Starting phenix.real_space_refine on Wed Mar 20 07:10:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i00_0320/03_2024/6i00_0320.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i00_0320/03_2024/6i00_0320.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i00_0320/03_2024/6i00_0320.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i00_0320/03_2024/6i00_0320.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i00_0320/03_2024/6i00_0320.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i00_0320/03_2024/6i00_0320.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 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 156 5.16 5 C 17100 2.51 5 N 4572 2.21 5 O 4884 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "J ARG 225": "NH1" <-> "NH2" Residue "J ARG 297": "NH1" <-> "NH2" Residue "I ARG 225": "NH1" <-> "NH2" Residue "I ARG 297": "NH1" <-> "NH2" Residue "H ARG 225": "NH1" <-> "NH2" Residue "H ARG 297": "NH1" <-> "NH2" Residue "G PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 225": "NH1" <-> "NH2" Residue "G ARG 297": "NH1" <-> "NH2" Residue "F ARG 225": "NH1" <-> "NH2" Residue "F ARG 297": "NH1" <-> "NH2" Residue "E ARG 225": "NH1" <-> "NH2" Residue "E ARG 297": "NH1" <-> "NH2" Residue "D ARG 225": "NH1" <-> "NH2" Residue "D ARG 297": "NH1" <-> "NH2" Residue "C ARG 225": "NH1" <-> "NH2" Residue "C ARG 297": "NH1" <-> "NH2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B ARG 297": "NH1" <-> "NH2" Residue "A ARG 225": "NH1" <-> "NH2" Residue "A ARG 297": "NH1" <-> "NH2" Residue "L ARG 225": "NH1" <-> "NH2" Residue "L ARG 297": "NH1" <-> "NH2" Residue "K ARG 225": "NH1" <-> "NH2" Residue "K ARG 297": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 26712 Number of models: 1 Model: "" Number of chains: 12 Chain: "J" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2226 Classifications: {'peptide': 289} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 274} Chain breaks: 1 Chain: "I" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2226 Classifications: {'peptide': 289} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 273} Chain breaks: 1 Chain: "H" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2226 Classifications: {'peptide': 289} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 274} Chain breaks: 1 Chain: "G" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2226 Classifications: {'peptide': 289} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 273} Chain breaks: 1 Chain: "F" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2226 Classifications: {'peptide': 289} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 274} Chain breaks: 1 Chain: "E" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2226 Classifications: {'peptide': 289} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 273} Chain breaks: 1 Chain: "D" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2226 Classifications: {'peptide': 289} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 274} Chain breaks: 1 Chain: "C" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2226 Classifications: {'peptide': 289} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 273} Chain breaks: 1 Chain: "B" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2226 Classifications: {'peptide': 289} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 274} Chain breaks: 1 Chain: "A" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2226 Classifications: {'peptide': 289} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 273} Chain breaks: 1 Chain: "L" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2226 Classifications: {'peptide': 289} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 274} Chain breaks: 1 Chain: "K" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2226 Classifications: {'peptide': 289} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 273} Chain breaks: 1 Residues with excluded nonbonded symmetry interactions: 1020 residue: pdb=" N ARG J 37 " occ=0.97 ... (9 atoms not shown) pdb=" NH2 ARG J 37 " occ=0.93 residue: pdb=" N ALA J 38 " occ=0.97 ... (3 atoms not shown) pdb=" CB ALA J 38 " occ=0.97 residue: pdb=" N VAL J 41 " occ=0.97 ... (5 atoms not shown) pdb=" CG2 VAL J 41 " occ=0.93 residue: pdb=" N GLN J 42 " occ=0.97 ... (7 atoms not shown) pdb=" NE2 GLN J 42 " occ=0.95 residue: pdb=" N ALA J 43 " occ=0.97 ... (3 atoms not shown) pdb=" CB ALA J 43 " occ=0.97 residue: pdb=" N VAL J 46 " occ=0.97 ... (5 atoms not shown) pdb=" CG2 VAL J 46 " occ=0.94 residue: pdb=" N ALA J 52 " occ=0.96 ... (3 atoms not shown) pdb=" CB ALA J 52 " occ=0.93 residue: pdb=" N LYS J 56 " occ=0.97 ... (7 atoms not shown) pdb=" NZ LYS J 56 " occ=0.94 residue: pdb=" N ALA J 57 " occ=0.97 ... (3 atoms not shown) pdb=" CB ALA J 57 " occ=0.97 residue: pdb=" N LEU J 60 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU J 60 " occ=0.80 residue: pdb=" N GLU J 63 " occ=0.97 ... (7 atoms not shown) pdb=" OE2 GLU J 63 " occ=0.80 residue: pdb=" N ALA J 64 " occ=0.97 ... (3 atoms not shown) pdb=" CB ALA J 64 " occ=0.97 ... (remaining 1008 not shown) Time building chain proxies: 13.91, per 1000 atoms: 0.52 Number of scatterers: 26712 At special positions: 0 Unit cell: (137.7, 137.7, 182.75, 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 156 16.00 O 4884 8.00 N 4572 7.00 C 17100 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: 8.68 Conformation dependent library (CDL) restraints added in 5.1 seconds 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6312 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 32 sheets defined 22.5% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.97 Creating SS restraints... Processing helix chain 'J' and resid 55 through 66 removed outlier: 3.772A pdb=" N GLU J 66 " --> pdb=" O SER J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 108 removed outlier: 4.163A pdb=" N ARG J 100 " --> pdb=" O THR J 96 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP J 101 " --> pdb=" O ALA J 97 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ASP J 102 " --> pdb=" O LYS J 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 118 through 127 removed outlier: 3.573A pdb=" N LYS J 127 " --> pdb=" O LEU J 123 " (cutoff:3.500A) Processing helix chain 'J' and resid 202 through 210 removed outlier: 3.631A pdb=" N ARG J 206 " --> pdb=" O MET J 202 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR J 207 " --> pdb=" O PRO J 203 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA J 208 " --> pdb=" O SER J 204 " (cutoff:3.500A) Processing helix chain 'J' and resid 211 through 213 No H-bonds generated for 'chain 'J' and resid 211 through 213' Processing helix chain 'J' and resid 225 through 239 removed outlier: 4.196A pdb=" N LEU J 229 " --> pdb=" O ARG J 225 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA J 230 " --> pdb=" O GLU J 226 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR J 233 " --> pdb=" O LEU J 229 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N HIS J 234 " --> pdb=" O ALA J 230 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE J 235 " --> pdb=" O SER J 231 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 60 Processing helix chain 'I' and resid 60 through 66 Processing helix chain 'I' and resid 96 through 108 removed outlier: 4.150A pdb=" N ARG I 100 " --> pdb=" O THR I 96 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASP I 101 " --> pdb=" O ALA I 97 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ASP I 102 " --> pdb=" O LYS I 98 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR I 106 " --> pdb=" O ASP I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 118 through 127 removed outlier: 3.799A pdb=" N LYS I 127 " --> pdb=" O LEU I 123 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 210 Processing helix chain 'I' and resid 211 through 213 No H-bonds generated for 'chain 'I' and resid 211 through 213' Processing helix chain 'I' and resid 226 through 239 removed outlier: 4.298A pdb=" N ALA I 230 " --> pdb=" O GLU I 226 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N HIS I 234 " --> pdb=" O ALA I 230 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE I 235 " --> pdb=" O SER I 231 " (cutoff:3.500A) Processing helix chain 'I' and resid 313 through 317 removed outlier: 3.767A pdb=" N PHE I 316 " --> pdb=" O ARG I 313 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASP I 317 " --> pdb=" O ALA I 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 313 through 317' Processing helix chain 'H' and resid 55 through 66 removed outlier: 3.881A pdb=" N GLU H 66 " --> pdb=" O SER H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 108 removed outlier: 4.102A pdb=" N ARG H 100 " --> pdb=" O THR H 96 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASP H 101 " --> pdb=" O ALA H 97 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ASP H 102 " --> pdb=" O LYS H 98 " (cutoff:3.500A) Processing helix chain 'H' and resid 118 through 127 removed outlier: 3.551A pdb=" N LYS H 127 " --> pdb=" O LEU H 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 210 removed outlier: 3.615A pdb=" N ARG H 206 " --> pdb=" O MET H 202 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR H 207 " --> pdb=" O PRO H 203 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA H 208 " --> pdb=" O SER H 204 " (cutoff:3.500A) Processing helix chain 'H' and resid 211 through 213 No H-bonds generated for 'chain 'H' and resid 211 through 213' Processing helix chain 'H' and resid 225 through 239 removed outlier: 4.179A pdb=" N LEU H 229 " --> pdb=" O ARG H 225 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA H 230 " --> pdb=" O GLU H 226 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR H 233 " --> pdb=" O LEU H 229 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N HIS H 234 " --> pdb=" O ALA H 230 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE H 235 " --> pdb=" O SER H 231 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 60 Processing helix chain 'G' and resid 60 through 66 Processing helix chain 'G' and resid 96 through 108 removed outlier: 4.106A pdb=" N ARG G 100 " --> pdb=" O THR G 96 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP G 101 " --> pdb=" O ALA G 97 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ASP G 102 " --> pdb=" O LYS G 98 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR G 106 " --> pdb=" O ASP G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 127 removed outlier: 3.586A pdb=" N GLU G 119 " --> pdb=" O GLY G 115 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ARG G 120 " --> pdb=" O PRO G 116 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU G 121 " --> pdb=" O GLU G 117 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS G 127 " --> pdb=" O LEU G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 202 through 210 Processing helix chain 'G' and resid 211 through 213 No H-bonds generated for 'chain 'G' and resid 211 through 213' Processing helix chain 'G' and resid 226 through 239 removed outlier: 4.327A pdb=" N ALA G 230 " --> pdb=" O GLU G 226 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N HIS G 234 " --> pdb=" O ALA G 230 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE G 235 " --> pdb=" O SER G 231 " (cutoff:3.500A) Processing helix chain 'G' and resid 313 through 317 removed outlier: 3.772A pdb=" N PHE G 316 " --> pdb=" O ARG G 313 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASP G 317 " --> pdb=" O ALA G 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 313 through 317' Processing helix chain 'F' and resid 55 through 66 removed outlier: 3.740A pdb=" N GLU F 66 " --> pdb=" O SER F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 108 removed outlier: 4.128A pdb=" N ARG F 100 " --> pdb=" O THR F 96 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP F 101 " --> pdb=" O ALA F 97 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N ASP F 102 " --> pdb=" O LYS F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 127 removed outlier: 3.595A pdb=" N LYS F 127 " --> pdb=" O LEU F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 210 removed outlier: 3.627A pdb=" N ARG F 206 " --> pdb=" O MET F 202 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR F 207 " --> pdb=" O PRO F 203 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA F 208 " --> pdb=" O SER F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 213 No H-bonds generated for 'chain 'F' and resid 211 through 213' Processing helix chain 'F' and resid 225 through 239 removed outlier: 4.231A pdb=" N LEU F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA F 230 " --> pdb=" O GLU F 226 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR F 233 " --> pdb=" O LEU F 229 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N HIS F 234 " --> pdb=" O ALA F 230 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE F 235 " --> pdb=" O SER F 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 60 Processing helix chain 'E' and resid 60 through 66 Processing helix chain 'E' and resid 96 through 108 removed outlier: 4.130A pdb=" N ARG E 100 " --> pdb=" O THR E 96 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP E 101 " --> pdb=" O ALA E 97 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ASP E 102 " --> pdb=" O LYS E 98 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR E 106 " --> pdb=" O ASP E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 127 removed outlier: 3.930A pdb=" N LEU E 121 " --> pdb=" O GLU E 117 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS E 127 " --> pdb=" O LEU E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 210 Processing helix chain 'E' and resid 211 through 213 No H-bonds generated for 'chain 'E' and resid 211 through 213' Processing helix chain 'E' and resid 226 through 239 removed outlier: 4.281A pdb=" N ALA E 230 " --> pdb=" O GLU E 226 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N HIS E 234 " --> pdb=" O ALA E 230 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE E 235 " --> pdb=" O SER E 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 66 removed outlier: 3.804A pdb=" N GLU D 66 " --> pdb=" O SER D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 108 removed outlier: 4.055A pdb=" N ARG D 100 " --> pdb=" O THR D 96 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP D 101 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ASP D 102 " --> pdb=" O LYS