Starting phenix.real_space_refine (version: dev) on Thu Dec 15 17:15:30 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i00_0320/12_2022/6i00_0320.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i00_0320/12_2022/6i00_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_0320/12_2022/6i00_0320.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i00_0320/12_2022/6i00_0320.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i00_0320/12_2022/6i00_0320.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i00_0320/12_2022/6i00_0320.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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 Convert atoms to be neutral 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: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 14.25, per 1000 atoms: 0.53 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: 9.79 Conformation dependent library (CDL) restraints added in 4.0 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: 1.51 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: 7.82 Time building geometry restraints manager: 10.66 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 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. 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: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 6.500 Check model and map are aligned: 0.410 Convert atoms to be neutral: 0.230 Process input model: 64.060 Find NCS groups from input model: 1.810 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9064 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 : 1.584 15.791 36972 Z= 0.963 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 : 7.17 Ramachandran Plot: Outliers : 0.73 % Allowed : 16.23 % Favored : 83.04 % Rotamer Outliers : 2.72 % 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 *********************** 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 : 3.324 Fit side-chains outliers start: 76 outliers final: 16 residues processed: 734 average time/residue: 0.4336 time to fit residues: 476.6410 Evaluate side-chains 380 residues out of total 2796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 364 time to evaluate : 3.212 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2223 time to fit residues: 11.0757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 141 optimal weight: 2.9990 chunk 86 optimal weight: 9.9990 chunk 171 optimal weight: 2.9990 chunk 136 optimal weight: 8.9990 chunk 263 optimal weight: 3.9990 chunk 101 optimal weight: 0.6980 chunk 160 optimal weight: 3.9990 chunk 196 optimal weight: 9.9990 chunk 305 optimal weight: 1.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 200 ASN ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 70 GLN I 200 ASN H 200 ASN G 200 ASN F 200 ASN E 200 ASN D 70 GLN D 200 ASN ** D 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 ASN B 200 ASN ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 ASN L 161 HIS L 200 ASN ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 200 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8962 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 27312 Z= 0.235 Angle : 0.731 12.144 36972 Z= 0.373 Chirality : 0.047 0.172 4116 Planarity : 0.005 0.093 4740 Dihedral : 6.516 53.735 3804 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.35 % Allowed : 11.81 % Favored : 87.84 % Rotamer Outliers : 4.29 % 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: -4.46 (0.12), residues: 3420 helix: -2.51 (0.15), residues: 816 sheet: -2.14 (0.18), residues: 780 loop : -3.67 (0.11), residues: 1824 *********************** 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 537 residues out of total 2796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 417 time to evaluate : 3.433 Fit side-chains outliers start: 120 outliers final: 53 residues processed: 511 average time/residue: 0.4082 time to fit residues: 320.8801 Evaluate side-chains 415 residues out of total 2796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 362 time to evaluate : 3.295 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 0 residues processed: 53 average time/residue: 0.2271 time to fit residues: 27.3987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 169 optimal weight: 9.9990 chunk 94 optimal weight: 8.9990 chunk 253 optimal weight: 8.9990 chunk 207 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 chunk 305 optimal weight: 7.9990 chunk 330 optimal weight: 10.0000 chunk 272 optimal weight: 10.0000 chunk 303 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 chunk 245 optimal weight: 1.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 333 ASN ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 333 ASN ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9049 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.080 27312 Z= 0.513 Angle : 0.849 12.220 36972 Z= 0.431 Chirality : 0.053 0.202 4116 Planarity : 0.006 0.072 4740 Dihedral : 6.534 51.196 3804 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.53 % Allowed : 15.03 % Favored : 84.44 % Rotamer Outliers : 3.90 % 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: -4.11 (0.12), residues: 3420 helix: -2.22 (0.16), residues: 804 sheet: -1.66 (0.18), residues: 780 loop : -3.59 (0.11), residues: 1836 *********************** 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 459 residues out of total 2796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 350 time to evaluate : 3.636 Fit side-chains outliers start: 109 outliers final: 80 residues processed: 430 average time/residue: 0.3978 time to fit residues: 266.7825 Evaluate side-chains 395 residues out of total 2796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 315 time to evaluate : 3.159 Switching outliers to nearest non-outliers outliers start: 80 outliers final: 0 residues processed: 80 average time/residue: 0.2432 time to fit residues: 40.2512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 302 optimal weight: 6.9990 chunk 229 optimal weight: 9.9990 chunk 158 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 145 optimal weight: 7.9990 chunk 205 optimal weight: 7.9990 chunk 306 optimal weight: 9.9990 chunk 324 optimal weight: 6.9990 chunk 160 optimal weight: 4.9990 chunk 290 optimal weight: 5.9990 chunk 87 optimal weight: 0.