Starting phenix.real_space_refine on Sat Sep 28 08:49:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cej_45503/09_2024/9cej_45503.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cej_45503/09_2024/9cej_45503.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cej_45503/09_2024/9cej_45503.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cej_45503/09_2024/9cej_45503.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cej_45503/09_2024/9cej_45503.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cej_45503/09_2024/9cej_45503.cif" } resolution = 2.53 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= 0.005 sd= 0.116 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 144 5.16 5 C 42768 2.51 5 N 12060 2.21 5 O 14724 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 332 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 69696 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "B" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "C" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "D" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "E" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "F" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "G" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "H" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "I" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "J" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "K" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "L" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "M" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "O" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "P" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "T" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "Q" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "R" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "S" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "U" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "V" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "W" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "X" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "Y" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "Z" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "N" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "a" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "b" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "c" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "d" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "e" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "f" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "h" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "i" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "j" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "g" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Time building chain proxies: 31.11, per 1000 atoms: 0.45 Number of scatterers: 69696 At special positions: 0 Unit cell: (138.444, 136.776, 330.264, 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 144 16.00 O 14724 8.00 N 12060 7.00 C 42768 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.97 Conformation dependent library (CDL) restraints added in 7.4 seconds 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 18000 Finding SS restraints... Secondary structure from input PDB file: 277 helices and 36 sheets defined 76.5% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.29 Creating SS restraints... Processing helix chain 'A' and resid 9 through 36 Processing helix chain 'A' and resid 45 through 61 Processing helix chain 'A' and resid 61 through 101 removed outlier: 4.011A pdb=" N VAL A 65 " --> pdb=" O SER A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 130 Processing helix chain 'A' and resid 179 through 234 removed outlier: 3.994A pdb=" N GLY A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 263 removed outlier: 3.608A pdb=" N GLU A 240 " --> pdb=" O ASP A 236 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA A 242 " --> pdb=" O ALA A 238 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLN A 245 " --> pdb=" O SER A 241 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLN A 263 " --> pdb=" O SER A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 272 removed outlier: 3.813A pdb=" N SER A 267 " --> pdb=" O SER A 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 36 Processing helix chain 'B' and resid 45 through 61 Processing helix chain 'B' and resid 61 through 102 removed outlier: 4.034A pdb=" N VAL B 65 " --> pdb=" O SER B 61 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASP B 102 " --> pdb=" O LEU B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 130 Processing helix chain 'B' and resid 179 through 234 removed outlier: 4.100A pdb=" N GLY B 188 " --> pdb=" O LYS B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 263 removed outlier: 3.582A pdb=" N GLU B 240 " --> pdb=" O ASP B 236 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA B 242 " --> pdb=" O ALA B 238 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLN B 245 " --> pdb=" O SER B 241 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLN B 263 " --> pdb=" O SER B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 271 removed outlier: 4.099A pdb=" N LEU B 269 " --> pdb=" O SER B 265 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N SER B 270 " --> pdb=" O SER B 266 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU B 271 " --> pdb=" O SER B 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 265 through 271' Processing helix chain 'C' and resid 9 through 36 removed outlier: 3.955A pdb=" N MET C 13 " --> pdb=" O ASN C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 61 Processing helix chain 'C' and resid 61 through 101 removed outlier: 4.097A pdb=" N VAL C 65 " --> pdb=" O SER C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 130 Processing helix chain 'C' and resid 179 through 234 removed outlier: 3.977A pdb=" N GLY C 188 " --> pdb=" O LYS C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 263 removed outlier: 3.968A pdb=" N GLU C 240 " --> pdb=" O ASP C 236 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA C 242 " --> pdb=" O ALA C 238 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLN C 245 " --> pdb=" O SER C 241 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLN C 263 " --> pdb=" O SER C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 271 removed outlier: 3.877A pdb=" N LEU C 269 " --> pdb=" O SER C 265 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N SER C 270 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU C 271 " --> pdb=" O SER C 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 265 through 271' Processing helix chain 'D' and resid 9 through 36 Processing helix chain 'D' and resid 45 through 61 Processing helix chain 'D' and resid 61 through 102 removed outlier: 4.066A pdb=" N VAL D 65 " --> pdb=" O SER D 61 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ASP D 102 " --> pdb=" O LEU D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 130 Processing helix chain 'D' and resid 166 through 170 removed outlier: 3.568A pdb=" N ILE D 169 " --> pdb=" O LEU D 166 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY D 170 " --> pdb=" O ALA D 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 166 through 170' Processing helix chain 'D' and resid 179 through 234 removed outlier: 4.060A pdb=" N GLY D 188 " --> pdb=" O LYS D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 263 removed outlier: 3.988A pdb=" N GLU D 240 " --> pdb=" O ASP D 236 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA D 242 " --> pdb=" O ALA D 238 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLN D 245 " --> pdb=" O SER D 241 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLN D 263 " --> pdb=" O SER D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 272 removed outlier: 4.005A pdb=" N SER D 267 " --> pdb=" O SER D 264 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU D 269 " --> pdb=" O SER D 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 36 Processing helix chain 'E' and resid 45 through 61 Processing helix chain 'E' and resid 61 through 101 removed outlier: 3.939A pdb=" N VAL E 65 " --> pdb=" O SER E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 130 Processing helix chain 'E' and resid 179 through 234 removed outlier: 4.080A pdb=" N GLY E 188 " --> pdb=" O LYS E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 263 removed outlier: 4.153A pdb=" N GLU E 240 " --> pdb=" O ASP E 236 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA E 242 " --> pdb=" O ALA E 238 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLN E 245 " --> pdb=" O SER E 241 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLN E 263 " --> pdb=" O SER E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 271 removed outlier: 4.314A pdb=" N LEU E 269 " --> pdb=" O SER E 265 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N SER E 270 " --> pdb=" O SER E 266 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU E 271 " --> pdb=" O SER E 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 265 through 271' Processing helix chain 'F' and resid 9 through 36 removed outlier: 3.533A pdb=" N MET F 13 " --> pdb=" O ASN F 9 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 61 Processing helix chain 'F' and resid 61 through 101 removed outlier: 4.060A pdb=" N VAL F 65 " --> pdb=" O SER F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 130 Processing helix chain 'F' and resid 179 through 234 removed outlier: 4.123A pdb=" N GLY F 188 " --> pdb=" O LYS F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 236 through 263 removed outlier: 3.734A pdb=" N GLU F 240 " --> pdb=" O ASP F 236 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ALA F 242 " --> pdb=" O ALA F 238 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLN F 245 " --> pdb=" O SER F 241 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLN F 263 " --> pdb=" O SER F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 264 through 272 Processing helix chain 'G' and resid 9 through 36 Processing helix chain 'G' and resid 45 through 61 Processing helix chain 'G' and resid 61 through 102 removed outlier: 4.222A pdb=" N VAL G 65 " --> pdb=" O SER G 61 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASP G 102 " --> pdb=" O LEU G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 130 removed outlier: 3.612A pdb=" N PHE G 110 " --> pdb=" O ASN G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 170 removed outlier: 3.531A pdb=" N GLY G 170 " --> pdb=" O ALA G 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 179 through 234 removed outlier: 3.857A pdb=" N GLY G 188 " --> pdb=" O LYS G 184 " (cutoff:3.500A) Processing helix chain 'G' and resid 236 through 262 removed outlier: 3.818A pdb=" N GLU G 240 " --> pdb=" O ASP G 236 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA G 242 " --> pdb=" O ALA G 238 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLN G 245 " --> pdb=" O SER G 241 " (cutoff:3.500A) Processing helix chain 'G' and resid 263 through 272 removed outlier: 3.656A pdb=" N SER G 267 " --> pdb=" O SER G 264 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 36 Processing helix chain 'H' and resid 45 through 61 Processing helix chain 'H' and resid 61 through 101 removed outlier: 4.163A pdb=" N VAL H 65 " --> pdb=" O SER H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 131 removed outlier: 3.643A pdb=" N ALA H 131 " --> pdb=" O ALA H 127 " (cutoff:3.500A) Processing helix chain 'H' and resid 179 through 234 removed outlier: 4.063A pdb=" N GLY H 188 " --> pdb=" O LYS H 184 " (cutoff:3.500A) Processing helix chain 'H' and resid 236 through 262 removed outlier: 3.569A pdb=" N GLU H 240 " --> pdb=" O ASP H 236 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ALA H 242 " --> pdb=" O ALA H 238 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN H 245 " --> pdb=" O SER H 241 " (cutoff:3.500A) Processing helix chain 'H' and resid 263 through 272 removed outlier: 3.880A pdb=" N SER H 267 " --> pdb=" O SER H 264 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU H 269 " --> pdb=" O SER H 266 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 36 Processing helix chain 'I' and resid 45 through 61 Processing helix chain 'I' and resid 61 through 101 removed outlier: 4.167A pdb=" N VAL I 65 " --> pdb=" O SER I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 130 Processing helix chain 'I' and resid 179 through 234 removed outlier: 4.094A pdb=" N GLY I 188 " --> pdb=" O LYS I 184 " (cutoff:3.500A) Processing helix chain 'I' and resid 236 through 262 removed outlier: 3.553A pdb=" N GLU I 240 " --> pdb=" O ASP I 236 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA I 242 " --> pdb=" O ALA I 238 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLN I 245 " --> pdb=" O SER I 241 " (cutoff:3.500A) Processing helix chain 'I' and resid 263 through 272 removed outlier: 4.020A pdb=" N SER I 267 " --> pdb=" O SER I 264 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE I 268 " --> pdb=" O SER I 265 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU I 269 " --> pdb=" O SER I 266 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 36 Processing helix chain 'J' and resid 45 through 61 Processing helix chain 'J' and resid 61 through 102 removed outlier: 4.039A pdb=" N VAL J 65 " --> pdb=" O SER J 61 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASP J 102 " --> pdb=" O LEU J 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 106 through 130 Processing helix chain 'J' and resid 166 through 170 removed outlier: 3.647A pdb=" N ILE J 169 " --> pdb=" O LEU J 166 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY J 170 " --> pdb=" O ALA J 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 166 through 170' Processing helix chain 'J' and resid 179 through 234 removed outlier: 4.047A pdb=" N GLY J 188 " --> pdb=" O LYS J 184 " (cutoff:3.500A) Processing helix chain 'J' and resid 236 through 263 removed outlier: 4.077A pdb=" N GLU J 240 " --> pdb=" O ASP J 236 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA J 242 " --> pdb=" O ALA J 238 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLN J 245 " --> pdb=" O SER J 241 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLN J 263 " --> pdb=" O SER J 259 " (cutoff:3.500A) Processing helix chain 'J' and resid 266 through 271 removed outlier: 3.954A pdb=" N SER J 270 " --> pdb=" O SER J 266 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU J 271 " --> pdb=" O SER J 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 266 through 271' Processing helix chain 'K' and resid 9 through 36 Processing helix chain 'K' and resid 45 through 61 Processing helix chain 'K' and resid 62 through 101 Processing helix chain 'K' and resid 106 through 130 Processing helix chain 'K' and resid 165 through 170 removed outlier: 3.689A pdb=" N GLY K 170 " --> pdb=" O ALA K 167 " (cutoff:3.500A) Processing helix chain 'K' and resid 179 through 234 removed outlier: 3.922A pdb=" N GLY K 188 " --> pdb=" O LYS K 184 " (cutoff:3.500A) Processing helix chain 'K' and resid 236 through 263 removed outlier: 3.557A pdb=" N GLU K 240 " --> pdb=" O ASP K 236 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA K 242 " --> pdb=" O ALA K 238 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN K 245 " --> pdb=" O SER K 241 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLN K 263 " --> pdb=" O SER K 259 " (cutoff:3.500A) Processing helix chain 'K' and resid 264 through 272 removed outlier: 3.775A pdb=" N SER K 267 " --> pdb=" O SER K 264 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE K 268 " --> pdb=" O SER K 265 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 36 removed outlier: 3.590A pdb=" N MET L 13 " --> pdb=" O ASN L 9 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 61 Processing helix chain 'L' and resid 61 through 101 removed outlier: 4.235A pdb=" N VAL L 65 " --> pdb=" O SER L 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 106 through 130 Processing helix chain 'L' and resid 179 through 234 removed outlier: 3.960A pdb=" N GLY L 188 " --> pdb=" O LYS L 184 " (cutoff:3.500A) Processing helix chain 'L' and resid 237 through 263 removed outlier: 3.862A pdb=" N ALA L 242 " --> pdb=" O ALA L 238 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN L 245 " --> pdb=" O SER L 241 " (cutoff:3.500A) Processing helix chain 'L' and resid 264 through 266 No H-bonds generated for 'chain 'L' and resid 264 through 266' Processing helix chain 'L' and resid 267 through 272 removed outlier: 4.013A pdb=" N LEU L 271 " --> pdb=" O SER L 267 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N PHE L 272 " --> pdb=" O ILE L 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 267 through 272' Processing helix chain 'M' and resid 9 through 36 removed outlier: 3.584A pdb=" N MET M 13 " --> pdb=" O ASN M 9 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 61 Processing helix chain 'M' and resid 61 through 102 removed outlier: 4.131A pdb=" N VAL M 65 " --> pdb=" O SER M 61 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASP M 102 " --> pdb=" O LEU M 98 " (cutoff:3.500A) Processing helix chain 'M' and resid 106 through 131 removed outlier: 3.640A pdb=" N ALA M 131 " --> pdb=" O ALA M 127 " (cutoff:3.500A) Processing helix chain 'M' and resid 166 through 170 removed outlier: 3.518A pdb=" N ILE M 169 " --> pdb=" O LEU M 166 " (cutoff:3.500A) Processing helix chain 'M' and resid 179 through 234 removed outlier: 4.128A pdb=" N GLY M 188 " --> pdb=" O LYS M 184 " (cutoff:3.500A) Processing helix chain 'M' and