D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 127 removed outlier: 3.593A pdb=" N LYS D 127 " --> pdb=" O LEU D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 210 removed outlier: 3.633A pdb=" N ARG D 206 " --> pdb=" O MET D 202 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA D 208 " --> pdb=" O SER D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 213 No H-bonds generated for 'chain 'D' and resid 211 through 213' Processing helix chain 'D' and resid 225 through 239 removed outlier: 4.312A pdb=" N LEU D 229 " --> pdb=" O ARG D 225 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA D 230 " --> pdb=" O GLU D 226 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR D 233 " --> pdb=" O LEU D 229 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N HIS D 234 " --> pdb=" O ALA D 230 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE D 235 " --> pdb=" O SER D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 311 removed outlier: 4.059A pdb=" N ILE D 311 " --> pdb=" O LEU D 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 60 Processing helix chain 'C' and resid 60 through 66 Processing helix chain 'C' and resid 96 through 108 removed outlier: 4.108A pdb=" N ARG C 100 " --> pdb=" O THR C 96 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASP C 101 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N ASP C 102 " --> pdb=" O LYS C 98 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR C 106 " --> pdb=" O ASP C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 127 removed outlier: 3.598A pdb=" N GLU C 119 " --> pdb=" O GLY C 115 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG C 120 " --> pdb=" O PRO C 116 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU C 121 " --> pdb=" O GLU C 117 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS C 127 " --> pdb=" O LEU C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 173 Processing helix chain 'C' and resid 202 through 210 Processing helix chain 'C' and resid 211 through 213 No H-bonds generated for 'chain 'C' and resid 211 through 213' Processing helix chain 'C' and resid 226 through 239 removed outlier: 4.242A pdb=" N ALA C 230 " --> pdb=" O GLU C 226 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N HIS C 234 " --> pdb=" O ALA C 230 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE C 235 " --> pdb=" O SER C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 317 removed outlier: 3.739A pdb=" N PHE C 316 " --> pdb=" O ARG C 313 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP C 317 " --> pdb=" O ALA C 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 313 through 317' Processing helix chain 'B' and resid 55 through 66 removed outlier: 3.779A pdb=" N GLU B 66 " --> pdb=" O SER B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 108 removed outlier: 4.141A pdb=" N ARG B 100 " --> pdb=" O THR B 96 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP B 101 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ASP B 102 " --> pdb=" O LYS B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 127 removed outlier: 3.605A pdb=" N LYS B 127 " --> pdb=" O LEU B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 210 removed outlier: 3.628A pdb=" N ARG B 206 " --> pdb=" O MET B 202 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR B 207 " --> pdb=" O PRO B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 213 No H-bonds generated for 'chain 'B' and resid 211 through 213' Processing helix chain 'B' and resid 225 through 239 removed outlier: 4.207A pdb=" N LEU B 229 " --> pdb=" O ARG B 225 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR B 233 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N HIS B 234 " --> pdb=" O ALA B 230 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE B 235 " --> pdb=" O SER B 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 60 Processing helix chain 'A' and resid 60 through 66 Processing helix chain 'A' and resid 96 through 108 removed outlier: 4.226A pdb=" N ARG A 100 " --> pdb=" O THR A 96 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ASP A 101 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ASP A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR A 106 " --> pdb=" O ASP A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 127 removed outlier: 3.835A pdb=" N LYS A 127 " --> pdb=" O LEU A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 211 removed outlier: 3.644A pdb=" N ALA A 211 " --> pdb=" O THR A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 239 removed outlier: 4.300A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N HIS A 234 " --> pdb=" O ALA A 230 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 317 removed outlier: 3.743A pdb=" N PHE A 316 " --> pdb=" O ARG A 313 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASP A 317 " --> pdb=" O ALA A 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 313 through 317' Processing helix chain 'L' and resid 55 through 66 removed outlier: 3.782A pdb=" N GLU L 66 " --> pdb=" O SER L 62 " (cutoff:3.500A) Processing helix chain 'L' and resid 96 through 108 removed outlier: 4.120A pdb=" N ARG L 100 " --> pdb=" O THR L 96 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP L 101 " --> pdb=" O ALA L 97 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ASP L 102 " --> pdb=" O LYS L 98 " (cutoff:3.500A) Processing helix chain 'L' and resid 118 through 127 removed outlier: 3.603A pdb=" N LYS L 127 " --> pdb=" O LEU L 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 202 through 210 removed outlier: 3.621A pdb=" N ARG L 206 " --> pdb=" O MET L 202 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR L 207 " --> pdb=" O PRO L 203 " (cutoff:3.500A) Processing helix chain 'L' and resid 211 through 213 No H-bonds generated for 'chain 'L' and resid 211 through 213' Processing helix chain 'L' and resid 225 through 239 removed outlier: 4.197A pdb=" N LEU L 229 " --> pdb=" O ARG L 225 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA L 230 " --> pdb=" O GLU L 226 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR L 233 " --> pdb=" O LEU L 229 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N HIS L 234 " --> pdb=" O ALA L 230 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE L 235 " --> pdb=" O SER L 231 " (cutoff:3.500A) Processing helix chain 'K' and resid 55 through 60 Processing helix chain 'K' and resid 60 through 66 Processing helix chain 'K' and resid 96 through 108 removed outlier: 4.228A pdb=" N ARG K 100 " --> pdb=" O THR K 96 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASP K 101 " --> pdb=" O ALA K 97 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ASP K 102 " --> pdb=" O LYS K 98 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR K 106 " --> pdb=" O ASP K 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 118 through 127 removed outlier: 3.837A pdb=" N LYS K 127 " --> pdb=" O LEU K 123 " (cutoff:3.500A) Processing helix chain 'K' and resid 202 through 211 removed outlier: 3.643A pdb=" N ALA K 211 " --> pdb=" O THR K 207 " (cutoff:3.500A) Processing helix chain 'K' and resid 226 through 239 removed outlier: 4.305A pdb=" N ALA K 230 " --> pdb=" O GLU K 226 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N HIS K 234 " --> pdb=" O ALA K 230 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE K 235 " --> pdb=" O SER K 231 " (cutoff:3.500A) Processing helix chain 'K' and resid 313 through 317 removed outlier: 3.747A pdb=" N PHE K 316 " --> pdb=" O ARG K 313 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASP K 317 " --> pdb=" O ALA K 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 313 through 317' Processing sheet with id=AA1, first strand: chain 'J' and resid 157 through 160 removed outlier: 6.914A pdb=" N PHE J 150 " --> pdb=" O LEU J 158 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LYS J 160 " --> pdb=" O VAL J 148 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL J 148 " --> pdb=" O LYS J 160 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU J 71 " --> pdb=" O ARG J 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 186 through 187 removed outlier: 6.326A pdb=" N LYS J 191 " --> pdb=" O ILE J 216 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N CYS J 218 " --> pdb=" O LYS J 191 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N GLY J 193 " --> pdb=" O CYS J 218 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N TYR J 217 " --> pdb=" O LEU J 244 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ALA J 246 " --> pdb=" O TYR J 217 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ALA J 219 " --> pdb=" O ALA J 246 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ILE J 283 " --> pdb=" O LEU J 291 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 342 through 346 removed outlier: 8.708A pdb=" N SER K 343 " --> pdb=" O PHE I 330 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU I 332 " --> pdb=" O SER K 343 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N LYS K 345 " --> pdb=" O LEU I 332 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ILE I 334 " --> pdb=" O LYS K 345 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 342 through 346 removed outlier: 6.819A pdb=" N SER J 343 " --> pdb=" O ILE L 334 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N GLU L 336 " --> pdb=" O SER J 343 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LYS J 345 " --> pdb=" O GLU L 336 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 157 through 160 removed outlier: 7.069A pdb=" N PHE I 150 " --> pdb=" O LEU I 158 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LYS I 160 " --> pdb=" O VAL I 148 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL I 148 " --> pdb=" O LYS I 160 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU I 71 " --> pdb=" O ARG I 37 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA I 304 " --> pdb=" O ALA I 38 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 186 through 187 removed outlier: 6.505A pdb=" N LYS I 191 " --> pdb=" O ILE I 216 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N CYS I 218 " --> pdb=" O LYS I 191 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLY I 193 " --> pdb=" O CYS I 218 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA I 246 " --> pdb=" O ALA I 219 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ILE I 283 " --> pdb=" O LEU I 291 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 342 through 345 Processing sheet with id=AA8, first strand: chain 'H' and resid 157 through 160 removed outlier: 3.918A pdb=" N GLY H 159 " --> pdb=" O PHE H 150 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU H 71 " --> pdb=" O ARG H 37 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 186 through 187 removed outlier: 6.236A pdb=" N LYS H 191 " --> pdb=" O ILE H 216 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N CYS H 218 " --> pdb=" O LYS H 191 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLY H 193 " --> pdb=" O CYS H 218 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N TYR H 217 " --> pdb=" O LEU H 244 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ALA H 246 " --> pdb=" O TYR H 217 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ALA H 219 " --> pdb=" O ALA H 246 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ILE H 283 " --> pdb=" O LEU H 291 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 157 through 160 removed outlier: 4.138A pdb=" N GLY G 159 " --> pdb=" O PHE G 150 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU G 71 " --> pdb=" O ARG G 37 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA G 304 " --> pdb=" O ALA G 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 186 through 187 removed outlier: 3.677A pdb=" N ALA G 246 " --> pdb=" O ALA G 219 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ILE G 283 " --> pdb=" O LEU G 291 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 342 through 345 Processing sheet with id=AB4, first strand: chain 'F' and resid 157 through 160 removed outlier: 3.880A pdb=" N GLY F 159 " --> pdb=" O PHE F 150 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU F 71 " --> pdb=" O ARG F 37 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 186 through 187 removed outlier: 6.252A pdb=" N LYS F 191 " --> pdb=" O ILE F 216 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N CYS F 218 " --> pdb=" O LYS F 191 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N GLY F 193 " --> pdb=" O CYS F 218 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N TYR F 217 " --> pdb=" O LEU F 244 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N ALA F 246 " --> pdb=" O TYR F 217 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ALA F 219 " --> pdb=" O ALA F 246 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE F 283 " --> pdb=" O LEU F 291 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 157 through 160 removed outlier: 7.016A pdb=" N PHE E 150 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LYS E 160 " --> pdb=" O VAL E 148 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL E 148 " --> pdb=" O LYS E 160 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU E 71 " --> pdb=" O ARG E 37 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA E 304 " --> pdb=" O ALA E 38 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 192 through 194 removed outlier: 6.362A pdb=" N GLY E 193 " --> pdb=" O CYS E 218 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N TYR E 217 " --> pdb=" O LEU E 244 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N ALA E 246 " --> pdb=" O TYR E 217 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ALA E 219 " --> pdb=" O ALA E 246 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ILE E 283 " --> pdb=" O LEU E 291 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 342 through 345 Processing sheet with id=AB9, first strand: chain 'D' and resid 157 through 160 removed outlier: 6.875A pdb=" N PHE D 150 " --> pdb=" O LEU D 158 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LYS D 160 " --> pdb=" O VAL D 148 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL D 148 " --> pdb=" O LYS D 160 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR D 147 " --> pdb=" O VAL D 136 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL D 136 " --> pdb=" O THR D 147 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU D 71 " --> pdb=" O ARG D 37 