start: 0.8222 (tptt) cc_final: 0.7536 (mttp) REVERT: e 367 ASN cc_start: 0.8732 (OUTLIER) cc_final: 0.8439 (t0) REVERT: f 133 HIS cc_start: 0.7696 (OUTLIER) cc_final: 0.6827 (m-70) REVERT: f 246 ARG cc_start: 0.7399 (ptm160) cc_final: 0.7093 (ptm160) REVERT: f 282 THR cc_start: 0.9191 (m) cc_final: 0.8964 (p) REVERT: f 367 ASN cc_start: 0.8755 (OUTLIER) cc_final: 0.8326 (t0) REVERT: g 127 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9086 (mt) REVERT: h 48 LEU cc_start: 0.9063 (tp) cc_final: 0.8752 (tp) REVERT: h 371 ARG cc_start: 0.8710 (mtp85) cc_final: 0.8401 (mtp85) REVERT: l 177 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.8230 (mtt90) REVERT: k 48 LEU cc_start: 0.9056 (tp) cc_final: 0.8747 (tp) REVERT: k 177 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.8022 (mtt90) REVERT: k 257 THR cc_start: 0.9192 (OUTLIER) cc_final: 0.8890 (p) REVERT: j 127 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.9096 (mt) REVERT: j 234 ARG cc_start: 0.8126 (ttp80) cc_final: 0.7351 (tmm-80) REVERT: j 287 MET cc_start: 0.8889 (tpt) cc_final: 0.8525 (tpt) REVERT: i 177 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.8205 (mtt90) REVERT: i 287 MET cc_start: 0.8936 (tpt) cc_final: 0.8648 (tpt) REVERT: m 14 ILE cc_start: 0.8654 (pt) cc_final: 0.8391 (pt) REVERT: m 96 SER cc_start: 0.8803 (m) cc_final: 0.8278 (p) REVERT: m 127 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.9107 (mt) REVERT: m 282 THR cc_start: 0.9186 (OUTLIER) cc_final: 0.8740 (p) REVERT: m 327 ASN cc_start: 0.8512 (p0) cc_final: 0.8191 (m110) REVERT: m 383 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8147 (mp) REVERT: n 75 ARG cc_start: 0.9190 (OUTLIER) cc_final: 0.8823 (tpt90) REVERT: n 96 SER cc_start: 0.8731 (m) cc_final: 0.7943 (p) REVERT: n 151 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7627 (mtt90) REVERT: n 260 ARG cc_start: 0.7512 (mtp85) cc_final: 0.6928 (mtp85) REVERT: r 96 SER cc_start: 0.8392 (m) cc_final: 0.7878 (p) REVERT: r 327 ASN cc_start: 0.8337 (p0) cc_final: 0.8046 (m-40) REVERT: q 75 ARG cc_start: 0.9206 (OUTLIER) cc_final: 0.8843 (tpt90) REVERT: q 96 SER cc_start: 0.8271 (m) cc_final: 0.7587 (p) REVERT: q 151 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7687 (mtt90) REVERT: q 260 ARG cc_start: 0.7529 (mtp85) cc_final: 0.6866 (mtp85) REVERT: q 328 GLN cc_start: 0.8520 (tt0) cc_final: 0.8296 (tt0) REVERT: p 75 ARG cc_start: 0.9128 (OUTLIER) cc_final: 0.8791 (tpt90) REVERT: p 96 SER cc_start: 0.8821 (m) cc_final: 0.8290 (p) REVERT: p 127 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9125 (mt) REVERT: p 282 THR cc_start: 0.9161 (OUTLIER) cc_final: 0.8580 (p) REVERT: p 383 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8120 (mp) REVERT: o 75 ARG cc_start: 0.9133 (OUTLIER) cc_final: 0.8922 (tpt170) REVERT: o 96 SER cc_start: 0.8573 (m) cc_final: 0.7829 (p) REVERT: o 327 ASN cc_start: 0.8353 (p0) cc_final: 0.8074 (m-40) outliers start: 285 outliers final: 201 residues processed: 1050 average time/residue: 0.5628 time to fit residues: 998.9786 Evaluate side-chains 1045 residues out of total 6144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 809 time to evaluate : 4.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain a residue 133 HIS Chi-restraints excluded: chain a residue 230 THR Chi-restraints excluded: chain a residue 257 THR Chi-restraints excluded: chain a residue 258 ILE Chi-restraints excluded: chain a residue 282 THR Chi-restraints excluded: chain a residue 335 GLU Chi-restraints excluded: chain a residue 367 ASN Chi-restraints excluded: chain a residue 372 VAL Chi-restraints excluded: chain a residue 381 GLU Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 135 ASP Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 135 ASP Chi-restraints excluded: chain E residue 71 MET Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 135 ASP Chi-restraints excluded: chain b residue 10 THR Chi-restraints excluded: chain b residue 34 THR Chi-restraints excluded: chain b residue 133 HIS Chi-restraints excluded: chain b residue 161 SER Chi-restraints excluded: chain b residue 207 LEU Chi-restraints excluded: chain b residue 257 THR Chi-restraints excluded: chain b residue 259 ILE Chi-restraints excluded: chain b residue 289 LEU Chi-restraints excluded: chain b residue 326 LYS Chi-restraints excluded: chain b residue 367 ASN Chi-restraints excluded: chain b residue 372 VAL Chi-restraints excluded: chain c residue 10 THR Chi-restraints excluded: chain c residue 34 THR Chi-restraints excluded: chain c residue 133 HIS Chi-restraints excluded: chain c residue 146 LEU Chi-restraints excluded: chain c residue 257 THR Chi-restraints excluded: chain c residue 259 ILE Chi-restraints excluded: chain c residue 289 LEU Chi-restraints excluded: chain c residue 298 HIS Chi-restraints excluded: chain c residue 335 GLU Chi-restraints excluded: chain c residue 367 ASN Chi-restraints excluded: chain c residue 372 VAL Chi-restraints excluded: chain d residue 61 ILE Chi-restraints excluded: chain d residue 133 HIS Chi-restraints excluded: chain d residue 236 VAL Chi-restraints excluded: chain d residue 258 ILE Chi-restraints excluded: chain d residue 259 ILE Chi-restraints excluded: chain d residue 282 THR Chi-restraints excluded: chain d residue 318 LEU Chi-restraints excluded: chain d residue 335 GLU Chi-restraints excluded: chain d residue 362 VAL Chi-restraints excluded: chain d residue 367 ASN Chi-restraints excluded: chain d residue 369 ASN Chi-restraints excluded: chain d residue 372 VAL Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 133 HIS Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain e residue 161 SER Chi-restraints excluded: chain e residue 257 THR Chi-restraints excluded: chain e residue 289 LEU Chi-restraints excluded: chain e residue 335 GLU Chi-restraints excluded: chain e residue 367 ASN Chi-restraints excluded: chain e residue 372 VAL Chi-restraints excluded: chain f residue 10 THR Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 133 HIS Chi-restraints excluded: chain f residue 156 LEU Chi-restraints excluded: chain f residue 164 GLU Chi-restraints excluded: chain f residue 236 VAL Chi-restraints excluded: chain f residue 257 THR Chi-restraints excluded: chain f residue 289 LEU Chi-restraints excluded: chain f residue 367 ASN Chi-restraints excluded: chain f residue 372 VAL Chi-restraints excluded: chain g residue 64 SER Chi-restraints excluded: chain g residue 116 ASP Chi-restraints excluded: chain g residue 127 LEU Chi-restraints excluded: chain g residue 181 VAL Chi-restraints excluded: chain g residue 211 THR Chi-restraints excluded: chain g residue 252 ASN Chi-restraints excluded: chain g residue 275 ASP Chi-restraints excluded: chain g residue 282 THR Chi-restraints excluded: chain g residue 309 THR Chi-restraints excluded: chain g residue 325 LEU Chi-restraints excluded: chain g residue 344 SER Chi-restraints excluded: chain g residue 353 VAL Chi-restraints excluded: chain g residue 375 THR Chi-restraints excluded: chain g residue 383 LEU Chi-restraints excluded: chain h residue 64 SER Chi-restraints excluded: chain h residue 127 LEU Chi-restraints excluded: chain h residue 181 VAL Chi-restraints excluded: chain h residue 232 THR Chi-restraints excluded: chain h residue 236 VAL Chi-restraints excluded: chain h residue 245 CYS Chi-restraints excluded: chain h residue 275 ASP Chi-restraints excluded: chain h residue 282 THR Chi-restraints excluded: chain h residue 307 THR Chi-restraints excluded: chain h residue 325 LEU Chi-restraints excluded: chain h residue 353 VAL Chi-restraints excluded: chain h residue 362 VAL Chi-restraints excluded: chain l residue 64 SER Chi-restraints excluded: chain l residue 177 ARG Chi-restraints excluded: chain l residue 181 VAL Chi-restraints excluded: chain l residue 245 CYS Chi-restraints excluded: chain l residue 252 ASN Chi-restraints excluded: chain l residue 275 ASP Chi-restraints excluded: chain l residue 302 VAL