resid 236 through 263 removed outlier: 3.756A pdb=" N ALA M 242 " --> pdb=" O ALA M 238 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLN M 245 " --> pdb=" O SER M 241 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLN M 263 " --> pdb=" O SER M 259 " (cutoff:3.500A) Processing helix chain 'M' and resid 264 through 266 No H-bonds generated for 'chain 'M' and resid 264 through 266' Processing helix chain 'M' and resid 267 through 272 removed outlier: 4.106A pdb=" N LEU M 271 " --> pdb=" O SER M 267 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE M 272 " --> pdb=" O ILE M 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 267 through 272' Processing helix chain 'O' and resid 9 through 36 removed outlier: 3.841A pdb=" N MET O 13 " --> pdb=" O ASN O 9 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 61 Processing helix chain 'O' and resid 61 through 101 removed outlier: 4.243A pdb=" N VAL O 65 " --> pdb=" O SER O 61 " (cutoff:3.500A) Processing helix chain 'O' and resid 106 through 130 Processing helix chain 'O' and resid 165 through 170 removed outlier: 3.674A pdb=" N GLY O 170 " --> pdb=" O ALA O 167 " (cutoff:3.500A) Processing helix chain 'O' and resid 179 through 234 removed outlier: 3.978A pdb=" N GLY O 188 " --> pdb=" O LYS O 184 " (cutoff:3.500A) Processing helix chain 'O' and resid 236 through 263 removed outlier: 3.810A pdb=" N THR O 249 " --> pdb=" O GLN O 245 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN O 263 " --> pdb=" O SER O 259 " (cutoff:3.500A) Processing helix chain 'O' and resid 264 through 266 No H-bonds generated for 'chain 'O' and resid 264 through 266' Processing helix chain 'O' and resid 267 through 272 removed outlier: 3.888A pdb=" N LEU O 271 " --> pdb=" O SER O 267 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE O 272 " --> pdb=" O ILE O 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 267 through 272' Processing helix chain 'P' and resid 9 through 36 removed outlier: 3.702A pdb=" N MET P 13 " --> pdb=" O ASN P 9 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 61 Processing helix chain 'P' and resid 61 through 102 removed outlier: 4.350A pdb=" N VAL P 65 " --> pdb=" O SER P 61 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ASP P 102 " --> pdb=" O LEU P 98 " (cutoff:3.500A) Processing helix chain 'P' and resid 106 through 130 Processing helix chain 'P' and resid 165 through 170 removed outlier: 3.699A pdb=" N GLY P 170 " --> pdb=" O ALA P 167 " (cutoff:3.500A) Processing helix chain 'P' and resid 179 through 234 removed outlier: 3.896A pdb=" N GLY P 188 " --> pdb=" O LYS P 184 " (cutoff:3.500A) Processing helix chain 'P' and resid 236 through 263 removed outlier: 3.646A pdb=" N ALA P 242 " --> pdb=" O ALA P 238 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN P 263 " --> pdb=" O SER P 259 " (cutoff:3.500A) Processing helix chain 'P' and resid 264 through 272 removed outlier: 4.055A pdb=" N SER P 267 " --> pdb=" O SER P 264 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE P 272 " --> pdb=" O LEU P 269 " (cutoff:3.500A) Processing helix chain 'T' and resid 9 through 36 removed outlier: 3.555A pdb=" N MET T 13 " --> pdb=" O ASN T 9 " (cutoff:3.500A) Processing helix chain 'T' and resid 45 through 61 Processing helix chain 'T' and resid 61 through 102 removed outlier: 4.186A pdb=" N VAL T 65 " --> pdb=" O SER T 61 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASP T 102 " --> pdb=" O LEU T 98 " (cutoff:3.500A) Processing helix chain 'T' and resid 106 through 130 Processing helix chain 'T' and resid 165 through 170 removed outlier: 3.695A pdb=" N GLY T 170 " --> pdb=" O ALA T 167 " (cutoff:3.500A) Processing helix chain 'T' and resid 179 through 234 removed outlier: 4.367A pdb=" N GLY T 188 " --> pdb=" O LYS T 184 " (cutoff:3.500A) Processing helix chain 'T' and resid 236 through 263 removed outlier: 3.719A pdb=" N GLN T 263 " --> pdb=" O SER T 259 " (cutoff:3.500A) Processing helix chain 'T' and resid 264 through 266 No H-bonds generated for 'chain 'T' and resid 264 through 266' Processing helix chain 'T' and resid 267 through 272 removed outlier: 3.722A pdb=" N LEU T 271 " --> pdb=" O SER T 267 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE T 272 " --> pdb=" O ILE T 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 267 through 272' Processing helix chain 'Q' and resid 9 through 36 removed outlier: 3.758A pdb=" N MET Q 13 " --> pdb=" O ASN Q 9 " (cutoff:3.500A) Processing helix chain 'Q' and resid 45 through 61 Processing helix chain 'Q' and resid 61 through 101 removed outlier: 4.153A pdb=" N VAL Q 65 " --> pdb=" O SER Q 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 106 through 130 Processing helix chain 'Q' and resid 165 through 170 removed outlier: 3.752A pdb=" N GLY Q 170 " --> pdb=" O ALA Q 167 " (cutoff:3.500A) Processing helix chain 'Q' and resid 179 through 234 removed outlier: 4.141A pdb=" N GLY Q 188 " --> pdb=" O LYS Q 184 " (cutoff:3.500A) Processing helix chain 'Q' and resid 236 through 264 removed outlier: 3.800A pdb=" N ALA Q 242 " --> pdb=" O ALA Q 238 " (cutoff:3.500A) Processing helix chain 'Q' and resid 266 through 271 removed outlier: 3.727A pdb=" N SER Q 270 " --> pdb=" O SER Q 266 " (cutoff:3.500A) Processing helix chain 'R' and resid 9 through 36 removed outlier: 3.798A pdb=" N MET R 13 " --> pdb=" O ASN R 9 " (cutoff:3.500A) Processing helix chain 'R' and resid 45 through 61 Processing helix chain 'R' and resid 61 through 101 removed outlier: 4.173A pdb=" N VAL R 65 " --> pdb=" O SER R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 106 through 130 Processing helix chain 'R' and resid 165 through 170 removed outlier: 3.977A pdb=" N GLY R 170 " --> pdb=" O ALA R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 179 through 234 removed outlier: 3.981A pdb=" N GLY R 188 " --> pdb=" O LYS R 184 " (cutoff:3.500A) Processing helix chain 'R' and resid 236 through 263 removed outlier: 3.650A pdb=" N GLU R 240 " --> pdb=" O ASP R 236 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN R 263 " --> pdb=" O SER R 259 " (cutoff:3.500A) Processing helix chain 'R' and resid 264 through 272 removed outlier: 4.270A pdb=" N SER R 267 " --> pdb=" O SER R 264 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE R 272 " --> pdb=" O LEU R 269 " (cutoff:3.500A) Processing helix chain 'S' and resid 9 through 36 removed outlier: 3.749A pdb=" N MET S 13 " --> pdb=" O ASN S 9 " (cutoff:3.500A) Processing helix chain 'S' and resid 45 through 61 Processing helix chain 'S' and resid 61 through 102 removed outlier: 4.155A pdb=" N VAL S 65 " --> pdb=" O SER S 61 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASP S 102 " --> pdb=" O LEU S 98 " (cutoff:3.500A) Processing helix chain 'S' and resid 106 through 130 Processing helix chain 'S' and resid 165 through 170 removed outlier: 3.882A pdb=" N GLY S 170 " --> pdb=" O ALA S 167 " (cutoff:3.500A) Processing helix chain 'S' and resid 179 through 234 removed outlier: 4.092A pdb=" N GLY S 188 " --> pdb=" O LYS S 184 " (cutoff:3.500A) Processing helix chain 'S' and resid 236 through 264 Processing helix chain 'S' and resid 265 through 272 removed outlier: 3.886A pdb=" N ILE S 268 " --> pdb=" O SER S 265 " (cutoff:3.500A) Processing helix chain 'U' and resid 9 through 36 removed outlier: 3.556A pdb=" N MET U 13 " --> pdb=" O ASN U 9 " (cutoff:3.500A) Processing helix chain 'U' and resid 45 through 61 Processing helix chain 'U' and resid 61 through 101 removed outlier: 4.191A pdb=" N VAL U 65 " --> pdb=" O SER U 61 " (cutoff:3.500A) Processing helix chain 'U' and resid 106 through 131 removed outlier: 3.690A pdb=" N ALA U 131 " --> pdb=" O ALA U 127 " (cutoff:3.500A) Processing helix chain 'U' and resid 179 through 234 removed outlier: 4.024A pdb=" N GLY U 188 " --> pdb=" O LYS U 184 " (cutoff:3.500A) Processing helix chain 'U' and resid 236 through 263 removed outlier: 3.872A pdb=" N GLU U 240 " --> pdb=" O ASP U 236 " (cutoff:3.500A) Processing helix chain 'U' and resid 266 through 272 removed outlier: 4.149A pdb=" N SER U 270 " --> pdb=" O SER U 266 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU U 271 " --> pdb=" O SER U 267 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N PHE U 272 " --> pdb=" O ILE U 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 266 through 272' Processing helix chain 'V' and resid 9 through 36 removed outlier: 3.601A pdb=" N MET V 13 " --> pdb=" O ASN V 9 " (cutoff:3.500A) Processing helix chain 'V' and resid 45 through 61 Processing helix chain 'V' and resid 62 through 101 Processing helix chain 'V' and resid 106 through 130 Processing helix chain 'V' and resid 179 through 234 removed outlier: 3.988A pdb=" N GLY V 188 " --> pdb=" O LYS V 184 " (cutoff:3.500A) Processing helix chain 'V' and resid 236 through 264 Processing helix chain 'V' and resid 265 through 272 Processing helix chain 'W' and resid 9 through 36 removed outlier: 3.575A pdb=" N MET W 13 " --> pdb=" O ASN W 9 " (cutoff:3.500A) Processing helix chain 'W' and resid 45 through 61 Processing helix chain 'W' and resid 61 through 101 removed outlier: 4.256A pdb=" N VAL W 65 " --> pdb=" O SER W 61 " (cutoff:3.500A) Processing helix chain 'W' and resid 106 through 130 Processing helix chain 'W' and resid 165 through 170 removed outlier: 3.803A pdb=" N GLY W 170 " --> pdb=" O ALA W 167 " (cutoff:3.500A) Processing helix chain 'W' and resid 179 through 234 removed outlier: 3.980A pdb=" N GLY W 188 " --> pdb=" O LYS W 184 " (cutoff:3.500A) Processing helix chain 'W' and resid 236 through 263 removed outlier: 3.905A pdb=" N GLN W 263 " --> pdb=" O SER W 259 " (cutoff:3.500A) Processing helix chain 'W' and resid 264 through 266 No H-bonds generated for 'chain 'W' and resid 264 through 266' Processing helix chain 'W' and resid 267 through 272 removed outlier: 4.134A pdb=" N LEU W 271 " --> pdb=" O SER W 267 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE W 272 " --> pdb=" O ILE W 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 267 through 272' Processing helix chain 'X' and resid 9 through 36 Processing helix chain 'X' and resid 45 through 61 Processing helix chain 'X' and resid 61 through 102 removed outlier: 4.200A pdb=" N VAL X 65 " --> pdb=" O SER X 61 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ASP X 102 " --> pdb=" O LEU X 98 " (cutoff:3.500A) Processing helix chain 'X' and resid 106 through 130 Processing helix chain 'X' and resid 165 through 170 removed outlier: 3.766A pdb=" N GLY X 170 " --> pdb=" O ALA X 167 " (cutoff:3.500A) Processing helix chain 'X' and resid 179 through 234 removed outlier: 3.889A pdb=" N GLY X 188 " --> pdb=" O LYS X 184 " (cutoff:3.500A) Processing helix chain 'X' and resid 236 through 263 removed outlier: 3.755A pdb=" N GLN X 263 " --> pdb=" O SER X 259 " (cutoff:3.500A) Processing helix chain 'X' and resid 264 through 272 removed outlier: 3.697A pdb=" N SER X 267 " --> pdb=" O SER X 264 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE X 272 " --> pdb=" O LEU X 269 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 36 Processing helix chain 'Y' and resid 45 through 61 Processing helix chain 'Y' and resid 61 through 101 removed outlier: 4.217A pdb=" N VAL Y 65 " --> pdb=" O SER Y 61 " (cutoff:3.500A) Processing helix chain 'Y' and resid 106 through 130 Processing helix chain 'Y' and resid 165 through 170 removed outlier: 3.812A pdb=" N GLY Y 170 " --> pdb=" O ALA Y 167 " (cutoff:3.500A) Processing helix chain 'Y' and resid 179 through 234 removed outlier: 4.055A pdb=" N GLY Y 188 " --> pdb=" O LYS Y 184 " (cutoff:3.500A) Processing helix chain 'Y' and resid 236 through 263 removed outlier: 3.510A pdb=" N GLU Y 240 " --> pdb=" O ASP Y 236 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN Y 263 " --> pdb=" O SER Y 259 " (cutoff:3.500A) Processing helix chain 'Y' and resid 266 through 271 removed outlier: 4.117A pdb=" N SER Y 270 " --> pdb=" O SER Y 266 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU Y 271 " --> pdb=" O SER Y 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 266 through 271' Processing helix chain 'Z' and resid 9 through 36 Processing helix chain 'Z' and resid 45 through 61 Processing helix chain 'Z' and resid 62 through 101 Processing helix chain 'Z' and resid 106 through 130 Processing helix chain 'Z' and resid 179 through 234 removed outlier: 4.107A pdb=" N GLY Z 188 " --> pdb=" O LYS Z 184 " (cutoff:3.500A) Processing helix chain 'Z' and resid 236 through 263 removed outlier: 3.544A pdb=" N GLN Z 245 " --> pdb=" O SER Z 241 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN Z 263 " --> pdb=" O SER Z 259 " (cutoff:3.500A) Processing helix chain 'Z' and resid 264 through 272 removed outlier: 3.811A pdb=" N SER Z 267 " --> pdb=" O SER Z 264 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE Z 268 " --> pdb=" O SER Z 265 " (cutoff:3.500A) Processing helix chain 'N' and resid 9 through 36 removed outlier: 4.176A pdb=" N MET N 13 " --> pdb=" O ASN N 9 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 61 Processing helix chain 'N' and resid 61 through 101 removed outlier: 4.217A pdb=" N VAL N 65 " --> pdb=" O SER N 61 " (cutoff:3.500A) Processing helix chain 'N' and resid 106 through 130 Processing helix chain 'N' and resid 179 through 234 removed outlier: 3.990A pdb=" N GLY N 188 " --> pdb=" O LYS N 184 " (cutoff:3.500A) Processing helix chain 'N' and resid 236 through 263 Processing helix chain 'N' and resid 264 through 270 removed outlier: 3.976A pdb=" N SER N 267 " --> pdb=" O SER N 264 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE N 268 " --> pdb=" O SER N 265 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU N 269 " --> pdb=" O SER N 266 " (cutoff:3.500A) Processing helix chain 'a' and resid 9 through 36 removed outlier: 3.633A pdb=" N MET a 13 " --> pdb=" O ASN a 9 " (cutoff:3.500A) Processing helix chain 'a' and resid 45 through 61 Processing helix chain 'a' and resid 61 through 101 removed outlier: 4.125A pdb=" N VAL a 65 " --> pdb=" O SER a 61 " (cutoff:3.500A) Processing helix chain 'a' and resid 106 through 130 Processing helix chain 'a' and resid 165 through 170 Processing helix chain 'a' and resid 179 through 234 removed outlier: 3.808A pdb=" N GLY a 188 " --> pdb=" O LYS a 184 " (cutoff:3.500A) Processing helix chain 'a' and resid 236 through 263 removed outlier: 3.568A pdb=" N GLU a 240 " --> pdb=" O ASP a 236 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN a 245 " --> pdb=" O SER a 241 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN a 263 " --> pdb=" O SER a 259 " (cutoff:3.500A) Processing helix chain 'a' and resid 264 through 272 removed outlier: 3.704A pdb=" N SER a 267 " --> pdb=" O SER a 264 " (cutoff:3.500A) Processing helix chain 'b' and resid 9 through 36 removed outlier: 3.605A pdb=" N MET b 13 " --> pdb=" O ASN b 9 " (cutoff:3.500A) Processing helix chain 'b' and resid 45 through 61 Processing helix chain 'b' and resid 61 through 101 removed outlier: 4.261A pdb=" N VAL b 65 " --> pdb=" O SER b 61 " (cutoff:3.500A) Processing helix chain 'b' and resid 106 through 130 Processing helix chain 'b' and resid 166 through 170 removed outlier: 3.709A pdb=" N GLY b 170 " --> pdb=" O ALA b 167 " (cutoff:3.500A) Processing helix chain 'b' and resid 179 through 234 removed outlier: 3.958A pdb=" N GLY b 188 " --> pdb=" O LYS b 184 " (cutoff:3.500A) Processing helix chain 'b' and resid 236 through 263 removed outlier: 3.555A pdb=" N GLU b 240 " --> pdb=" O ASP b 236 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLN b 263 " --> pdb=" O SER b 259 " (cutoff:3.500A) Processing helix chain 'b' and resid 266 through 271 removed outlier: 4.130A pdb=" N SER b 270 " --> pdb=" O SER b 266 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU b 271 " --> pdb=" O SER b 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 266 through 271' Processing helix chain 'c' and resid 9 through 36 removed outlier: 3.522A pdb=" N MET c 13 " --> pdb=" O ASN c 9 " (cutoff:3.500A) Processing helix chain 'c' and resid 45 through 61 Processing helix chain 'c' and resid 61 through 101 removed outlier: 4.263A pdb=" N VAL c 65 " --> pdb=" O SER c 61 " (cutoff:3.500A) Processing helix chain 'c' and resid 106 through 130 Processing helix chain 'c' and resid 179 through 234 removed outlier: 3.928A pdb=" N GLY c 188 " --> pdb=" O LYS c 184 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL c 233 " --> pdb=" O VAL c 229 " (cutoff:3.500A) Processing helix chain 'c' and resid 236 through 263 removed outlier: 3.513A pdb=" N GLU c 240 " --> pdb=" O ASP c 236 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN c 245 " --> pdb=" O SER c 241 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN c 263 " --> pdb=" O SER c 259 " (cutoff:3.500A) Processing helix chain 'c' and resid 264 through 272 removed outlier: 3.895A pdb=" N SER c 267 " --> pdb=" O SER c 264 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE c 268 " --> pdb=" O SER c 265 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU c 269 " --> pdb=" O SER c 266 " (cutoff:3.500A) Processing helix chain 'd' and resid 9 through 36 Processing helix chain 'd' and resid 45 through 61 Processing helix chain 'd' and resid 61 through 102 removed outlier: 4.226A pdb=" N VAL d 65 " --> pdb=" O SER d 61 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ASP d 102 " --> pdb=" O LEU d 98 " (cutoff:3.500A) Processing helix chain 'd' and resid 106 through 130 Processing helix chain 'd' and resid 166 through 170 Processing helix chain 'd' and resid 179 through 234 removed outlier: 4.134A pdb=" N GLY d 188 " --> pdb=" O LYS d 184 " (cutoff:3.500A) Processing helix chain 'd' and resid 236 through 263 removed outlier: 3.531A pdb=" N GLU d 240 " --> pdb=" O