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 186 through 187 removed outlier: 6.226A pdb=" N LYS D 191 " --> pdb=" O ILE D 216 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N CYS D 218 " --> pdb=" O LYS D 191 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N GLY D 193 " --> pdb=" O CYS D 218 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N TYR D 217 " --> pdb=" O LEU D 244 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ALA D 246 " --> pdb=" O TYR D 217 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ALA D 219 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL D 243 " --> pdb=" O ILE D 284 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ILE D 283 " --> pdb=" O LEU D 291 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 157 through 162 removed outlier: 6.977A pdb=" N PHE C 150 " --> pdb=" O LEU C 158 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LYS C 160 " --> pdb=" O VAL C 148 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL C 148 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ARG C 162 " --> pdb=" O CYS C 146 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N CYS C 146 " --> pdb=" O ARG C 162 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU C 71 " --> pdb=" O ARG C 37 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA C 304 " --> pdb=" O ALA C 38 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 186 through 187 removed outlier: 3.669A pdb=" N ALA C 246 " --> pdb=" O ALA C 219 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ILE C 283 " --> pdb=" O LEU C 291 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 342 through 345 Processing sheet with id=AC5, first strand: chain 'B' and resid 157 through 160 removed outlier: 3.849A pdb=" N GLY B 159 " --> pdb=" O PHE B 150 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B 132 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU B 71 " --> pdb=" O ARG B 37 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 137 through 139 Processing sheet with id=AC7, first strand: chain 'B' and resid 186 through 187 removed outlier: 6.222A pdb=" N LYS B 191 " --> pdb=" O ILE B 216 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N CYS B 218 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLY B 193 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TYR B 217 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N ALA B 246 " --> pdb=" O TYR B 217 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ALA B 219 " --> pdb=" O ALA B 246 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE B 283 " --> pdb=" O LEU B 291 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 157 through 160 removed outlier: 4.049A pdb=" N GLY A 159 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU A 71 " --> pdb=" O ARG A 37 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA A 304 " --> pdb=" O ALA A 38 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 186 through 187 removed outlier: 6.458A pdb=" N LYS A 191 " --> pdb=" O ILE A 216 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N CYS A 218 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N GLY A 193 " --> pdb=" O CYS A 218 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TYR A 217 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N ALA A 246 " --> pdb=" O TYR A 217 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ALA A 219 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE A 283 " --> pdb=" O LEU A 291 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 157 through 160 removed outlier: 3.851A pdb=" N GLY L 159 " --> pdb=" O PHE L 150 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU L 132 " --> pdb=" O PHE L 151 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU L 71 " --> pdb=" O ARG L 37 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 137 through 139 Processing sheet with id=AD3, first strand: chain 'L' and resid 186 through 187 removed outlier: 6.213A pdb=" N LYS L 191 " --> pdb=" O ILE L 216 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N CYS L 218 " --> pdb=" O LYS L 191 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLY L 193 " --> pdb=" O CYS L 218 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TYR L 217 " --> pdb=" O LEU L 244 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N ALA L 246 " --> pdb=" O TYR L 217 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ALA L 219 " --> pdb=" O ALA L 246 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ILE L 283 " --> pdb=" O LEU L 291 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 157 through 160 removed outlier: 4.048A pdb=" N GLY K 159 " --> pdb=" O PHE K 150 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU K 71 " --> pdb=" O ARG K 37 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA K 304 " --> pdb=" O ALA K 38 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 186 through 187 removed outlier: 6.476A pdb=" N LYS K 191 " --> pdb=" O ILE K 216 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N CYS K 218 " --> pdb=" O LYS K 191 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N GLY K 193 " --> pdb=" O CYS K 218 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TYR K 217 " --> pdb=" O LEU K 244 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N ALA K 246 " --> pdb=" O TYR K 217 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ALA K 219 " --> pdb=" O ALA K 246 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE K 283 " --> pdb=" O LEU K 291 " (cutoff:3.500A) 668 hydrogen bonds defined for protein. 1896 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: 7.89 Time building geometry restraints manager: 9.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 8246 1.34 - 1.48: 7520 1.48 - 1.62: 11318 1.62 - 1.77: 0 1.77 - 1.91: 228 Bond restraints: 27312 Sorted by residual: bond pdb=" C ARG D 251 " pdb=" O ARG D 251 " ideal model delta sigma weight residual 1.231 1.537 -0.306 2.00e-02 2.50e+03 2.34e+02 bond pdb=" C ARG B 251 " pdb=" O ARG B 251 " ideal model delta sigma weight residual 1.231 1.490 -0.259 2.00e-02 2.50e+03 1.68e+02 bond pdb=" C ARG H 251 " pdb=" O ARG H 251 " ideal model delta sigma weight residual 1.231 1.435 -0.204 2.00e-02 2.50e+03 1.05e+02 bond pdb=" C ARG L 251 " pdb=" O ARG L 251 " ideal model delta sigma weight residual 1.231 1.355 -0.124 2.00e-02 2.50e+03 3.85e+01 bond pdb=" C ARG J 251 " pdb=" O ARG J 251 " ideal model delta sigma weight residual 1.231 1.336 -0.105 2.00e-02 2.50e+03 2.76e+01 ... (remaining 27307 not shown) Histogram of bond angle deviations from ideal: 96.13 - 104.23: 547 104.23 - 112.32: 12040 112.32 - 120.41: 14006 120.41 - 128.50: 10221 128.50 - 136.59: 158 Bond angle restraints: 36972 Sorted by residual: angle pdb=" CA ARG B 251 " pdb=" C ARG B 251 " pdb=" O ARG B 251 " ideal model delta sigma weight residual 120.80 136.59 -15.79 1.70e+00 3.46e-01 8.63e+01 angle pdb=" OG1 THR D 207 " pdb=" CB THR D 207 " pdb=" CG2 THR D 207 " ideal model delta sigma weight residual 109.30 96.13 13.17 2.00e+00 2.50e-01 4.33e+01 angle pdb=" OG1 THR F 207 " pdb=" CB THR F 207 " pdb=" CG2 THR F 207 " ideal model delta sigma weight residual 109.30 96.31 12.99 2.00e+00 2.50e-01 4.22e+01 angle pdb=" CB ARG J 326 " pdb=" CG ARG J 326 " pdb=" CD ARG J 326 " ideal model delta sigma weight residual 111.30 126.23 -14.93 2.30e+00 1.89e-01 4.21e+01 angle pdb=" OG1 THR H 207 " pdb=" CB THR H 207 " pdb=" CG2 THR H 207 " ideal model delta sigma weight residual 109.30 96.43 12.87 2.00e+00 2.50e-01 4.14e+01 ... (remaining 36967 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.98: 13033 9.98 - 19.96: 2277 19.96 - 29.94: 566 29.94 - 39.92: 253 39.92 - 49.89: 83 Dihedral angle restraints: 16212 sinusoidal: 6324 harmonic: 9888 Sorted by residual: dihedral pdb=" CA VAL K 320 " pdb=" C VAL K 320 " pdb=" N VAL K 321 " pdb=" CA VAL K 321 " ideal model delta harmonic sigma weight residual -180.00 -130.11 -49.89 0 5.00e+00 4.00e-02 9.96e+01 dihedral pdb=" CA VAL E 320 " pdb=" C VAL E 320 " pdb=" N VAL E 321 " pdb=" CA VAL E 321 " ideal model delta harmonic sigma weight residual -180.00 -130.67 -49.33 0 5.00e+00 4.00e-02 9.73e+01 dihedral pdb=" CA VAL A 320 " pdb=" C VAL A 320 " pdb=" N VAL A 321 " pdb=" CA VAL A 321 " ideal model delta harmonic sigma weight residual -180.00 -130.85 -49.15 0 5.00e+00 4.00e-02 9.66e+01 ... (remaining 16209 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 2807 0.106 - 0.212: 1062 0.212 - 0.318: 200 0.318 - 0.424: 31 0.424 - 0.530: 16 Chirality restraints: 4116 Sorted by residual: chirality pdb=" CA PHE G 318 " pdb=" N PHE G 318 " pdb=" C PHE G 318 " pdb=" CB PHE G 318 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.04e+00 chirality pdb=" CA PHE C 318 " pdb=" N PHE C 318 " pdb=" C PHE C 318 " pdb=" CB PHE C 318 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.22e+00 chirality pdb=" CA PHE I 318 " pdb=" N PHE I 318 " pdb=" C PHE I 318 " pdb=" CB PHE I 318 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.15e+00 ... (remaining 4113 not shown) Planarity restraints: 4740 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR J 217 " -0.018 2.00e-02 2.50e+03 3.88e-02 3.01e+01 pdb=" CG TYR J 217 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 TYR J 217 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 TYR J 217 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR J 217 " 0.033 2.00e-02 2.50e+03 pdb=" CE2 TYR J 217 " 0.044 2.00e-02 2.50e+03 pdb=" CZ TYR J 217 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR J 217 " -0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 326 " 0.491 9.50e-02 1.11e+02 2.20e-01 2.97e+01 pdb=" NE ARG A 326 " -0.031 2.00e-02 2.50e+03 pdb=" CZ ARG A 326 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 326 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 326 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG I 201 " -0.487 9.50e-02 1.11e+02 2.18e-01 2.93e+01 pdb=" NE ARG I 201 " 0.030 2.00e-02 2.50e+03 pdb=" CZ ARG I 201 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG I 201 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG I 201 " -0.017 2.00e-02 2.50e+03 ... (remaining 4737 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 7014 2.81 - 3.33: 21592 3.33 - 3.85: 40260 3.85 - 4.38: 47971 4.38 - 4.90: 84769 Nonbonded interactions: 201606 Sorted by model distance: nonbonded pdb=" OG1 THR I 187 " pdb=" O GLY I 190 " model vdw 2.285 2.440 nonbonded pdb=" OG1 THR E 187 " pdb=" O GLY E 190 " model vdw 2.287 2.440 nonbonded pdb=" OG1 THR C 187 " pdb=" O GLY C 190 " model vdw 2.295 2.440 nonbonded pdb=" OG1 THR G 187 " pdb=" O GLY G 190 " model vdw 2.310 2.440 nonbonded pdb=" OG1 THR K 187 " pdb=" O GLY K 190 " model vdw 2.319 2.440 ... (remaining 201601 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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=0.50 max=1.00 mean=0.97 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.380 Check model and map are aligned: 0.390 Set scattering table: 0.250 Process input model: 66.320 Find NCS groups from input model: 1.560 Set up NCS constraints: 0.150 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:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 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 : 0.010 0.306 27312 Z= 0.648 Angle : 1.585 15.791 36972 Z= 0.964 Chirality : 0.114 0.530 4116 Planarity : 0.016 0.220 4740 Dihedral : 11.837 49.895 9900 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.73 % Allowed : 16.23 % Favored : 83.04 % Rotamer: Outliers : 2.72 % Allowed : 7.69 % Favored : 89.59 % Cbeta Deviations : 0.79 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -5.33 (0.11), residues: 3420 helix: -3.58 (0.11), residues: 888 sheet: -3.23 (0.18), residues: 588 loop : -3.74 (0.11), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.013 TRP A 198 HIS 0.026 0.007 HIS F 337 PHE 0.043 0.009 PHE K 318 TYR 0.063 0.012 TYR B 217 ARG 0.019 0.002 ARG D 339 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 747 residues out of total 2796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 671 time to evaluate : 3.164 Fit side-chains REVERT: J 58 GLU cc_start: 0.8022 (tp30) cc_final: 0.7540 (tt0) REVERT: J 169 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8889 (tp) REVERT: J 191 LYS cc_start: 0.9028 (mttt) cc_final: 0.8766 (mtpt) REVERT: J 297 ARG cc_start: 0.8237 (mtp85) cc_final: 0.7863 (ppt170) REVERT: J 305 ASP cc_start: 0.9016 (p0) cc_final: 0.8784 (t0) REVERT: J 310 ASP cc_start: 0.9308 (t0) cc_final: 0.9010 (t0) REVERT: I 63 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7457 (tm-30) REVERT: I 295 ASN cc_start: 0.8658 (t0) cc_final: 0.8351 (t0) REVERT: I 301 LEU cc_start: 0.8494 (mt) cc_final: 0.8286 (mp) REVERT: H 58 GLU cc_start: 0.7998 (tp30) cc_final: 0.7492 (tt0) REVERT: H 63 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7978 (tp30) REVERT: H 95 ARG cc_start: 0.8035 (mpt-90) cc_final: 0.7803 (mmt90) REVERT: H 295 ASN cc_start: 0.8775 (t0) cc_final: 0.8396 (t0) REVERT: H 297 ARG cc_start: 0.8122 (mtp85) cc_final: 0.7654 (ppt170) REVERT: G 61 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7774 (tt) REVERT: G 63 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7405 (tm-30) REVERT: G 123 LEU cc_start: 0.8457 (tt) cc_final: 0.8244 (pp) REVERT: G 169 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.9115 (tp) REVERT: G 295 ASN cc_start: 0.8691 (t0) cc_final: 0.8222 (t0) REVERT: G 340 LYS cc_start: 0.8578 (ttmp) cc_final: 0.8370 (ttpt) REVERT: F 89 GLU cc_start: 0.9316 (mt-10) cc_final: 0.9067 (mp0) REVERT: F 127 LYS cc_start: 0.7147 (mtmt) cc_final: 0.6851 (pttm) REVERT: F 169 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8861 (tp) REVERT: F 295 ASN cc_start: 0.8686 (t0) cc_final: 0.8472 (t0) REVERT: F 297 ARG cc_start: 0.7889 (mtp85) cc_final: 0.7508 (ptt-90) REVERT: E 55 ASP cc_start: 0.8517 (m-30) cc_final: 0.8293 (m-30) REVERT: E 192 ILE cc_start: 0.9115 (pt) cc_final: 0.8875 (mt) REVERT: E 295 ASN cc_start: 0.8697 (t0) cc_final: 0.8337 (t0) REVERT: D 58 GLU cc_start: 0.8007 (tp30) cc_final: 0.7754 (tt0) REVERT: D 63 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7832 (tp30) REVERT: D 95 ARG cc_start: 0.8039 (mpt-90) cc_final: 0.7630 (mmt90) REVERT: D 127 LYS cc_start: 0.7166 (mtmt) cc_final: 0.6867 (pttt) REVERT: D 169 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8873 (tp) REVERT: D 297 ARG cc_start: 0.7846 (mtp85) cc_final: 0.7523 (ptt-90) REVERT: C 55 ASP cc_start: 0.8669 (m-30) cc_final: 0.8424 (m-30) REVERT: C 63 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7486 (tm-30) REVERT: C 95 ARG cc_start: 0.8025 (mpt-90) cc_final: 0.6415 (mpt-90) REVERT: C 169 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.9143 (tp) REVERT: C 225 ARG cc_start: 0.8209 (mpt-90) cc_final: 0.7981 (mtt-85) REVERT: C 295 ASN cc_start: 0.8713 (t0) cc_final: 0.8402 (t0) REVERT: B 58 GLU cc_start: 0.7927 (tp30) cc_final: 0.7330 (tt0) REVERT: B 169 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8981 (tp) REVERT: B 191 LYS cc_start: 0.9008 (mttt) cc_final: 0.8612 (mtpt) REVERT: B 283 ILE cc_start: 0.9025 (OUTLIER) cc_final: 0.8810 (mt) REVERT: B 297 ARG cc_start: 0.7785 (mtp85) cc_final: 0.7404 (ptt90) REVERT: A 63 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7640 (tm-30) REVERT: A 95 ARG cc_start: 0.7460 (mpt-90) cc_final: 0.6558 (mtt180) REVERT: A 169 LEU cc_start: 0.9453 (OUTLIER) cc_final: 0.9068 (tp) REVERT: A 197 CYS cc_start: 0.9271 (t) cc_final: 0.8962 (t) REVERT: A 289 ILE cc_start: 0.8193 (mt) cc_final: 0.7990 (pt) REVERT: A 295 ASN cc_start: 0.8687 (t0) cc_final: 0.8394 (t0) REVERT: A 299 GLU cc_start: 0.8400 (pt0) cc_final: 0.8177 (pt0) REVERT: L 58 GLU cc_start: 0.8049 (tp30) cc_final: 0.7557 (tt0) REVERT: L 89 GLU cc_start: 0.9221 (mt-10) cc_final: 0.8802 (tt0) REVERT: L 225 ARG cc_start: 0.7722 (mpt-90) cc_final: 0.7451 (mtt-85) REVERT: L 297 ARG cc_start: 0.7879 (mtp85) cc_final: 0.7468 (ptp90) REVERT: K 63 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7605 (tm-30) REVERT: K 169 LEU cc_start: 0.9455 (OUTLIER) cc_final: 0.9221 (tp) REVERT: K 184 VAL cc_start: 0.8155 (OUTLIER) cc_final: 0.7835 (p) REVERT: K 289 ILE cc_start: 0.8180 (mt) cc_final: 0.7968 (pt) REVERT: K 295 ASN cc_start: 0.8651 (t0) cc_final: 0.8381 (t0) outliers start: 76 outliers final: 16 residues processed: 734 average time/residue: 0.4636 time to fit residues: 511.2017 Evaluate side-chains 405 residues out of total 2796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 378 time to evaluate : 3.