Chi-restraints excluded: chain l residue 325 LEU Chi-restraints excluded: chain l residue 344 SER Chi-restraints excluded: chain l residue 353 VAL Chi-restraints excluded: chain l residue 362 VAL Chi-restraints excluded: chain l residue 376 ASP Chi-restraints excluded: chain k residue 64 SER Chi-restraints excluded: chain k residue 127 LEU Chi-restraints excluded: chain k residue 177 ARG Chi-restraints excluded: chain k residue 181 VAL Chi-restraints excluded: chain k residue 232 THR Chi-restraints excluded: chain k residue 245 CYS Chi-restraints excluded: chain k residue 257 THR Chi-restraints excluded: chain k residue 275 ASP Chi-restraints excluded: chain k residue 282 THR Chi-restraints excluded: chain k residue 307 THR Chi-restraints excluded: chain k residue 309 THR Chi-restraints excluded: chain k residue 325 LEU Chi-restraints excluded: chain k residue 353 VAL Chi-restraints excluded: chain k residue 362 VAL Chi-restraints excluded: chain k residue 376 ASP Chi-restraints excluded: chain j residue 64 SER Chi-restraints excluded: chain j residue 116 ASP Chi-restraints excluded: chain j residue 127 LEU Chi-restraints excluded: chain j residue 181 VAL Chi-restraints excluded: chain j residue 236 VAL Chi-restraints excluded: chain j residue 252 ASN Chi-restraints excluded: chain j residue 282 THR Chi-restraints excluded: chain j residue 309 THR Chi-restraints excluded: chain j residue 325 LEU Chi-restraints excluded: chain j residue 344 SER Chi-restraints excluded: chain j residue 353 VAL Chi-restraints excluded: chain j residue 383 LEU Chi-restraints excluded: chain i residue 10 THR Chi-restraints excluded: chain i residue 64 SER Chi-restraints excluded: chain i residue 177 ARG Chi-restraints excluded: chain i residue 181 VAL Chi-restraints excluded: chain i residue 245 CYS Chi-restraints excluded: chain i residue 275 ASP Chi-restraints excluded: chain i residue 302 VAL Chi-restraints excluded: chain i residue 307 THR Chi-restraints excluded: chain i residue 325 LEU Chi-restraints excluded: chain i residue 344 SER Chi-restraints excluded: chain i residue 353 VAL Chi-restraints excluded: chain i residue 362 VAL Chi-restraints excluded: chain i residue 376 ASP Chi-restraints excluded: chain m residue 10 THR Chi-restraints excluded: chain m residue 18 THR Chi-restraints excluded: chain m residue 25 SER Chi-restraints excluded: chain m residue 127 LEU Chi-restraints excluded: chain m residue 148 GLU Chi-restraints excluded: chain m residue 222 SER Chi-restraints excluded: chain m residue 229 VAL Chi-restraints excluded: chain m residue 230 THR Chi-restraints excluded: chain m residue 282 THR Chi-restraints excluded: chain m residue 307 THR Chi-restraints excluded: chain m residue 325 LEU Chi-restraints excluded: chain m residue 344 SER Chi-restraints excluded: chain m residue 379 LEU Chi-restraints excluded: chain m residue 380 THR Chi-restraints excluded: chain m residue 382 VAL Chi-restraints excluded: chain m residue 383 LEU Chi-restraints excluded: chain n residue 10 THR Chi-restraints excluded: chain n residue 25 SER Chi-restraints excluded: chain n residue 54 ASP Chi-restraints excluded: chain n residue 75 ARG Chi-restraints excluded: chain n residue 151 ARG Chi-restraints excluded: chain n residue 222 SER Chi-restraints excluded: chain n residue 229 VAL Chi-restraints excluded: chain n residue 233 SER Chi-restraints excluded: chain n residue 257 THR Chi-restraints excluded: chain n residue 282 THR Chi-restraints excluded: chain n residue 307 THR Chi-restraints excluded: chain n residue 344 SER Chi-restraints excluded: chain n residue 379 LEU Chi-restraints excluded: chain r residue 10 THR Chi-restraints excluded: chain r residue 34 THR Chi-restraints excluded: chain r residue 70 GLU Chi-restraints excluded: chain r residue 162 THR Chi-restraints excluded: chain r residue 243 GLU Chi-restraints excluded: chain r residue 282 THR Chi-restraints excluded: chain r residue 291 MET Chi-restraints excluded: chain r residue 307 THR Chi-restraints excluded: chain r residue 344 SER Chi-restraints excluded: chain q residue 10 THR Chi-restraints excluded: chain q residue 54 ASP Chi-restraints excluded: chain q residue 75 ARG Chi-restraints excluded: chain q residue 92 GLU Chi-restraints excluded: chain q residue 151 ARG Chi-restraints excluded: chain q residue 162 THR Chi-restraints excluded: chain q residue 222 SER Chi-restraints excluded: chain q residue 229 VAL Chi-restraints excluded: chain q residue 282 THR Chi-restraints excluded: chain q residue 307 THR Chi-restraints excluded: chain q residue 344 SER Chi-restraints excluded: chain q residue 379 LEU Chi-restraints excluded: chain q residue 380 THR Chi-restraints excluded: chain p residue 10 THR Chi-restraints excluded: chain p residue 12 VAL Chi-restraints excluded: chain p residue 18 THR Chi-restraints excluded: chain p residue 25 SER Chi-restraints excluded: chain p residue 75 ARG Chi-restraints excluded: chain p residue 127 LEU Chi-restraints excluded: chain p residue 222 SER Chi-restraints excluded: chain p residue 229 VAL Chi-restraints excluded: chain p residue 230 THR Chi-restraints excluded: chain p residue 244 THR Chi-restraints excluded: chain p residue 282 THR Chi-restraints excluded: chain p residue 307 THR Chi-restraints excluded: chain p residue 344 SER Chi-restraints excluded: chain p residue 376 ASP Chi-restraints excluded: chain p residue 379 LEU Chi-restraints excluded: chain p residue 382 VAL Chi-restraints excluded: chain p residue 383 LEU Chi-restraints excluded: chain o residue 10 THR Chi-restraints excluded: chain o residue 75 ARG Chi-restraints excluded: chain o residue 162 THR Chi-restraints excluded: chain o residue 230 THR Chi-restraints excluded: chain o residue 282 THR Chi-restraints excluded: chain o residue 291 MET Chi-restraints excluded: chain o residue 307 THR Chi-restraints excluded: chain o residue 344 SER Chi-restraints excluded: chain o residue 376 ASP Chi-restraints excluded: chain o residue 383 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 465 optimal weight: 9.9990 chunk 300 optimal weight: 10.0000 chunk 449 optimal weight: 4.9990 chunk 226 optimal weight: 3.9990 chunk 147 optimal weight: 0.0570 chunk 145 optimal weight: 10.0000 chunk 477 optimal weight: 0.4980 chunk 512 optimal weight: 0.0670 chunk 371 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 590 optimal weight: 7.9990 overall best weight: 1.9240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 186 GLN ** c 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 74 ASN ** f 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 74 ASN l 369 ASN k 122 ASN i 369 ASN m 197 ASN m 343 ASN n 327 ASN r 77 GLN q 172 ASN p 197 ASN ** o 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 60864 Z= 0.178 Angle : 0.509 10.789 82998 Z= 0.267 Chirality : 0.043 0.168 9444 Planarity : 0.004 0.072 10908 Dihedral : 5.186 45.635 8507 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 4.26 % Allowed : 18.05 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.10), residues: 7830 helix: -0.23 (0.10), residues: 2736 sheet: -2.41 (0.15), residues: 1044 loop : -1.43 (0.10), residues: 4050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP r 210 HIS 0.002 0.001 HIS b 133 PHE 0.019 0.001 PHE i 238 TYR 0.021 0.001 TYR B 12 ARG 0.006 0.000 ARG o 260 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15660 Ramachandran restraints generated. 7830 Oldfield, 0 Emsley, 7830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15660 Ramachandran restraints generated. 7830 Oldfield, 0 Emsley, 7830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1109 residues out of total 6144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 262 poor density : 847 time to evaluate : 4.