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 333 ASN ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 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: 0.9018 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.064 27312 Z= 0.357 Angle : 0.731 9.910 36972 Z= 0.373 Chirality : 0.049 0.238 4116 Planarity : 0.005 0.068 4740 Dihedral : 6.240 52.199 3804 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.35 % Allowed : 13.54 % Favored : 86.11 % Rotamer Outliers : 2.22 % 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: -3.84 (0.13), residues: 3420 helix: -1.97 (0.16), residues: 816 sheet: -1.45 (0.19), residues: 804 loop : -3.47 (0.12), residues: 1800 *********************** 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 417 residues out of total 2796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 355 time to evaluate : 3.469 Fit side-chains revert: symmetry clash outliers start: 62 outliers final: 30 residues processed: 401 average time/residue: 0.4070 time to fit residues: 251.3491 Evaluate side-chains 342 residues out of total 2796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 312 time to evaluate : 3.240 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.2420 time to fit residues: 17.4290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 270 optimal weight: 1.9990 chunk 184 optimal weight: 0.4980 chunk 4 optimal weight: 10.0000 chunk 241 optimal weight: 0.9980 chunk 134 optimal weight: 7.9990 chunk 277 optimal weight: 5.9990 chunk 224 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 165 optimal weight: 6.9990 chunk 291 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 323 HIS D 323 HIS ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 67 ASN B 323 HIS ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8962 moved from start: 0.3333 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= 0.197 Angle : 0.631 9.679 36972 Z= 0.322 Chirality : 0.045 0.222 4116 Planarity : 0.005 0.040 4740 Dihedral : 5.698 52.538 3804 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.35 % Allowed : 12.19 % Favored : 87.46 % Rotamer Outliers : 1.54 % 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: -3.43 (0.13), residues: 3420 helix: -1.51 (0.18), residues: 804 sheet: -1.21 (0.19), residues: 804 loop : -3.27 (0.12), residues: 1812 *********************** 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 400 residues out of total 2796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 357 time to evaluate : 3.249 Fit side-chains outliers start: 43 outliers final: 25 residues processed: 380 average time/residue: 0.3995 time to fit residues: 236.2662 Evaluate side-chains 346 residues out of total 2796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 321 time to evaluate : 3.349 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.2353 time to fit residues: 15.4068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 64 optimal weight: 7.9990 chunk 190 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 325 optimal weight: 7.9990 chunk 269 optimal weight: 9.9990 chunk 150 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 107 optimal weight: 10.0000 chunk 170 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 67 ASN I 42 GLN H 67 ASN ** H 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 337 HIS ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9024 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.059 27312 Z= 0.380 Angle : 0.744 10.638 36972 Z= 0.377 Chirality : 0.050 0.250 4116 Planarity : 0.005 0.046 4740 Dihedral : 5.934 50.272 3804 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.35 % Allowed : 14.53 % Favored : 85.12 % Rotamer Outliers : 1.79 % 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: -3.36 (0.13), residues: 3420 helix: -1.49 (0.18), residues: 792 sheet: -1.04 (0.18), residues: 876 loop : -3.33 (0.12), residues: 1752 *********************** 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 369 residues out of total 2796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 319 time to evaluate : 3.249 Fit side-chains outliers start: 50 outliers final: 27 residues processed: 359 average time/residue: 0.4072 time to fit residues: 224.6596 Evaluate side-chains 329 residues out of total 2796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 302 time to evaluate : 3.373 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.2545 time to fit residues: 17.1259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 313 optimal weight: 0.0050 chunk 36 optimal weight: 1.9990 chunk 185 optimal weight: 1.9990 chunk 237 optimal weight: 4.9990 chunk 183 optimal weight: 0.9980 chunk 273 optimal weight: 6.9990 chunk 181 optimal weight: 0.0470 chunk 323 optimal weight: 7.9990 chunk 202 optimal weight: 20.0000 chunk 197 optimal weight: 20.0000 chunk 149 optimal weight: 9.9990 overall best weight: 1.0096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 323 HIS ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 323 HIS ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 27312 Z= 0.164 Angle : 0.605 10.015 36972 Z= 0.309 Chirality : 0.044 0.222 4116 Planarity : 0.004 0.042 4740 Dihedral : 5.405 51.060 3804 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.35 % Allowed : 10.96 % Favored : 88.68 % Rotamer Outliers : 1.25 % 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: -3.06 (0.14), residues: 3420 helix: -1.34 (0.18), residues: 828 sheet: -0.77 (0.19), residues: 876 loop : -3.17 (0.12), residues: 1716 *********************** 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 391 residues out of total 2796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 356 time to evaluate : 3.306 Fit side-chains outliers start: 35 outliers final: 21 residues processed: 374 average time/residue: 0.4062 time to fit residues: 235.8299 Evaluate side-chains 339 residues out of total 2796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 318 time to evaluate : 3.408 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2418 time to fit residues: 14.0947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 200 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 193 optimal weight: 9.9990 chunk 97 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 205 optimal weight: 9.9990 chunk 220 optimal weight: 4.9990 chunk 160 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 chunk 254 optimal weight: 0.0770 overall best weight: 2.