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain I residue 184 VAL Chi-restraints excluded: chain H residue 283 ILE Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain K residue 169 LEU Chi-restraints excluded: chain K residue 184 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 283 optimal weight: 5.9990 chunk 254 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 86 optimal weight: 7.9990 chunk 171 optimal weight: 5.9990 chunk 136 optimal weight: 8.9990 chunk 263 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 160 optimal weight: 3.9990 chunk 196 optimal weight: 10.0000 chunk 305 optimal weight: 1.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 200 ASN I 70 GLN I 200 ASN H 200 ASN G 200 ASN F 200 ASN E 200 ASN D 70 GLN D 200 ASN C 200 ASN B 200 ASN A 200 ASN L 161 HIS L 200 ASN K 200 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 27312 Z= 0.238 Angle : 0.716 11.895 36972 Z= 0.365 Chirality : 0.047 0.199 4116 Planarity : 0.005 0.088 4740 Dihedral : 7.129 54.029 3848 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.35 % Allowed : 11.35 % Favored : 88.30 % Rotamer: Outliers : 5.19 % Allowed : 11.16 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -4.44 (0.12), residues: 3420 helix: -2.46 (0.15), residues: 816 sheet: -2.14 (0.18), residues: 780 loop : -3.67 (0.11), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP L 198 HIS 0.003 0.001 HIS A 337 PHE 0.012 0.001 PHE A 318 TYR 0.019 0.002 TYR A 128 ARG 0.004 0.001 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 2796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 434 time to evaluate : 2.925 Fit side-chains REVERT: J 58 GLU cc_start: 0.7842 (tp30) cc_final: 0.7403 (tt0) REVERT: J 63 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7859 (tp30) REVERT: J 169 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8788 (tp) REVERT: J 191 LYS cc_start: 0.8884 (mttt) cc_final: 0.8513 (mtpt) REVERT: J 227 THR cc_start: 0.8296 (OUTLIER) cc_final: 0.7916 (p) REVERT: J 287 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8855 (mm) REVERT: J 295 ASN cc_start: 0.8495 (t0) cc_final: 0.8209 (t0) REVERT: J 297 ARG cc_start: 0.8096 (mtp85) cc_final: 0.7854 (ptp90) REVERT: J 305 ASP cc_start: 0.8585 (p0) cc_final: 0.8360 (t0) REVERT: I 63 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7456 (tm-30) REVERT: I 169 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.9138 (tp) REVERT: I 184 VAL cc_start: 0.7952 (OUTLIER) cc_final: 0.7689 (p) REVERT: I 301 LEU cc_start: 0.8674 (mt) cc_final: 0.8323 (mp) REVERT: H 58 GLU cc_start: 0.7867 (tp30) cc_final: 0.7408 (tt0) REVERT: H 63 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7716 (tp30) REVERT: H 95 ARG cc_start: 0.7946 (mpt-90) cc_final: 0.7675 (mmt90) REVERT: H 283 ILE cc_start: 0.8911 (OUTLIER) cc_final: 0.8684 (mt) REVERT: H 295 ASN cc_start: 0.8860 (t0) cc_final: 0.8624 (t0) REVERT: H 297 ARG cc_start: 0.7985 (mtp85) cc_final: 0.7563 (ppt170) REVERT: G 63 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7473 (tm-30) REVERT: G 95 ARG cc_start: 0.8019 (mpt-90) cc_final: 0.6661 (mpt-90) REVERT: G 117 GLU cc_start: 0.8847 (mp0) cc_final: 0.8546 (mp0) REVERT: G 169 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.8953 (tp) REVERT: G 184 VAL cc_start: 0.7962 (OUTLIER) cc_final: 0.7675 (p) REVERT: G 295 ASN cc_start: 0.8618 (t0) cc_final: 0.8268 (t0) REVERT: G 340 LYS cc_start: 0.8142 (ttmp) cc_final: 0.7933 (ttpt) REVERT: F 58 GLU cc_start: 0.7611 (tp30) cc_final: 0.7388 (tt0) REVERT: F 169 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8799 (tp) REVERT: F 209 MET cc_start: 0.9248 (mmm) cc_final: 0.9009 (mtp) REVERT: F 227 THR cc_start: 0.8185 (OUTLIER) cc_final: 0.7813 (p) REVERT: F 287 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8791 (mm) REVERT: F 295 ASN cc_start: 0.8672 (t0) cc_final: 0.8453 (t0) REVERT: F 297 ARG cc_start: 0.7819 (mtp85) cc_final: 0.7452 (ptt-90) REVERT: E 63 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7568 (tm-30) REVERT: E 169 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.9074 (tp) REVERT: E 184 VAL cc_start: 0.8001 (OUTLIER) cc_final: 0.7775 (p) REVERT: E 192 ILE cc_start: 0.9107 (OUTLIER) cc_final: 0.8878 (mt) REVERT: E 225 ARG cc_start: 0.8011 (mtm-85) cc_final: 0.7799 (mtt-85) REVERT: E 297 ARG cc_start: 0.8432 (mtp85) cc_final: 0.8220 (ptt-90) REVERT: D 58 GLU cc_start: 0.8008 (tp30) cc_final: 0.7607 (tt0) REVERT: D 63 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7676 (tp30) REVERT: D 95 ARG cc_start: 0.7892 (mpt-90) cc_final: 0.7635 (mmt90) REVERT: D 169 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8736 (tp) REVERT: D 209 MET cc_start: 0.9203 (mmm) cc_final: 0.8925 (mtp) REVERT: D 227 THR cc_start: 0.8218 (OUTLIER) cc_final: 0.7889 (p) REVERT: D 232 MET cc_start: 0.8963 (mmp) cc_final: 0.8730 (mmt) REVERT: D 283 ILE cc_start: 0.9053 (OUTLIER) cc_final: 0.8713 (mt) REVERT: C 63 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7502 (tm-30) REVERT: C 95 ARG cc_start: 0.8110 (mpt-90) cc_final: 0.6507 (mpt-90) REVERT: C 169 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8818 (tp) REVERT: C 184 VAL cc_start: 0.7895 (OUTLIER) cc_final: 0.7600 (p) REVERT: C 295 ASN cc_start: 0.8628 (t0) cc_final: 0.8292 (t0) REVERT: B 58 GLU cc_start: 0.7770 (tp30) cc_final: 0.7290 (tt0) REVERT: B 117 GLU cc_start: 0.9121 (mp0) cc_final: 0.8811 (mp0) REVERT: B 169 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8905 (tp) REVERT: B 209 MET cc_start: 0.9066 (mmm) cc_final: 0.8716 (mtp) REVERT: B 227 THR cc_start: 0.8209 (OUTLIER) cc_final: 0.7842 (p) REVERT: B 283 ILE cc_start: 0.8906 (OUTLIER) cc_final: 0.8682 (mt) REVERT: B 287 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8778 (mm) REVERT: A 63 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7645 (tm-30) REVERT: A 95 ARG cc_start: 0.7569 (mpt-90) cc_final: 0.6487 (mtt180) REVERT: A 124 MET cc_start: 0.7779 (ttm) cc_final: 0.7495 (ttm) REVERT: A 169 LEU cc_start: 0.9434 (OUTLIER) cc_final: 0.9138 (tp) REVERT: A 184 VAL cc_start: 0.7993 (OUTLIER) cc_final: 0.7781 (p) REVERT: A 299 GLU cc_start: 0.8400 (pt0) cc_final: 0.8115 (pt0) REVERT: L 225 ARG cc_start: 0.7784 (mpt-90) cc_final: 0.7398 (mtt-85) REVERT: L 227 THR cc_start: 0.8235 (OUTLIER) cc_final: 0.7915 (p) REVERT: L 297 ARG cc_start: 0.7604 (mtp85) cc_final: 0.7373 (ptp90) REVERT: K 63 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7601 (tm-30) REVERT: K 169 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9101 (tp) REVERT: K 184 VAL cc_start: 0.7963 (OUTLIER) cc_final: 0.7757 (p) outliers start: 145 outliers final: 51 residues processed: 548 average time/residue: 0.4295 time to fit residues: 363.3723 Evaluate side-chains 439 residues out of total 2796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 360 time to evaluate : 3.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 227 THR Chi-restraints excluded: chain J residue 287 LEU Chi-restraints excluded: chain J residue 308 LEU Chi-restraints excluded: chain J residue 317 ASP Chi-restraints excluded: chain J residue 329 VAL Chi-restraints excluded: chain I residue 35 ILE Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain I residue 184 VAL Chi-restraints excluded: chain I residue 192 ILE Chi-restraints excluded: chain I residue 224 SER Chi-restraints excluded: chain I residue 276 VAL Chi-restraints excluded: chain I residue 320 VAL Chi-restraints excluded: chain I residue 321 VAL Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain H residue 214 ILE Chi-restraints excluded: chain H residue 283 ILE Chi-restraints excluded: chain H residue 301 LEU Chi-restraints excluded: chain H residue 317 ASP Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 276 VAL Chi-restraints excluded: chain G residue 289 ILE Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 317 ASP Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain E residue 138 GLU Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 299 GLU Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 317 ASP Chi-restraints excluded: chain D residue 333 ASN Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain L residue 214 ILE Chi-restraints excluded: chain L residue 227 THR Chi-restraints excluded: chain L residue 317 ASP Chi-restraints excluded: chain L residue 329 VAL Chi-restraints excluded: chain L residue 333 ASN Chi-restraints excluded: chain K residue 138 GLU Chi-restraints excluded: chain K residue 169 LEU Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 224 SER Chi-restraints excluded: chain K residue 276 VAL Chi-restraints excluded: chain K residue 333 ASN Chi-restraints excluded: chain K residue 343 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 169 optimal weight: 8.9990 chunk 94 optimal weight: 6.9990 chunk 253 optimal weight: 6.9990 chunk 207 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 305 optimal weight: 4.9990 chunk 330 optimal weight: 9.9990 chunk 272 optimal weight: 10.0000 chunk 303 optimal weight: 6.9990 chunk 104 optimal weight: 10.0000 chunk 245 optimal weight: 3.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 333 ASN ** F 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 27312 Z= 0.411 Angle : 0.773 10.589 36972 Z= 0.396 Chirality : 0.050 0.191 4116 Planarity : 0.006 0.063 4740 Dihedral : 7.050 52.732 3838 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.35 % Allowed : 14.74 % Favored : 84.91 % Rotamer: Outliers : 5.79 % Allowed : 12.27 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -4.00 (0.12), residues: 3420 helix: -2.07 (0.16), residues: 804 sheet: -1.65 (0.18), residues: 780 loop : -3.52 (0.11), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 228 HIS 0.008 0.001 HIS G 337 PHE 0.020 0.002 PHE A 318 TYR 0.029 0.002 TYR K 128 ARG 0.003 0.001 ARG F 84 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 2796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 371 time to evaluate : 3.051 Fit side-chains REVERT: J 58 GLU cc_start: 0.7957 (tp30) cc_final: 0.7553 (tt0) REVERT: J 63 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7754 (tp30) REVERT: J 169 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8895 (tp) REVERT: J 287 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8924 (mm) REVERT: J 295 ASN cc_start: 0.8509 (t0) cc_final: 0.8238 (t0) REVERT: J 297 ARG cc_start: 0.8014 (mtp85) cc_final: 0.7761 (ptp90) REVERT: I 63 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7494 (tm-30) REVERT: I 184 VAL cc_start: 0.8020 (OUTLIER) cc_final: 0.7660 (p) REVERT: I 301 LEU cc_start: 0.8762 (mt) cc_final: 0.8434 (mp) REVERT: H 58 GLU cc_start: 0.7988 (tp30) cc_final: 0.7461 (tt0) REVERT: H 95 ARG cc_start: 0.8047 (mpt-90) cc_final: 0.7398 (mmt90) REVERT: H 227 THR cc_start: 0.8281 (OUTLIER) cc_final: 0.7787 (p) REVERT: H 295 ASN cc_start: 0.8855 (t0) cc_final: 0.8533 (t0) REVERT: H 297 ARG cc_start: 0.7960 (mtp85) cc_final: 0.7515 (ppt170) REVERT: G 63 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7397 (tm-30) REVERT: G 95 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.6697 (mpt-90) REVERT: G 124 MET cc_start: 0.7987 (ttm) cc_final: 0.7727 (ttm) REVERT: G 184 VAL cc_start: 0.8006 (OUTLIER) cc_final: 0.7669 (p) REVERT: G 295 ASN cc_start: 0.8648 (t0) cc_final: 0.8288 (t0) REVERT: F 58 GLU cc_start: 0.7672 (tp30) cc_final: 0.7387 (tt0) REVERT: F 169 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8936 (tp) REVERT: F 287 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8902 (mm) REVERT: F 295 ASN cc_start: 0.8632 (t0) cc_final: 0.8423 (t0) REVERT: F 297 ARG cc_start: 0.7887 (mtp85) cc_final: 0.7512 (ptt-90) REVERT: E 63 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7588 (tm-30) REVERT: E 184 VAL cc_start: 0.8057 (OUTLIER) cc_final: 0.7714 (p) REVERT: E 192 ILE cc_start: 0.9165 (OUTLIER) cc_final: 0.8905 (mt) REVERT: E 223 ASP cc_start: 0.7852 (p0) cc_final: 0.7612 (p0) REVERT: D 58 GLU cc_start: 0.8067 (tp30) cc_final: 0.7644 (tt0) REVERT: D 63 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7648 (tp30) REVERT: D 95 ARG cc_start: 0.7949 (mpt-90) cc_final: 0.7392 (mmt90) REVERT: D 169 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8812 (tp) REVERT: D 227 THR cc_start: 0.8320 (OUTLIER) cc_final: 0.7832 (p) REVERT: C 42 GLN cc_start: 0.8662 (tt0) cc_final: 0.8444 (tt0) REVERT: C 63 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7607 (tm-30) REVERT: C 95 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7162 (mpt-90) REVERT: C 184 VAL cc_start: 0.8000 (OUTLIER) cc_final: 0.7686 (p) REVERT: C 295 ASN cc_start: 0.8721 (t0) cc_final: 0.8338 (t0) REVERT: C 345 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8306 (mtmt) REVERT: B 169 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8916 (tp) REVERT: B 209 MET cc_start: 0.9104 (mmm) cc_final: 0.8884 (mtp) REVERT: B 287 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8858 (mm) REVERT: A 63 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7716 (tm-30) REVERT: A 95 ARG cc_start: 0.7667 (mpt-90) cc_final: 0.6268 (mtt180) REVERT: A 169 LEU cc_start: 0.9426 (OUTLIER) cc_final: 0.9083 (tp) REVERT: A 184 VAL cc_start: 0.7993 (OUTLIER) cc_final: 0.7708 (p) REVERT: L 58 GLU cc_start: 0.7828 (tp30) cc_final: 0.7516 (tt0) REVERT: L 89 GLU cc_start: 0.9134 (mp0) cc_final: 0.8727 (tt0) REVERT: K 63 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7574 (tm-30) REVERT: K 169 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.9096 (tp) REVERT: K 184 VAL cc_start: 0.8129 (OUTLIER) cc_final: 0.7855 (p) outliers start: 162 outliers final: 111 residues processed: 502 average time/residue: 0.3843 time to fit residues: 300.1492 Evaluate side-chains 468 residues out of total 2796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 336 time to evaluate : 3.