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 ASP cc_start: -0.1588 (OUTLIER) cc_final: -0.2292 (t70) REVERT: a 61 ILE cc_start: 0.8313 (OUTLIER) cc_final: 0.8059 (mp) REVERT: a 180 MET cc_start: 0.8685 (tpp) cc_final: 0.8348 (ttt) REVERT: B 135 ASP cc_start: -0.1832 (OUTLIER) cc_final: -0.2363 (t70) REVERT: C 135 ASP cc_start: -0.1957 (OUTLIER) cc_final: -0.2344 (t70) REVERT: D 135 ASP cc_start: -0.1397 (OUTLIER) cc_final: -0.1955 (t70) REVERT: D 149 MET cc_start: 0.8692 (mmm) cc_final: 0.8464 (mmm) REVERT: E 135 ASP cc_start: -0.2082 (OUTLIER) cc_final: -0.2614 (t70) REVERT: F 135 ASP cc_start: -0.2074 (OUTLIER) cc_final: -0.2410 (t70) REVERT: F 149 MET cc_start: 0.8552 (mmm) cc_final: 0.8167 (mmm) REVERT: b 180 MET cc_start: 0.8568 (tpp) cc_final: 0.7984 (ttt) REVERT: b 246 ARG cc_start: 0.7339 (ptm160) cc_final: 0.6805 (mtp180) REVERT: b 259 ILE cc_start: 0.7885 (OUTLIER) cc_final: 0.7618 (pp) REVERT: b 282 THR cc_start: 0.9079 (m) cc_final: 0.8859 (p) REVERT: b 312 LYS cc_start: 0.8226 (tptp) cc_final: 0.7552 (mttp) REVERT: b 367 ASN cc_start: 0.8727 (OUTLIER) cc_final: 0.8425 (t0) REVERT: c 133 HIS cc_start: 0.7497 (OUTLIER) cc_final: 0.6847 (m-70) REVERT: c 259 ILE cc_start: 0.7674 (OUTLIER) cc_final: 0.7395 (pp) REVERT: c 367 ASN cc_start: 0.8721 (OUTLIER) cc_final: 0.8288 (t0) REVERT: d 61 ILE cc_start: 0.8335 (OUTLIER) cc_final: 0.8070 (mp) REVERT: d 180 MET cc_start: 0.8535 (tpp) cc_final: 0.8263 (ttt) REVERT: d 246 ARG cc_start: 0.7577 (ptm160) cc_final: 0.7230 (ptm-80) REVERT: d 259 ILE cc_start: 0.7864 (OUTLIER) cc_final: 0.7542 (pp) REVERT: d 312 LYS cc_start: 0.8350 (tptp) cc_final: 0.7580 (mttp) REVERT: e 180 MET cc_start: 0.8525 (tpp) cc_final: 0.7942 (ttt) REVERT: e 246 ARG cc_start: 0.7280 (ptm160) cc_final: 0.6970 (mtm180) REVERT: e 282 THR cc_start: 0.9113 (m) cc_final: 0.8878 (p) REVERT: e 312 LYS cc_start: 0.8243 (tptt) cc_final: 0.7547 (mttp) REVERT: e 367 ASN cc_start: 0.8732 (OUTLIER) cc_final: 0.8467 (t0) REVERT: f 133 HIS cc_start: 0.7527 (OUTLIER) cc_final: 0.6730 (m-70) REVERT: f 215 TYR cc_start: 0.8492 (m-10) cc_final: 0.8251 (m-80) REVERT: f 246 ARG cc_start: 0.7388 (ptm160) cc_final: 0.7098 (ptm160) REVERT: f 282 THR cc_start: 0.9156 (m) cc_final: 0.8950 (p) REVERT: f 367 ASN cc_start: 0.8733 (OUTLIER) cc_final: 0.8304 (t0) REVERT: g 127 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.9064 (mt) REVERT: g 234 ARG cc_start: 0.8121 (ttp80) cc_final: 0.7752 (tmm-80) REVERT: h 48 LEU cc_start: 0.9055 (tp) cc_final: 0.8733 (tp) REVERT: h 371 ARG cc_start: 0.8674 (mtp85) cc_final: 0.8232 (mtp85) REVERT: l 177 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.8213 (mtt90) REVERT: l 287 MET cc_start: 0.8973 (tpt) cc_final: 0.8565 (tpt) REVERT: k 48 LEU cc_start: 0.9042 (tp) cc_final: 0.8729 (tp) REVERT: k 177 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.8064 (mtt90) REVERT: k 257 THR cc_start: 0.9188 (OUTLIER) cc_final: 0.8877 (p) REVERT: j 234 ARG cc_start: 0.8100 (ttp80) cc_final: 0.7333 (tmm-80) REVERT: j 287 MET cc_start: 0.8866 (tpt) cc_final: 0.8437 (tpt) REVERT: i 177 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.8219 (mtt90) REVERT: i 287 MET cc_start: 0.8919 (tpt) cc_final: 0.8587 (tpt) REVERT: m 14 ILE cc_start: 0.8649 (pt) cc_final: 0.8385 (pt) REVERT: m 96 SER cc_start: 0.8822 (m) cc_final: 0.8387 (p) REVERT: m 127 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9084 (mt) REVERT: m 282 THR cc_start: 0.9177 (OUTLIER) cc_final: 0.8729 (p) REVERT: m 327 ASN cc_start: 0.8482 (p0) cc_final: 0.8196 (m110) REVERT: m 383 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8070 (mp) REVERT: n 75 ARG cc_start: 0.9216 (OUTLIER) cc_final: 0.8834 (tpt90) REVERT: n 96 SER cc_start: 0.8819 (m) cc_final: 0.8180 (p) REVERT: n 151 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7558 (mtt90) REVERT: n 260 ARG cc_start: 0.7487 (mtp85) cc_final: 0.6918 (mtp85) REVERT: n 289 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8938 (mm) REVERT: r 96 SER cc_start: 0.8367 (m) cc_final: 0.7834 (p) REVERT: r 327 ASN cc_start: 0.8253 (p0) cc_final: 0.8035 (m-40) REVERT: q 75 ARG cc_start: 0.9203 (OUTLIER) cc_final: 0.8820 (tpt90) REVERT: q 96 SER cc_start: 0.8235 (m) cc_final: 0.7426 (p) REVERT: q 151 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7588 (mtt90) REVERT: q 260 ARG cc_start: 0.7536 (mtp85) cc_final: 0.6946 (mtp85) REVERT: q 282 THR cc_start: 0.9215 (OUTLIER) cc_final: 0.8709 (p) REVERT: q 328 GLN cc_start: 0.8492 (tt0) cc_final: 0.8218 (tt0) REVERT: p 75 ARG cc_start: 0.9112 (OUTLIER) cc_final: 0.8755 (tpt90) REVERT: p 96 SER cc_start: 0.8901 (m) cc_final: 0.8458 (p) REVERT: p 127 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.9119 (mt) REVERT: p 282 THR cc_start: 0.9155 (OUTLIER) cc_final: 0.8569 (p) REVERT: p 383 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8106 (mp) REVERT: o 75 ARG cc_start: 0.9109 (OUTLIER) cc_final: 0.8735 (tpt170) REVERT: o 96 SER cc_start: 0.8694 (m) cc_final: 0.8012 (p) REVERT: o 327 ASN cc_start: 0.8277 (p0) cc_final: 0.8060 (m-40) outliers start: 262 outliers final: 193 residues processed: 1026 average time/residue: 0.5683 time to fit residues: 984.2163 Evaluate side-chains 1043 residues out of total 6144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 814 time to evaluate : 4.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain a residue 61 ILE Chi-restraints excluded: chain a residue 133 HIS Chi-restraints excluded: chain a residue 230 THR Chi-restraints excluded: chain a residue 257 THR Chi-restraints excluded: chain a residue 258 ILE Chi-restraints excluded: chain a residue 282 THR Chi-restraints excluded: chain a residue 335 GLU Chi-restraints excluded: chain a residue 367 ASN Chi-restraints excluded: chain a residue 369 ASN Chi-restraints excluded: chain a residue 372 VAL Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 135 ASP Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 135 ASP Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 135 ASP Chi-restraints excluded: chain b residue 10 THR Chi-restraints excluded: chain b residue 34 THR Chi-restraints excluded: chain b residue 133 HIS Chi-restraints excluded: chain b residue 146 LEU Chi-restraints excluded: chain b residue 161 SER Chi-restraints excluded: chain b residue 207 LEU Chi-restraints excluded: chain b residue 257 THR Chi-restraints excluded: chain b residue 259 ILE Chi-restraints excluded: chain b residue 326 LYS Chi-restraints excluded: chain b residue 335 GLU Chi-restraints excluded: chain b residue 367 ASN Chi-restraints excluded: chain b residue 372 VAL Chi-restraints excluded: chain c residue 10 THR Chi-restraints excluded: chain c residue 34 THR Chi-restraints excluded: chain c residue 133 HIS Chi-restraints excluded: chain c residue 257 THR Chi-restraints excluded: chain c residue 259 ILE Chi-restraints excluded: chain c residue 289 LEU Chi-restraints excluded: chain c residue 298 HIS Chi-restraints excluded: chain c residue 367 ASN Chi-restraints excluded: chain c residue 372 VAL Chi-restraints excluded: chain d residue 61 ILE Chi-restraints excluded: chain d residue 133 HIS Chi-restraints excluded: chain d residue 236 VAL Chi-restraints excluded: chain d residue 258 ILE Chi-restraints excluded: chain d residue 259 ILE Chi-restraints excluded: chain d residue 282 THR Chi-restraints excluded: chain d residue 335 GLU Chi-restraints excluded: chain d residue 362 VAL Chi-restraints excluded: chain d residue 367 ASN Chi-restraints excluded: chain d residue 369 ASN Chi-restraints excluded: chain d residue 372 VAL Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 61 ILE Chi-restraints excluded: chain e residue 133 HIS Chi-restraints excluded: chain e residue 161 SER Chi-restraints excluded: chain e residue 257 THR Chi-restraints excluded: chain e residue 289 LEU Chi-restraints excluded: chain e residue 335 GLU Chi-restraints excluded: chain e residue 367 ASN Chi-restraints excluded: chain e residue 372 VAL Chi-restraints excluded: chain f residue 10 THR Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 133 HIS Chi-restraints excluded: chain f residue 156 LEU Chi-restraints excluded: chain f residue 164 GLU Chi-restraints excluded: chain f residue 