ASP d 236 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA d 242 " --> pdb=" O ALA d 238 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN d 263 " --> pdb=" O SER d 259 " (cutoff:3.500A) Processing helix chain 'd' and resid 266 through 271 removed outlier: 4.109A pdb=" N SER d 270 " --> pdb=" O SER d 266 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU d 271 " --> pdb=" O SER d 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 266 through 271' Processing helix chain 'e' and resid 9 through 36 removed outlier: 3.632A pdb=" N MET e 13 " --> pdb=" O ASN e 9 " (cutoff:3.500A) Processing helix chain 'e' and resid 45 through 61 Processing helix chain 'e' and resid 61 through 101 removed outlier: 4.112A pdb=" N VAL e 65 " --> pdb=" O SER e 61 " (cutoff:3.500A) Processing helix chain 'e' and resid 106 through 130 Processing helix chain 'e' and resid 179 through 234 removed outlier: 4.125A pdb=" N GLY e 188 " --> pdb=" O LYS e 184 " (cutoff:3.500A) Processing helix chain 'e' and resid 236 through 264 removed outlier: 3.771A pdb=" N GLN e 245 " --> pdb=" O SER e 241 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER e 264 " --> pdb=" O ILE e 260 " (cutoff:3.500A) Processing helix chain 'e' and resid 265 through 272 removed outlier: 3.505A pdb=" N ILE e 268 " --> pdb=" O SER e 265 " (cutoff:3.500A) Processing helix chain 'f' and resid 9 through 36 removed outlier: 3.934A pdb=" N MET f 13 " --> pdb=" O ASN f 9 " (cutoff:3.500A) Processing helix chain 'f' and resid 45 through 101 removed outlier: 4.713A pdb=" N ASN f 63 " --> pdb=" O ALA f 59 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N ALA f 64 " --> pdb=" O ALA f 60 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL f 65 " --> pdb=" O SER f 61 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N THR f 85 " --> pdb=" O ALA f 81 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LYS f 94 " --> pdb=" O LEU f 90 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLU f 95 " --> pdb=" O GLY f 91 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS f 96 " --> pdb=" O LYS f 92 " (cutoff:3.500A) Processing helix chain 'f' and resid 106 through 131 removed outlier: 3.655A pdb=" N THR f 129 " --> pdb=" O GLU f 125 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA f 131 " --> pdb=" O ALA f 127 " (cutoff:3.500A) Processing helix chain 'f' and resid 165 through 170 Processing helix chain 'f' and resid 179 through 234 removed outlier: 4.463A pdb=" N GLY f 188 " --> pdb=" O LYS f 184 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N THR f 189 " --> pdb=" O THR f 185 " (cutoff:3.500A) Processing helix chain 'f' and resid 236 through 263 removed outlier: 4.439A pdb=" N ALA f 242 " --> pdb=" O ALA f 238 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS f 243 " --> pdb=" O LYS f 239 " (cutoff:3.500A) Processing helix chain 'f' and resid 265 through 272 removed outlier: 4.058A pdb=" N LEU f 269 " --> pdb=" O SER f 265 " (cutoff:3.500A) Processing helix chain 'h' and resid 9 through 36 Processing helix chain 'h' and resid 45 through 61 Processing helix chain 'h' and resid 61 through 101 removed outlier: 4.346A pdb=" N VAL h 65 " --> pdb=" O SER h 61 " (cutoff:3.500A) Processing helix chain 'h' and resid 106 through 130 Processing helix chain 'h' and resid 166 through 170 removed outlier: 3.591A pdb=" N GLY h 170 " --> pdb=" O ALA h 167 " (cutoff:3.500A) Processing helix chain 'h' and resid 179 through 234 removed outlier: 4.095A pdb=" N GLY h 188 " --> pdb=" O LYS h 184 " (cutoff:3.500A) Processing helix chain 'h' and resid 236 through 263 removed outlier: 3.553A pdb=" N GLU h 240 " --> pdb=" O ASP h 236 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA h 242 " --> pdb=" O ALA h 238 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLN h 245 " --> pdb=" O SER h 241 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLN h 263 " --> pdb=" O SER h 259 " (cutoff:3.500A) Processing helix chain 'h' and resid 265 through 271 removed outlier: 4.084A pdb=" N LEU h 269 " --> pdb=" O SER h 265 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N SER h 270 " --> pdb=" O SER h 266 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU h 271 " --> pdb=" O SER h 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 265 through 271' Processing helix chain 'i' and resid 9 through 36 removed outlier: 3.622A pdb=" N MET i 13 " --> pdb=" O ASN i 9 " (cutoff:3.500A) Processing helix chain 'i' and resid 45 through 61 Processing helix chain 'i' and resid 61 through 102 removed outlier: 4.171A pdb=" N VAL i 65 " --> pdb=" O SER i 61 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASP i 102 " --> pdb=" O LEU i 98 " (cutoff:3.500A) Processing helix chain 'i' and resid 106 through 130 Processing helix chain 'i' and resid 179 through 234 removed outlier: 4.109A pdb=" N GLY i 188 " --> pdb=" O LYS i 184 " (cutoff:3.500A) Processing helix chain 'i' and resid 236 through 262 removed outlier: 3.674A pdb=" N GLU i 240 " --> pdb=" O ASP i 236 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA i 242 " --> pdb=" O ALA i 238 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLN i 245 " --> pdb=" O SER i 241 " (cutoff:3.500A) Processing helix chain 'i' and resid 265 through 272 removed outlier: 4.198A pdb=" N LEU i 269 " --> pdb=" O SER i 265 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N SER i 270 " --> pdb=" O SER i 266 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU i 271 " --> pdb=" O SER i 267 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE i 272 " --> pdb=" O ILE i 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 265 through 272' Processing helix chain 'j' and resid 9 through 36 Processing helix chain 'j' and resid 45 through 61 Processing helix chain 'j' and resid 61 through 101 removed outlier: 4.101A pdb=" N VAL j 65 " --> pdb=" O SER j 61 " (cutoff:3.500A) Processing helix chain 'j' and resid 106 through 130 Processing helix chain 'j' and resid 166 through 170 removed outlier: 3.694A pdb=" N ILE j 169 " --> pdb=" O LEU j 166 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY j 170 " --> pdb=" O ALA j 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 166 through 170' Processing helix chain 'j' and resid 179 through 234 removed outlier: 4.042A pdb=" N GLY j 188 " --> pdb=" O LYS j 184 " (cutoff:3.500A) Processing helix chain 'j' and resid 236 through 263 removed outlier: 3.573A pdb=" N GLU j 240 " --> pdb=" O ASP j 236 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA j 242 " --> pdb=" O ALA j 238 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLN j 263 " --> pdb=" O SER j 259 " (cutoff:3.500A) Processing helix chain 'j' and resid 264 through 272 removed outlier: 3.888A pdb=" N SER j 267 " --> pdb=" O SER j 264 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE j 268 " --> pdb=" O SER j 265 " (cutoff:3.500A) Processing helix chain 'g' and resid 9 through 36 Processing helix chain 'g' and resid 45 through 61 Processing helix chain 'g' and resid 61 through 101 removed outlier: 4.156A pdb=" N VAL g 65 " --> pdb=" O SER g 61 " (cutoff:3.500A) Processing helix chain 'g' and resid 106 through 130 Processing helix chain 'g' and resid 166 through 170 removed outlier: 3.525A pdb=" N GLY g 170 " --> pdb=" O ALA g 167 " (cutoff:3.500A) Processing helix chain 'g' and resid 179 through 234 removed outlier: 4.095A pdb=" N GLY g 188 " --> pdb=" O LYS g 184 " (cutoff:3.500A) Processing helix chain 'g' and resid 236 through 263 removed outlier: 3.641A pdb=" N GLU g 240 " --> pdb=" O ASP g 236 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA g 242 " --> pdb=" O ALA g 238 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLN g 245 " --> pdb=" O SER g 241 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN g 263 " --> pdb=" O SER g 259 " (cutoff:3.500A) Processing helix chain 'g' and resid 265 through 271 removed outlier: 4.218A pdb=" N LEU g 269 " --> pdb=" O SER g 265 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER g 270 " --> pdb=" O SER g 266 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU g 271 " --> pdb=" O SER g 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 265 through 271' Processing sheet with id=AA1, first strand: chain 'A' and resid 145 through 146 Processing sheet with id=AA2, first strand: chain 'B' and resid 145 through 149 Processing sheet with id=AA3, first strand: chain 'C' and resid 145 through 146 Processing sheet with id=AA4, first strand: chain 'D' and resid 145 through 149 Processing sheet with id=AA5, first strand: chain 'E' and resid 145 through 149 Processing sheet with id=AA6, first strand: chain 'F' and resid 145 through 149 removed outlier: 3.532A pdb=" N PHE F 148 " --> pdb=" O PHE F 157 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 145 through 149 Processing sheet with id=AA8, first strand: chain 'H' and resid 145 through 149 Processing sheet with id=AA9, first strand: chain 'I' and resid 145 through 146 Processing sheet with id=AB1, first strand: chain 'J' and resid 145 through 146 Processing sheet with id=AB2, first strand: chain 'K' and resid 145 through 149 Processing sheet with id=AB3, first strand: chain 'L' and resid 145 through 149 Processing sheet with id=AB4, first strand: chain 'M' and resid 145 through 149 Processing sheet with id=AB5, first strand: chain 'O' and resid 145 through 149 Processing sheet with id=AB6, first strand: chain 'P' and resid 148 through 149 Processing sheet with id=AB7, first strand: chain 'T' and resid 145 through 149 Processing sheet with id=AB8, first strand: chain 'Q' and resid 145 through 149 Processing sheet with id=AB9, first strand: chain 'R' and resid 145 through 149 Processing sheet with id=AC1, first strand: chain 'S' and resid 145 through 149 Processing sheet with id=AC2, first strand: chain 'U' and resid 145 through 149 Processing sheet with id=AC3, first strand: chain 'V' and resid 145 through 149 Processing sheet with id=AC4, first strand: chain 'W' and resid 145 through 149 Processing sheet with id=AC5, first strand: chain 'X' and resid 145 through 149 Processing sheet with id=AC6, first strand: chain 'Y' and resid 145 through 149 Processing sheet with id=AC7, first strand: chain 'Z' and resid 145 through 149 Processing sheet with id=AC8, first strand: chain 'N' and resid 145 through 149 Processing sheet with id=AC9, first strand: chain 'a' and resid 145 through 149 Processing sheet with id=AD1, first strand: chain 'b' and resid 145 through 149 Processing sheet with id=AD2, first strand: chain 'c' and resid 145 through 149 removed outlier: 3.563A pdb=" N PHE c 148 " --> pdb=" O PHE c 157 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'd' and resid 145 through 149 Processing sheet with id=AD4, first strand: chain 'e' and resid 145 through 149 Processing sheet with id=AD5, first strand: chain 'f' and resid 145 through 149 Processing sheet with id=AD6, first strand: chain 'h' and resid 145 through 149 Processing sheet with id=AD7, first strand: chain 'i' and resid 145 through 146 Processing sheet with id=AD8, first strand: chain 'j' and resid 145 through 146 Processing sheet with id=AD9, first strand: chain 'g' and resid 145 through 146 6203 hydrogen bonds defined for protein. 18276 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: 27.70 Time building geometry restraints manager: 16.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 16891 1.33 - 1.45: 11741 1.45 - 1.57: 41136 1.57 - 1.69: 0 1.69 - 1.81: 288 Bond restraints: 70056 Sorted by residual: bond pdb=" CB GLN f 70 " pdb=" CG GLN f 70 " ideal model delta sigma weight residual 1.520 1.451 0.069 3.00e-02 1.11e+03 5.30e+00 bond pdb=" N LEU W 26 " pdb=" CA LEU W 26 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.23e-02 6.61e+03 4.73e+00 bond pdb=" CG1 ILE b 124 " pdb=" CD1 ILE b 124 " ideal model delta sigma weight residual 1.513 1.450 0.063 3.90e-02 6.57e+02 2.58e+00 bond pdb=" CG1 ILE S 124 " pdb=" CD1 ILE S 124 " ideal model delta sigma weight residual 1.513 1.460 0.053 3.90e-02 6.57e+02 1.82e+00 bond pdb=" CB MET f 93 " pdb=" CG MET f 93 " ideal model delta sigma weight residual 1.520 1.481 0.039 3.00e-02 1.11e+03 1.72e+00 ... (remaining 70051 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 93751 2.15 - 4.30: 973 4.30 - 6.44: 82 6.44 - 8.59: 14 8.59 - 10.74: 4 Bond angle restraints: 94824 Sorted by residual: angle pdb=" C LEU D 232 " pdb=" N VAL D 233 " pdb=" CA VAL D 233 " ideal model delta sigma weight residual 122.77 118.61 4.16 1.05e+00 9.07e-01 1.57e+01 angle pdb=" N GLU F 95 " pdb=" CA GLU F 95 " pdb=" CB GLU F 95 " ideal model delta sigma weight residual 110.28 115.89 -5.61 1.55e+00 4.16e-01 1.31e+01 angle pdb=" CB MET X 93 " pdb=" CG MET X 93 " pdb=" SD MET X 93 " ideal model delta sigma weight residual 112.70 101.96 10.74 3.00e+00 1.11e-01 1.28e+01 angle pdb=" C LYS F 94 " pdb=" N GLU F 95 " pdb=" CA GLU F 95 " ideal model delta sigma weight residual 120.31 114.88 5.43 1.52e+00 4.33e-01 1.28e+01 angle pdb=" N ILE G 164 " pdb=" CA ILE G 164 " pdb=" C ILE G 164 " ideal model delta sigma weight residual 112.43 109.26 3.17 9.20e-01 1.18e+00 1.19e+01 ... (remaining 94819 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 39638 17.99 - 35.99: 2562 35.99 - 53.98: 311 53.98 - 71.98: 102 71.98 - 89.97: 83 Dihedral angle restraints: 42696 sinusoidal: 15012 harmonic: 27684 Sorted by residual: dihedral pdb=" CA GLN f 263 " pdb=" C GLN f 263 " pdb=" N SER f 264 " pdb=" CA SER f 264 " ideal model delta harmonic sigma weight residual -180.00 -155.54 -24.46 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA GLN e 263 " pdb=" C GLN e 263 " pdb=" N SER e 264 " pdb=" CA SER e 264 " ideal model delta harmonic sigma weight residual 180.00 -159.82 -20.18 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA ASP U 236 " pdb=" C ASP U 236 " pdb=" N LEU U 237 " pdb=" CA LEU U 237 " ideal model delta harmonic sigma weight residual -180.00 -160.47 -19.53 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 42693 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 10531 0.054 - 0.109: 1485 0.109 - 0.163: 177 0.163 - 0.217: 10 0.217 - 0.271: 1 Chirality restraints: 12204 Sorted by residual: chirality pdb=" CB ILE W 124 " pdb=" CA ILE W 124 " pdb=" CG1 ILE W 124 " pdb=" CG2 ILE W 124 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CB THR j 87 " pdb=" CA THR j 87 " pdb=" OG1 THR j 87 " pdb=" CG2 THR j 87 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.88e-01 chirality pdb=" CB ILE R 86 " pdb=" CA ILE R 86 " pdb=" CG1 ILE R 86 " pdb=" CG2 ILE R 86 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.43e-01 ... (remaining 12201 not shown) Planarity restraints: 12132 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU W 25 " -0.013 2.00e-02 2.50e+03 2.56e-02 6.57e+00 pdb=" C GLU W 25 " 0.044 2.00e-02 2.50e+03 pdb=" O GLU W 25 " -0.017 2.00e-02 2.50e+03 pdb=" N LEU W 26 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP f 49 " 0.022 2.00e-02 2.50e+03 1.54e-02 5.90e+00 pdb=" CG TRP f 49 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP f 49 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP f 49 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP f 49 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP f 49 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP f 49 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP f 49 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP f 49 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP f 49 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN Q 245 " -0.010 2.00e-02 2.50e+03 1.98e-02 3.92e+00 pdb=" CD GLN Q 245 " 0.034 2.00e-02 2.50e+03 pdb=" OE1 GLN Q 245 " -0.013 2.00e-02 2.50e+03 pdb=" NE2 GLN Q 245 " -0.012 2.00e-02 2.50e+03 ... (remaining 12129 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 523 2.63 - 3.20: 65656 3.20 - 3.76: 113479 3.76 - 4.33: 150264 4.33 - 4.90: 247032 Nonbonded interactions: 576954 Sorted by model distance: nonbonded pdb=" NE2 GLN N 73 " pdb=" OD1 ASP N 212 " model vdw 2.060 3.120 nonbonded pdb=" NZ LYS P 94 " pdb=" OD1 ASP P 191 " model vdw 2.094 3.120 nonbonded pdb=" O ILE C 6 " pdb=" OG SER j 246 " model vdw 2.134 3.040 nonbonded pdb=" OD1 ASP f 118 " pdb=" NE ARG f 121 " model vdw 2.140 3.120 nonbonded pdb=" OG SER e 152 " pdb=" NZ LYS f 94 " model vdw 2.151 3.120 ... (remaining 576949 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 7.270 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: 0.070 Extract box with map and model: 2.030 Check model and map are aligned: 0.390 Set scattering table: 0.500 Process input model: 125.700 Find NCS groups from input model: 2.340 Set up NCS constraints: 0.830 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: 0.020 Load rotamer database and sin/cos tables:13.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 152.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 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 : 0.003 0.069 70056 Z= 0.208 Angle : 0.604 10.739 94824 Z= 0.358 Chirality : 0.037 0.271 12204 Planarity : 0.004 0.050 12132 Dihedral : 12.854 89.969 24696 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.71 % Favored : 98.23 % Rotamer: Outliers : 0.04 % Allowed : 0.25 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.07), residues: 9648 helix: 0.18 (0.05), residues: 6948 sheet: -3.46 (0.18), residues: 432 loop : 1.98 (0.15), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP f 49 HIS 0.004 0.001 HIS Z 214 PHE 0.032 0.002 PHE c 117 ARG 0.014 0.001 ARG a 71 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1090 residues out of total 7560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1087 time to evaluate : 5.