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 102 ASP Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 276 VAL Chi-restraints excluded: chain J residue 287 LEU Chi-restraints excluded: chain J residue 308 LEU Chi-restraints excluded: chain J residue 317 ASP Chi-restraints excluded: chain J residue 331 SER Chi-restraints excluded: chain J residue 333 ASN Chi-restraints excluded: chain I residue 35 ILE Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 95 ARG Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 138 GLU Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain I residue 184 VAL Chi-restraints excluded: chain I residue 192 ILE Chi-restraints excluded: chain I residue 224 SER Chi-restraints excluded: chain I residue 276 VAL Chi-restraints excluded: chain I residue 289 ILE Chi-restraints excluded: chain I residue 320 VAL Chi-restraints excluded: chain I residue 321 VAL Chi-restraints excluded: chain I residue 333 ASN Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 214 ILE Chi-restraints excluded: chain H residue 227 THR Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain H residue 283 ILE Chi-restraints excluded: chain H residue 301 LEU Chi-restraints excluded: chain H residue 317 ASP Chi-restraints excluded: chain H residue 333 ASN Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 95 ARG Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 224 SER Chi-restraints excluded: chain G residue 289 ILE Chi-restraints excluded: chain G residue 321 VAL Chi-restraints excluded: chain G residue 331 SER Chi-restraints excluded: chain G residue 333 ASN Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 317 ASP Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 331 SER Chi-restraints excluded: chain F residue 333 ASN Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 138 GLU Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 333 ASN Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 317 ASP Chi-restraints excluded: chain D residue 333 ASN Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain C residue 345 LYS Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain L residue 276 VAL Chi-restraints excluded: chain L residue 317 ASP Chi-restraints excluded: chain L residue 329 VAL Chi-restraints excluded: chain L residue 331 SER Chi-restraints excluded: chain L residue 333 ASN Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 124 MET Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 138 GLU Chi-restraints excluded: chain K residue 169 LEU Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 192 ILE Chi-restraints excluded: chain K residue 224 SER Chi-restraints excluded: chain K residue 276 VAL Chi-restraints excluded: chain K residue 289 ILE Chi-restraints excluded: chain K residue 321 VAL Chi-restraints excluded: chain K residue 333 ASN Chi-restraints excluded: chain K residue 343 SER Chi-restraints excluded: chain K residue 345 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 302 optimal weight: 10.0000 chunk 229 optimal weight: 10.0000 chunk 158 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 145 optimal weight: 8.9990 chunk 205 optimal weight: 10.0000 chunk 306 optimal weight: 0.8980 chunk 324 optimal weight: 6.9990 chunk 160 optimal weight: 0.9990 chunk 290 optimal weight: 10.0000 chunk 87 optimal weight: 6.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 161 HIS ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 27312 Z= 0.352 Angle : 0.725 9.358 36972 Z= 0.371 Chirality : 0.049 0.240 4116 Planarity : 0.005 0.076 4740 Dihedral : 6.993 52.657 3838 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.35 % Allowed : 13.42 % Favored : 86.23 % Rotamer: Outliers : 6.26 % Allowed : 13.66 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -3.70 (0.13), residues: 3420 helix: -1.85 (0.17), residues: 816 sheet: -1.32 (0.19), residues: 780 loop : -3.39 (0.12), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 228 HIS 0.006 0.001 HIS E 337 PHE 0.019 0.002 PHE A 318 TYR 0.025 0.002 TYR A 128 ARG 0.006 0.000 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 2796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 361 time to evaluate : 2.987 Fit side-chains REVERT: J 58 GLU cc_start: 0.7869 (tp30) cc_final: 0.7470 (tt0) REVERT: J 169 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8906 (tp) REVERT: J 295 ASN cc_start: 0.8539 (t0) cc_final: 0.8253 (t0) REVERT: J 297 ARG cc_start: 0.7981 (mtp85) cc_final: 0.7732 (ptp90) REVERT: J 333 ASN cc_start: 0.9046 (p0) cc_final: 0.8772 (p0) REVERT: I 63 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7390 (tm-30) REVERT: I 184 VAL cc_start: 0.8028 (OUTLIER) cc_final: 0.7705 (p) REVERT: I 301 LEU cc_start: 0.8778 (mt) cc_final: 0.8495 (mp) REVERT: H 95 ARG cc_start: 0.8018 (mpt-90) cc_final: 0.7366 (mmt90) REVERT: H 227 THR cc_start: 0.8254 (OUTLIER) cc_final: 0.7747 (p) REVERT: H 295 ASN cc_start: 0.8872 (t0) cc_final: 0.8669 (t0) REVERT: H 297 ARG cc_start: 0.7899 (mtp85) cc_final: 0.7490 (ptt-90) REVERT: G 63 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7442 (tm-30) REVERT: G 95 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.6645 (mpt-90) REVERT: G 124 MET cc_start: 0.8064 (ttm) cc_final: 0.7776 (ttm) REVERT: G 184 VAL cc_start: 0.8000 (OUTLIER) cc_final: 0.7668 (p) REVERT: G 295 ASN cc_start: 0.8680 (t0) cc_final: 0.8328 (t0) REVERT: F 58 GLU cc_start: 0.7625 (tp30) cc_final: 0.7398 (tt0) REVERT: F 169 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8954 (tp) REVERT: F 287 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8858 (mm) REVERT: F 297 ARG cc_start: 0.7855 (mtp85) cc_final: 0.7485 (ptt-90) REVERT: E 169 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.9008 (tp) REVERT: E 184 VAL cc_start: 0.8095 (OUTLIER) cc_final: 0.7786 (p) REVERT: E 192 ILE cc_start: 0.9155 (OUTLIER) cc_final: 0.8898 (mt) REVERT: D 58 GLU cc_start: 0.7980 (tp30) cc_final: 0.7603 (tt0) REVERT: D 95 ARG cc_start: 0.8024 (mpt-90) cc_final: 0.7396 (mmt90) REVERT: D 169 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8777 (tp) REVERT: C 42 GLN cc_start: 0.8656 (tt0) cc_final: 0.8449 (tt0) REVERT: C 63 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7623 (tm-30) REVERT: C 95 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.6935 (mpt-90) REVERT: C 184 VAL cc_start: 0.8023 (OUTLIER) cc_final: 0.7742 (p) REVERT: C 295 ASN cc_start: 0.8720 (t0) cc_final: 0.8345 (t0) REVERT: C 345 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8269 (mtmt) REVERT: B 58 GLU cc_start: 0.7702 (tp30) cc_final: 0.7381 (tt0) REVERT: B 169 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8974 (tp) REVERT: B 209 MET cc_start: 0.9062 (mmm) cc_final: 0.8858 (mtp) REVERT: B 287 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8829 (mm) REVERT: A 63 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7659 (tm-30) REVERT: A 95 ARG cc_start: 0.7688 (mpt-90) cc_final: 0.6192 (mtt180) REVERT: A 169 LEU cc_start: 0.9404 (OUTLIER) cc_final: 0.9047 (tp) REVERT: A 184 VAL cc_start: 0.8120 (OUTLIER) cc_final: 0.7885 (p) REVERT: K 63 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7615 (tm-30) REVERT: K 169 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.9079 (tp) REVERT: K 184 VAL cc_start: 0.8224 (OUTLIER) cc_final: 0.7990 (p) outliers start: 175 outliers final: 113 residues processed: 498 average time/residue: 0.3763 time to fit residues: 293.1531 Evaluate side-chains 462 residues out of total 2796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 329 time to evaluate : 2.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 102 ASP Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 276 VAL Chi-restraints excluded: chain J residue 308 LEU Chi-restraints excluded: chain J residue 317 ASP Chi-restraints excluded: chain J residue 329 VAL Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 95 ARG Chi-restraints excluded: chain I residue 138 GLU Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain I residue 184 VAL Chi-restraints excluded: chain I residue 192 ILE Chi-restraints excluded: chain I residue 224 SER Chi-restraints excluded: chain I residue 276 VAL Chi-restraints excluded: chain I residue 289 ILE Chi-restraints excluded: chain I residue 320 VAL Chi-restraints excluded: chain I residue 321 VAL Chi-restraints excluded: chain I residue 333 ASN Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 147 THR Chi-restraints excluded: chain H residue 214 ILE Chi-restraints excluded: chain H residue 227 THR Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain H residue 283 ILE Chi-restraints excluded: chain H residue 317 ASP Chi-restraints excluded: chain H residue 333 ASN Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 95 ARG Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 224 SER Chi-restraints excluded: chain G residue 289 ILE Chi-restraints excluded: chain G residue 301 LEU Chi-restraints excluded: chain G residue 331 SER Chi-restraints excluded: chain G residue 333 ASN Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 317 ASP Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 331 SER Chi-restraints excluded: chain F residue 333 ASN Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 124 MET Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 138 GLU Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 333 ASN Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 297 ARG Chi-restraints excluded: chain D residue 317 ASP Chi-restraints excluded: chain D residue 333 ASN Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain C residue 345 LYS Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain L residue 276 VAL Chi-restraints excluded: chain L residue 317 ASP Chi-restraints excluded: chain L residue 329 VAL Chi-restraints excluded: chain L residue 333 ASN Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 124 MET Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 138 GLU Chi-restraints excluded: chain K residue 169 LEU Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 192 ILE Chi-restraints excluded: chain K residue 224 SER Chi-restraints excluded: chain K residue 276 VAL Chi-restraints excluded: chain K residue 289 ILE Chi-restraints excluded: chain K residue 321 VAL Chi-restraints excluded: chain K residue 333 ASN Chi-restraints excluded: chain K residue 343 SER Chi-restraints excluded: chain K residue 345 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 270 optimal weight: 10.0000 chunk 184 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 chunk 241 optimal weight: 3.9990 chunk 134 optimal weight: 9.9990 chunk 277 optimal weight: 1.9990 chunk 224 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 165 optimal weight: 3.9990 chunk 291 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 323 HIS ** F 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 27312 Z= 0.232 Angle : 0.646 9.607 36972 Z= 0.330 Chirality : 0.046 0.239 4116 Planarity : 0.005 0.057 4740 Dihedral : 6.576 52.309 3838 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.35 % Allowed : 12.46 % Favored : 87.19 % Rotamer: Outliers : 4.94 % Allowed : 16.13 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -3.38 (0.13), residues: 3420 helix: -1.51 (0.18), residues: 816 sheet: -1.01 (0.18), residues: 876 loop : -3.40 (0.12), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 228 HIS 0.003 0.001 HIS E 337 PHE 0.013 0.001 PHE A 318 TYR 0.021 0.001 TYR A 128 ARG 0.004 0.000 ARG C 225 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 2796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 362 time to evaluate : 3.152 Fit side-chains REVERT: J 58 GLU cc_start: 0.7700 (tp30) cc_final: 0.7380 (tt0) REVERT: J 63 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7750 (tp30) REVERT: J 169 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8828 (tp) REVERT: J 297 ARG cc_start: 0.8094 (mtp85) cc_final: 0.7859 (ptt-90) REVERT: I 63 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7356 (tm-30) REVERT: I 95 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7103 (mpt-90) REVERT: I 184 VAL cc_start: 0.8026 (OUTLIER) cc_final: 0.7731 (p) REVERT: I 215 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8394 (pt0) REVERT: I 276 VAL cc_start: 0.5636 (OUTLIER) cc_final: 0.5235 (t) REVERT: I 301 LEU cc_start: 0.8786 (mt) cc_final: 0.8498 (mp) REVERT: H 58 GLU cc_start: 0.7861 (tp30) cc_final: 0.7526 (tt0) REVERT: H 95 ARG cc_start: 0.7981 (mpt-90) cc_final: 0.7329 (mmt90) REVERT: H 227 THR cc_start: 0.8186 (OUTLIER) cc_final: 0.7702 (p) REVERT: H 297 ARG cc_start: 0.7903 (mtp85) cc_final: 0.7456 (pmt170) REVERT: G 63 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7390 (tm-30) REVERT: G 95 ARG cc_start: 0.8066 (mpt-90) cc_final: 0.6476 (mpt-90) REVERT: G 124 MET cc_start: 0.8044 (ttm) cc_final: 0.7751 (ttm) REVERT: G 169 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.8879 (tp) REVERT: G 184 VAL cc_start: 0.8047 (OUTLIER) cc_final: 0.7758 (p) REVERT: G 295 ASN cc_start: 0.8584 (t0) cc_final: 0.8310 (t0) REVERT: F 58 GLU cc_start: 0.7594 (tp30) cc_final: 0.7374 (tt0) REVERT: F 169 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8844 (tp) REVERT: F 287 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8755 (mm) REVERT: F 297 ARG cc_start: 0.7637 (mtp85) cc_final: 0.7415 (ptt-90) REVERT: E 169 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.8983 (tp) REVERT: E 184 VAL cc_start: 0.8055 (OUTLIER) cc_final: 0.7750 (p) REVERT: E 192 ILE cc_start: 0.9100 (OUTLIER) cc_final: 0.8876 (mt) REVERT: D 58 GLU cc_start: 0.7830 (tp30) cc_final: 0.7481 (tt0) REVERT: D 95 ARG cc_start: 0.7877 (mpt-90) cc_final: 0.7245 (mmt90) REVERT: D 169 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8698 (tp) REVERT: D 178 ASP cc_start: 0.8112 (p0) cc_final: 0.7683 (m-30) REVERT: C 42 GLN cc_start: 0.8589 (tt0) cc_final: 0.8382 (tt0) REVERT: C 95 ARG cc_start: 0.8054 (mpt-90) cc_final: 0.6533 (mpt-90) REVERT: C 184 VAL cc_start: 0.8092 (OUTLIER) cc_final: 0.7845 (p) REVERT: C 295 ASN cc_start: 0.8647 (t0) cc_final: 0.8320 (t0) REVERT: C 345 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.8286 (mtmt) REVERT: B 117 GLU cc_start: 0.9128 (mp0) cc_final: 0.8824 (mp0) REVERT: B 169 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8897 (tp) REVERT: B 287 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8745 (mm) REVERT: A 63 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7699 (tm-30) REVERT: A 95 ARG cc_start: 0.7643 (mpt-90) cc_final: 0.6101 (mtt180) REVERT: A 169 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9016 (tp) REVERT: A 184 VAL cc_start: 0.8198 (OUTLIER) cc_final: 0.7985 (p) REVERT: K 169 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.9024 (tp) REVERT: K 184 VAL cc_start: 0.8172 (OUTLIER) cc_final: 0.7947 (p) outliers start: 138 outliers final: 93 residues processed: 466 average time/residue: 0.3890 time to fit residues: 282.8484 Evaluate side-chains 448 residues out of total 2796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 333 time to evaluate : 3.