236 VAL Chi-restraints excluded: chain f residue 257 THR Chi-restraints excluded: chain f residue 289 LEU Chi-restraints excluded: chain f residue 367 ASN Chi-restraints excluded: chain f residue 372 VAL Chi-restraints excluded: chain f residue 380 THR Chi-restraints excluded: chain g residue 116 ASP Chi-restraints excluded: chain g residue 127 LEU Chi-restraints excluded: chain g residue 181 VAL Chi-restraints excluded: chain g residue 211 THR Chi-restraints excluded: chain g residue 236 VAL Chi-restraints excluded: chain g residue 243 GLU Chi-restraints excluded: chain g residue 275 ASP Chi-restraints excluded: chain g residue 282 THR Chi-restraints excluded: chain g residue 309 THR Chi-restraints excluded: chain g residue 325 LEU Chi-restraints excluded: chain g residue 344 SER Chi-restraints excluded: chain g residue 353 VAL Chi-restraints excluded: chain g residue 375 THR Chi-restraints excluded: chain h residue 64 SER Chi-restraints excluded: chain h residue 127 LEU Chi-restraints excluded: chain h residue 181 VAL Chi-restraints excluded: chain h residue 232 THR Chi-restraints excluded: chain h residue 236 VAL Chi-restraints excluded: chain h residue 245 CYS Chi-restraints excluded: chain h residue 282 THR Chi-restraints excluded: chain h residue 307 THR Chi-restraints excluded: chain h residue 309 THR Chi-restraints excluded: chain h residue 325 LEU Chi-restraints excluded: chain h residue 353 VAL Chi-restraints excluded: chain h residue 362 VAL Chi-restraints excluded: chain l residue 64 SER Chi-restraints excluded: chain l residue 177 ARG Chi-restraints excluded: chain l residue 181 VAL Chi-restraints excluded: chain l residue 245 CYS Chi-restraints excluded: chain l residue 275 ASP Chi-restraints excluded: chain l residue 302 VAL Chi-restraints excluded: chain l residue 307 THR Chi-restraints excluded: chain l residue 325 LEU Chi-restraints excluded: chain l residue 344 SER Chi-restraints excluded: chain l residue 353 VAL Chi-restraints excluded: chain l residue 362 VAL Chi-restraints excluded: chain k residue 64 SER Chi-restraints excluded: chain k residue 127 LEU Chi-restraints excluded: chain k residue 177 ARG Chi-restraints excluded: chain k residue 181 VAL Chi-restraints excluded: chain k residue 245 CYS Chi-restraints excluded: chain k residue 257 THR Chi-restraints excluded: chain k residue 275 ASP Chi-restraints excluded: chain k residue 282 THR Chi-restraints excluded: chain k residue 307 THR Chi-restraints excluded: chain k residue 309 THR Chi-restraints excluded: chain k residue 325 LEU Chi-restraints excluded: chain k residue 353 VAL Chi-restraints excluded: chain k residue 362 VAL Chi-restraints excluded: chain k residue 376 ASP Chi-restraints excluded: chain j residue 64 SER Chi-restraints excluded: chain j residue 116 ASP Chi-restraints excluded: chain j residue 181 VAL Chi-restraints excluded: chain j residue 236 VAL Chi-restraints excluded: chain j residue 252 ASN Chi-restraints excluded: chain j residue 282 THR Chi-restraints excluded: chain j residue 309 THR Chi-restraints excluded: chain j residue 325 LEU Chi-restraints excluded: chain j residue 344 SER Chi-restraints excluded: chain j residue 353 VAL Chi-restraints excluded: chain i residue 64 SER Chi-restraints excluded: chain i residue 177 ARG Chi-restraints excluded: chain i residue 181 VAL Chi-restraints excluded: chain i residue 275 ASP Chi-restraints excluded: chain i residue 302 VAL Chi-restraints excluded: chain i residue 307 THR Chi-restraints excluded: chain i residue 325 LEU Chi-restraints excluded: chain i residue 344 SER Chi-restraints excluded: chain i residue 353 VAL Chi-restraints excluded: chain i residue 362 VAL Chi-restraints excluded: chain i residue 374 VAL Chi-restraints excluded: chain i residue 376 ASP Chi-restraints excluded: chain m residue 10 THR Chi-restraints excluded: chain m residue 18 THR Chi-restraints excluded: chain m residue 25 SER Chi-restraints excluded: chain m residue 34 THR Chi-restraints excluded: chain m residue 127 LEU Chi-restraints excluded: chain m residue 148 GLU Chi-restraints excluded: chain m residue 222 SER Chi-restraints excluded: chain m residue 229 VAL Chi-restraints excluded: chain m residue 230 THR Chi-restraints excluded: chain m residue 244 THR Chi-restraints excluded: chain m residue 282 THR Chi-restraints excluded: chain m residue 325 LEU Chi-restraints excluded: chain m residue 344 SER Chi-restraints excluded: chain m residue 379 LEU Chi-restraints excluded: chain m residue 380 THR Chi-restraints excluded: chain m residue 382 VAL Chi-restraints excluded: chain m residue 383 LEU Chi-restraints excluded: chain n residue 10 THR Chi-restraints excluded: chain n residue 25 SER Chi-restraints excluded: chain n residue 54 ASP Chi-restraints excluded: chain n residue 75 ARG Chi-restraints excluded: chain n residue 143 MET Chi-restraints excluded: chain n residue 151 ARG Chi-restraints excluded: chain n residue 222 SER Chi-restraints excluded: chain n residue 229 VAL Chi-restraints excluded: chain n residue 282 THR Chi-restraints excluded: chain n residue 289 LEU Chi-restraints excluded: chain n residue 307 THR Chi-restraints excluded: chain n residue 344 SER Chi-restraints excluded: chain n residue 379 LEU Chi-restraints excluded: chain r residue 10 THR Chi-restraints excluded: chain r residue 70 GLU Chi-restraints excluded: chain r residue 92 GLU Chi-restraints excluded: chain r residue 148 GLU Chi-restraints excluded: chain r residue 162 THR Chi-restraints excluded: chain r residue 230 THR Chi-restraints excluded: chain r residue 243 GLU Chi-restraints excluded: chain r residue 282 THR Chi-restraints excluded: chain r residue 307 THR Chi-restraints excluded: chain r residue 344 SER Chi-restraints excluded: chain q residue 10 THR Chi-restraints excluded: chain q residue 54 ASP Chi-restraints excluded: chain q residue 75 ARG Chi-restraints excluded: chain q residue 92 GLU Chi-restraints excluded: chain q residue 151 ARG Chi-restraints excluded: chain q residue 162 THR Chi-restraints excluded: chain q residue 229 VAL Chi-restraints excluded: chain q residue 233 SER Chi-restraints excluded: chain q residue 282 THR Chi-restraints excluded: chain q residue 307 THR Chi-restraints excluded: chain q residue 344 SER Chi-restraints excluded: chain q residue 379 LEU Chi-restraints excluded: chain q residue 380 THR Chi-restraints excluded: chain p residue 10 THR Chi-restraints excluded: chain p residue 18 THR Chi-restraints excluded: chain p residue 25 SER Chi-restraints excluded: chain p residue 75 ARG Chi-restraints excluded: chain p residue 127 LEU Chi-restraints excluded: chain p residue 222 SER Chi-restraints excluded: chain p residue 229 VAL Chi-restraints excluded: chain p residue 230 THR Chi-restraints excluded: chain p residue 244 THR Chi-restraints excluded: chain p residue 282 THR Chi-restraints excluded: chain p residue 307 THR Chi-restraints excluded: chain p residue 344 SER Chi-restraints excluded: chain p residue 379 LEU Chi-restraints excluded: chain p residue 382 VAL Chi-restraints excluded: chain p residue 383 LEU Chi-restraints excluded: chain o residue 10 THR Chi-restraints excluded: chain o residue 34 THR Chi-restraints excluded: chain o residue 75 ARG Chi-restraints excluded: chain o residue 162 THR Chi-restraints excluded: chain o residue 282 THR Chi-restraints excluded: chain o residue 291 MET Chi-restraints excluded: chain o residue 307 THR Chi-restraints excluded: chain o residue 344 SER Chi-restraints excluded: chain o residue 376 ASP Chi-restraints excluded: chain o residue 383 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 683 optimal weight: 8.9990 chunk 720 optimal weight: 0.9990 chunk 657 optimal weight: 0.2980 chunk 700 optimal weight: 1.9990 chunk 421 optimal weight: 5.9990 chunk 305 optimal weight: 5.9990 chunk 550 optimal weight: 5.9990 chunk 214 optimal weight: 20.0000 chunk 633 optimal weight: 10.0000 chunk 662 optimal weight: 2.9990 chunk 698 optimal weight: 0.9980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 67 GLN ** c 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 74 ASN ** f 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 74 ASN h 369 ASN j 343 ASN m 197 ASN m 343 ASN r 77 GLN q 172 ASN p 197 ASN o 77 GLN ** o 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 60864 Z= 0.160 Angle : 0.502 11.637 82998 Z= 0.264 Chirality : 0.043 0.170 9444 Planarity : 0.004 0.077 10908 Dihedral : 5.139 57.155 8507 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 3.66 % Allowed : 18.83 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.10), residues: 7830 helix: 0.02 (0.10), residues: 2724 sheet: -2.37 (0.15), residues: 1044 loop : -1.38 (0.10), residues: 4062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP h 355 HIS 0.002 0.000 HIS e 133 PHE 0.021 0.001 PHE i 238 TYR 0.024 0.001 TYR B 12 ARG 0.006 0.000 ARG p 260 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15660 Ramachandran restraints generated. 