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASN cc_start: 0.7865 (t0) cc_final: 0.7046 (p0) REVERT: B 95 GLU cc_start: 0.7592 (mm-30) cc_final: 0.6920 (mt-10) REVERT: B 256 GLN cc_start: 0.7823 (tt0) cc_final: 0.7594 (tt0) REVERT: D 95 GLU cc_start: 0.5390 (mm-30) cc_final: 0.4961 (mt-10) REVERT: E 13 MET cc_start: 0.8443 (mtt) cc_final: 0.8237 (mtm) REVERT: E 240 GLU cc_start: 0.8119 (mp0) cc_final: 0.7887 (mm-30) REVERT: E 256 GLN cc_start: 0.7968 (tt0) cc_final: 0.7556 (mt0) REVERT: F 18 ASN cc_start: 0.7991 (m110) cc_final: 0.7709 (m-40) REVERT: H 191 ASP cc_start: 0.8115 (t0) cc_final: 0.7748 (m-30) REVERT: I 31 GLN cc_start: 0.6880 (pp30) cc_final: 0.6261 (mm-40) REVERT: J 43 LYS cc_start: 0.5343 (mmmt) cc_final: 0.4747 (mmpt) REVERT: K 71 ARG cc_start: 0.7614 (ttt90) cc_final: 0.6733 (mtm110) REVERT: K 77 ASP cc_start: 0.7768 (p0) cc_final: 0.7249 (m-30) REVERT: K 130 ASN cc_start: 0.8313 (m-40) cc_final: 0.8035 (m-40) REVERT: M 93 MET cc_start: 0.7968 (mtp) cc_final: 0.7730 (mtp) REVERT: M 195 GLN cc_start: 0.7319 (tt0) cc_final: 0.6889 (tm-30) REVERT: O 84 ASP cc_start: 0.7548 (m-30) cc_final: 0.7213 (t0) REVERT: O 136 VAL cc_start: 0.8631 (t) cc_final: 0.8381 (m) REVERT: P 116 ASP cc_start: 0.7128 (m-30) cc_final: 0.6819 (m-30) REVERT: T 8 THR cc_start: 0.8402 (t) cc_final: 0.7984 (m) REVERT: Q 38 LYS cc_start: 0.8201 (ptmm) cc_final: 0.7783 (pttm) REVERT: Q 123 GLN cc_start: 0.8421 (mt0) cc_final: 0.7688 (tm-30) REVERT: Q 186 MET cc_start: 0.8860 (tpp) cc_final: 0.8571 (tpt) REVERT: Q 220 LYS cc_start: 0.6816 (mmmt) cc_final: 0.5859 (mttt) REVERT: R 67 ASP cc_start: 0.7335 (m-30) cc_final: 0.7115 (m-30) REVERT: R 263 GLN cc_start: 0.7328 (mp10) cc_final: 0.6688 (mm-40) REVERT: U 123 GLN cc_start: 0.7951 (tp40) cc_final: 0.7660 (tp-100) REVERT: U 226 ASP cc_start: 0.7796 (m-30) cc_final: 0.7545 (m-30) REVERT: V 30 GLN cc_start: 0.7523 (tp40) cc_final: 0.7204 (tp-100) REVERT: V 34 ASN cc_start: 0.7590 (p0) cc_final: 0.7235 (p0) REVERT: V 88 ASP cc_start: 0.7674 (m-30) cc_final: 0.7460 (m-30) REVERT: V 123 GLN cc_start: 0.7504 (tp40) cc_final: 0.6588 (mt0) REVERT: V 173 THR cc_start: 0.8538 (m) cc_final: 0.8243 (p) REVERT: V 245 GLN cc_start: 0.7449 (mm-40) cc_final: 0.7095 (mm110) REVERT: W 123 GLN cc_start: 0.7525 (tp40) cc_final: 0.6727 (mt0) REVERT: W 195 GLN cc_start: 0.8302 (mt0) cc_final: 0.7982 (mm-40) REVERT: X 151 ASN cc_start: 0.7811 (p0) cc_final: 0.7330 (t0) REVERT: Z 53 LYS cc_start: 0.8549 (tppt) cc_final: 0.6843 (pttt) REVERT: N 3 LEU cc_start: 0.5897 (tp) cc_final: 0.5322 (tt) REVERT: N 67 ASP cc_start: 0.7717 (m-30) cc_final: 0.7451 (m-30) REVERT: a 87 THR cc_start: 0.7668 (m) cc_final: 0.6983 (p) REVERT: a 220 LYS cc_start: 0.7848 (mtmt) cc_final: 0.6935 (mmtt) REVERT: b 73 GLN cc_start: 0.6904 (mt0) cc_final: 0.6508 (mt0) REVERT: b 116 ASP cc_start: 0.7177 (m-30) cc_final: 0.6815 (m-30) REVERT: c 263 GLN cc_start: 0.8504 (mm110) cc_final: 0.7279 (tp40) REVERT: d 123 GLN cc_start: 0.6248 (tp-100) cc_final: 0.5583 (mt0) REVERT: e 252 GLN cc_start: 0.8399 (mt0) cc_final: 0.8049 (mm-40) REVERT: h 95 GLU cc_start: 0.7371 (tt0) cc_final: 0.6976 (mt-10) REVERT: h 178 THR cc_start: 0.8467 (m) cc_final: 0.7961 (p) REVERT: j 243 LYS cc_start: 0.7589 (ttmt) cc_final: 0.7125 (tptt) REVERT: j 263 GLN cc_start: 0.7286 (pt0) cc_final: 0.6942 (mp-120) REVERT: g 93 MET cc_start: 0.8123 (mtp) cc_final: 0.7723 (mtp) REVERT: g 106 ASN cc_start: 0.7745 (t0) cc_final: 0.6357 (p0) REVERT: g 174 THR cc_start: 0.8366 (m) cc_final: 0.8024 (p) REVERT: g 184 LYS cc_start: 0.7141 (tttp) cc_final: 0.6616 (tptt) outliers start: 3 outliers final: 1 residues processed: 1090 average time/residue: 1.4465 time to fit residues: 2076.4321 Evaluate side-chains 679 residues out of total 7560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 678 time to evaluate : 5.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 236 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 820 optimal weight: 5.9990 chunk 736 optimal weight: 10.0000 chunk 408 optimal weight: 4.9990 chunk 251 optimal weight: 7.9990 chunk 496 optimal weight: 3.9990 chunk 393 optimal weight: 0.9990 chunk 761 optimal weight: 10.0000 chunk 294 optimal weight: 0.9990 chunk 463 optimal weight: 9.9990 chunk 567 optimal weight: 30.0000 chunk 882 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 73 GLN B 30 GLN B 262 ASN C 262 ASN D 256 GLN E 23 ASN E 31 GLN E 55 GLN E 130 ASN F 30 GLN H 4 ASN H 18 ASN H 248 GLN I 195 GLN I 222 GLN J 30 GLN K 18 ASN K 123 GLN K 134 ASN K 263 GLN L 23 ASN L 30 GLN L 123 GLN L 231 ASN L 251 GLN M 199 ASN M 256 GLN O 4 ASN O 18 ASN O 195 GLN P 18 ASN P 231 ASN T 70 GLN ** Q 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 45 ASN R 123 GLN R 245 GLN S 9 ASN S 23 ASN S 123 GLN S 256 GLN S 262 ASN U 18 ASN U 151 ASN V 30 GLN V 31 GLN V 55 GLN V 130 ASN V 151 ASN V 251 GLN V 263 GLN W 251 GLN X 9 ASN X 31 GLN X 45 ASN ** X 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 262 ASN Z 31 GLN Z 70 GLN Z 123 GLN Z 151 ASN N 7 ASN N 17 GLN N 31 GLN N 231 ASN N 256 GLN a 30 GLN a 31 GLN a 134 ASN a 256 GLN d 18 ASN d 245 GLN d 256 GLN d 262 ASN e 9 ASN e 31 GLN ** f 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 73 GLN f 214 HIS f 252 GLN h 18 ASN h 134 ASN h 151 ASN j 130 ASN j 262 ASN g 31 GLN g 256 GLN Total number of N/Q/H flips: 85 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 70056 Z= 0.255 Angle : 0.526 9.211 94824 Z= 0.299 Chirality : 0.037 0.159 12204 Planarity : 0.003 0.033 12132 Dihedral : 4.011 47.430 9794 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Rotamer: Outliers : 2.18 % Allowed : 6.49 % Favored : 91.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.19 (0.08), residues: 9648 helix: 2.67 (0.06), residues: 7020 sheet: -3.09 (0.19), residues: 432 loop : 1.51 (0.15), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP f 49 HIS 0.005 0.002 HIS C 214 PHE 0.020 0.002 PHE P 217 ARG 0.007 0.001 ARG a 71 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 864 residues out of total 7560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 699 time to evaluate : 5.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7723 (tm130) REVERT: B 35 THR cc_start: 0.8493 (m) cc_final: 0.8255 (p) REVERT: B 95 GLU cc_start: 0.7713 (mm-30) cc_final: 0.7205 (mt-10) REVERT: B 126 LYS cc_start: 0.7722 (OUTLIER) cc_final: 0.7449 (tppp) REVERT: C 248 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.8158 (mt0) REVERT: D 95 GLU cc_start: 0.5578 (mm-30) cc_final: 0.5053 (mt-10) REVERT: E 256 GLN cc_start: 0.7989 (tt0) cc_final: 0.7593 (mt0) REVERT: F 253 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7490 (mt) REVERT: F 264 SER cc_start: 0.7568 (t) cc_final: 0.7294 (p) REVERT: G 220 LYS cc_start: 0.7779 (mtmt) cc_final: 0.6712 (mmtt) REVERT: H 191 ASP cc_start: 0.8107 (t0) cc_final: 0.7744 (m-30) REVERT: H 226 ASP cc_start: 0.7440 (m-30) cc_final: 0.7123 (m-30) REVERT: I 31 GLN cc_start: 0.6994 (pp30) cc_final: 0.6324 (mm-40) REVERT: I 67 ASP cc_start: 0.8276 (m-30) cc_final: 0.8063 (m-30) REVERT: J 32 ARG cc_start: 0.7519 (ttm-80) cc_final: 0.7261 (ttt180) REVERT: J 43 LYS cc_start: 0.5195 (mmmt) cc_final: 0.4668 (mmpt) REVERT: K 71 ARG cc_start: 0.7714 (ttt90) cc_final: 0.6658 (mtm110) REVERT: K 77 ASP cc_start: 0.7705 (p0) cc_final: 0.7321 (m-30) REVERT: L 253 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8301 (mm) REVERT: M 93 MET cc_start: 0.8060 (mtp) cc_final: 0.7726 (mtp) REVERT: M 145 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.8021 (pttm) REVERT: M 195 GLN cc_start: 0.7429 (tt0) cc_final: 0.7014 (tm-30) REVERT: O 31 GLN cc_start: 0.7744 (OUTLIER) cc_final: 0.7187 (tm-30) REVERT: O 84 ASP cc_start: 0.7610 (m-30) cc_final: 0.7267 (t0) REVERT: P 256 GLN cc_start: 0.8227 (tt0) cc_final: 0.7995 (mt0) REVERT: Q 38 LYS cc_start: 0.8311 (ptmm) cc_final: 0.7803 (pttm) REVERT: Q 132 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8471 (mtpp) REVERT: Q 220 LYS cc_start: 0.6928 (mmmt) cc_final: 0.5849 (mttp) REVERT: Q 267 SER cc_start: 0.8078 (OUTLIER) cc_final: 0.7870 (p) REVERT: R 67 ASP cc_start: 0.7648 (m-30) cc_final: 0.7323 (m-30) REVERT: R 240 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7380 (mp0) REVERT: R 263 GLN cc_start: 0.7359 (mp10) cc_final: 0.6897 (mm-40) REVERT: S 14 ILE cc_start: 0.7383 (OUTLIER) cc_final: 0.7157 (mm) REVERT: S 31 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7420 (tp40) REVERT: U 123 GLN cc_start: 0.7946 (tp40) cc_final: 0.7745 (tp-100) REVERT: V 34 ASN cc_start: 0.7762 (p0) cc_final: 0.7441 (p0) REVERT: V 88 ASP cc_start: 0.7774 (m-30) cc_final: 0.7494 (m-30) REVERT: V 123 GLN cc_start: 0.7489 (tp40) cc_final: 0.6543 (mt0) REVERT: V 173 THR cc_start: 0.8724 (m) cc_final: 0.8438 (p) REVERT: W 123 GLN cc_start: 0.7488 (tp40) cc_final: 0.6686 (mt0) REVERT: W 195 GLN cc_start: 0.8301 (mt0) cc_final: 0.8010 (mm-40) REVERT: X 151 ASN cc_start: 0.8054 (p0) cc_final: 0.7357 (t0) REVERT: X 226 ASP cc_start: 0.7888 (m-30) cc_final: 0.7662 (m-30) REVERT: N 3 LEU cc_start: 0.5868 (tp) cc_final: 0.5222 (tt) REVERT: N 31 GLN cc_start: 0.7602 (OUTLIER) cc_final: 0.7352 (mm110) REVERT: N 67 ASP cc_start: 0.7826 (m-30) cc_final: 0.7540 (m-30) REVERT: N 245 GLN cc_start: 0.6373 (pt0) cc_final: 0.6117 (tp-100) REVERT: a 62 MET cc_start: 0.7138 (OUTLIER) cc_final: 0.6736 (tpp) REVERT: a 87 THR cc_start: 0.7937 (m) cc_final: 0.7274 (p) REVERT: a 220 LYS cc_start: 0.7928 (mtmt) cc_final: 0.7009 (mmtt) REVERT: b 73 GLN cc_start: 0.6992 (mt0) cc_final: 0.6718 (mt0) REVERT: b 256 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7584 (tm-30) REVERT: c 263 GLN cc_start: 0.8486 (mm110) cc_final: 0.7343 (tp40) REVERT: d 31 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.7552 (pt0) REVERT: d 123 GLN cc_start: 0.6154 (tp-100) cc_final: 0.5526 (mt0) REVERT: e 252 GLN cc_start: 0.8408 (mt0) cc_final: 0.8054 (mm-40) REVERT: f 62 MET cc_start: 0.6424 (mpt) cc_final: 0.6218 (mpp) REVERT: f 89 LEU cc_start: 0.6622 (OUTLIER) cc_final: 0.6158 (mp) REVERT: h 95 GLU cc_start: 0.7381 (tt0) cc_final: 0.6810 (mt-10) REVERT: i 31 GLN cc_start: 0.7164 (OUTLIER) cc_final: 0.6792 (mt0) REVERT: i 175 SER cc_start: 0.8735 (m) cc_final: 0.8463 (m) REVERT: j 243 LYS cc_start: 0.7671 (ttmt) cc_final: 0.7183 (tptt) REVERT: j 263 GLN cc_start: 0.7513 (pt0) cc_final: 0.7114 (mp-120) REVERT: g 93 MET cc_start: 0.8076 (mtp) cc_final: 0.7724 (mtp) REVERT: g 106 ASN cc_start: 0.7314 (t0) cc_final: 0.5545 (p0) REVERT: g 174 THR cc_start: 0.8349 (m) cc_final: 0.8136 (p) REVERT: g 184 LYS cc_start: 0.7215 (tttp) cc_final: 0.6692 (tptt) REVERT: g 252 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7451 (mp10) outliers start: 165 outliers final: 79 residues processed: 824 average time/residue: 1.3072 time to fit residues: 1458.7617 Evaluate side-chains 732 residues out of total 7560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 634 time to evaluate : 6.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain C residue 5 SER Chi-restraints excluded: chain C residue 248 GLN Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain E residue 126 LYS Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 116 ASP Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain I residue 56 SER Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain I residue 264 SER Chi-restraints excluded: chain J residue 77 ASP Chi-restraints excluded: chain J residue 260 ILE Chi-restraints excluded: chain K residue 27 THR Chi-restraints excluded: chain K residue 38 LYS Chi-restraints excluded: chain K residue 253 LEU Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain L residue 253 LEU Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 145 LYS Chi-restraints excluded: chain M residue 253 LEU Chi-restraints excluded: chain M residue 259 SER Chi-restraints excluded: chain O residue 31 GLN Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain O residue 267 SER Chi-restraints excluded: chain P residue 85 THR Chi-restraints excluded: chain P residue 259 SER Chi-restraints excluded: chain T residue 98 LEU Chi-restraints excluded: chain T residue 173 THR Chi-restraints excluded: chain T residue 223 ASP Chi-restraints excluded: chain Q residue 132 LYS Chi-restraints excluded: chain Q residue 267 SER Chi-restraints excluded: chain R residue 240 GLU Chi-restraints excluded: chain S residue 6 ILE Chi-restraints excluded: chain S residue 14 ILE Chi-restraints excluded: chain S residue 31 GLN Chi-restraints excluded: chain S residue 65 VAL Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 159 VAL Chi-restraints excluded: chain S residue 243 LYS Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 31 GLN Chi-restraints excluded: chain U residue 84 ASP Chi-restraints excluded: chain V residue 159 VAL Chi-restraints excluded: chain V residue 259 SER Chi-restraints excluded: chain W residue 6 ILE Chi-restraints excluded: chain W residue 198 THR Chi-restraints excluded: chain X residue 29 VAL Chi-restraints excluded: chain X residue 249 THR Chi-restraints excluded: chain X residue 253 LEU Chi-restraints excluded: chain Y residue 29 VAL Chi-restraints excluded: chain Y residue 233 VAL Chi-restraints excluded: chain N residue 31 GLN Chi-restraints excluded: chain N residue 84 ASP Chi-restraints excluded: chain N residue 268 ILE Chi-restraints excluded: chain a residue 62 MET Chi-restraints excluded: chain b residue 159 VAL Chi-restraints excluded: chain b residue 256 GLN Chi-restraints excluded: chain b residue 264 SER Chi-restraints excluded: chain c residue 132 LYS Chi-restraints excluded: chain c residue 159 VAL Chi-restraints excluded: chain d residue 31 GLN Chi-restraints excluded: chain d residue 101 SER Chi-restraints excluded: chain e residue 101 SER Chi-restraints excluded: chain f residue 31 GLN Chi-restraints excluded: chain f residue 89 LEU Chi-restraints excluded: chain f residue 107 THR Chi-restraints excluded: chain f residue 164 ILE Chi-restraints excluded: chain f residue 189 THR Chi-restraints excluded: chain f residue 268 ILE Chi-restraints excluded: chain h residue 3 LEU Chi-restraints excluded: chain h residue 16 LEU Chi-restraints excluded: chain h residue 195 GLN Chi-restraints excluded: chain h residue 198 THR Chi-restraints excluded: chain i residue 5 SER Chi-restraints excluded: chain i residue 31 GLN Chi-restraints excluded: chain i residue 103 THR Chi-restraints excluded: chain i residue 265 SER Chi-restraints excluded: chain g residue 124 ILE Chi-restraints excluded: chain g residue 172 THR Chi-restraints excluded: chain g residue 196 THR Chi-restraints excluded: chain g residue 252 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 490 optimal weight: 1.9990 chunk 273 optimal weight: 0.8980 chunk 734 optimal weight: 10.0000 chunk 601 optimal weight: 0.9980 chunk 243 optimal weight: 30.0000 chunk 884 optimal weight: 7.9990 chunk 955 optimal weight: 10.0000 chunk 787 optimal weight: 8.9990 chunk 876 optimal weight: 1.9990 chunk 301 optimal weight: 3.9990 chunk 709 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 256 GLN E 31 GLN E 251 GLN F 151 ASN H 245 GLN J 30 GLN J 55 GLN K 134 ASN K 199 ASN K 263 GLN L 130 ASN L 195 GLN L 231 ASN M 45 ASN ** Q 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 123 GLN R 245 GLN S 130 ASN S 251 GLN U 151 ASN V 18 ASN V 151 ASN V 245 GLN V 251 GLN V 256 GLN V 263 GLN W 4 ASN W 55 GLN X 130 ASN Y 30 GLN Z 31 GLN Z 54 ASN Z 151 ASN N 31 GLN N 73 GLN a 134 ASN ** b 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 30 GLN d 256 GLN f 73 GLN f 151 ASN i 4 ASN j 262 ASN g 31 GLN g 262 ASN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 70056 Z= 0.203 Angle : 0.456 8.180 94824 Z= 0.263 Chirality : 0.034 0.154 12204 Planarity : 0.002 0.030 12132 Dihedral : 3.806 22.117 9792 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 2.17 % Allowed : 8.19 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.92 (0.09), residues: 9648 helix: 3.37 (0.06), residues: 7020 sheet: -2.81 (0.19), residues: 432 loop : 1.17 (0.15), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP f 49 HIS 0.004 0.001 HIS C 214 PHE 0.016 0.002 PHE P 217 ARG 0.010 0.000 ARG j 71 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 866 residues out of total 7560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 702 time to evaluate : 5.