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 102 ASP Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 276 VAL Chi-restraints excluded: chain J residue 308 LEU Chi-restraints excluded: chain J residue 317 ASP Chi-restraints excluded: chain J residue 329 VAL Chi-restraints excluded: chain J residue 333 ASN Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 95 ARG Chi-restraints excluded: chain I residue 128 TYR Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain I residue 184 VAL Chi-restraints excluded: chain I residue 192 ILE Chi-restraints excluded: chain I residue 215 GLU Chi-restraints excluded: chain I residue 224 SER Chi-restraints excluded: chain I residue 276 VAL Chi-restraints excluded: chain I residue 289 ILE Chi-restraints excluded: chain I residue 321 VAL Chi-restraints excluded: chain I residue 333 ASN Chi-restraints excluded: chain H residue 102 ASP Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 214 ILE Chi-restraints excluded: chain H residue 227 THR Chi-restraints excluded: chain H residue 283 ILE Chi-restraints excluded: chain H residue 317 ASP Chi-restraints excluded: chain H residue 333 ASN Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 224 SER Chi-restraints excluded: chain G residue 289 ILE Chi-restraints excluded: chain G residue 320 VAL Chi-restraints excluded: chain G residue 333 ASN Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 317 ASP Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 333 ASN Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 124 MET Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 333 ASN Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 317 ASP Chi-restraints excluded: chain D residue 333 ASN Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain C residue 345 LYS Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain L residue 102 ASP Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain L residue 276 VAL Chi-restraints excluded: chain L residue 317 ASP Chi-restraints excluded: chain L residue 329 VAL Chi-restraints excluded: chain L residue 333 ASN Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 124 MET Chi-restraints excluded: chain K residue 169 LEU Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 224 SER Chi-restraints excluded: chain K residue 276 VAL Chi-restraints excluded: chain K residue 321 VAL Chi-restraints excluded: chain K residue 333 ASN Chi-restraints excluded: chain K residue 343 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 109 optimal weight: 3.9990 chunk 292 optimal weight: 9.9990 chunk 64 optimal weight: 4.9990 chunk 190 optimal weight: 10.0000 chunk 80 optimal weight: 9.9990 chunk 325 optimal weight: 0.7980 chunk 269 optimal weight: 2.9990 chunk 150 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 107 optimal weight: 0.0870 chunk 170 optimal weight: 6.9990 overall best weight: 2.5764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 67 ASN ** J 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 ASN ** F 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 323 HIS ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27312 Z= 0.221 Angle : 0.634 10.399 36972 Z= 0.323 Chirality : 0.046 0.218 4116 Planarity : 0.005 0.052 4740 Dihedral : 6.456 58.297 3838 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.35 % Allowed : 12.40 % Favored : 87.25 % Rotamer: Outliers : 4.97 % Allowed : 17.42 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -3.12 (0.13), residues: 3420 helix: -1.24 (0.19), residues: 804 sheet: -0.86 (0.19), residues: 876 loop : -3.24 (0.12), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 198 HIS 0.003 0.001 HIS E 337 PHE 0.014 0.001 PHE E 318 TYR 0.018 0.001 TYR A 128 ARG 0.004 0.000 ARG E 95 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 2796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 348 time to evaluate : 3.076 Fit side-chains REVERT: J 58 GLU cc_start: 0.7686 (tp30) cc_final: 0.7362 (tt0) REVERT: J 63 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7692 (tp30) REVERT: J 169 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8833 (tp) REVERT: J 295 ASN cc_start: 0.8534 (t0) cc_final: 0.8284 (t0) REVERT: J 297 ARG cc_start: 0.8039 (mtp85) cc_final: 0.7752 (pmt170) REVERT: I 63 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7355 (tm-30) REVERT: I 95 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7150 (mpt-90) REVERT: I 184 VAL cc_start: 0.8070 (OUTLIER) cc_final: 0.7789 (p) REVERT: I 215 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8274 (pt0) REVERT: I 276 VAL cc_start: 0.5675 (OUTLIER) cc_final: 0.5245 (t) REVERT: I 301 LEU cc_start: 0.8801 (mt) cc_final: 0.8519 (mp) REVERT: H 95 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7490 (mmt90) REVERT: H 227 THR cc_start: 0.8145 (OUTLIER) cc_final: 0.7652 (p) REVERT: H 297 ARG cc_start: 0.7775 (mtp85) cc_final: 0.7553 (pmt170) REVERT: G 63 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7411 (tm-30) REVERT: G 95 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7802 (mpt-90) REVERT: G 124 MET cc_start: 0.7917 (ttm) cc_final: 0.7621 (ttm) REVERT: G 128 TYR cc_start: 0.5124 (OUTLIER) cc_final: 0.4200 (p90) REVERT: G 184 VAL cc_start: 0.8173 (OUTLIER) cc_final: 0.7929 (p) REVERT: G 295 ASN cc_start: 0.8518 (t0) cc_final: 0.8300 (t0) REVERT: F 169 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8847 (tp) REVERT: F 287 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8728 (mm) REVERT: F 297 ARG cc_start: 0.7812 (mtp85) cc_final: 0.7605 (ptt-90) REVERT: E 184 VAL cc_start: 0.8093 (OUTLIER) cc_final: 0.7800 (p) REVERT: E 192 ILE cc_start: 0.9118 (OUTLIER) cc_final: 0.8893 (mt) REVERT: D 58 GLU cc_start: 0.7812 (tp30) cc_final: 0.7474 (tt0) REVERT: D 95 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.7328 (mmt90) REVERT: D 169 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8674 (tp) REVERT: D 178 ASP cc_start: 0.8087 (p0) cc_final: 0.7721 (m-30) REVERT: C 42 GLN cc_start: 0.8599 (tt0) cc_final: 0.8398 (tt0) REVERT: C 209 MET cc_start: 0.8936 (OUTLIER) cc_final: 0.8686 (mmt) REVERT: C 295 ASN cc_start: 0.8626 (t0) cc_final: 0.8374 (t0) REVERT: C 345 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.8300 (mtmt) REVERT: B 117 GLU cc_start: 0.9112 (mp0) cc_final: 0.8813 (mp0) REVERT: B 169 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8890 (tp) REVERT: B 287 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8744 (mm) REVERT: B 317 ASP cc_start: 0.8507 (OUTLIER) cc_final: 0.8255 (m-30) REVERT: A 63 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7594 (tm-30) REVERT: A 169 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.8978 (tp) REVERT: A 184 VAL cc_start: 0.8128 (OUTLIER) cc_final: 0.7849 (p) REVERT: L 178 ASP cc_start: 0.8171 (p0) cc_final: 0.7730 (m-30) REVERT: K 169 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.8994 (tp) outliers start: 139 outliers final: 99 residues processed: 451 average time/residue: 0.3786 time to fit residues: 266.6885 Evaluate side-chains 454 residues out of total 2796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 331 time to evaluate : 2.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 102 ASP Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 276 VAL Chi-restraints excluded: chain J residue 308 LEU Chi-restraints excluded: chain J residue 317 ASP Chi-restraints excluded: chain J residue 329 VAL Chi-restraints excluded: chain J residue 333 ASN Chi-restraints excluded: chain I residue 35 ILE Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 95 ARG Chi-restraints excluded: chain I residue 128 TYR Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain I residue 184 VAL Chi-restraints excluded: chain I residue 192 ILE Chi-restraints excluded: chain I residue 215 GLU Chi-restraints excluded: chain I residue 276 VAL Chi-restraints excluded: chain I residue 289 ILE Chi-restraints excluded: chain I residue 321 VAL Chi-restraints excluded: chain I residue 333 ASN Chi-restraints excluded: chain H residue 95 ARG Chi-restraints excluded: chain H residue 102 ASP Chi-restraints excluded: chain H residue 214 ILE Chi-restraints excluded: chain H residue 227 THR Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain H residue 283 ILE Chi-restraints excluded: chain H residue 317 ASP Chi-restraints excluded: chain H residue 333 ASN Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 95 ARG Chi-restraints excluded: chain G residue 128 TYR Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 224 SER Chi-restraints excluded: chain G residue 289 ILE Chi-restraints excluded: chain G residue 299 GLU Chi-restraints excluded: chain G residue 320 VAL Chi-restraints excluded: chain G residue 333 ASN Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 317 ASP Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 333 ASN Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 124 MET Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 333 ASN Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 317 ASP Chi-restraints excluded: chain D residue 333 ASN Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 128 TYR Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain C residue 345 LYS Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 102 ASP Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain L residue 276 VAL Chi-restraints excluded: chain L residue 317 ASP Chi-restraints excluded: chain L residue 329 VAL Chi-restraints excluded: chain L residue 333 ASN Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 124 MET Chi-restraints excluded: chain K residue 148 VAL Chi-restraints excluded: chain K residue 169 LEU Chi-restraints excluded: chain K residue 276 VAL Chi-restraints excluded: chain K residue 321 VAL Chi-restraints excluded: chain K residue 333 ASN Chi-restraints excluded: chain K residue 343 SER Chi-restraints excluded: chain K residue 345 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 313 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 185 optimal weight: 0.9980 chunk 237 optimal weight: 7.9990 chunk 183 optimal weight: 6.9990 chunk 273 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 chunk 323 optimal weight: 10.0000 chunk 202 optimal weight: 20.0000 chunk 197 optimal weight: 0.4980 chunk 149 optimal weight: 7.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 27312 Z= 0.226 Angle : 0.636 10.859 36972 Z= 0.323 Chirality : 0.046 0.228 4116 Planarity : 0.005 0.048 4740 Dihedral : 6.285 55.835 3836 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.35 % Allowed : 12.11 % Favored : 87.54 % Rotamer: Outliers : 5.15 % Allowed : 17.88 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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 (0.14), residues: 3420 helix: -1.15 (0.19), residues: 804 sheet: -0.75 (0.19), residues: 876 loop : -3.15 (0.12), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP G 228 HIS 0.003 0.001 HIS E 337 PHE 0.014 0.001 PHE I 318 TYR 0.019 0.001 TYR A 128 ARG 0.004 0.000 ARG C 225 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 2796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 356 time to evaluate : 2.966 Fit side-chains REVERT: J 63 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7676 (tp30) REVERT: J 169 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8832 (tp) REVERT: J 295 ASN cc_start: 0.8541 (t0) cc_final: 0.8278 (t0) REVERT: J 297 ARG cc_start: 0.8098 (mtp85) cc_final: 0.7829 (pmt170) REVERT: I 63 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7346 (tm-30) REVERT: I 95 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.7152 (mpt-90) REVERT: I 128 TYR cc_start: 0.5316 (OUTLIER) cc_final: 0.4977 (p90) REVERT: I 184 VAL cc_start: 0.8083 (OUTLIER) cc_final: 0.7815 (p) REVERT: I 215 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8273 (pt0) REVERT: I 276 VAL cc_start: 0.5623 (OUTLIER) cc_final: 0.5206 (t) REVERT: I 301 LEU cc_start: 0.8785 (mt) cc_final: 0.8480 (mp) REVERT: H 95 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7523 (mmt90) REVERT: H 209 MET cc_start: 0.9203 (mmm) cc_final: 0.8998 (mtp) REVERT: H 227 THR cc_start: 0.8141 (OUTLIER) cc_final: 0.7644 (p) REVERT: H 297 ARG cc_start: 0.7781 (mtp85) cc_final: 0.7566 (pmt170) REVERT: G 63 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7439 (tm-30) REVERT: G 95 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7758 (mpt-90) REVERT: G 124 MET cc_start: 0.7980 (ttm) cc_final: 0.7736 (ttm) REVERT: G 128 TYR cc_start: 0.5323 (OUTLIER) cc_final: 0.4164 (p90) REVERT: G 184 VAL cc_start: 0.8185 (OUTLIER) cc_final: 0.7948 (p) REVERT: F 169 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8848 (tp) REVERT: F 287 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8723 (mm) REVERT: F 297 ARG cc_start: 0.7847 (mtp85) cc_final: 0.7639 (ptt-90) REVERT: E 128 TYR cc_start: 0.4952 (OUTLIER) cc_final: 0.4600 (p90) REVERT: E 184 VAL cc_start: 0.8128 (OUTLIER) cc_final: 0.7814 (p) REVERT: E 192 ILE cc_start: 0.9127 (OUTLIER) cc_final: 0.8913 (mt) REVERT: D 58 GLU cc_start: 0.7790 (tp30) cc_final: 0.7464 (tt0) REVERT: D 95 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.7367 (mmt90) REVERT: D 169 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8673 (tp) REVERT: D 178 ASP cc_start: 0.8068 (p0) cc_final: 0.7712 (m-30) REVERT: C 42 GLN cc_start: 0.8606 (tt0) cc_final: 0.8405 (tt0) REVERT: C 63 GLU cc_start: 0.7666 (tm-30) cc_final: 0.7301 (tm-30) REVERT: C 209 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8688 (mmt) REVERT: C 295 ASN cc_start: 0.8587 (t0) cc_final: 0.8364 (t0) REVERT: B 117 GLU cc_start: 0.9095 (mp0) cc_final: 0.8813 (mp0) REVERT: B 169 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8882 (tp) REVERT: B 287 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8753 (mm) REVERT: B 317 ASP cc_start: 0.8486 (OUTLIER) cc_final: 0.8224 (m-30) REVERT: A 63 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7520 (tm-30) REVERT: A 169 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.8943 (tp) REVERT: A 184 VAL cc_start: 0.8076 (OUTLIER) cc_final: 0.7845 (p) REVERT: L 178 ASP cc_start: 0.8153 (p0) cc_final: 0.7729 (m-30) REVERT: K 63 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7388 (tm-30) outliers start: 144 outliers final: 102 residues processed: 463 average time/residue: 0.3813 time to fit residues: 275.9655 Evaluate side-chains 464 residues out of total 2796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 338 time to evaluate : 3.