7830 Oldfield, 0 Emsley, 7830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15660 Ramachandran restraints generated. 7830 Oldfield, 0 Emsley, 7830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1074 residues out of total 6144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 849 time to evaluate : 5.032 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 ASP cc_start: -0.1634 (OUTLIER) cc_final: -0.2367 (t70) REVERT: a 61 ILE cc_start: 0.8278 (OUTLIER) cc_final: 0.8007 (mp) REVERT: B 135 ASP cc_start: -0.1877 (OUTLIER) cc_final: -0.2395 (t70) REVERT: D 149 MET cc_start: 0.8668 (mmm) cc_final: 0.8461 (mmm) REVERT: E 135 ASP cc_start: -0.2282 (OUTLIER) cc_final: -0.2706 (t70) REVERT: F 149 MET cc_start: 0.8559 (mmm) cc_final: 0.8137 (mmm) REVERT: b 180 MET cc_start: 0.8564 (tpp) cc_final: 0.7967 (ttt) REVERT: b 246 ARG cc_start: 0.7265 (ptm160) cc_final: 0.6904 (mtm180) REVERT: b 259 ILE cc_start: 0.7781 (OUTLIER) cc_final: 0.7528 (pp) REVERT: b 282 THR cc_start: 0.9096 (m) cc_final: 0.8874 (p) REVERT: b 287 MET cc_start: 0.8412 (tpt) cc_final: 0.8189 (tpt) REVERT: b 312 LYS cc_start: 0.8175 (tptp) cc_final: 0.7512 (mttp) REVERT: b 367 ASN cc_start: 0.8720 (OUTLIER) cc_final: 0.8452 (t0) REVERT: c 133 HIS cc_start: 0.7371 (OUTLIER) cc_final: 0.6670 (m-70) REVERT: c 259 ILE cc_start: 0.7541 (OUTLIER) cc_final: 0.7330 (pp) REVERT: c 367 ASN cc_start: 0.8619 (OUTLIER) cc_final: 0.8128 (t0) REVERT: d 61 ILE cc_start: 0.8296 (OUTLIER) cc_final: 0.8038 (mp) REVERT: d 180 MET cc_start: 0.8515 (tpp) cc_final: 0.8280 (ttm) REVERT: d 246 ARG cc_start: 0.7552 (ptm160) cc_final: 0.7257 (ptm160) REVERT: d 312 LYS cc_start: 0.8333 (tptp) cc_final: 0.7559 (mttp) REVERT: e 180 MET cc_start: 0.8534 (tpp) cc_final: 0.7919 (ttt) REVERT: e 246 ARG cc_start: 0.7271 (ptm160) cc_final: 0.7040 (ptm160) REVERT: e 282 THR cc_start: 0.9112 (m) cc_final: 0.8883 (p) REVERT: e 312 LYS cc_start: 0.8321 (tptt) cc_final: 0.7549 (mttp) REVERT: e 367 ASN cc_start: 0.8723 (OUTLIER) cc_final: 0.8460 (t0) REVERT: f 133 HIS cc_start: 0.7486 (OUTLIER) cc_final: 0.6763 (m-70) REVERT: f 215 TYR cc_start: 0.8441 (m-10) cc_final: 0.8200 (m-80) REVERT: f 246 ARG cc_start: 0.7368 (ptm160) cc_final: 0.7100 (ptm160) REVERT: f 367 ASN cc_start: 0.8636 (OUTLIER) cc_final: 0.8141 (t0) REVERT: g 234 ARG cc_start: 0.8093 (ttp80) cc_final: 0.7340 (tmm-80) REVERT: h 48 LEU cc_start: 0.9034 (tp) cc_final: 0.8730 (tp) REVERT: h 227 LYS cc_start: 0.8160 (mmtt) cc_final: 0.7067 (mmmt) REVERT: h 371 ARG cc_start: 0.8625 (mtp85) cc_final: 0.8199 (mtp85) REVERT: l 177 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.8297 (mtt90) REVERT: l 287 MET cc_start: 0.8917 (tpt) cc_final: 0.8604 (tpt) REVERT: k 48 LEU cc_start: 0.9027 (tp) cc_final: 0.8700 (tp) REVERT: k 177 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.8049 (mtt90) REVERT: k 257 THR cc_start: 0.9197 (OUTLIER) cc_final: 0.8872 (p) REVERT: j 127 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.9036 (mt) REVERT: j 234 ARG cc_start: 0.8070 (ttp80) cc_final: 0.7315 (tmm-80) REVERT: j 287 MET cc_start: 0.8869 (tpt) cc_final: 0.8466 (tpt) REVERT: i 177 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.8274 (mtt90) REVERT: i 287 MET cc_start: 0.8928 (tpt) cc_final: 0.8588 (tpt) REVERT: m 14 ILE cc_start: 0.8555 (pt) cc_final: 0.8298 (pt) REVERT: m 96 SER cc_start: 0.8867 (m) cc_final: 0.8480 (p) REVERT: m 127 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9089 (mt) REVERT: m 282 THR cc_start: 0.9165 (OUTLIER) cc_final: 0.8724 (p) REVERT: m 327 ASN cc_start: 0.8433 (p0) cc_final: 0.8210 (m110) REVERT: m 383 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8043 (mp) REVERT: n 96 SER cc_start: 0.8808 (m) cc_final: 0.8256 (p) REVERT: n 151 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7553 (mtt90) REVERT: n 260 ARG cc_start: 0.7437 (mtp85) cc_final: 0.6888 (mtp85) REVERT: n 289 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8949 (mm) REVERT: r 96 SER cc_start: 0.8343 (m) cc_final: 0.7620 (p) REVERT: q 96 SER cc_start: 0.8247 (m) cc_final: 0.7591 (p) REVERT: q 260 ARG cc_start: 0.7452 (mtp85) cc_final: 0.6894 (mtp85) REVERT: q 282 THR cc_start: 0.9204 (OUTLIER) cc_final: 0.8734 (p) REVERT: p 75 ARG cc_start: 0.9097 (OUTLIER) cc_final: 0.8691 (tpt90) REVERT: p 96 SER cc_start: 0.8891 (m) cc_final: 0.8525 (p) REVERT: p 127 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.9095 (mt) REVERT: p 180 MET cc_start: 0.8722 (ttm) cc_final: 0.8521 (ttt) REVERT: p 282 THR cc_start: 0.9159 (OUTLIER) cc_final: 0.8569 (p) REVERT: p 383 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8098 (mp) REVERT: o 75 ARG cc_start: 0.9091 (OUTLIER) cc_final: 0.8812 (tpt170) REVERT: o 96 SER cc_start: 0.8748 (m) cc_final: 0.8112 (p) outliers start: 225 outliers final: 163 residues processed: 999 average time/residue: 0.5871 time to fit residues: 980.1887 Evaluate side-chains 999 residues out of total 6144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 807 time to evaluate : 4.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain a residue 61 ILE Chi-restraints excluded: chain a residue 133 HIS Chi-restraints excluded: chain a residue 257 THR Chi-restraints excluded: chain a residue 282 THR Chi-restraints excluded: chain a residue 335 GLU Chi-restraints excluded: chain a residue 367 ASN Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain b residue 34 THR Chi-restraints excluded: chain b residue 133 HIS Chi-restraints excluded: chain b residue 146 LEU Chi-restraints excluded: chain b residue 207 LEU Chi-restraints excluded: chain b residue 257 THR Chi-restraints excluded: chain b residue 259 ILE Chi-restraints excluded: chain b residue 335 GLU Chi-restraints excluded: chain b residue 367 ASN Chi-restraints excluded: chain b residue 372 VAL Chi-restraints excluded: chain c residue 10 THR Chi-restraints excluded: chain c residue 34 THR Chi-restraints excluded: chain c residue 133 HIS Chi-restraints excluded: chain c residue 257 THR Chi-restraints excluded: chain c residue 259 ILE Chi-restraints excluded: chain c residue 289 LEU Chi-restraints excluded: chain c residue 298 HIS Chi-restraints excluded: chain c residue 335 GLU Chi-restraints excluded: chain c residue 367 ASN Chi-restraints excluded: chain c residue 372 VAL Chi-restraints excluded: chain d residue 61 ILE Chi-restraints excluded: chain d residue 133 HIS Chi-restraints excluded: chain d residue 236 VAL Chi-restraints excluded: chain d residue 282 THR Chi-restraints excluded: chain d residue 335 GLU Chi-restraints excluded: chain d residue 362 VAL Chi-restraints excluded: chain d residue 367 ASN Chi-restraints excluded: chain d residue 369 ASN Chi-restraints excluded: chain d residue 372 VAL Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 133 HIS Chi-restraints excluded: chain e residue 161 SER Chi-restraints excluded: chain e residue 257 THR Chi-restraints excluded: chain e residue 289 LEU Chi-restraints excluded: chain e residue 335 GLU Chi-restraints excluded: chain e residue 367 ASN Chi-restraints excluded: chain e residue 372 VAL Chi-restraints excluded: chain f residue 10 THR Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 133 HIS Chi-restraints excluded: chain f residue 156 LEU Chi-restraints excluded: chain f residue 164 GLU Chi-restraints excluded: chain f residue 236 VAL Chi-restraints excluded: chain f residue 257 THR Chi-restraints excluded: chain f residue 289 LEU Chi-restraints excluded: chain f residue 367 ASN Chi-restraints excluded: chain f residue 372 VAL Chi-restraints excluded: chain g residue 64 SER Chi-restraints excluded: chain g residue 116 ASP Chi-restraints excluded: chain g residue 181 VAL Chi-restraints excluded: chain g residue 236 VAL Chi-restraints excluded: chain g residue 275 ASP Chi-restraints excluded: chain g residue 282 THR Chi-restraints excluded: chain g residue 309 THR Chi-restraints excluded: chain g residue 325 LEU Chi-restraints excluded: chain g residue 344 SER Chi-restraints excluded: chain g residue 353 VAL Chi-restraints excluded: chain g residue 383 LEU Chi-restraints excluded: chain h residue 127 LEU Chi-restraints excluded: chain h residue 181 VAL Chi-restraints excluded: chain h residue 236 VAL Chi-restraints excluded: chain h residue 325 LEU Chi-restraints excluded: chain h residue 353 VAL Chi-restraints excluded: chain h residue 362 VAL Chi-restraints excluded: chain l residue 64 SER Chi-restraints excluded: chain l residue 177 ARG Chi-restraints excluded: chain l residue 181 VAL Chi-restraints excluded: chain l residue 243 GLU Chi-restraints excluded: chain l residue 275 ASP Chi-restraints excluded: chain l residue 302 VAL Chi-restraints excluded: chain l residue 307 THR Chi-restraints excluded: chain l residue 325 LEU Chi-restraints excluded: chain l residue 344 SER Chi-restraints excluded: chain l residue 353 VAL Chi-restraints excluded: chain l residue 362 VAL Chi-restraints excluded: chain l residue 376 ASP Chi-restraints excluded: chain k residue 64 SER Chi-restraints excluded: chain k residue 177 ARG Chi-restraints excluded: chain k residue 181 VAL Chi-restraints excluded: chain k residue 257 THR Chi-restraints excluded: chain k residue 307 THR Chi-restraints excluded: chain k residue 309 THR Chi-restraints excluded: chain k residue 325 LEU Chi-restraints excluded: chain k residue 353 VAL Chi-restraints excluded: chain k residue 362 VAL Chi-restraints excluded: chain k residue 376 ASP Chi-restraints excluded: chain j residue 64 SER Chi-restraints excluded: chain j residue 116 ASP Chi-restraints excluded: chain j residue 127 LEU Chi-restraints excluded: chain j residue 181 VAL Chi-restraints excluded: chain j residue 236 VAL Chi-restraints excluded: chain j residue 252 ASN Chi-restraints excluded: chain j residue 282 THR Chi-restraints excluded: chain j residue 309 THR Chi-restraints excluded: chain j residue 325 LEU Chi-restraints excluded: chain j residue 344 SER Chi-restraints excluded: chain j residue 353 VAL Chi-restraints excluded: chain i residue 10 THR Chi-restraints excluded: chain i residue 64 SER Chi-restraints excluded: chain i residue 177 ARG Chi-restraints excluded: chain i residue 181 VAL Chi-restraints excluded: chain i residue 275 ASP Chi-restraints excluded: chain i residue 325 LEU Chi-restraints excluded: chain i residue 353 VAL Chi-restraints excluded: chain i residue 362 VAL Chi-restraints excluded: chain i residue 374 VAL Chi-restraints excluded: chain i residue 376 ASP Chi-restraints excluded: chain m residue 10 THR Chi-restraints excluded: chain m residue 18 THR Chi-restraints excluded: chain m residue 25 SER Chi-restraints excluded: chain m residue 127 LEU Chi-restraints excluded: chain m residue 148 GLU Chi-restraints excluded: chain m residue 222 SER Chi-restraints excluded: chain m residue 229 VAL Chi-restraints excluded: chain m residue 230 THR Chi-restraints excluded: chain m residue 244 THR Chi-restraints excluded: chain m residue 282 THR Chi-restraints excluded: chain m residue 307 THR Chi-restraints excluded: chain m residue 325 LEU Chi-restraints excluded: chain m residue 344 SER Chi-restraints excluded: chain m residue 380 THR Chi-restraints excluded: chain m residue 382 VAL Chi-restraints excluded: chain m residue 383 LEU Chi-restraints excluded: chain n residue 10 THR Chi-restraints excluded: chain n residue 54 ASP Chi-restraints excluded: chain n residue 143 MET Chi-restraints excluded: chain n residue 151 ARG Chi-restraints excluded: chain n residue 222 SER Chi-restraints excluded: chain n residue 233 SER Chi-restraints excluded: chain n residue 282 THR Chi-restraints excluded: chain n residue 289 LEU Chi-restraints excluded: chain n residue 307 THR Chi-restraints excluded: chain n residue 344 SER Chi-restraints excluded: chain n residue 379 LEU Chi-restraints excluded: chain r residue 70 GLU Chi-restraints excluded: chain r residue 148 GLU Chi-restraints excluded: chain r residue 162 THR Chi-restraints excluded: chain r residue 230 THR Chi-restraints excluded: chain r residue 243 GLU Chi-restraints excluded: chain r residue 282 THR Chi-restraints excluded: chain r residue 291 MET Chi-restraints excluded: chain r residue 307 THR Chi-restraints excluded: chain r residue 344 SER Chi-restraints excluded: chain q residue 10 THR Chi-restraints excluded: chain q residue 54 ASP Chi-restraints excluded: chain q residue 162 THR Chi-restraints excluded: chain q residue 233 SER Chi-restraints excluded: chain q residue 282 THR Chi-restraints excluded: chain q residue 307 THR Chi-restraints excluded: chain q residue 344 SER Chi-restraints excluded: chain q residue 379 LEU Chi-restraints excluded: chain q residue 380 THR Chi-restraints excluded: chain p residue 10 THR Chi-restraints excluded: chain p residue 18 THR Chi-restraints excluded: chain p residue 25 SER Chi-restraints excluded: chain p residue 75 ARG Chi-restraints excluded: chain p residue 127 LEU Chi-restraints excluded: chain p residue 229 VAL Chi-restraints excluded: chain p residue 230 THR Chi-restraints excluded: chain p residue 244 THR Chi-restraints excluded: chain p residue 282 THR Chi-restraints excluded: chain p residue 344 SER Chi-restraints excluded: chain p residue 376 ASP Chi-restraints excluded: chain p residue 382 VAL Chi-restraints excluded: chain p residue 383 LEU Chi-restraints excluded: chain o residue 10 THR Chi-restraints excluded: chain o residue 34 THR Chi-restraints excluded: chain o residue 75 ARG Chi-restraints excluded: chain o residue 282 THR Chi-restraints excluded: chain o residue 291 MET Chi-restraints excluded: chain o residue 307 THR Chi-restraints excluded: chain o residue 344 SER Chi-restraints excluded: chain o residue 376 ASP Chi-restraints excluded: chain o residue 383 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 460 optimal weight: 1.9990 chunk 740 optimal weight: 3.9990 chunk 452 optimal weight: 6.9990 chunk 351 optimal weight: 7.9990 chunk 514 optimal weight: 9.9990 chunk 777 optimal weight: 2.9990 chunk 715 optimal weight: 1.9990 chunk 618 optimal weight: 0.9990 chunk 64 optimal weight: 8.9990 chunk 477 optimal weight: 10.0000 chunk 379 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 67 GLN ** c 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 74 ASN ** f 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 74 ASN m 197 ASN m 343 ASN ** n 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 77 GLN r 327 ASN q 172 ASN p 197 ASN ** o 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 60864 Z= 0.205 Angle : 0.525 11.512 82998 Z= 0.276 Chirality : 0.044 0.167 9444 Planarity : 0.004 0.082 10908 Dihedral : 5.148 58.202 8499 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 3.42 % Allowed : 19.25 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.10), residues: 7830 helix: 0.05 (0.10), residues: 2736 sheet: -2.33 (0.15), residues: 1044 loop : -1.35 (0.10), residues: 4050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP p 210 HIS 0.003 0.001 HIS a 133 PHE 0.024 0.001 PHE i 238 TYR 0.025 0.002 TYR B 12 ARG 0.016 0.000 ARG F 107 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15660 Ramachandran restraints generated. 