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7705 (tm130) REVERT: B 95 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7266 (mt-10) REVERT: B 126 LYS cc_start: 0.7567 (OUTLIER) cc_final: 0.7329 (tppp) REVERT: D 95 GLU cc_start: 0.6200 (mm-30) cc_final: 0.5631 (mt-10) REVERT: E 256 GLN cc_start: 0.7956 (tt0) cc_final: 0.7550 (mt0) REVERT: F 256 GLN cc_start: 0.7094 (OUTLIER) cc_final: 0.6148 (mt0) REVERT: F 264 SER cc_start: 0.7479 (t) cc_final: 0.7210 (p) REVERT: G 32 ARG cc_start: 0.8818 (OUTLIER) cc_final: 0.8391 (mtt180) REVERT: G 220 LYS cc_start: 0.7698 (mtmt) cc_final: 0.6679 (mmtt) REVERT: H 191 ASP cc_start: 0.8146 (t0) cc_final: 0.7815 (m-30) REVERT: H 226 ASP cc_start: 0.7430 (m-30) cc_final: 0.7071 (m-30) REVERT: I 31 GLN cc_start: 0.7010 (pp30) cc_final: 0.6279 (mm-40) REVERT: I 67 ASP cc_start: 0.8263 (m-30) cc_final: 0.8036 (m-30) REVERT: J 32 ARG cc_start: 0.7508 (ttm-80) cc_final: 0.7174 (ttt180) REVERT: J 43 LYS cc_start: 0.5125 (mmmt) cc_final: 0.4669 (mmpt) REVERT: K 71 ARG cc_start: 0.7694 (ttt90) cc_final: 0.6634 (mtm110) REVERT: K 77 ASP cc_start: 0.7620 (p0) cc_final: 0.7398 (m-30) REVERT: K 92 LYS cc_start: 0.8693 (mtpp) cc_final: 0.8433 (mtmt) REVERT: M 145 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.8006 (pttm) REVERT: M 195 GLN cc_start: 0.7439 (tt0) cc_final: 0.7018 (tm-30) REVERT: M 243 LYS cc_start: 0.8333 (tppt) cc_final: 0.8075 (mmmm) REVERT: O 31 GLN cc_start: 0.7661 (OUTLIER) cc_final: 0.7077 (tm-30) REVERT: O 84 ASP cc_start: 0.7577 (m-30) cc_final: 0.7302 (t0) REVERT: T 8 THR cc_start: 0.8416 (t) cc_final: 0.8073 (m) REVERT: Q 38 LYS cc_start: 0.8318 (ptmm) cc_final: 0.7821 (pttm) REVERT: Q 220 LYS cc_start: 0.6863 (mmmt) cc_final: 0.5809 (mttt) REVERT: Q 267 SER cc_start: 0.8107 (OUTLIER) cc_final: 0.7841 (p) REVERT: R 67 ASP cc_start: 0.7599 (m-30) cc_final: 0.7287 (m-30) REVERT: R 240 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7331 (mp0) REVERT: R 263 GLN cc_start: 0.7421 (mp10) cc_final: 0.6892 (mm-40) REVERT: S 14 ILE cc_start: 0.7375 (OUTLIER) cc_final: 0.7146 (mm) REVERT: S 25 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7399 (mt-10) REVERT: S 95 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7512 (tt0) REVERT: U 123 GLN cc_start: 0.7915 (tp40) cc_final: 0.7703 (tp-100) REVERT: V 34 ASN cc_start: 0.7641 (p0) cc_final: 0.7257 (p0) REVERT: V 88 ASP cc_start: 0.7734 (m-30) cc_final: 0.7440 (m-30) REVERT: V 123 GLN cc_start: 0.7457 (tp40) cc_final: 0.6501 (mt0) REVERT: V 173 THR cc_start: 0.8732 (m) cc_final: 0.8463 (p) REVERT: W 123 GLN cc_start: 0.7495 (tp40) cc_final: 0.6684 (mt0) REVERT: W 195 GLN cc_start: 0.8273 (mt0) cc_final: 0.7972 (mm-40) REVERT: X 93 MET cc_start: 0.8637 (ttm) cc_final: 0.8053 (mtp) REVERT: X 151 ASN cc_start: 0.8122 (p0) cc_final: 0.7361 (t0) REVERT: N 3 LEU cc_start: 0.5933 (tp) cc_final: 0.5301 (tt) REVERT: N 31 GLN cc_start: 0.7594 (OUTLIER) cc_final: 0.7285 (tt0) REVERT: N 67 ASP cc_start: 0.7805 (m-30) cc_final: 0.7506 (m-30) REVERT: a 62 MET cc_start: 0.7173 (OUTLIER) cc_final: 0.6681 (tpp) REVERT: a 87 THR cc_start: 0.7894 (m) cc_final: 0.7238 (p) REVERT: a 220 LYS cc_start: 0.7962 (mtmt) cc_final: 0.7065 (mmtt) REVERT: b 73 GLN cc_start: 0.7007 (mt0) cc_final: 0.6763 (mt0) REVERT: b 95 GLU cc_start: 0.7477 (tp30) cc_final: 0.6922 (tt0) REVERT: b 256 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7592 (tm-30) REVERT: c 30 GLN cc_start: 0.7658 (tp40) cc_final: 0.7334 (tp40) REVERT: c 263 GLN cc_start: 0.8444 (mm110) cc_final: 0.7362 (tp40) REVERT: d 31 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7536 (pt0) REVERT: d 123 GLN cc_start: 0.6176 (tp-100) cc_final: 0.5548 (mt0) REVERT: e 252 GLN cc_start: 0.8392 (mt0) cc_final: 0.8041 (mm-40) REVERT: f 89 LEU cc_start: 0.6524 (OUTLIER) cc_final: 0.6041 (mp) REVERT: h 95 GLU cc_start: 0.7347 (tt0) cc_final: 0.6666 (mt-10) REVERT: i 31 GLN cc_start: 0.7125 (OUTLIER) cc_final: 0.6795 (mt0) REVERT: i 175 SER cc_start: 0.8772 (m) cc_final: 0.8488 (m) REVERT: j 62 MET cc_start: 0.8198 (OUTLIER) cc_final: 0.7924 (mmt) REVERT: j 243 LYS cc_start: 0.7655 (ttmt) cc_final: 0.7128 (tptt) REVERT: j 263 GLN cc_start: 0.7617 (pt0) cc_final: 0.7121 (mp-120) REVERT: g 67 ASP cc_start: 0.8064 (m-30) cc_final: 0.7702 (m-30) REVERT: g 93 MET cc_start: 0.8095 (mtp) cc_final: 0.7757 (mtp) REVERT: g 106 ASN cc_start: 0.7207 (t0) cc_final: 0.5446 (p0) REVERT: g 174 THR cc_start: 0.8416 (m) cc_final: 0.8200 (p) REVERT: g 184 LYS cc_start: 0.7082 (tttp) cc_final: 0.6549 (tptt) REVERT: g 252 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7480 (mp10) outliers start: 164 outliers final: 79 residues processed: 823 average time/residue: 1.3191 time to fit residues: 1466.5340 Evaluate side-chains 733 residues out of total 7560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 635 time to evaluate : 5.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain C residue 5 SER Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 256 GLN Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 32 ARG Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 116 ASP Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain I residue 56 SER Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain I residue 264 SER Chi-restraints excluded: chain J residue 77 ASP Chi-restraints excluded: chain J residue 260 ILE Chi-restraints excluded: chain K residue 27 THR Chi-restraints excluded: chain K residue 253 LEU Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain L residue 267 SER Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 145 LYS Chi-restraints excluded: chain M residue 253 LEU Chi-restraints excluded: chain M residue 259 SER Chi-restraints excluded: chain O residue 31 GLN Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain O residue 267 SER Chi-restraints excluded: chain P residue 85 THR Chi-restraints excluded: chain P residue 259 SER Chi-restraints excluded: chain T residue 98 LEU Chi-restraints excluded: chain T residue 173 THR Chi-restraints excluded: chain T residue 223 ASP Chi-restraints excluded: chain Q residue 267 SER Chi-restraints excluded: chain R residue 240 GLU Chi-restraints excluded: chain S residue 6 ILE Chi-restraints excluded: chain S residue 14 ILE Chi-restraints excluded: chain S residue 25 GLU Chi-restraints excluded: chain S residue 65 VAL Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 95 GLU Chi-restraints excluded: chain S residue 159 VAL Chi-restraints excluded: chain S residue 243 LYS Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 31 GLN Chi-restraints excluded: chain U residue 84 ASP Chi-restraints excluded: chain V residue 159 VAL Chi-restraints excluded: chain V residue 246 SER Chi-restraints excluded: chain V residue 259 SER Chi-restraints excluded: chain W residue 6 ILE Chi-restraints excluded: chain W residue 198 THR Chi-restraints excluded: chain X residue 29 VAL Chi-restraints excluded: chain X residue 249 THR Chi-restraints excluded: chain X residue 253 LEU Chi-restraints excluded: chain Y residue 29 VAL Chi-restraints excluded: chain Y residue 232 LEU Chi-restraints excluded: chain Y residue 233 VAL Chi-restraints excluded: chain Z residue 27 THR Chi-restraints excluded: chain N residue 31 GLN Chi-restraints excluded: chain N residue 84 ASP Chi-restraints excluded: chain N residue 268 ILE Chi-restraints excluded: chain a residue 62 MET Chi-restraints excluded: chain b residue 6 ILE Chi-restraints excluded: chain b residue 159 VAL Chi-restraints excluded: chain b residue 256 GLN Chi-restraints excluded: chain b residue 264 SER Chi-restraints excluded: chain c residue 33 ILE Chi-restraints excluded: chain c residue 132 LYS Chi-restraints excluded: chain c residue 159 VAL Chi-restraints excluded: chain d residue 4 ASN Chi-restraints excluded: chain d residue 31 GLN Chi-restraints excluded: chain d residue 101 SER Chi-restraints excluded: chain d residue 159 VAL Chi-restraints excluded: chain e residue 101 SER Chi-restraints excluded: chain f residue 89 LEU Chi-restraints excluded: chain f residue 107 THR Chi-restraints excluded: chain f residue 164 ILE Chi-restraints excluded: chain f residue 189 THR Chi-restraints excluded: chain f residue 268 ILE Chi-restraints excluded: chain h residue 3 LEU Chi-restraints excluded: chain h residue 16 LEU Chi-restraints excluded: chain h residue 116 ASP Chi-restraints excluded: chain h residue 195 GLN Chi-restraints excluded: chain h residue 198 THR Chi-restraints excluded: chain i residue 31 GLN Chi-restraints excluded: chain i residue 84 ASP Chi-restraints excluded: chain i residue 103 THR Chi-restraints excluded: chain i residue 265 SER Chi-restraints excluded: chain j residue 62 MET Chi-restraints excluded: chain g residue 124 ILE Chi-restraints excluded: chain g residue 172 THR Chi-restraints excluded: chain g residue 196 THR Chi-restraints excluded: chain g residue 252 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 873 optimal weight: 6.9990 chunk 664 optimal weight: 2.9990 chunk 458 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 422 optimal weight: 6.9990 chunk 593 optimal weight: 10.0000 chunk 887 optimal weight: 8.9990 chunk 939 optimal weight: 0.8980 chunk 463 optimal weight: 5.9990 chunk 841 optimal weight: 6.9990 chunk 253 optimal weight: 7.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 256 GLN E 31 GLN E 251 GLN F 151 ASN H 245 GLN J 30 GLN K 45 ASN K 263 GLN L 20 ASN L 231 ASN T 151 ASN T 231 ASN R 123 GLN R 245 GLN U 151 ASN U 252 GLN V 31 GLN V 151 ASN V 245 GLN V 251 GLN V 256 GLN V 263 GLN W 199 ASN X 30 GLN X 130 ASN X 263 GLN Y 17 GLN Z 31 GLN Z 151 ASN N 31 GLN N 73 GLN a 134 ASN ** b 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 4 ASN d 256 GLN h 130 ASN i 7 ASN j 262 ASN g 31 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 70056 Z= 0.282 Angle : 0.508 8.582 94824 Z= 0.288 Chirality : 0.037 0.214 12204 Planarity : 0.002 0.024 12132 Dihedral : 3.945 22.632 9792 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 2.45 % Allowed : 8.98 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.78 (0.08), residues: 9648 helix: 3.30 (0.06), residues: 7020 sheet: -2.53 (0.19), residues: 432 loop : 0.87 (0.15), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP f 49 HIS 0.006 0.002 HIS S 214 PHE 0.020 0.002 PHE M 217 ARG 0.005 0.001 ARG G 32 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 856 residues out of total 7560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 671 time to evaluate : 6.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7978 (OUTLIER) cc_final: 0.7752 (tm130) REVERT: A 106 ASN cc_start: 0.7622 (t0) cc_final: 0.6600 (p0) REVERT: B 95 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7471 (mt-10) REVERT: B 126 LYS cc_start: 0.7640 (OUTLIER) cc_final: 0.7396 (tppp) REVERT: B 256 GLN cc_start: 0.7940 (tt0) cc_final: 0.7612 (tt0) REVERT: C 31 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.7796 (tt0) REVERT: D 95 GLU cc_start: 0.6183 (mm-30) cc_final: 0.5757 (mt-10) REVERT: E 256 GLN cc_start: 0.8010 (tt0) cc_final: 0.7584 (mt0) REVERT: F 256 GLN cc_start: 0.7133 (OUTLIER) cc_final: 0.6131 (mt0) REVERT: F 264 SER cc_start: 0.7540 (t) cc_final: 0.7257 (p) REVERT: G 32 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.8393 (mtt180) REVERT: G 220 LYS cc_start: 0.7789 (mtmt) cc_final: 0.6711 (mmtt) REVERT: H 191 ASP cc_start: 0.8131 (t0) cc_final: 0.7780 (m-30) REVERT: H 226 ASP cc_start: 0.7500 (m-30) cc_final: 0.7093 (m-30) REVERT: I 31 GLN cc_start: 0.7120 (pp30) cc_final: 0.6356 (mm-40) REVERT: J 32 ARG cc_start: 0.7555 (ttm-80) cc_final: 0.7208 (ttt180) REVERT: K 71 ARG cc_start: 0.7826 (ttt90) cc_final: 0.6644 (mtm110) REVERT: K 77 ASP cc_start: 0.7647 (p0) cc_final: 0.7432 (m-30) REVERT: K 92 LYS cc_start: 0.8700 (mtpp) cc_final: 0.8448 (mtmt) REVERT: M 145 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.8024 (pttm) REVERT: M 195 GLN cc_start: 0.7462 (tt0) cc_final: 0.7018 (tm-30) REVERT: M 243 LYS cc_start: 0.8394 (tppt) cc_final: 0.8120 (mmmm) REVERT: O 31 GLN cc_start: 0.7746 (OUTLIER) cc_final: 0.7193 (tm-30) REVERT: O 84 ASP cc_start: 0.7638 (m-30) cc_final: 0.7331 (t0) REVERT: O 136 VAL cc_start: 0.8754 (t) cc_final: 0.8513 (m) REVERT: T 8 THR cc_start: 0.8460 (t) cc_final: 0.8141 (m) REVERT: Q 38 LYS cc_start: 0.8312 (ptmm) cc_final: 0.7808 (pttm) REVERT: Q 123 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.7736 (tp-100) REVERT: Q 220 LYS cc_start: 0.6978 (mmmt) cc_final: 0.5881 (mttp) REVERT: R 240 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7423 (mp0) REVERT: R 263 GLN cc_start: 0.7477 (mp10) cc_final: 0.6856 (mm-40) REVERT: S 14 ILE cc_start: 0.7389 (OUTLIER) cc_final: 0.7168 (mm) REVERT: S 25 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7418 (mt-10) REVERT: S 31 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7407 (tp40) REVERT: U 123 GLN cc_start: 0.7973 (tp40) cc_final: 0.7724 (tp-100) REVERT: V 34 ASN cc_start: 0.7885 (p0) cc_final: 0.7562 (p0) REVERT: V 88 ASP cc_start: 0.7753 (m-30) cc_final: 0.7476 (m-30) REVERT: V 123 GLN cc_start: 0.7469 (tp40) cc_final: 0.6518 (mt0) REVERT: V 173 THR cc_start: 0.8841 (m) cc_final: 0.8579 (p) REVERT: W 95 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8251 (tm-30) REVERT: W 123 GLN cc_start: 0.7538 (tp40) cc_final: 0.6707 (mt0) REVERT: W 195 GLN cc_start: 0.8300 (mt0) cc_final: 0.8007 (mm-40) REVERT: X 93 MET cc_start: 0.8760 (ttm) cc_final: 0.8049 (mtp) REVERT: X 151 ASN cc_start: 0.8161 (p0) cc_final: 0.7466 (t0) REVERT: Z 123 GLN cc_start: 0.7644 (OUTLIER) cc_final: 0.6475 (tm-30) REVERT: N 3 LEU cc_start: 0.5981 (tp) cc_final: 0.5361 (tt) REVERT: N 67 ASP cc_start: 0.7875 (m-30) cc_final: 0.7639 (m-30) REVERT: a 87 THR cc_start: 0.7953 (m) cc_final: 0.7336 (p) REVERT: a 220 LYS cc_start: 0.7961 (mtmt) cc_final: 0.7050 (mmtt) REVERT: b 73 GLN cc_start: 0.7041 (mt0) cc_final: 0.6759 (mt0) REVERT: b 95 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7002 (tt0) REVERT: b 231 ASN cc_start: 0.7383 (t0) cc_final: 0.7121 (t0) REVERT: b 256 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.7580 (tm-30) REVERT: c 30 GLN cc_start: 0.7891 (tp40) cc_final: 0.7608 (tm-30) REVERT: c 263 GLN cc_start: 0.8426 (mm110) cc_final: 0.7421 (tp40) REVERT: d 31 GLN cc_start: 0.7950 (OUTLIER) cc_final: 0.7610 (pt0) REVERT: e 252 GLN cc_start: 0.8414 (mt0) cc_final: 0.8049 (mm-40) REVERT: f 89 LEU cc_start: 0.6648 (OUTLIER) cc_final: 0.6167 (mp) REVERT: h 95 GLU cc_start: 0.7402 (tt0) cc_final: 0.6694 (mt-10) REVERT: h 178 THR cc_start: 0.8406 (m) cc_final: 0.7936 (p) REVERT: i 31 GLN cc_start: 0.7177 (OUTLIER) cc_final: 0.6878 (mt0) REVERT: i 175 SER cc_start: 0.8759 (m) cc_final: 0.8430 (m) REVERT: j 243 LYS cc_start: 0.7858 (ttmt) cc_final: 0.7226 (tptt) REVERT: j 263 GLN cc_start: 0.7694 (pt0) cc_final: 0.7192 (mp-120) REVERT: g 67 ASP cc_start: 0.8131 (m-30) cc_final: 0.7736 (m-30) REVERT: g 93 MET cc_start: 0.8087 (mtp) cc_final: 0.7792 (mtp) REVERT: g 106 ASN cc_start: 0.7405 (t0) cc_final: 0.5731 (p0) REVERT: g 184 LYS cc_start: 0.7185 (tttp) cc_final: 0.6663 (tptt) REVERT: g 252 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.7461 (mp10) outliers start: 185 outliers final: 95 residues processed: 814 average time/residue: 1.3603 time to fit residues: 1481.9845 Evaluate side-chains 750 residues out of total 7560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 635 time to evaluate : 5.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain C residue 5 SER Chi-restraints excluded: chain C residue 31 GLN Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 126 LYS Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 256 GLN Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 32 ARG Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 199 ASN Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain I residue 56 SER Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain I residue 264 SER Chi-restraints excluded: chain J residue 77 ASP Chi-restraints excluded: chain J residue 260 ILE Chi-restraints excluded: chain K residue 27 THR Chi-restraints excluded: chain K residue 38 LYS Chi-restraints excluded: chain K residue 253 LEU Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain L residue 225 LEU Chi-restraints excluded: chain L residue 253 LEU Chi-restraints excluded: chain L residue 267 SER Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 88 ASP Chi-restraints excluded: chain M residue 145 LYS Chi-restraints excluded: chain M residue 253 LEU Chi-restraints excluded: chain M residue 259 SER Chi-restraints excluded: chain O residue 31 GLN Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain O residue 267 SER Chi-restraints excluded: chain P residue 85 THR Chi-restraints excluded: chain P residue 208 SER Chi-restraints excluded: chain P residue 259 SER Chi-restraints excluded: chain T residue 98 LEU Chi-restraints excluded: chain T residue 173 THR Chi-restraints excluded: chain T residue 223 ASP Chi-restraints excluded: chain Q residue 123 GLN Chi-restraints excluded: chain R residue 240 GLU Chi-restraints excluded: chain S residue 6 ILE Chi-restraints excluded: chain S residue 14 ILE Chi-restraints excluded: chain S residue 25 GLU Chi-restraints excluded: chain S residue 31 GLN Chi-restraints excluded: chain S residue 65 VAL Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 159 VAL Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 31 GLN Chi-restraints excluded: chain U residue 84 ASP Chi-restraints excluded: chain U residue 265 SER Chi-restraints excluded: chain V residue 159 VAL Chi-restraints excluded: chain V residue 246 SER Chi-restraints excluded: chain V residue 259 SER Chi-restraints excluded: chain W residue 6 ILE Chi-restraints excluded: chain W residue 95 GLU Chi-restraints excluded: chain W residue 198 THR Chi-restraints excluded: chain X residue 29 VAL Chi-restraints excluded: chain X residue 249 THR Chi-restraints excluded: chain X residue 253 LEU Chi-restraints excluded: chain Y residue 29 VAL Chi-restraints excluded: chain Y residue 232 LEU Chi-restraints excluded: chain Y residue 233 VAL Chi-restraints excluded: chain Z residue 27 THR Chi-restraints excluded: chain Z residue 123 GLN Chi-restraints excluded: chain N residue 84 ASP Chi-restraints excluded: chain N residue 268 ILE Chi-restraints excluded: chain a residue 179 THR Chi-restraints excluded: chain b residue 95 GLU Chi-restraints excluded: chain b residue 159 VAL Chi-restraints excluded: chain b residue 256 GLN Chi-restraints excluded: chain b residue 264 SER Chi-restraints excluded: chain c residue 33 ILE Chi-restraints excluded: chain c residue 132 LYS Chi-restraints excluded: chain c residue 159 VAL Chi-restraints excluded: chain d residue 4 ASN Chi-restraints excluded: chain d residue 31 GLN Chi-restraints excluded: chain d residue 101 SER Chi-restraints excluded: chain d residue 159 VAL Chi-restraints excluded: chain e residue 6 ILE Chi-restraints excluded: chain e residue 33 ILE Chi-restraints excluded: chain e residue 101 SER Chi-restraints excluded: chain f residue 89 LEU Chi-restraints excluded: chain f residue 107 THR Chi-restraints excluded: chain f residue 124 ILE Chi-restraints excluded: chain f residue 164 ILE Chi-restraints excluded: chain f residue 189 THR Chi-restraints excluded: chain h residue 3 LEU Chi-restraints excluded: chain h residue 16 LEU Chi-restraints excluded: chain h residue 116 ASP Chi-restraints excluded: chain h residue 195 GLN Chi-restraints excluded: chain h residue 198 THR Chi-restraints excluded: chain i residue 31 GLN Chi-restraints excluded: chain i residue 98 LEU Chi-restraints excluded: chain i residue 103 THR Chi-restraints excluded: chain g residue 124 ILE Chi-restraints excluded: chain g residue 172 THR Chi-restraints excluded: chain g residue 196 THR Chi-restraints excluded: chain g residue 252 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 782 optimal weight: 9.9990 chunk 533 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 chunk 699 optimal weight: 1.9990 chunk 387 optimal weight: 0.9980 chunk 801 optimal weight: 0.7980 chunk 649 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 479 optimal weight: 0.8980 chunk 843 optimal weight: 5.9990 chunk 237 optimal weight: 5.