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 102 ASP Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 276 VAL Chi-restraints excluded: chain J residue 308 LEU Chi-restraints excluded: chain J residue 317 ASP Chi-restraints excluded: chain J residue 329 VAL Chi-restraints excluded: chain J residue 333 ASN Chi-restraints excluded: chain I residue 35 ILE Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 95 ARG Chi-restraints excluded: chain I residue 128 TYR Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain I residue 184 VAL Chi-restraints excluded: chain I residue 192 ILE Chi-restraints excluded: chain I residue 215 GLU Chi-restraints excluded: chain I residue 224 SER Chi-restraints excluded: chain I residue 276 VAL Chi-restraints excluded: chain I residue 289 ILE Chi-restraints excluded: chain I residue 321 VAL Chi-restraints excluded: chain I residue 333 ASN Chi-restraints excluded: chain H residue 95 ARG Chi-restraints excluded: chain H residue 102 ASP Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 214 ILE Chi-restraints excluded: chain H residue 227 THR Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain H residue 283 ILE Chi-restraints excluded: chain H residue 317 ASP Chi-restraints excluded: chain H residue 333 ASN Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 95 ARG Chi-restraints excluded: chain G residue 128 TYR Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 224 SER Chi-restraints excluded: chain G residue 289 ILE Chi-restraints excluded: chain G residue 299 GLU Chi-restraints excluded: chain G residue 320 VAL Chi-restraints excluded: chain G residue 333 ASN Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 317 ASP Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 333 ASN Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 124 MET Chi-restraints excluded: chain E residue 128 TYR Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 299 GLU Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 333 ASN Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 297 ARG Chi-restraints excluded: chain D residue 317 ASP Chi-restraints excluded: chain D residue 333 ASN Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 102 ASP Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain L residue 276 VAL Chi-restraints excluded: chain L residue 317 ASP Chi-restraints excluded: chain L residue 329 VAL Chi-restraints excluded: chain L residue 333 ASN Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 124 MET Chi-restraints excluded: chain K residue 147 THR Chi-restraints excluded: chain K residue 148 VAL Chi-restraints excluded: chain K residue 169 LEU Chi-restraints excluded: chain K residue 224 SER Chi-restraints excluded: chain K residue 276 VAL Chi-restraints excluded: chain K residue 321 VAL Chi-restraints excluded: chain K residue 333 ASN Chi-restraints excluded: chain K residue 343 SER Chi-restraints excluded: chain K residue 345 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 200 optimal weight: 7.9990 chunk 129 optimal weight: 0.6980 chunk 193 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 chunk 63 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 205 optimal weight: 5.9990 chunk 220 optimal weight: 10.0000 chunk 160 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 254 optimal weight: 1.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 333 ASN G 42 GLN ** F 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 42 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 27312 Z= 0.270 Angle : 0.657 10.367 36972 Z= 0.335 Chirality : 0.047 0.224 4116 Planarity : 0.005 0.047 4740 Dihedral : 6.429 57.503 3836 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.35 % Allowed : 13.07 % Favored : 86.58 % Rotamer: Outliers : 5.58 % Allowed : 17.81 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -2.94 (0.14), residues: 3420 helix: -1.16 (0.19), residues: 804 sheet: -0.66 (0.18), residues: 948 loop : -3.24 (0.13), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 228 HIS 0.004 0.001 HIS E 337 PHE 0.015 0.001 PHE E 318 TYR 0.021 0.001 TYR A 128 ARG 0.004 0.000 ARG K 171 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 2796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 336 time to evaluate : 3.040 Fit side-chains REVERT: J 54 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8837 (mp) REVERT: J 58 GLU cc_start: 0.7781 (tm-30) cc_final: 0.7566 (tt0) REVERT: J 169 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8857 (tp) REVERT: J 289 ILE cc_start: 0.8584 (mt) cc_final: 0.8333 (mm) REVERT: J 295 ASN cc_start: 0.8546 (t0) cc_final: 0.8275 (t0) REVERT: J 297 ARG cc_start: 0.7880 (mtp85) cc_final: 0.7591 (pmt170) REVERT: I 63 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7345 (tm-30) REVERT: I 184 VAL cc_start: 0.8102 (OUTLIER) cc_final: 0.7834 (p) REVERT: I 215 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8320 (pt0) REVERT: I 276 VAL cc_start: 0.5684 (OUTLIER) cc_final: 0.5261 (t) REVERT: I 301 LEU cc_start: 0.8792 (mt) cc_final: 0.8483 (mp) REVERT: H 95 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7579 (mmt90) REVERT: H 297 ARG cc_start: 0.7799 (mtp85) cc_final: 0.7554 (pmt170) REVERT: G 63 GLU cc_start: 0.7695 (mt-10) cc_final: 0.7436 (tm-30) REVERT: G 95 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7790 (mpt-90) REVERT: G 124 MET cc_start: 0.7964 (ttm) cc_final: 0.7746 (ttm) REVERT: G 128 TYR cc_start: 0.5472 (OUTLIER) cc_final: 0.4259 (p90) REVERT: G 184 VAL cc_start: 0.8188 (OUTLIER) cc_final: 0.7952 (p) REVERT: F 54 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8705 (mp) REVERT: F 169 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8905 (tp) REVERT: F 287 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8785 (mm) REVERT: F 297 ARG cc_start: 0.7856 (mtp85) cc_final: 0.7636 (ptt-90) REVERT: F 328 GLU cc_start: 0.9390 (OUTLIER) cc_final: 0.9155 (mp0) REVERT: E 128 TYR cc_start: 0.5263 (OUTLIER) cc_final: 0.4666 (p90) REVERT: E 184 VAL cc_start: 0.8137 (OUTLIER) cc_final: 0.7859 (p) REVERT: E 192 ILE cc_start: 0.9130 (OUTLIER) cc_final: 0.8896 (mt) REVERT: D 58 GLU cc_start: 0.7787 (tp30) cc_final: 0.7465 (tt0) REVERT: D 95 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.7387 (mmt90) REVERT: D 169 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8759 (tp) REVERT: D 178 ASP cc_start: 0.8083 (p0) cc_final: 0.7738 (m-30) REVERT: C 128 TYR cc_start: 0.5457 (OUTLIER) cc_final: 0.4906 (p90) REVERT: C 209 MET cc_start: 0.8956 (OUTLIER) cc_final: 0.8689 (mmt) REVERT: C 295 ASN cc_start: 0.8589 (t0) cc_final: 0.8356 (t0) REVERT: B 58 GLU cc_start: 0.7830 (tp30) cc_final: 0.7477 (tt0) REVERT: B 117 GLU cc_start: 0.9093 (mp0) cc_final: 0.8810 (mp0) REVERT: B 127 LYS cc_start: 0.5048 (pttm) cc_final: 0.4801 (pttm) REVERT: B 169 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8952 (tp) REVERT: B 287 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8824 (mm) REVERT: A 63 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7570 (tm-30) REVERT: A 169 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.8951 (tp) REVERT: A 184 VAL cc_start: 0.8155 (OUTLIER) cc_final: 0.7943 (p) REVERT: L 178 ASP cc_start: 0.8164 (p0) cc_final: 0.7733 (m-30) REVERT: K 63 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7413 (tm-30) REVERT: K 169 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.8983 (tp) outliers start: 156 outliers final: 116 residues processed: 459 average time/residue: 0.3935 time to fit residues: 282.9062 Evaluate side-chains 464 residues out of total 2796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 323 time to evaluate : 3.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 102 ASP Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 276 VAL Chi-restraints excluded: chain J residue 308 LEU Chi-restraints excluded: chain J residue 317 ASP Chi-restraints excluded: chain J residue 329 VAL Chi-restraints excluded: chain J residue 333 ASN Chi-restraints excluded: chain I residue 35 ILE Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 95 ARG Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain I residue 184 VAL Chi-restraints excluded: chain I residue 192 ILE Chi-restraints excluded: chain I residue 215 GLU Chi-restraints excluded: chain I residue 224 SER Chi-restraints excluded: chain I residue 276 VAL Chi-restraints excluded: chain I residue 289 ILE Chi-restraints excluded: chain I residue 321 VAL Chi-restraints excluded: chain I residue 333 ASN Chi-restraints excluded: chain H residue 95 ARG Chi-restraints excluded: chain H residue 102 ASP Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 147 THR Chi-restraints excluded: chain H residue 214 ILE Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain H residue 283 ILE Chi-restraints excluded: chain H residue 287 LEU Chi-restraints excluded: chain H residue 317 ASP Chi-restraints excluded: chain H residue 333 ASN Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 95 ARG Chi-restraints excluded: chain G residue 128 TYR Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 224 SER Chi-restraints excluded: chain G residue 289 ILE Chi-restraints excluded: chain G residue 299 GLU Chi-restraints excluded: chain G residue 320 VAL Chi-restraints excluded: chain G residue 333 ASN Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 317 ASP Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 333 ASN Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 124 MET Chi-restraints excluded: chain E residue 128 TYR Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 333 ASN Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 317 ASP Chi-restraints excluded: chain D residue 333 ASN Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 128 TYR Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 333 ASN Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 102 ASP Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain L residue 276 VAL Chi-restraints excluded: chain L residue 317 ASP Chi-restraints excluded: chain L residue 329 VAL Chi-restraints excluded: chain L residue 333 ASN Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 124 MET Chi-restraints excluded: chain K residue 147 THR Chi-restraints excluded: chain K residue 148 VAL Chi-restraints excluded: chain K residue 169 LEU Chi-restraints excluded: chain K residue 192 ILE Chi-restraints excluded: chain K residue 224 SER Chi-restraints excluded: chain K residue 276 VAL Chi-restraints excluded: chain K residue 289 ILE Chi-restraints excluded: chain K residue 321 VAL Chi-restraints excluded: chain K residue 333 ASN Chi-restraints excluded: chain K residue 343 SER Chi-restraints excluded: chain K residue 345 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 294 optimal weight: 20.0000 chunk 310 optimal weight: 6.9990 chunk 283 optimal weight: 5.9990 chunk 301 optimal weight: 3.9990 chunk 181 optimal weight: 2.9990 chunk 131 optimal weight: 9.9990 chunk 236 optimal weight: 0.8980 chunk 92 optimal weight: 8.9990 chunk 272 optimal weight: 8.9990 chunk 285 optimal weight: 0.9980 chunk 300 optimal weight: 7.