7830 Oldfield, 0 Emsley, 7830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15660 Ramachandran restraints generated. 7830 Oldfield, 0 Emsley, 7830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1026 residues out of total 6144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 816 time to evaluate : 5.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 ASP cc_start: -0.1859 (OUTLIER) cc_final: -0.2422 (t70) REVERT: a 61 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.8107 (mp) REVERT: a 225 GLU cc_start: 0.8111 (tp30) cc_final: 0.7599 (tp30) REVERT: B 135 ASP cc_start: -0.1810 (OUTLIER) cc_final: -0.2335 (t70) REVERT: D 135 ASP cc_start: -0.1577 (OUTLIER) cc_final: -0.2151 (t70) REVERT: D 149 MET cc_start: 0.8673 (mmm) cc_final: 0.8458 (mmm) REVERT: E 135 ASP cc_start: -0.2171 (OUTLIER) cc_final: -0.2679 (t70) REVERT: F 149 MET cc_start: 0.8505 (mmm) cc_final: 0.8135 (mmm) REVERT: b 180 MET cc_start: 0.8555 (tpp) cc_final: 0.7934 (ttt) REVERT: b 246 ARG cc_start: 0.7227 (ptm160) cc_final: 0.6748 (mtp180) REVERT: b 282 THR cc_start: 0.9098 (m) cc_final: 0.8872 (p) REVERT: b 312 LYS cc_start: 0.8316 (tptp) cc_final: 0.7550 (mttp) REVERT: b 367 ASN cc_start: 0.8753 (OUTLIER) cc_final: 0.8481 (t0) REVERT: c 133 HIS cc_start: 0.7462 (OUTLIER) cc_final: 0.6798 (m-70) REVERT: c 259 ILE cc_start: 0.7526 (OUTLIER) cc_final: 0.7294 (pp) REVERT: c 367 ASN cc_start: 0.8719 (OUTLIER) cc_final: 0.8301 (t0) REVERT: d 61 ILE cc_start: 0.8357 (OUTLIER) cc_final: 0.8093 (mp) REVERT: d 180 MET cc_start: 0.8541 (tpp) cc_final: 0.8307 (ttm) REVERT: d 246 ARG cc_start: 0.7518 (ptm160) cc_final: 0.7277 (ptm160) REVERT: d 259 ILE cc_start: 0.7769 (OUTLIER) cc_final: 0.7464 (pp) REVERT: d 312 LYS cc_start: 0.8364 (tptp) cc_final: 0.7539 (mttp) REVERT: e 180 MET cc_start: 0.8550 (tpp) cc_final: 0.7939 (ttt) REVERT: e 282 THR cc_start: 0.9112 (m) cc_final: 0.8897 (p) REVERT: e 312 LYS cc_start: 0.8337 (tptt) cc_final: 0.7562 (mttp) REVERT: e 367 ASN cc_start: 0.8745 (OUTLIER) cc_final: 0.8491 (t0) REVERT: f 133 HIS cc_start: 0.7494 (OUTLIER) cc_final: 0.6816 (m-70) REVERT: f 215 TYR cc_start: 0.8481 (m-10) cc_final: 0.8249 (m-80) REVERT: f 246 ARG cc_start: 0.7398 (ptm160) cc_final: 0.7111 (ptm160) REVERT: f 367 ASN cc_start: 0.8728 (OUTLIER) cc_final: 0.8304 (t0) REVERT: g 234 ARG cc_start: 0.8085 (ttp80) cc_final: 0.7333 (tmm-80) REVERT: h 48 LEU cc_start: 0.9070 (tp) cc_final: 0.8741 (tp) REVERT: h 371 ARG cc_start: 0.8658 (mtp85) cc_final: 0.8358 (mtp85) REVERT: l 177 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.8252 (mtt90) REVERT: l 287 MET cc_start: 0.8935 (tpt) cc_final: 0.8543 (tpt) REVERT: k 48 LEU cc_start: 0.9059 (tp) cc_final: 0.8741 (tp) REVERT: k 177 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.8055 (mtt90) REVERT: k 257 THR cc_start: 0.9198 (OUTLIER) cc_final: 0.8883 (p) REVERT: j 127 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.9032 (mt) REVERT: j 234 ARG cc_start: 0.8064 (ttp80) cc_final: 0.7309 (tmm-80) REVERT: j 287 MET cc_start: 0.8863 (tpt) cc_final: 0.8622 (tpt) REVERT: i 177 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.8247 (mtt90) REVERT: i 287 MET cc_start: 0.8929 (tpt) cc_final: 0.8581 (tpt) REVERT: m 14 ILE cc_start: 0.8500 (pt) cc_final: 0.8296 (pt) REVERT: m 96 SER cc_start: 0.8895 (m) cc_final: 0.8601 (p) REVERT: m 127 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.9089 (mt) REVERT: m 282 THR cc_start: 0.9197 (OUTLIER) cc_final: 0.8752 (p) REVERT: m 327 ASN cc_start: 0.8480 (p0) cc_final: 0.8228 (m110) REVERT: m 383 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8042 (mp) REVERT: n 96 SER cc_start: 0.8862 (m) cc_final: 0.8302 (p) REVERT: n 151 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7556 (mtt90) REVERT: n 260 ARG cc_start: 0.7490 (mtp85) cc_final: 0.6904 (mtp85) REVERT: n 289 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8979 (mm) REVERT: r 96 SER cc_start: 0.8509 (m) cc_final: 0.7819 (p) REVERT: q 96 SER cc_start: 0.8614 (m) cc_final: 0.7840 (p) REVERT: q 151 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7570 (mtt90) REVERT: q 260 ARG cc_start: 0.7508 (mtp85) cc_final: 0.6916 (mtp85) REVERT: q 282 THR cc_start: 0.9222 (OUTLIER) cc_final: 0.8727 (p) REVERT: p 75 ARG cc_start: 0.9130 (OUTLIER) cc_final: 0.8768 (tpt90) REVERT: p 96 SER cc_start: 0.8918 (m) cc_final: 0.8582 (p) REVERT: p 127 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.9077 (mt) REVERT: p 260 ARG cc_start: 0.7475 (mtp85) cc_final: 0.6963 (mtp85) REVERT: p 282 THR cc_start: 0.9172 (OUTLIER) cc_final: 0.8587 (p) REVERT: p 383 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8088 (mp) REVERT: o 75 ARG cc_start: 0.9105 (OUTLIER) cc_final: 0.8849 (tpt170) REVERT: o 96 SER cc_start: 0.8803 (m) cc_final: 0.8278 (p) outliers start: 210 outliers final: 165 residues processed: 960 average time/residue: 0.5585 time to fit residues: 901.1917 Evaluate side-chains 991 residues out of total 6144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 795 time to evaluate : 4.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain a residue 61 ILE Chi-restraints excluded: chain a residue 133 HIS Chi-restraints excluded: chain a residue 257 THR Chi-restraints excluded: chain a residue 282 THR Chi-restraints excluded: chain a residue 335 GLU Chi-restraints excluded: chain a residue 367 ASN Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 135 ASP Chi-restraints excluded: chain E residue 71 MET Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain b residue 34 THR Chi-restraints excluded: chain b residue 133 HIS Chi-restraints excluded: chain b residue 146 LEU Chi-restraints excluded: chain b residue 161 SER Chi-restraints excluded: chain b residue 207 LEU Chi-restraints excluded: chain b residue 257 THR Chi-restraints excluded: chain b residue 258 ILE Chi-restraints excluded: chain b residue 289 LEU Chi-restraints excluded: chain b residue 335 GLU Chi-restraints excluded: chain b residue 367 ASN Chi-restraints excluded: chain b residue 372 VAL Chi-restraints excluded: chain c residue 10 THR Chi-restraints excluded: chain c residue 34 THR Chi-restraints excluded: chain c residue 133 HIS Chi-restraints excluded: chain c residue 257 THR Chi-restraints excluded: chain c residue 259 ILE Chi-restraints excluded: chain c residue 289 LEU Chi-restraints excluded: chain c residue 298 HIS Chi-restraints excluded: chain c residue 335 GLU Chi-restraints excluded: chain c residue 367 ASN Chi-restraints excluded: chain c residue 372 VAL Chi-restraints excluded: chain d residue 61 ILE Chi-restraints excluded: chain d residue 133 HIS Chi-restraints excluded: chain d residue 236 VAL Chi-restraints excluded: chain d residue 259 ILE Chi-restraints excluded: chain d residue 282 THR Chi-restraints excluded: chain d residue 335 GLU Chi-restraints excluded: chain d residue 362 VAL Chi-restraints excluded: chain d residue 367 ASN Chi-restraints excluded: chain d residue 369 ASN Chi-restraints excluded: chain d residue 372 VAL Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 133 HIS Chi-restraints excluded: chain e residue 161 SER Chi-restraints excluded: chain e residue 257 THR Chi-restraints excluded: chain e residue 289 LEU Chi-restraints excluded: chain e residue 335 GLU Chi-restraints excluded: chain e residue 367 ASN Chi-restraints excluded: chain e residue 372 VAL Chi-restraints excluded: chain f residue 10 THR Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 133 HIS Chi-restraints excluded: chain f residue 156 LEU Chi-restraints excluded: chain f residue 164 GLU Chi-restraints excluded: chain f residue 236 VAL Chi-restraints excluded: chain f residue 257 THR Chi-restraints excluded: chain f residue 289 LEU Chi-restraints excluded: chain f residue 367 ASN Chi-restraints excluded: chain f residue 372 VAL Chi-restraints excluded: chain