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 106 ASN D 256 GLN E 31 GLN E 251 GLN F 151 ASN G 151 ASN H 245 GLN H 263 GLN K 134 ASN K 263 GLN ** T 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 31 GLN R 123 GLN R 245 GLN U 151 ASN U 252 GLN V 151 ASN V 245 GLN V 251 GLN V 263 GLN W 20 ASN ** X 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 263 GLN Y 151 ASN Z 31 GLN Z 73 GLN Z 151 ASN N 31 GLN a 54 ASN a 134 ASN e 9 ASN j 9 ASN j 262 ASN g 31 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 70056 Z= 0.149 Angle : 0.399 8.615 94824 Z= 0.234 Chirality : 0.031 0.148 12204 Planarity : 0.002 0.041 12132 Dihedral : 3.594 21.509 9792 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 1.73 % Allowed : 10.25 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.44 (0.09), residues: 9648 helix: 3.84 (0.06), residues: 7020 sheet: -2.21 (0.19), residues: 432 loop : 0.87 (0.15), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP f 49 HIS 0.003 0.001 HIS C 214 PHE 0.013 0.001 PHE G 157 ARG 0.010 0.000 ARG j 71 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 868 residues out of total 7560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 737 time to evaluate : 5.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 95 GLU cc_start: 0.7406 (mm-30) cc_final: 0.7148 (mt-10) REVERT: B 256 GLN cc_start: 0.7917 (tt0) cc_final: 0.7645 (tt0) REVERT: D 95 GLU cc_start: 0.6040 (mm-30) cc_final: 0.5561 (mt-10) REVERT: F 256 GLN cc_start: 0.6952 (OUTLIER) cc_final: 0.5813 (mp10) REVERT: F 264 SER cc_start: 0.7431 (t) cc_final: 0.7176 (p) REVERT: G 220 LYS cc_start: 0.7612 (mtmt) cc_final: 0.6613 (mmtt) REVERT: H 191 ASP cc_start: 0.7955 (t0) cc_final: 0.7695 (m-30) REVERT: H 226 ASP cc_start: 0.7214 (m-30) cc_final: 0.6834 (m-30) REVERT: I 31 GLN cc_start: 0.6973 (pp30) cc_final: 0.6193 (mm-40) REVERT: J 43 LYS cc_start: 0.5199 (mmmt) cc_final: 0.4595 (mmpt) REVERT: K 71 ARG cc_start: 0.7682 (ttt90) cc_final: 0.6671 (mtm110) REVERT: K 77 ASP cc_start: 0.7563 (p0) cc_final: 0.7278 (m-30) REVERT: K 92 LYS cc_start: 0.8658 (mtpp) cc_final: 0.8360 (mtmt) REVERT: L 39 ILE cc_start: 0.8236 (mp) cc_final: 0.8033 (mp) REVERT: M 13 MET cc_start: 0.7408 (mtp) cc_final: 0.7073 (mtt) REVERT: M 195 GLN cc_start: 0.7418 (tt0) cc_final: 0.6919 (tm-30) REVERT: M 256 GLN cc_start: 0.7521 (tt0) cc_final: 0.7258 (tt0) REVERT: O 31 GLN cc_start: 0.7574 (OUTLIER) cc_final: 0.7197 (tm-30) REVERT: O 231 ASN cc_start: 0.8435 (t0) cc_final: 0.8163 (t0) REVERT: T 8 THR cc_start: 0.8482 (t) cc_final: 0.8281 (m) REVERT: Q 38 LYS cc_start: 0.8344 (ptmm) cc_final: 0.7885 (pttm) REVERT: Q 123 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.7706 (tp-100) REVERT: Q 220 LYS cc_start: 0.6845 (mmmt) cc_final: 0.5876 (mttt) REVERT: R 240 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7476 (mp0) REVERT: S 14 ILE cc_start: 0.7339 (OUTLIER) cc_final: 0.7098 (mm) REVERT: S 25 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7365 (mt-10) REVERT: S 31 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.7367 (tp40) REVERT: S 95 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7214 (tt0) REVERT: U 123 GLN cc_start: 0.7892 (tp40) cc_final: 0.7644 (tp-100) REVERT: V 34 ASN cc_start: 0.7370 (p0) cc_final: 0.7087 (p0) REVERT: V 123 GLN cc_start: 0.7443 (tp40) cc_final: 0.6486 (mt0) REVERT: V 173 THR cc_start: 0.8725 (m) cc_final: 0.8454 (p) REVERT: W 123 GLN cc_start: 0.7474 (tp40) cc_final: 0.6678 (mt0) REVERT: W 195 GLN cc_start: 0.8199 (mt0) cc_final: 0.7919 (mm-40) REVERT: X 151 ASN cc_start: 0.7972 (p0) cc_final: 0.7213 (t0) REVERT: Z 38 LYS cc_start: 0.8161 (mtmm) cc_final: 0.7875 (mtmm) REVERT: Z 243 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.8199 (tttp) REVERT: N 3 LEU cc_start: 0.5946 (tp) cc_final: 0.5327 (tt) REVERT: N 151 ASN cc_start: 0.8464 (t0) cc_final: 0.8061 (t0) REVERT: a 62 MET cc_start: 0.7402 (mmt) cc_final: 0.7074 (mmt) REVERT: a 87 THR cc_start: 0.7744 (m) cc_final: 0.7072 (p) REVERT: a 220 LYS cc_start: 0.7951 (mtmt) cc_final: 0.7052 (tptt) REVERT: b 73 GLN cc_start: 0.6884 (mt0) cc_final: 0.6638 (mt0) REVERT: b 95 GLU cc_start: 0.7366 (tp30) cc_final: 0.6814 (tt0) REVERT: b 116 ASP cc_start: 0.7107 (m-30) cc_final: 0.6728 (m-30) REVERT: b 256 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7622 (tm-30) REVERT: c 30 GLN cc_start: 0.7601 (tp40) cc_final: 0.7358 (tp40) REVERT: c 263 GLN cc_start: 0.8407 (mm110) cc_final: 0.7358 (tp40) REVERT: d 31 GLN cc_start: 0.7889 (OUTLIER) cc_final: 0.7535 (pt0) REVERT: d 123 GLN cc_start: 0.5962 (tp-100) cc_final: 0.5415 (mt0) REVERT: e 252 GLN cc_start: 0.8368 (mt0) cc_final: 0.8042 (mm-40) REVERT: f 16 LEU cc_start: 0.6958 (OUTLIER) cc_final: 0.6457 (tt) REVERT: h 95 GLU cc_start: 0.7293 (tt0) cc_final: 0.6550 (mt-10) REVERT: i 31 GLN cc_start: 0.7152 (OUTLIER) cc_final: 0.6892 (mt0) REVERT: i 175 SER cc_start: 0.8790 (m) cc_final: 0.8466 (m) REVERT: j 67 ASP cc_start: 0.6810 (m-30) cc_final: 0.6404 (m-30) REVERT: j 243 LYS cc_start: 0.7678 (ttmt) cc_final: 0.7183 (tptt) REVERT: j 256 GLN cc_start: 0.6856 (OUTLIER) cc_final: 0.6647 (tt0) REVERT: j 263 GLN cc_start: 0.7656 (pt0) cc_final: 0.7072 (mp-120) REVERT: g 67 ASP cc_start: 0.8106 (m-30) cc_final: 0.7781 (m-30) REVERT: g 93 MET cc_start: 0.8002 (mtp) cc_final: 0.7749 (mtp) REVERT: g 184 LYS cc_start: 0.6716 (tttp) cc_final: 0.6234 (tptt) REVERT: g 252 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7490 (mp10) outliers start: 131 outliers final: 60 residues processed: 838 average time/residue: 1.2938 time to fit residues: 1463.3444 Evaluate side-chains 719 residues out of total 7560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 644 time to evaluate : 5.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain C residue 5 SER Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 126 LYS Chi-restraints excluded: chain F residue 256 GLN Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain K residue 253 LEU Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain L residue 225 LEU Chi-restraints excluded: chain L residue 267 SER Chi-restraints excluded: chain M residue 88 ASP Chi-restraints excluded: chain M residue 253 LEU Chi-restraints excluded: chain O residue 31 GLN Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain O residue 267 SER Chi-restraints excluded: chain P residue 208 SER Chi-restraints excluded: chain P residue 259 SER Chi-restraints excluded: chain T residue 105 LEU Chi-restraints excluded: chain T residue 223 ASP Chi-restraints excluded: chain Q residue 123 GLN Chi-restraints excluded: chain R residue 240 GLU Chi-restraints excluded: chain S residue 14 ILE Chi-restraints excluded: chain S residue 25 GLU Chi-restraints excluded: chain S residue 31 GLN Chi-restraints excluded: chain S residue 65 VAL Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 95 GLU Chi-restraints excluded: chain S residue 159 VAL Chi-restraints excluded: chain U residue 31 GLN Chi-restraints excluded: chain V residue 159 VAL Chi-restraints excluded: chain V residue 246 SER Chi-restraints excluded: chain V residue 259 SER Chi-restraints excluded: chain W residue 198 THR Chi-restraints excluded: chain X residue 29 VAL Chi-restraints excluded: chain X residue 249 THR Chi-restraints excluded: chain X residue 253 LEU Chi-restraints excluded: chain Y residue 29 VAL Chi-restraints excluded: chain Y residue 232 LEU Chi-restraints excluded: chain Z residue 27 THR Chi-restraints excluded: chain Z residue 232 LEU Chi-restraints excluded: chain Z residue 243 LYS Chi-restraints excluded: chain a residue 179 THR Chi-restraints excluded: chain b residue 159 VAL Chi-restraints excluded: chain b residue 256 GLN Chi-restraints excluded: chain b residue 264 SER Chi-restraints excluded: chain c residue 33 ILE Chi-restraints excluded: chain c residue 159 VAL Chi-restraints excluded: chain d residue 31 GLN Chi-restraints excluded: chain d residue 159 VAL Chi-restraints excluded: chain e residue 33 ILE Chi-restraints excluded: chain f residue 16 LEU Chi-restraints excluded: chain f residue 107 THR Chi-restraints excluded: chain f residue 124 ILE Chi-restraints excluded: chain f residue 164 ILE Chi-restraints excluded: chain f residue 189 THR Chi-restraints excluded: chain h residue 16 LEU Chi-restraints excluded: chain h residue 116 ASP Chi-restraints excluded: chain h residue 195 GLN Chi-restraints excluded: chain h residue 198 THR Chi-restraints excluded: chain i residue 31 GLN Chi-restraints excluded: chain i residue 98 LEU Chi-restraints excluded: chain i residue 103 THR Chi-restraints excluded: chain j residue 256 GLN Chi-restraints excluded: chain g residue 172 THR Chi-restraints excluded: chain g residue 252 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 316 optimal weight: 1.9990 chunk 846 optimal weight: 1.9990 chunk 185 optimal weight: 0.9990 chunk 551 optimal weight: 0.9990 chunk 231 optimal weight: 10.0000 chunk 940 optimal weight: 0.9990 chunk 780 optimal weight: 3.9990 chunk 435 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 chunk 311 optimal weight: 9.9990 chunk 493 optimal weight: 2.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN B 30 GLN D 106 ASN D 256 GLN E 31 GLN F 31 GLN F 151 ASN F 262 ASN ** G 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 151 ASN H 245 GLN K 134 ASN ** T 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 123 GLN R 245 GLN U 151 ASN V 151 ASN V 245 GLN V 251 GLN V 256 GLN V 263 GLN ** X 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 263 GLN Z 31 GLN Z 151 ASN N 31 GLN N 263 GLN a 134 ASN a 231 ASN c 9 ASN d 256 GLN f 151 ASN h 18 ASN j 262 ASN g 31 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 70056 Z= 0.158 Angle : 0.404 9.268 94824 Z= 0.236 Chirality : 0.032 0.142 12204 Planarity : 0.002 0.015 12132 Dihedral : 3.556 19.727 9792 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 1.90 % Allowed : 10.81 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.51 (0.09), residues: 9648 helix: 3.90 (0.06), residues: 7020 sheet: -2.01 (0.20), residues: 432 loop : 0.83 (0.15), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP f 49 HIS 0.003 0.001 HIS D 214 PHE 0.015 0.001 PHE a 177 ARG 0.002 0.000 ARG G 121 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 825 residues out of total 7560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 681 time to evaluate : 5.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7838 (OUTLIER) cc_final: 0.7592 (tm130) REVERT: B 95 GLU cc_start: 0.7484 (mm-30) cc_final: 0.7257 (mt-10) REVERT: B 191 ASP cc_start: 0.8029 (m-30) cc_final: 0.7807 (m-30) REVERT: B 256 GLN cc_start: 0.7941 (tt0) cc_final: 0.7659 (tt0) REVERT: D 95 GLU cc_start: 0.6047 (mm-30) cc_final: 0.5573 (mt-10) REVERT: F 256 GLN cc_start: 0.6928 (OUTLIER) cc_final: 0.5789 (mp10) REVERT: F 264 SER cc_start: 0.7451 (t) cc_final: 0.7189 (p) REVERT: G 220 LYS cc_start: 0.7621 (mtmt) cc_final: 0.6695 (mmtt) REVERT: H 191 ASP cc_start: 0.7932 (t0) cc_final: 0.7669 (m-30) REVERT: H 226 ASP cc_start: 0.7257 (OUTLIER) cc_final: 0.6872 (m-30) REVERT: I 31 GLN cc_start: 0.6973 (pp30) cc_final: 0.6225 (mm-40) REVERT: K 71 ARG cc_start: 0.7700 (ttt90) cc_final: 0.6683 (mtm110) REVERT: K 77 ASP cc_start: 0.7598 (p0) cc_final: 0.7302 (m-30) REVERT: K 92 LYS cc_start: 0.8657 (mtpp) cc_final: 0.8351 (mtmt) REVERT: L 39 ILE cc_start: 0.8233 (mp) cc_final: 0.8024 (mp) REVERT: L 253 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8246 (mm) REVERT: M 13 MET cc_start: 0.7440 (mtp) cc_final: 0.7132 (mtt) REVERT: M 195 GLN cc_start: 0.7464 (tt0) cc_final: 0.6973 (tm-30) REVERT: M 256 GLN cc_start: 0.7517 (tt0) cc_final: 0.7294 (tt0) REVERT: O 31 GLN cc_start: 0.7745 (OUTLIER) cc_final: 0.7173 (tm-30) REVERT: O 231 ASN cc_start: 0.8428 (t0) cc_final: 0.8195 (t0) REVERT: Q 38 LYS cc_start: 0.8294 (ptmm) cc_final: 0.7801 (pttt) REVERT: Q 123 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.7711 (tp-100) REVERT: Q 220 LYS cc_start: 0.6853 (mmmt) cc_final: 0.5886 (mttt) REVERT: S 14 ILE cc_start: 0.7344 (OUTLIER) cc_final: 0.7117 (mm) REVERT: S 25 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7383 (mt-10) REVERT: S 31 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7363 (tp40) REVERT: U 123 GLN cc_start: 0.7906 (tp40) cc_final: 0.7653 (tp-100) REVERT: V 34 ASN cc_start: 0.7419 (p0) cc_final: 0.7097 (p0) REVERT: V 123 GLN cc_start: 0.7428 (tp40) cc_final: 0.6457 (mt0) REVERT: V 173 THR cc_start: 0.8743 (m) cc_final: 0.8471 (p) REVERT: W 123 GLN cc_start: 0.7481 (tp40) cc_final: 0.6685 (mt0) REVERT: W 195 GLN cc_start: 0.8183 (mt0) cc_final: 0.7888 (mm-40) REVERT: X 151 ASN cc_start: 0.7984 (p0) cc_final: 0.7265 (t0) REVERT: Z 38 LYS cc_start: 0.8174 (mtmm) cc_final: 0.7868 (mtmm) REVERT: Z 123 GLN cc_start: 0.7539 (OUTLIER) cc_final: 0.6471 (mm-40) REVERT: N 3 LEU cc_start: 0.5881 (tp) cc_final: 0.5281 (tt) REVERT: N 151 ASN cc_start: 0.8456 (t0) cc_final: 0.8153 (t0) REVERT: a 62 MET cc_start: 0.7414 (mmt) cc_final: 0.6986 (mmt) REVERT: a 87 THR cc_start: 0.7839 (m) cc_final: 0.7175 (p) REVERT: a 220 LYS cc_start: 0.7949 (mtmt) cc_final: 0.7057 (tptt) REVERT: b 73 GLN cc_start: 0.6870 (mt0) cc_final: 0.6644 (mt0) REVERT: b 95 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6788 (tt0) REVERT: b 116 ASP cc_start: 0.7114 (m-30) cc_final: 0.6686 (m-30) REVERT: b 256 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7639 (tm-30) REVERT: c 30 GLN cc_start: 0.7707 (tp40) cc_final: 0.7467 (tp40) REVERT: c 263 GLN cc_start: 0.8384 (mm110) cc_final: 0.7436 (tp40) REVERT: d 31 GLN cc_start: 0.7871 (OUTLIER) cc_final: 0.7502 (pt0) REVERT: d 123 GLN cc_start: 0.6027 (tp-100) cc_final: 0.5469 (mt0) REVERT: e 252 GLN cc_start: 0.8345 (mt0) cc_final: 0.8007 (mm-40) REVERT: f 16 LEU cc_start: 0.6971 (OUTLIER) cc_final: 0.6471 (tt) REVERT: h 95 GLU cc_start: 0.7339 (tt0) cc_final: 0.6597 (mt-10) REVERT: i 31 GLN cc_start: 0.7109 (OUTLIER) cc_final: 0.6903 (mt0) REVERT: j 67 ASP cc_start: 0.6750 (m-30) cc_final: 0.6433 (m-30) REVERT: j 212 ASP cc_start: 0.8245 (m-30) cc_final: 0.7975 (m-30) REVERT: j 243 LYS cc_start: 0.7718 (ttmt) cc_final: 0.7400 (tmtt) REVERT: j 263 GLN cc_start: 0.7718 (pt0) cc_final: 0.7130 (mp-120) REVERT: g 67 ASP cc_start: 0.8128 (m-30) cc_final: 0.7757 (m-30) REVERT: g 93 MET cc_start: 0.8008 (mtp) cc_final: 0.7783 (mtp) REVERT: g 184 LYS cc_start: 0.6697 (tttp) cc_final: 0.6262 (mmtt) REVERT: g 252 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7421 (mp10) outliers start: 144 outliers final: 74 residues processed: 791 average time/residue: 1.2784 time to fit residues: 1373.0342 Evaluate side-chains 730 residues out of total 7560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 640 time to evaluate : 5.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain C residue 5 SER Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 126 LYS Chi-restraints excluded: chain E residue 233 VAL Chi-restraints excluded: chain F residue 256 GLN Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 199 ASN Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 226 ASP Chi-restraints excluded: chain I residue 56 SER Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain I residue 264 SER Chi-restraints excluded: chain K residue 253 LEU Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain L residue 225 LEU Chi-restraints excluded: chain L residue 253 LEU Chi-restraints excluded: chain L residue 267 SER Chi-restraints excluded: chain M residue 88 ASP Chi-restraints excluded: chain M residue 253 LEU Chi-restraints excluded: chain M residue 259 SER Chi-restraints excluded: chain O residue 31 GLN Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain O residue 267 SER Chi-restraints excluded: chain P residue 208 SER Chi-restraints excluded: chain P residue 259 SER Chi-restraints excluded: chain T residue 105 LEU Chi-restraints excluded: chain T residue 223 ASP Chi-restraints excluded: chain Q residue 123 GLN Chi-restraints excluded: chain S residue 14 ILE Chi-restraints excluded: chain S residue 25 GLU Chi-restraints excluded: chain S residue 31 GLN Chi-restraints excluded: chain S residue 65 VAL Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 159 VAL Chi-restraints excluded: chain U residue 33 ILE Chi-restraints excluded: chain U residue 84 ASP Chi-restraints excluded: chain U residue 87 THR Chi-restraints excluded: chain V residue 159 VAL Chi-restraints excluded: chain V residue 259 SER Chi-restraints excluded: chain W residue 6 ILE Chi-restraints excluded: chain W residue 198 THR Chi-restraints excluded: chain X residue 29 VAL Chi-restraints excluded: chain X residue 249 THR Chi-restraints excluded: chain X residue 253 LEU Chi-restraints excluded: chain Y residue 29 VAL Chi-restraints excluded: chain Y residue 233 VAL Chi-restraints excluded: chain Z residue 27 THR Chi-restraints excluded: chain Z residue 123 GLN Chi-restraints excluded: chain a residue 179 THR Chi-restraints excluded: chain b residue 95 GLU Chi-restraints excluded: chain b residue 256 GLN Chi-restraints excluded: chain b residue 268 ILE Chi-restraints excluded: chain c residue 33 ILE Chi-restraints excluded: chain c residue 159 VAL Chi-restraints excluded: chain d residue 4 ASN Chi-restraints excluded: chain d residue 31 GLN Chi-restraints excluded: chain d residue 101 SER Chi-restraints excluded: chain d residue 159 VAL Chi-restraints excluded: chain e residue 31 GLN Chi-restraints excluded: chain e residue 33 ILE Chi-restraints excluded: chain e residue 101 SER Chi-restraints excluded: chain f residue 16 LEU Chi-restraints excluded: chain f residue 107 THR Chi-restraints excluded: chain f residue 124 ILE Chi-restraints excluded: chain f residue 164 ILE Chi-restraints excluded: chain f residue 189 THR Chi-restraints excluded: chain h residue 16 LEU Chi-restraints excluded: chain h residue 116 ASP Chi-restraints excluded: chain h residue 198 THR Chi-restraints excluded: chain i residue 31 GLN Chi-restraints excluded: chain i residue 98 LEU Chi-restraints excluded: chain i residue 103 THR Chi-restraints excluded: chain g residue 89 LEU Chi-restraints excluded: chain g residue 172 THR Chi-restraints excluded: chain g residue 252 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 906 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 chunk 535 optimal weight: 0.9980 chunk 686 optimal weight: 0.7980 chunk 532 optimal weight: 5.9990 chunk 791 optimal weight: 2.9990 chunk 525 optimal weight: 3.9990 chunk 936 optimal weight: 8.9990 chunk 586 optimal weight: 1.9990 chunk 571 optimal weight: 5.9990 chunk 432 optimal weight: 10.