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 333 ASN ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 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: 0.8959 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 27312 Z= 0.224 Angle : 0.641 11.122 36972 Z= 0.324 Chirality : 0.046 0.231 4116 Planarity : 0.005 0.037 4740 Dihedral : 5.316 49.825 3804 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.35 % Allowed : 12.34 % Favored : 87.31 % Rotamer Outliers : 0.86 % 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: -2.91 (0.14), residues: 3420 helix: -1.18 (0.19), residues: 816 sheet: -0.69 (0.19), residues: 876 loop : -3.08 (0.12), residues: 1728 *********************** 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 368 residues out of total 2796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 344 time to evaluate : 3.015 Fit side-chains outliers start: 24 outliers final: 10 residues processed: 357 average time/residue: 0.4248 time to fit residues: 238.2072 Evaluate side-chains 334 residues out of total 2796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 324 time to evaluate : 3.260 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2425 time to fit residues: 9.1087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 294 optimal weight: 8.9990 chunk 310 optimal weight: 5.9990 chunk 283 optimal weight: 5.9990 chunk 301 optimal weight: 6.9990 chunk 181 optimal weight: 5.9990 chunk 131 optimal weight: 6.9990 chunk 236 optimal weight: 4.9990 chunk 92 optimal weight: 10.0000 chunk 272 optimal weight: 8.9990 chunk 285 optimal weight: 0.0170 chunk 300 optimal weight: 5.9990 overall best weight: 4.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 42 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9008 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 27312 Z= 0.330 Angle : 0.719 10.508 36972 Z= 0.363 Chirality : 0.049 0.268 4116 Planarity : 0.005 0.038 4740 Dihedral : 5.673 49.191 3804 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.35 % Allowed : 13.22 % Favored : 86.43 % Rotamer Outliers : 0.79 % 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: -2.88 (0.14), residues: 3420 helix: -0.84 (0.19), residues: 732 sheet: -0.89 (0.19), residues: 804 loop : -2.96 (0.12), residues: 1884 *********************** 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 355 residues out of total 2796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 333 time to evaluate : 3.387 Fit side-chains outliers start: 22 outliers final: 18 residues processed: 342 average time/residue: 0.4210 time to fit residues: 221.9687 Evaluate side-chains 324 residues out of total 2796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 306 time to evaluate : 3.381 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2405 time to fit residues: 12.3701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 198 optimal weight: 5.9990 chunk 319 optimal weight: 9.9990 chunk 194 optimal weight: 0.4980 chunk 151 optimal weight: 9.9990 chunk 221 optimal weight: 4.9990 chunk 334 optimal weight: 0.0270 chunk 308 optimal weight: 10.0000 chunk 266 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 205 optimal weight: 5.9990 chunk 163 optimal weight: 4.9990 overall best weight: 3.1044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8981 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 27312 Z= 0.248 Angle : 0.667 10.281 36972 Z= 0.337 Chirality : 0.047 0.246 4116 Planarity : 0.005 0.038 4740 Dihedral : 5.513 49.672 3804 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.35 % Allowed : 12.02 % Favored : 87.63 % Rotamer Outliers : 0.36 % 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: -0.73 (0.20), residues: 732 sheet: -0.65 (0.19), residues: 876 loop : -2.95 (0.13), residues: 1812 ********************** 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 332 residues out of total 2796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 322 time to evaluate : 3.401 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 327 average time/residue: 0.4182 time to fit residues: 212.8035 Evaluate side-chains 314 residues out of total 2796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 308 time to evaluate : 3.285 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2330 time to fit residues: 6.7520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 211 optimal weight: 8.9990 chunk 283 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 chunk 245 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 266 optimal weight: 10.0000 chunk 111 optimal weight: 8.9990 chunk 274 optimal weight: 0.9990 chunk 33 optimal weight: 8.9990 chunk 49 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 107 HIS ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.137111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.112364 restraints weight = 35954.981| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.18 r_work: 0.3026 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3532 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3532 r_free = 0.3532 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 133 | |-----------------------------------------------------------------------------| r_final: 0.3233 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.3760 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= 0.235 Angle : 0.660 10.065 36972 Z= 0.333 Chirality : 0.046 0.235 4116 Planarity : 0.004 0.038 4740 Dihedral : 5.406 49.655 3804 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.35 % Allowed : 11.93 % Favored : 87.72 % Rotamer Outliers : 0.43 % 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: -2.64 (0.14), residues: 3420 helix: -0.74 (0.20), residues: 744 sheet: -0.62 (0.19), residues: 876 loop : -2.89 (0.13), residues: 1800 =============================================================================== Job complete usr+sys time: 5715.09 seconds wall clock time: 104 minutes 8.87 seconds (6248.87 seconds total)