g residue 64 SER Chi-restraints excluded: chain g residue 116 ASP Chi-restraints excluded: chain g residue 181 VAL Chi-restraints excluded: chain g residue 236 VAL Chi-restraints excluded: chain g residue 275 ASP Chi-restraints excluded: chain g residue 282 THR Chi-restraints excluded: chain g residue 309 THR Chi-restraints excluded: chain g residue 325 LEU Chi-restraints excluded: chain g residue 344 SER Chi-restraints excluded: chain g residue 353 VAL Chi-restraints excluded: chain h residue 127 LEU Chi-restraints excluded: chain h residue 181 VAL Chi-restraints excluded: chain h residue 236 VAL Chi-restraints excluded: chain h residue 282 THR Chi-restraints excluded: chain h residue 325 LEU Chi-restraints excluded: chain h residue 353 VAL Chi-restraints excluded: chain h residue 362 VAL Chi-restraints excluded: chain l residue 64 SER Chi-restraints excluded: chain l residue 177 ARG Chi-restraints excluded: chain l residue 181 VAL Chi-restraints excluded: chain l residue 243 GLU Chi-restraints excluded: chain l residue 275 ASP Chi-restraints excluded: chain l residue 302 VAL Chi-restraints excluded: chain l residue 325 LEU Chi-restraints excluded: chain l residue 344 SER Chi-restraints excluded: chain l residue 353 VAL Chi-restraints excluded: chain l residue 362 VAL Chi-restraints excluded: chain l residue 376 ASP Chi-restraints excluded: chain k residue 64 SER Chi-restraints excluded: chain k residue 177 ARG Chi-restraints excluded: chain k residue 181 VAL Chi-restraints excluded: chain k residue 257 THR Chi-restraints excluded: chain k residue 282 THR Chi-restraints excluded: chain k residue 307 THR Chi-restraints excluded: chain k residue 309 THR Chi-restraints excluded: chain k residue 325 LEU Chi-restraints excluded: chain k residue 353 VAL Chi-restraints excluded: chain k residue 362 VAL Chi-restraints excluded: chain k residue 376 ASP Chi-restraints excluded: chain j residue 64 SER Chi-restraints excluded: chain j residue 116 ASP Chi-restraints excluded: chain j residue 127 LEU Chi-restraints excluded: chain j residue 181 VAL Chi-restraints excluded: chain j residue 236 VAL Chi-restraints excluded: chain j residue 252 ASN Chi-restraints excluded: chain j residue 282 THR Chi-restraints excluded: chain j residue 309 THR Chi-restraints excluded: chain j residue 325 LEU Chi-restraints excluded: chain j residue 344 SER Chi-restraints excluded: chain j residue 353 VAL Chi-restraints excluded: chain i residue 10 THR Chi-restraints excluded: chain i residue 64 SER Chi-restraints excluded: chain i residue 177 ARG Chi-restraints excluded: chain i residue 181 VAL Chi-restraints excluded: chain i residue 275 ASP Chi-restraints excluded: chain i residue 325 LEU Chi-restraints excluded: chain i residue 353 VAL Chi-restraints excluded: chain i residue 362 VAL Chi-restraints excluded: chain i residue 374 VAL Chi-restraints excluded: chain i residue 376 ASP Chi-restraints excluded: chain m residue 10 THR Chi-restraints excluded: chain m residue 18 THR Chi-restraints excluded: chain m residue 25 SER Chi-restraints excluded: chain m residue 34 THR Chi-restraints excluded: chain m residue 127 LEU Chi-restraints excluded: chain m residue 222 SER Chi-restraints excluded: chain m residue 229 VAL Chi-restraints excluded: chain m residue 230 THR Chi-restraints excluded: chain m residue 244 THR Chi-restraints excluded: chain m residue 282 THR Chi-restraints excluded: chain m residue 307 THR Chi-restraints excluded: chain m residue 325 LEU Chi-restraints excluded: chain m residue 344 SER Chi-restraints excluded: chain m residue 380 THR Chi-restraints excluded: chain m residue 382 VAL Chi-restraints excluded: chain m residue 383 LEU Chi-restraints excluded: chain n residue 10 THR Chi-restraints excluded: chain n residue 25 SER Chi-restraints excluded: chain n residue 54 ASP Chi-restraints excluded: chain n residue 151 ARG Chi-restraints excluded: chain n residue 222 SER Chi-restraints excluded: chain n residue 233 SER Chi-restraints excluded: chain n residue 282 THR Chi-restraints excluded: chain n residue 289 LEU Chi-restraints excluded: chain n residue 307 THR Chi-restraints excluded: chain n residue 344 SER Chi-restraints excluded: chain n residue 379 LEU Chi-restraints excluded: chain r residue 34 THR Chi-restraints excluded: chain r residue 70 GLU Chi-restraints excluded: chain r residue 148 GLU Chi-restraints excluded: chain r residue 162 THR Chi-restraints excluded: chain r residue 243 GLU Chi-restraints excluded: chain r residue 282 THR Chi-restraints excluded: chain r residue 291 MET Chi-restraints excluded: chain r residue 307 THR Chi-restraints excluded: chain r residue 344 SER Chi-restraints excluded: chain q residue 10 THR Chi-restraints excluded: chain q residue 54 ASP Chi-restraints excluded: chain q residue 151 ARG Chi-restraints excluded: chain q residue 162 THR Chi-restraints excluded: chain q residue 233 SER Chi-restraints excluded: chain q residue 282 THR Chi-restraints excluded: chain q residue 307 THR Chi-restraints excluded: chain q residue 344 SER Chi-restraints excluded: chain q residue 379 LEU Chi-restraints excluded: chain q residue 380 THR Chi-restraints excluded: chain p residue 10 THR Chi-restraints excluded: chain p residue 18 THR Chi-restraints excluded: chain p residue 25 SER Chi-restraints excluded: chain p residue 75 ARG Chi-restraints excluded: chain p residue 127 LEU Chi-restraints excluded: chain p residue 229 VAL Chi-restraints excluded: chain p residue 230 THR Chi-restraints excluded: chain p residue 244 THR Chi-restraints excluded: chain p residue 282 THR Chi-restraints excluded: chain p residue 344 SER Chi-restraints excluded: chain p residue 382 VAL Chi-restraints excluded: chain p residue 383 LEU Chi-restraints excluded: chain o residue 10 THR Chi-restraints excluded: chain o residue 34 THR Chi-restraints excluded: chain o residue 75 ARG Chi-restraints excluded: chain o residue 282 THR Chi-restraints excluded: chain o residue 291 MET Chi-restraints excluded: chain o residue 307 THR Chi-restraints excluded: chain o residue 344 SER Chi-restraints excluded: chain o residue 383 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 491 optimal weight: 3.9990 chunk 659 optimal weight: 1.9990 chunk 189 optimal weight: 10.0000 chunk 570 optimal weight: 0.0770 chunk 91 optimal weight: 9.9990 chunk 171 optimal weight: 3.9990 chunk 619 optimal weight: 7.9990 chunk 259 optimal weight: 4.9990 chunk 636 optimal weight: 8.9990 chunk 78 optimal weight: 0.0270 chunk 114 optimal weight: 8.9990 overall best weight: 2.0202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 298 HIS ** c 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 74 ASN ** f 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 74 ASN h 124 GLN m 197 ASN m 343 ASN ** n 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 172 ASN p 197 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.142666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.115519 restraints weight = 77322.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.113519 restraints weight = 82005.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.114762 restraints weight = 70338.230| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 60864 Z= 0.185 Angle : 0.516 11.604 82998 Z= 0.271 Chirality : 0.043 0.164 9444 Planarity : 0.004 0.082 10908 Dihedral : 5.101 57.382 8499 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 3.56 % Allowed : 19.30 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.10), residues: 7830 helix: 0.17 (0.10), residues: 2736 sheet: -2.32 (0.15), residues: 1044 loop : -1.32 (0.10), residues: 4050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP b 267 HIS 0.002 0.001 HIS a 133 PHE 0.026 0.001 PHE i 238 TYR 0.024 0.001 TYR B 12 ARG 0.007 0.000 ARG m 304 =============================================================================== Job complete usr+sys time: 15555.52 seconds wall clock time: 272 minutes 13.71 seconds (16333.71 seconds total)