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN B 30 GLN ** C 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 256 GLN E 31 GLN E 251 GLN E 263 GLN F 151 ASN ** G 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 245 GLN K 134 ASN M 55 GLN O 20 ASN P 7 ASN P 256 GLN ** T 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 123 GLN R 245 GLN S 263 GLN U 151 ASN V 151 ASN V 245 GLN V 251 GLN V 263 GLN ** X 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 263 GLN Z 31 GLN Z 151 ASN N 31 GLN N 263 GLN a 134 ASN ** a 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 256 GLN f 73 GLN f 151 ASN g 31 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 70056 Z= 0.225 Angle : 0.458 9.555 94824 Z= 0.263 Chirality : 0.034 0.170 12204 Planarity : 0.002 0.048 12132 Dihedral : 3.725 20.622 9792 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 1.98 % Allowed : 11.28 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.23 (0.08), residues: 9648 helix: 3.69 (0.06), residues: 7020 sheet: -1.90 (0.20), residues: 432 loop : 0.71 (0.15), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP f 49 HIS 0.005 0.002 HIS G 214 PHE 0.018 0.002 PHE f 177 ARG 0.015 0.000 ARG j 71 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 795 residues out of total 7560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 645 time to evaluate : 6.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 95 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7367 (mt-10) REVERT: B 256 GLN cc_start: 0.7950 (tt0) cc_final: 0.7641 (tt0) REVERT: D 95 GLU cc_start: 0.6388 (mm-30) cc_final: 0.5908 (mt-10) REVERT: F 256 GLN cc_start: 0.7001 (OUTLIER) cc_final: 0.5752 (mp10) REVERT: F 264 SER cc_start: 0.7543 (t) cc_final: 0.7257 (p) REVERT: G 220 LYS cc_start: 0.7662 (mtmt) cc_final: 0.6714 (mmtt) REVERT: H 191 ASP cc_start: 0.8078 (t0) cc_final: 0.7800 (m-30) REVERT: H 226 ASP cc_start: 0.7454 (OUTLIER) cc_final: 0.7035 (m-30) REVERT: I 31 GLN cc_start: 0.7054 (pp30) cc_final: 0.6277 (mm-40) REVERT: J 31 GLN cc_start: 0.7383 (OUTLIER) cc_final: 0.6612 (mp10) REVERT: K 71 ARG cc_start: 0.7797 (ttt90) cc_final: 0.6633 (mtm110) REVERT: K 92 LYS cc_start: 0.8680 (mtpp) cc_final: 0.8410 (mtmt) REVERT: L 253 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8168 (mm) REVERT: M 13 MET cc_start: 0.7573 (mtp) cc_final: 0.7213 (mtt) REVERT: M 145 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.8039 (pttm) REVERT: M 195 GLN cc_start: 0.7457 (tt0) cc_final: 0.7025 (tm-30) REVERT: O 31 GLN cc_start: 0.7821 (OUTLIER) cc_final: 0.7241 (tm-30) REVERT: Q 38 LYS cc_start: 0.8328 (ptmm) cc_final: 0.7843 (pttm) REVERT: Q 123 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.7760 (tp-100) REVERT: Q 220 LYS cc_start: 0.6987 (mmmt) cc_final: 0.5902 (mttp) REVERT: R 240 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7520 (mp0) REVERT: S 14 ILE cc_start: 0.7370 (OUTLIER) cc_final: 0.7132 (mm) REVERT: S 25 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7399 (mt-10) REVERT: S 31 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7415 (tp40) REVERT: U 123 GLN cc_start: 0.7929 (tp40) cc_final: 0.7698 (tp-100) REVERT: V 34 ASN cc_start: 0.7735 (p0) cc_final: 0.7384 (p0) REVERT: V 88 ASP cc_start: 0.7760 (m-30) cc_final: 0.7446 (m-30) REVERT: V 123 GLN cc_start: 0.7448 (tp40) cc_final: 0.6480 (mt0) REVERT: V 173 THR cc_start: 0.8815 (m) cc_final: 0.8554 (p) REVERT: V 247 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7852 (mp) REVERT: W 95 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8210 (tm-30) REVERT: W 123 GLN cc_start: 0.7500 (tp40) cc_final: 0.6681 (mt0) REVERT: W 195 GLN cc_start: 0.8268 (mt0) cc_final: 0.7963 (mm-40) REVERT: X 151 ASN cc_start: 0.8092 (p0) cc_final: 0.7417 (t0) REVERT: N 3 LEU cc_start: 0.5900 (tp) cc_final: 0.5368 (tt) REVERT: N 67 ASP cc_start: 0.7818 (m-30) cc_final: 0.7553 (m-30) REVERT: N 151 ASN cc_start: 0.8479 (t0) cc_final: 0.8141 (t0) REVERT: a 62 MET cc_start: 0.7423 (mmt) cc_final: 0.6953 (mmt) REVERT: a 87 THR cc_start: 0.7923 (m) cc_final: 0.7265 (p) REVERT: a 220 LYS cc_start: 0.7951 (mtmt) cc_final: 0.7042 (tptt) REVERT: b 73 GLN cc_start: 0.6978 (mt0) cc_final: 0.6768 (mt0) REVERT: b 95 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.6895 (tt0) REVERT: b 256 GLN cc_start: 0.8095 (OUTLIER) cc_final: 0.7653 (tm-30) REVERT: c 30 GLN cc_start: 0.7828 (tp40) cc_final: 0.7519 (tp40) REVERT: c 263 GLN cc_start: 0.8366 (mm110) cc_final: 0.7503 (tp40) REVERT: d 31 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.7594 (pt0) REVERT: d 123 GLN cc_start: 0.6022 (tp-100) cc_final: 0.5439 (mt0) REVERT: e 125 GLU cc_start: 0.6954 (tp30) cc_final: 0.6690 (mm-30) REVERT: e 252 GLN cc_start: 0.8369 (mt0) cc_final: 0.8005 (mm-40) REVERT: f 16 LEU cc_start: 0.7133 (OUTLIER) cc_final: 0.6783 (tt) REVERT: h 95 GLU cc_start: 0.7436 (tt0) cc_final: 0.6710 (mt-10) REVERT: i 31 GLN cc_start: 0.7144 (OUTLIER) cc_final: 0.6913 (mt0) REVERT: j 243 LYS cc_start: 0.7853 (ttmt) cc_final: 0.7216 (tptt) REVERT: j 263 GLN cc_start: 0.7735 (pt0) cc_final: 0.7147 (mp-120) REVERT: g 67 ASP cc_start: 0.8124 (m-30) cc_final: 0.7743 (m-30) REVERT: g 93 MET cc_start: 0.8037 (mtp) cc_final: 0.7773 (mtp) REVERT: g 106 ASN cc_start: 0.7253 (t0) cc_final: 0.5519 (p0) REVERT: g 184 LYS cc_start: 0.6960 (tttp) cc_final: 0.6505 (mmtt) REVERT: g 252 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7470 (mp10) outliers start: 150 outliers final: 84 residues processed: 762 average time/residue: 1.3246 time to fit residues: 1365.4578 Evaluate side-chains 725 residues out of total 7560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 622 time to evaluate : 6.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain C residue 5 SER Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 126 LYS Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 256 GLN Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 226 ASP Chi-restraints excluded: chain I residue 56 SER Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain I residue 256 GLN Chi-restraints excluded: chain I residue 264 SER Chi-restraints excluded: chain J residue 31 GLN Chi-restraints excluded: chain J residue 260 ILE Chi-restraints excluded: chain K residue 8 THR Chi-restraints excluded: chain K residue 27 THR Chi-restraints excluded: chain K residue 253 LEU Chi-restraints excluded: chain L residue 225 LEU Chi-restraints excluded: chain L residue 253 LEU Chi-restraints excluded: chain L residue 267 SER Chi-restraints excluded: chain M residue 88 ASP Chi-restraints excluded: chain M residue 145 LYS Chi-restraints excluded: chain M residue 253 LEU Chi-restraints excluded: chain M residue 259 SER Chi-restraints excluded: chain O residue 31 GLN Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain O residue 267 SER Chi-restraints excluded: chain P residue 208 SER Chi-restraints excluded: chain P residue 259 SER Chi-restraints excluded: chain T residue 98 LEU Chi-restraints excluded: chain T residue 105 LEU Chi-restraints excluded: chain T residue 223 ASP Chi-restraints excluded: chain Q residue 123 GLN Chi-restraints excluded: chain R residue 240 GLU Chi-restraints excluded: chain S residue 14 ILE Chi-restraints excluded: chain S residue 25 GLU Chi-restraints excluded: chain S residue 31 GLN Chi-restraints excluded: chain S residue 51 THR Chi-restraints excluded: chain S residue 65 VAL Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 159 VAL Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 84 ASP Chi-restraints excluded: chain U residue 87 THR Chi-restraints excluded: chain V residue 159 VAL Chi-restraints excluded: chain V residue 246 SER Chi-restraints excluded: chain V residue 247 LEU Chi-restraints excluded: chain W residue 6 ILE Chi-restraints excluded: chain W residue 95 GLU Chi-restraints excluded: chain W residue 198 THR Chi-restraints excluded: chain X residue 29 VAL Chi-restraints excluded: chain X residue 249 THR Chi-restraints excluded: chain X residue 253 LEU Chi-restraints excluded: chain Y residue 29 VAL Chi-restraints excluded: chain Y residue 232 LEU Chi-restraints excluded: chain Y residue 233 VAL Chi-restraints excluded: chain Z residue 27 THR Chi-restraints excluded: chain Z residue 232 LEU Chi-restraints excluded: chain a residue 179 THR Chi-restraints excluded: chain b residue 95 GLU Chi-restraints excluded: chain b residue 256 GLN Chi-restraints excluded: chain b residue 264 SER Chi-restraints excluded: chain b residue 268 ILE Chi-restraints excluded: chain c residue 33 ILE Chi-restraints excluded: chain c residue 159 VAL Chi-restraints excluded: chain c residue 163 THR Chi-restraints excluded: chain d residue 4 ASN Chi-restraints excluded: chain d residue 31 GLN Chi-restraints excluded: chain d residue 101 SER Chi-restraints excluded: chain d residue 129 THR Chi-restraints excluded: chain d residue 159 VAL Chi-restraints excluded: chain e residue 33 ILE Chi-restraints excluded: chain e residue 101 SER Chi-restraints excluded: chain f residue 16 LEU Chi-restraints excluded: chain f residue 107 THR Chi-restraints excluded: chain f residue 124 ILE Chi-restraints excluded: chain f residue 164 ILE Chi-restraints excluded: chain f residue 189 THR Chi-restraints excluded: chain h residue 16 LEU Chi-restraints excluded: chain h residue 116 ASP Chi-restraints excluded: chain h residue 198 THR Chi-restraints excluded: chain i residue 31 GLN Chi-restraints excluded: chain i residue 98 LEU Chi-restraints excluded: chain i residue 103 THR Chi-restraints excluded: chain g residue 89 LEU Chi-restraints excluded: chain g residue 172 THR Chi-restraints excluded: chain g residue 252 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 579 optimal weight: 6.9990 chunk 374 optimal weight: 6.9990 chunk 559 optimal weight: 0.9980 chunk 282 optimal weight: 0.8980 chunk 184 optimal weight: 6.9990 chunk 181 optimal weight: 1.9990 chunk 595 optimal weight: 0.8980 chunk 638 optimal weight: 0.0370 chunk 463 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 736 optimal weight: 3.9990 overall best weight: 0.9660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 256 GLN E 31 GLN E 251 GLN F 151 ASN ** G 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 245 GLN K 18 ASN K 45 ASN K 134 ASN K 263 GLN M 55 GLN ** T 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 123 GLN U 151 ASN V 151 ASN V 245 GLN V 251 GLN V 256 GLN V 263 GLN ** X 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 70 GLN X 263 GLN Z 31 GLN Z 151 ASN N 31 GLN a 134 ASN a 231 ASN c 111 ASN e 9 ASN ** e 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 73 GLN f 151 ASN j 73 GLN g 31 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 70056 Z= 0.150 Angle : 0.397 9.748 94824 Z= 0.233 Chirality : 0.031 0.168 12204 Planarity : 0.002 0.041 12132 Dihedral : 3.519 19.595 9792 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 1.71 % Allowed : 11.73 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.59 (0.09), residues: 9648 helix: 3.97 (0.06), residues: 7020 sheet: -1.69 (0.21), residues: 432 loop : 0.74 (0.15), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP f 49 HIS 0.003 0.001 HIS C 214 PHE 0.014 0.001 PHE f 177 ARG 0.010 0.000 ARG j 71 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 807 residues out of total 7560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 678 time to evaluate : 5.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 191 ASP cc_start: 0.8027 (m-30) cc_final: 0.7796 (m-30) REVERT: B 256 GLN cc_start: 0.7911 (tt0) cc_final: 0.7654 (tt0) REVERT: D 95 GLU cc_start: 0.6188 (mm-30) cc_final: 0.5702 (mt-10) REVERT: F 256 GLN cc_start: 0.6887 (OUTLIER) cc_final: 0.5771 (mp10) REVERT: F 264 SER cc_start: 0.7487 (t) cc_final: 0.7211 (p) REVERT: G 220 LYS cc_start: 0.7550 (mtmt) cc_final: 0.6692 (mmtt) REVERT: H 191 ASP cc_start: 0.7950 (t0) cc_final: 0.7682 (m-30) REVERT: H 226 ASP cc_start: 0.7220 (OUTLIER) cc_final: 0.6841 (m-30) REVERT: I 31 GLN cc_start: 0.6934 (pp30) cc_final: 0.6185 (mm-40) REVERT: K 45 ASN cc_start: 0.8368 (t0) cc_final: 0.8157 (t0) REVERT: K 71 ARG cc_start: 0.7663 (ttt90) cc_final: 0.6628 (mtm110) REVERT: K 92 LYS cc_start: 0.8631 (mtpp) cc_final: 0.8327 (mtmt) REVERT: L 253 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8227 (mm) REVERT: M 13 MET cc_start: 0.7429 (mtp) cc_final: 0.7132 (mtt) REVERT: M 62 MET cc_start: 0.7785 (mmt) cc_final: 0.7411 (mtt) REVERT: M 195 GLN cc_start: 0.7430 (tt0) cc_final: 0.6948 (tm-30) REVERT: M 256 GLN cc_start: 0.7494 (tt0) cc_final: 0.7260 (tt0) REVERT: O 31 GLN cc_start: 0.7682 (OUTLIER) cc_final: 0.7100 (tm-30) REVERT: O 231 ASN cc_start: 0.8400 (t0) cc_final: 0.8179 (t0) REVERT: Q 38 LYS cc_start: 0.8294 (ptmm) cc_final: 0.7794 (pttt) REVERT: Q 62 MET cc_start: 0.8734 (mtt) cc_final: 0.8440 (mtt) REVERT: Q 123 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.7719 (tm-30) REVERT: Q 220 LYS cc_start: 0.6840 (mmmt) cc_final: 0.5884 (mttt) REVERT: R 240 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7533 (mp0) REVERT: S 14 ILE cc_start: 0.7320 (OUTLIER) cc_final: 0.7065 (mm) REVERT: S 25 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7393 (mt-10) REVERT: U 123 GLN cc_start: 0.7913 (tp40) cc_final: 0.7655 (tp-100) REVERT: V 123 GLN cc_start: 0.7423 (tp40) cc_final: 0.6480 (mt0) REVERT: V 173 THR cc_start: 0.8742 (m) cc_final: 0.8476 (p) REVERT: W 123 GLN cc_start: 0.7481 (tp40) cc_final: 0.6685 (mt0) REVERT: W 195 GLN cc_start: 0.8185 (mt0) cc_final: 0.7898 (mm-40) REVERT: X 151 ASN cc_start: 0.7957 (p0) cc_final: 0.7246 (t0) REVERT: Z 38 LYS cc_start: 0.8143 (mtmm) cc_final: 0.7892 (mtmm) REVERT: Z 123 GLN cc_start: 0.7524 (OUTLIER) cc_final: 0.6650 (tm-30) REVERT: N 151 ASN cc_start: 0.8401 (t0) cc_final: 0.8109 (t0) REVERT: a 62 MET cc_start: 0.7450 (mmt) cc_final: 0.6945 (mmt) REVERT: a 87 THR cc_start: 0.7764 (m) cc_final: 0.7092 (p) REVERT: a 220 LYS cc_start: 0.7952 (mtmt) cc_final: 0.7064 (tptt) REVERT: b 73 GLN cc_start: 0.6925 (mt0) cc_final: 0.6711 (mt0) REVERT: b 95 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6791 (tt0) REVERT: b 116 ASP cc_start: 0.7113 (m-30) cc_final: 0.6692 (m-30) REVERT: b 256 GLN cc_start: 0.8065 (OUTLIER) cc_final: 0.7643 (tm-30) REVERT: c 30 GLN cc_start: 0.7701 (tp40) cc_final: 0.7461 (tp40) REVERT: c 263 GLN cc_start: 0.8353 (mm110) cc_final: 0.7532 (tp40) REVERT: d 31 GLN cc_start: 0.7872 (OUTLIER) cc_final: 0.7525 (pt0) REVERT: d 123 GLN cc_start: 0.6000 (tp-100) cc_final: 0.5449 (mt0) REVERT: e 125 GLU cc_start: 0.6812 (tp30) cc_final: 0.6514 (mm-30) REVERT: e 252 GLN cc_start: 0.8348 (mt0) cc_final: 0.8025 (mm-40) REVERT: f 16 LEU cc_start: 0.6981 (OUTLIER) cc_final: 0.6403 (tt) REVERT: f 88 ASP cc_start: 0.6146 (m-30) cc_final: 0.5920 (m-30) REVERT: h 95 GLU cc_start: 0.7362 (tt0) cc_final: 0.6548 (mt-10) REVERT: j 67 ASP cc_start: 0.6867 (m-30) cc_final: 0.6450 (m-30) REVERT: j 212 ASP cc_start: 0.8182 (m-30) cc_final: 0.7951 (m-30) REVERT: j 243 LYS cc_start: 0.7706 (ttmt) cc_final: 0.7340 (tmtt) REVERT: j 263 GLN cc_start: 0.7714 (pt0) cc_final: 0.7127 (mp-120) REVERT: g 67 ASP cc_start: 0.8103 (m-30) cc_final: 0.7749 (m-30) REVERT: g 93 MET cc_start: 0.7955 (mtp) cc_final: 0.7742 (mtp) REVERT: g 184 LYS cc_start: 0.6622 (tttp) cc_final: 0.6219 (mmtt) REVERT: g 191 ASP cc_start: 0.7751 (m-30) cc_final: 0.7418 (m-30) REVERT: g 252 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7492 (mp10) outliers start: 129 outliers final: 70 residues processed: 780 average time/residue: 1.3557 time to fit residues: 1427.8224 Evaluate side-chains 723 residues out of total 7560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 639 time to evaluate : 5.