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 67 ASN ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 27312 Z= 0.240 Angle : 0.646 10.644 36972 Z= 0.329 Chirality : 0.046 0.262 4116 Planarity : 0.005 0.046 4740 Dihedral : 6.400 59.421 3836 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.35 % Allowed : 12.13 % Favored : 87.51 % Rotamer: Outliers : 5.36 % Allowed : 18.06 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -2.89 (0.14), residues: 3420 helix: -1.12 (0.19), residues: 804 sheet: -0.66 (0.19), residues: 876 loop : -3.09 (0.12), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 228 HIS 0.004 0.001 HIS E 337 PHE 0.014 0.001 PHE E 318 TYR 0.020 0.001 TYR A 128 ARG 0.004 0.000 ARG C 225 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 336 time to evaluate : 3.407 Fit side-chains REVERT: J 54 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8807 (mp) REVERT: J 58 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7509 (tt0) REVERT: J 169 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8843 (tp) REVERT: J 289 ILE cc_start: 0.8579 (mt) cc_final: 0.8329 (mm) REVERT: J 297 ARG cc_start: 0.7960 (mtp85) cc_final: 0.7681 (pmt170) REVERT: I 63 GLU cc_start: 0.7645 (mt-10) cc_final: 0.7331 (tm-30) REVERT: I 184 VAL cc_start: 0.8117 (OUTLIER) cc_final: 0.7871 (p) REVERT: I 215 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8270 (pt0) REVERT: I 276 VAL cc_start: 0.5677 (OUTLIER) cc_final: 0.5260 (t) REVERT: I 301 LEU cc_start: 0.8783 (mt) cc_final: 0.8470 (mp) REVERT: H 95 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7582 (mmt90) REVERT: H 297 ARG cc_start: 0.7791 (mtp85) cc_final: 0.7558 (pmt170) REVERT: G 63 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7436 (tm-30) REVERT: G 95 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7776 (mpt-90) REVERT: G 124 MET cc_start: 0.7984 (ttm) cc_final: 0.7728 (ttm) REVERT: G 128 TYR cc_start: 0.5551 (OUTLIER) cc_final: 0.4334 (p90) REVERT: G 184 VAL cc_start: 0.8128 (OUTLIER) cc_final: 0.7902 (p) REVERT: F 54 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8677 (mp) REVERT: F 169 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8894 (tp) REVERT: F 287 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8759 (mm) REVERT: F 297 ARG cc_start: 0.7866 (mtp85) cc_final: 0.7628 (pmt170) REVERT: F 328 GLU cc_start: 0.9380 (OUTLIER) cc_final: 0.9144 (mp0) REVERT: E 128 TYR cc_start: 0.5187 (OUTLIER) cc_final: 0.4531 (p90) REVERT: E 184 VAL cc_start: 0.8094 (OUTLIER) cc_final: 0.7858 (p) REVERT: E 192 ILE cc_start: 0.9130 (OUTLIER) cc_final: 0.8901 (mt) REVERT: D 58 GLU cc_start: 0.7772 (tp30) cc_final: 0.7458 (tt0) REVERT: D 95 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7373 (mmt90) REVERT: D 169 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8755 (tp) REVERT: D 178 ASP cc_start: 0.8080 (p0) cc_final: 0.7738 (m-30) REVERT: C 128 TYR cc_start: 0.5495 (OUTLIER) cc_final: 0.4779 (p90) REVERT: C 209 MET cc_start: 0.8946 (OUTLIER) cc_final: 0.8689 (mmt) REVERT: B 58 GLU cc_start: 0.7828 (tp30) cc_final: 0.7474 (tt0) REVERT: B 117 GLU cc_start: 0.9097 (mp0) cc_final: 0.8833 (mp0) REVERT: B 169 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8936 (tp) REVERT: B 287 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8788 (mm) REVERT: B 317 ASP cc_start: 0.8517 (OUTLIER) cc_final: 0.8264 (m-30) REVERT: A 63 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7565 (tm-30) REVERT: L 178 ASP cc_start: 0.8165 (p0) cc_final: 0.7737 (m-30) REVERT: K 63 GLU cc_start: 0.7620 (mt-10) cc_final: 0.7400 (tm-30) REVERT: K 169 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.9021 (tp) outliers start: 150 outliers final: 114 residues processed: 452 average time/residue: 0.3801 time to fit residues: 269.6954 Evaluate side-chains 464 residues out of total 2796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 326 time to evaluate : 2.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 102 ASP Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 276 VAL Chi-restraints excluded: chain J residue 308 LEU Chi-restraints excluded: chain J residue 317 ASP Chi-restraints excluded: chain J residue 329 VAL Chi-restraints excluded: chain J residue 333 ASN Chi-restraints excluded: chain I residue 35 ILE Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 95 ARG Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain I residue 184 VAL Chi-restraints excluded: chain I residue 192 ILE Chi-restraints excluded: chain I residue 215 GLU Chi-restraints excluded: chain I residue 224 SER Chi-restraints excluded: chain I residue 276 VAL Chi-restraints excluded: chain I residue 289 ILE Chi-restraints excluded: chain I residue 321 VAL Chi-restraints excluded: chain I residue 333 ASN Chi-restraints excluded: chain H residue 95 ARG Chi-restraints excluded: chain H residue 102 ASP Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 214 ILE Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain H residue 283 ILE Chi-restraints excluded: chain H residue 287 LEU Chi-restraints excluded: chain H residue 317 ASP Chi-restraints excluded: chain H residue 333 ASN Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 95 ARG Chi-restraints excluded: chain G residue 128 TYR Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 224 SER Chi-restraints excluded: chain G residue 289 ILE Chi-restraints excluded: chain G residue 299 GLU Chi-restraints excluded: chain G residue 320 VAL Chi-restraints excluded: chain G residue 321 VAL Chi-restraints excluded: chain G residue 333 ASN Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 317 ASP Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 333 ASN Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 124 MET Chi-restraints excluded: chain E residue 128 TYR Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 333 ASN Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 297 ARG Chi-restraints excluded: chain D residue 317 ASP Chi-restraints excluded: chain D residue 333 ASN Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 128 TYR Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 333 ASN Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 102 ASP Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain L residue 276 VAL Chi-restraints excluded: chain L residue 317 ASP Chi-restraints excluded: chain L residue 329 VAL Chi-restraints excluded: chain L residue 333 ASN Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 124 MET Chi-restraints excluded: chain K residue 147 THR Chi-restraints excluded: chain K residue 148 VAL Chi-restraints excluded: chain K residue 169 LEU Chi-restraints excluded: chain K residue 192 ILE Chi-restraints excluded: chain K residue 224 SER Chi-restraints excluded: chain K residue 276 VAL Chi-restraints excluded: chain K residue 321 VAL Chi-restraints excluded: chain K residue 333 ASN Chi-restraints excluded: chain K residue 343 SER Chi-restraints excluded: chain K residue 345 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 198 optimal weight: 0.0000 chunk 319 optimal weight: 0.8980 chunk 194 optimal weight: 2.9990 chunk 151 optimal weight: 10.0000 chunk 221 optimal weight: 0.9990 chunk 334 optimal weight: 0.0370 chunk 308 optimal weight: 10.0000 chunk 266 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 205 optimal weight: 10.0000 chunk 163 optimal weight: 2.9990 overall best weight: 0.9866 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 323 HIS ** J 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 323 HIS H 333 ASN G 42 GLN ** F 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 323 HIS L 323 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 27312 Z= 0.160 Angle : 0.587 10.166 36972 Z= 0.298 Chirality : 0.044 0.209 4116 Planarity : 0.004 0.040 4740 Dihedral : 5.811 53.007 3835 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.35 % Allowed : 10.15 % Favored : 89.50 % Rotamer: Outliers : 4.33 % Allowed : 19.42 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -2.69 (0.14), residues: 3420 helix: -0.98 (0.19), residues: 816 sheet: -0.59 (0.19), residues: 876 loop : -2.93 (0.13), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 198 HIS 0.004 0.001 HIS L 234 PHE 0.011 0.001 PHE A 318 TYR 0.014 0.001 TYR A 128 ARG 0.004 0.000 ARG C 225 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 2796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 393 time to evaluate : 3.329 Fit side-chains REVERT: J 58 GLU cc_start: 0.7723 (tm-30) cc_final: 0.7458 (tt0) REVERT: J 63 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7711 (tp30) REVERT: J 169 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8704 (tp) REVERT: J 289 ILE cc_start: 0.8562 (mt) cc_final: 0.8320 (mm) REVERT: J 295 ASN cc_start: 0.8559 (t0) cc_final: 0.8293 (t0) REVERT: J 297 ARG cc_start: 0.7999 (mtp85) cc_final: 0.7724 (pmt170) REVERT: J 310 ASP cc_start: 0.9245 (t0) cc_final: 0.9024 (t0) REVERT: I 63 GLU cc_start: 0.7696 (mt-10) cc_final: 0.7435 (tm-30) REVERT: I 128 TYR cc_start: 0.5424 (OUTLIER) cc_final: 0.4984 (p90) REVERT: I 276 VAL cc_start: 0.5201 (OUTLIER) cc_final: 0.4824 (t) REVERT: I 301 LEU cc_start: 0.8680 (mt) cc_final: 0.8328 (mp) REVERT: H 95 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7667 (mmt90) REVERT: H 215 GLU cc_start: 0.8922 (pt0) cc_final: 0.8634 (mt-10) REVERT: H 283 ILE cc_start: 0.8722 (OUTLIER) cc_final: 0.8496 (mt) REVERT: H 297 ARG cc_start: 0.7835 (mtp85) cc_final: 0.7598 (pmt170) REVERT: G 63 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7441 (tm-30) REVERT: G 95 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.7057 (mpt-90) REVERT: G 124 MET cc_start: 0.7858 (ttm) cc_final: 0.7633 (ttm) REVERT: G 128 TYR cc_start: 0.5456 (OUTLIER) cc_final: 0.4180 (p90) REVERT: F 169 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8752 (tp) REVERT: F 287 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8647 (mm) REVERT: F 297 ARG cc_start: 0.7914 (mtp85) cc_final: 0.7666 (pmt170) REVERT: E 128 TYR cc_start: 0.5263 (OUTLIER) cc_final: 0.4543 (p90) REVERT: E 192 ILE cc_start: 0.9120 (pt) cc_final: 0.8647 (mt) REVERT: E 276 VAL cc_start: 0.5004 (OUTLIER) cc_final: 0.4704 (t) REVERT: D 58 GLU cc_start: 0.7679 (tp30) cc_final: 0.7294 (tt0) REVERT: D 95 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.7521 (mmt90) REVERT: D 169 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8614 (tp) REVERT: D 333 ASN cc_start: 0.8791 (OUTLIER) cc_final: 0.8475 (m110) REVERT: B 58 GLU cc_start: 0.7736 (tp30) cc_final: 0.7405 (tt0) REVERT: B 117 GLU cc_start: 0.9060 (mp0) cc_final: 0.8804 (mp0) REVERT: B 127 LYS cc_start: 0.4937 (pttm) cc_final: 0.4709 (pttm) REVERT: B 169 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8818 (tp) REVERT: B 178 ASP cc_start: 0.8428 (p0) cc_final: 0.8020 (m-30) REVERT: B 283 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8457 (mt) REVERT: B 287 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8583 (mm) REVERT: A 63 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7578 (tm-30) REVERT: A 169 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.9043 (tp) REVERT: A 276 VAL cc_start: 0.4879 (OUTLIER) cc_final: 0.4632 (t) REVERT: K 63 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7356 (tm-30) REVERT: K 128 TYR cc_start: 0.5035 (OUTLIER) cc_final: 0.4232 (p90) outliers start: 121 outliers final: 84 residues processed: 480 average time/residue: 0.3841 time to fit residues: 291.6203 Evaluate side-chains 458 residues out of total 2796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 354 time to evaluate : 3.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 102 ASP Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 169 LEU Chi-restraints excluded: chain J residue 276 VAL Chi-restraints excluded: chain J residue 308 LEU Chi-restraints excluded: chain J residue 317 ASP Chi-restraints excluded: chain J residue 329 VAL Chi-restraints excluded: chain J residue 333 ASN Chi-restraints excluded: chain I residue 35 ILE Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 128 TYR Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain I residue 192 ILE Chi-restraints excluded: chain I residue 276 VAL Chi-restraints excluded: chain I residue 289 ILE Chi-restraints excluded: chain I residue 321 VAL Chi-restraints excluded: chain I residue 333 ASN Chi-restraints excluded: chain H residue 95 ARG Chi-restraints excluded: chain H residue 102 ASP Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 214 ILE Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain H residue 283 ILE Chi-restraints excluded: chain H residue 287 LEU Chi-restraints excluded: chain H residue 317 ASP Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 95 ARG Chi-restraints excluded: chain G residue 128 TYR Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 224 SER Chi-restraints excluded: chain G residue 289 ILE Chi-restraints excluded: chain G residue 299 GLU Chi-restraints excluded: chain G residue 321 VAL Chi-restraints excluded: chain G residue 333 ASN Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 317 ASP Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 128 TYR Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 299 GLU Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 333 ASN Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 297 ARG Chi-restraints excluded: chain D residue 317 ASP Chi-restraints excluded: chain D residue 333 ASN Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 333 ASN Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain L residue 113 VAL Chi-restraints excluded: chain L residue 276 VAL Chi-restraints excluded: chain L residue 317 ASP Chi-restraints excluded: chain L residue 329 VAL Chi-restraints excluded: chain L residue 333 ASN Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 124 MET Chi-restraints excluded: chain K residue 128 TYR Chi-restraints excluded: chain K residue 147 THR Chi-restraints excluded: chain K residue 169 LEU Chi-restraints excluded: chain K residue 224 SER Chi-restraints excluded: chain K residue 276 VAL Chi-restraints excluded: chain K residue 321 VAL Chi-restraints excluded: chain K residue 333 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 211 optimal weight: 5.9990 chunk 283 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 245 optimal weight: 7.9990 chunk 39 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 chunk 266 optimal weight: 8.9990 chunk 111 optimal weight: 2.9990 chunk 274 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 49 optimal weight: 0.3980 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 ASN H 333 ASN ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.135131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.111085 restraints weight = 35610.628| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.98 r_work: 0.3057 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2904 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2737 r_free = 0.2737 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2737 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27312 Z= 0.206 Angle : 0.627 10.644 36972 Z= 0.318 Chirality : 0.045 0.222 4116 Planarity : 0.004 0.039 4740 Dihedral : 5.683 50.050 3830 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.35 % Allowed : 11.67 % Favored : 87.98 % Rotamer: Outliers : 4.04 % Allowed : 19.56 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -2.67 (0.14), residues: 3420 helix: -0.99 (0.19), residues: 816 sheet: -0.54 (0.19), residues: 876 loop : -2.92 (0.13), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 198 HIS 0.003 0.001 HIS E 337 PHE 0.011 0.001 PHE I 318 TYR 0.017 0.001 TYR A 128 ARG 0.004 0.000 ARG C 225 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6299.20 seconds wall clock time: 113 minutes 46.30 seconds (6826.30 seconds total)