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain C residue 5 SER Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 126 LYS Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 256 GLN Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 226 ASP Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain J residue 31 GLN Chi-restraints excluded: chain K residue 253 LEU Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain L residue 225 LEU Chi-restraints excluded: chain L residue 253 LEU Chi-restraints excluded: chain L residue 267 SER Chi-restraints excluded: chain M residue 88 ASP Chi-restraints excluded: chain M residue 253 LEU Chi-restraints excluded: chain M residue 259 SER Chi-restraints excluded: chain O residue 31 GLN Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain O residue 267 SER Chi-restraints excluded: chain P residue 208 SER Chi-restraints excluded: chain P residue 259 SER Chi-restraints excluded: chain T residue 105 LEU Chi-restraints excluded: chain T residue 223 ASP Chi-restraints excluded: chain Q residue 123 GLN Chi-restraints excluded: chain R residue 240 GLU Chi-restraints excluded: chain S residue 14 ILE Chi-restraints excluded: chain S residue 25 GLU Chi-restraints excluded: chain S residue 51 THR Chi-restraints excluded: chain S residue 65 VAL Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 159 VAL Chi-restraints excluded: chain U residue 33 ILE Chi-restraints excluded: chain U residue 87 THR Chi-restraints excluded: chain V residue 159 VAL Chi-restraints excluded: chain W residue 6 ILE Chi-restraints excluded: chain W residue 56 SER Chi-restraints excluded: chain X residue 29 VAL Chi-restraints excluded: chain X residue 249 THR Chi-restraints excluded: chain X residue 253 LEU Chi-restraints excluded: chain Y residue 233 VAL Chi-restraints excluded: chain Z residue 27 THR Chi-restraints excluded: chain Z residue 123 GLN Chi-restraints excluded: chain Z residue 232 LEU Chi-restraints excluded: chain a residue 179 THR Chi-restraints excluded: chain b residue 95 GLU Chi-restraints excluded: chain b residue 256 GLN Chi-restraints excluded: chain b residue 264 SER Chi-restraints excluded: chain c residue 33 ILE Chi-restraints excluded: chain c residue 158 THR Chi-restraints excluded: chain c residue 159 VAL Chi-restraints excluded: chain c residue 163 THR Chi-restraints excluded: chain d residue 31 GLN Chi-restraints excluded: chain d residue 101 SER Chi-restraints excluded: chain d residue 159 VAL Chi-restraints excluded: chain e residue 33 ILE Chi-restraints excluded: chain e residue 101 SER Chi-restraints excluded: chain f residue 16 LEU Chi-restraints excluded: chain f residue 107 THR Chi-restraints excluded: chain f residue 124 ILE Chi-restraints excluded: chain f residue 164 ILE Chi-restraints excluded: chain f residue 189 THR Chi-restraints excluded: chain h residue 16 LEU Chi-restraints excluded: chain h residue 116 ASP Chi-restraints excluded: chain h residue 198 THR Chi-restraints excluded: chain i residue 98 LEU Chi-restraints excluded: chain i residue 103 THR Chi-restraints excluded: chain g residue 89 LEU Chi-restraints excluded: chain g residue 172 THR Chi-restraints excluded: chain g residue 252 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 852 optimal weight: 5.9990 chunk 897 optimal weight: 5.9990 chunk 818 optimal weight: 0.7980 chunk 873 optimal weight: 0.7980 chunk 525 optimal weight: 2.9990 chunk 380 optimal weight: 4.9990 chunk 685 optimal weight: 2.9990 chunk 267 optimal weight: 0.9980 chunk 788 optimal weight: 6.9990 chunk 825 optimal weight: 7.9990 chunk 869 optimal weight: 10.0000 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 GLN ** C 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 256 GLN E 31 GLN E 251 GLN F 151 ASN ** G 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 245 GLN K 134 ASN M 55 GLN P 256 GLN ** T 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 123 GLN U 151 ASN V 30 GLN V 151 ASN V 245 GLN V 251 GLN V 263 GLN ** X 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 263 GLN Z 31 GLN Z 151 ASN N 31 GLN a 134 ASN ** a 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 18 ASN d 256 GLN ** f 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 151 ASN j 73 GLN g 31 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 70056 Z= 0.197 Angle : 0.438 10.030 94824 Z= 0.253 Chirality : 0.033 0.202 12204 Planarity : 0.002 0.017 12132 Dihedral : 3.630 19.636 9792 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 1.56 % Allowed : 12.06 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.39 (0.08), residues: 9648 helix: 3.81 (0.06), residues: 7020 sheet: -1.63 (0.21), residues: 432 loop : 0.68 (0.15), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP f 49 HIS 0.004 0.002 HIS G 214 PHE 0.019 0.002 PHE P 110 ARG 0.002 0.000 ARG j 71 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 762 residues out of total 7560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 644 time to evaluate : 5.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7859 (OUTLIER) cc_final: 0.7615 (tm130) REVERT: B 256 GLN cc_start: 0.7938 (tt0) cc_final: 0.7659 (tt0) REVERT: D 30 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7858 (mt0) REVERT: D 95 GLU cc_start: 0.6328 (mm-30) cc_final: 0.5834 (mt-10) REVERT: F 256 GLN cc_start: 0.6979 (OUTLIER) cc_final: 0.5815 (mp10) REVERT: F 264 SER cc_start: 0.7578 (t) cc_final: 0.7282 (p) REVERT: G 199 ASN cc_start: 0.7702 (p0) cc_final: 0.7381 (m110) REVERT: G 220 LYS cc_start: 0.7604 (mtmt) cc_final: 0.6719 (mmtt) REVERT: H 191 ASP cc_start: 0.8040 (t0) cc_final: 0.7769 (m-30) REVERT: H 226 ASP cc_start: 0.7394 (OUTLIER) cc_final: 0.6969 (m-30) REVERT: I 31 GLN cc_start: 0.6984 (pp30) cc_final: 0.6227 (mm-40) REVERT: K 45 ASN cc_start: 0.8393 (t0) cc_final: 0.8180 (t0) REVERT: K 71 ARG cc_start: 0.7768 (ttt90) cc_final: 0.6570 (mtm110) REVERT: K 92 LYS cc_start: 0.8679 (mtpp) cc_final: 0.8372 (mtmt) REVERT: L 253 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8220 (mm) REVERT: M 13 MET cc_start: 0.7548 (mtp) cc_final: 0.7201 (mtt) REVERT: M 62 MET cc_start: 0.7950 (mmt) cc_final: 0.7573 (mtt) REVERT: M 195 GLN cc_start: 0.7483 (tt0) cc_final: 0.6993 (tm-30) REVERT: M 256 GLN cc_start: 0.7533 (tt0) cc_final: 0.7253 (tt0) REVERT: O 231 ASN cc_start: 0.8533 (t0) cc_final: 0.8213 (t0) REVERT: Q 38 LYS cc_start: 0.8293 (ptmm) cc_final: 0.7861 (pttm) REVERT: Q 62 MET cc_start: 0.8838 (mtt) cc_final: 0.8459 (mtt) REVERT: Q 123 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.7780 (tm-30) REVERT: Q 220 LYS cc_start: 0.6949 (mmmt) cc_final: 0.5874 (mttp) REVERT: R 123 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.7945 (mt0) REVERT: R 240 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7598 (mp0) REVERT: S 14 ILE cc_start: 0.7359 (OUTLIER) cc_final: 0.7107 (mm) REVERT: S 25 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7374 (mt-10) REVERT: S 31 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7386 (tp40) REVERT: S 186 MET cc_start: 0.8405 (tpt) cc_final: 0.8169 (tpp) REVERT: U 123 GLN cc_start: 0.7925 (tp40) cc_final: 0.7697 (tp-100) REVERT: V 88 ASP cc_start: 0.7731 (m-30) cc_final: 0.7441 (m-30) REVERT: V 123 GLN cc_start: 0.7437 (tp40) cc_final: 0.6465 (mt0) REVERT: V 173 THR cc_start: 0.8746 (m) cc_final: 0.8490 (p) REVERT: W 123 GLN cc_start: 0.7503 (tp40) cc_final: 0.6700 (mt0) REVERT: W 195 GLN cc_start: 0.8234 (mt0) cc_final: 0.7918 (mm-40) REVERT: X 151 ASN cc_start: 0.8071 (p0) cc_final: 0.7396 (t0) REVERT: Z 38 LYS cc_start: 0.8184 (mtmm) cc_final: 0.7968 (mtmm) REVERT: Z 123 GLN cc_start: 0.7575 (OUTLIER) cc_final: 0.6696 (tm-30) REVERT: N 67 ASP cc_start: 0.7800 (m-30) cc_final: 0.7501 (m-30) REVERT: N 151 ASN cc_start: 0.8457 (t0) cc_final: 0.8146 (t0) REVERT: a 62 MET cc_start: 0.7498 (mmt) cc_final: 0.7258 (mmt) REVERT: a 87 THR cc_start: 0.7892 (m) cc_final: 0.7239 (p) REVERT: a 220 LYS cc_start: 0.7933 (mtmt) cc_final: 0.7037 (tptt) REVERT: b 73 GLN cc_start: 0.7012 (mt0) cc_final: 0.6809 (mt0) REVERT: b 95 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.6917 (tt0) REVERT: b 256 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.7647 (tm-30) REVERT: c 30 GLN cc_start: 0.7763 (tp40) cc_final: 0.7486 (tp40) REVERT: c 263 GLN cc_start: 0.8353 (mm110) cc_final: 0.7544 (tp40) REVERT: d 31 GLN cc_start: 0.7902 (OUTLIER) cc_final: 0.7543 (pt0) REVERT: d 123 GLN cc_start: 0.6000 (tp-100) cc_final: 0.5438 (mt0) REVERT: e 125 GLU cc_start: 0.6913 (tp30) cc_final: 0.6654 (mm-30) REVERT: e 252 GLN cc_start: 0.8361 (mt0) cc_final: 0.8009 (mm-40) REVERT: f 16 LEU cc_start: 0.7061 (OUTLIER) cc_final: 0.6689 (tt) REVERT: f 263 GLN cc_start: 0.7536 (tm-30) cc_final: 0.7088 (tt0) REVERT: h 95 GLU cc_start: 0.7392 (tt0) cc_final: 0.6639 (mt-10) REVERT: j 67 ASP cc_start: 0.6818 (m-30) cc_final: 0.6480 (m-30) REVERT: j 212 ASP cc_start: 0.8213 (m-30) cc_final: 0.7922 (m-30) REVERT: j 243 LYS cc_start: 0.7815 (ttmt) cc_final: 0.7220 (tptt) REVERT: j 263 GLN cc_start: 0.7751 (pt0) cc_final: 0.7257 (mp-120) REVERT: g 67 ASP cc_start: 0.8103 (m-30) cc_final: 0.7735 (m-30) REVERT: g 93 MET cc_start: 0.8010 (mtp) cc_final: 0.7777 (mtp) REVERT: g 106 ASN cc_start: 0.7229 (t0) cc_final: 0.5468 (p0) REVERT: g 184 LYS cc_start: 0.6675 (tttp) cc_final: 0.6269 (mmtt) REVERT: g 191 ASP cc_start: 0.7818 (m-30) cc_final: 0.7490 (m-30) REVERT: g 252 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7450 (mp10) outliers start: 118 outliers final: 80 residues processed: 736 average time/residue: 1.4016 time to fit residues: 1390.7739 Evaluate side-chains 724 residues out of total 7560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 627 time to evaluate : 5.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain C residue 5 SER Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain D residue 30 GLN Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 126 LYS Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 256 GLN Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 226 ASP Chi-restraints excluded: chain I residue 56 SER Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain I residue 264 SER Chi-restraints excluded: chain J residue 31 GLN Chi-restraints excluded: chain J residue 116 ASP Chi-restraints excluded: chain K residue 253 LEU Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain L residue 225 LEU Chi-restraints excluded: chain L residue 253 LEU Chi-restraints excluded: chain L residue 267 SER Chi-restraints excluded: chain M residue 88 ASP Chi-restraints excluded: chain M residue 253 LEU Chi-restraints excluded: chain M residue 259 SER Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain O residue 267 SER Chi-restraints excluded: chain P residue 208 SER Chi-restraints excluded: chain P residue 259 SER Chi-restraints excluded: chain T residue 98 LEU Chi-restraints excluded: chain T residue 105 LEU Chi-restraints excluded: chain T residue 223 ASP Chi-restraints excluded: chain Q residue 123 GLN Chi-restraints excluded: chain R residue 123 GLN Chi-restraints excluded: chain R residue 240 GLU Chi-restraints excluded: chain S residue 14 ILE Chi-restraints excluded: chain S residue 25 GLU Chi-restraints excluded: chain S residue 31 GLN Chi-restraints excluded: chain S residue 51 THR Chi-restraints excluded: chain S residue 65 VAL Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 159 VAL Chi-restraints excluded: chain U residue 84 ASP Chi-restraints excluded: chain U residue 87 THR Chi-restraints excluded: chain V residue 159 VAL Chi-restraints excluded: chain W residue 6 ILE Chi-restraints excluded: chain W residue 56 SER Chi-restraints excluded: chain X residue 29 VAL Chi-restraints excluded: chain X residue 249 THR Chi-restraints excluded: chain X residue 253 LEU Chi-restraints excluded: chain Y residue 29 VAL Chi-restraints excluded: chain Y residue 232 LEU Chi-restraints excluded: chain Y residue 233 VAL Chi-restraints excluded: chain Z residue 27 THR Chi-restraints excluded: chain Z residue 123 GLN Chi-restraints excluded: chain Z residue 232 LEU Chi-restraints excluded: chain a residue 179 THR Chi-restraints excluded: chain b residue 95 GLU Chi-restraints excluded: chain b residue 256 GLN Chi-restraints excluded: chain b residue 264 SER Chi-restraints excluded: chain c residue 33 ILE Chi-restraints excluded: chain c residue 158 THR Chi-restraints excluded: chain c residue 159 VAL Chi-restraints excluded: chain c residue 163 THR Chi-restraints excluded: chain c residue 253 LEU Chi-restraints excluded: chain d residue 4 ASN Chi-restraints excluded: chain d residue 31 GLN Chi-restraints excluded: chain d residue 101 SER Chi-restraints excluded: chain d residue 159 VAL Chi-restraints excluded: chain e residue 33 ILE Chi-restraints excluded: chain e residue 101 SER Chi-restraints excluded: chain f residue 16 LEU Chi-restraints excluded: chain f residue 107 THR Chi-restraints excluded: chain f residue 124 ILE Chi-restraints excluded: chain f residue 164 ILE Chi-restraints excluded: chain f residue 189 THR Chi-restraints excluded: chain h residue 16 LEU Chi-restraints excluded: chain h residue 116 ASP Chi-restraints excluded: chain h residue 198 THR Chi-restraints excluded: chain i residue 98 LEU Chi-restraints excluded: chain i residue 103 THR Chi-restraints excluded: chain g residue 89 LEU Chi-restraints excluded: chain g residue 172 THR Chi-restraints excluded: chain g residue 252 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 573 optimal weight: 8.9990 chunk 923 optimal weight: 0.9990 chunk 563 optimal weight: 5.9990 chunk 437 optimal weight: 0.9980 chunk 641 optimal weight: 2.9990 chunk 968 optimal weight: 0.7980 chunk 891 optimal weight: 6.9990 chunk 771 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 595 optimal weight: 2.9990 chunk 472 optimal weight: 8.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 256 GLN E 31 GLN E 251 GLN F 151 ASN ** G 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 245 GLN K 134 ASN M 55 GLN P 256 GLN ** T 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 123 GLN U 151 ASN V 151 ASN V 245 GLN V 251 GLN V 263 GLN W 34 ASN ** X 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 263 GLN Z 31 GLN Z 151 ASN N 31 GLN a 134 ASN a 231 ASN d 256 GLN ** f 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 151 ASN f 251 GLN g 31 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 70056 Z= 0.176 Angle : 0.425 10.224 94824 Z= 0.247 Chirality : 0.033 0.287 12204 Planarity : 0.002 0.054 12132 Dihedral : 3.590 19.556 9792 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 1.43 % Allowed : 12.37 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.45 (0.08), residues: 9648 helix: 3.86 (0.06), residues: 7020 sheet: -1.56 (0.21), residues: 432 loop : 0.67 (0.15), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP f 49 HIS 0.004 0.001 HIS G 214 PHE 0.013 0.002 PHE f 177 ARG 0.016 0.000 ARG j 71 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 748 residues out of total 7560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 640 time to evaluate : 5.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7829 (OUTLIER) cc_final: 0.7547 (tm130) REVERT: B 256 GLN cc_start: 0.7925 (tt0) cc_final: 0.7655 (tt0) REVERT: D 30 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7864 (mt0) REVERT: D 95 GLU cc_start: 0.6308 (mm-30) cc_final: 0.5827 (mt-10) REVERT: F 256 GLN cc_start: 0.6943 (OUTLIER) cc_final: 0.5830 (mp10) REVERT: F 264 SER cc_start: 0.7575 (t) cc_final: 0.7276 (p) REVERT: G 199 ASN cc_start: 0.7677 (p0) cc_final: 0.7362 (m110) REVERT: G 220 LYS cc_start: 0.7591 (mtmt) cc_final: 0.6717 (mmtt) REVERT: H 191 ASP cc_start: 0.8028 (t0) cc_final: 0.7745 (m-30) REVERT: H 226 ASP cc_start: 0.7329 (OUTLIER) cc_final: 0.6932 (m-30) REVERT: I 31 GLN cc_start: 0.6972 (pp30) cc_final: 0.6218 (mm-40) REVERT: K 45 ASN cc_start: 0.8366 (t0) cc_final: 0.8155 (t0) REVERT: K 71 ARG cc_start: 0.7678 (ttt90) cc_final: 0.6590 (mtm110) REVERT: K 92 LYS cc_start: 0.8665 (mtpp) cc_final: 0.8358 (mtmt) REVERT: L 253 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8228 (mm) REVERT: M 13 MET cc_start: 0.7506 (mtp) cc_final: 0.7194 (mtt) REVERT: M 62 MET cc_start: 0.7902 (mmt) cc_final: 0.7552 (mtt) REVERT: M 195 GLN cc_start: 0.7460 (tt0) cc_final: 0.6971 (tm-30) REVERT: M 256 GLN cc_start: 0.7516 (tt0) cc_final: 0.7254 (tt0) REVERT: O 231 ASN cc_start: 0.8482 (t0) cc_final: 0.8209 (t0) REVERT: Q 38 LYS cc_start: 0.8286 (ptmm) cc_final: 0.7787 (pttt) REVERT: Q 62 MET cc_start: 0.8804 (mtt) cc_final: 0.8422 (mtt) REVERT: Q 123 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.7737 (tm-30) REVERT: Q 220 LYS cc_start: 0.6933 (mmmt) cc_final: 0.5891 (mttt) REVERT: R 245 GLN cc_start: 0.6772 (pt0) cc_final: 0.6551 (pt0) REVERT: S 14 ILE cc_start: 0.7340 (OUTLIER) cc_final: 0.7088 (mm) REVERT: S 25 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7384 (mt-10) REVERT: S 31 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.7384 (tp40) REVERT: S 186 MET cc_start: 0.8399 (tpt) cc_final: 0.8179 (tpp) REVERT: U 123 GLN cc_start: 0.7929 (tp40) cc_final: 0.7671 (tp-100) REVERT: V 88 ASP cc_start: 0.7721 (m-30) cc_final: 0.7425 (m-30) REVERT: V 123 GLN cc_start: 0.7421 (tp40) cc_final: 0.6462 (mt0) REVERT: V 173 THR cc_start: 0.8712 (m) cc_final: 0.8453 (p) REVERT: W 123 GLN cc_start: 0.7498 (tp40) cc_final: 0.6696 (mt0) REVERT: W 195 GLN cc_start: 0.8219 (mt0) cc_final: 0.7925 (mm-40) REVERT: X 151 ASN cc_start: 0.8037 (p0) cc_final: 0.7351 (t0) REVERT: Z 38 LYS cc_start: 0.8161 (mtmm) cc_final: 0.7956 (mtmm) REVERT: Z 93 MET cc_start: 0.8519 (mtp) cc_final: 0.8284 (mtm) REVERT: Z 123 GLN cc_start: 0.7540 (OUTLIER) cc_final: 0.6671 (tm-30) REVERT: N 67 ASP cc_start: 0.7770 (m-30) cc_final: 0.7441 (m-30) REVERT: N 151 ASN cc_start: 0.8405 (t0) cc_final: 0.8086 (t0) REVERT: a 62 MET cc_start: 0.7477 (mmt) cc_final: 0.7244 (mmt) REVERT: a 87 THR cc_start: 0.7869 (m) cc_final: 0.7211 (p) REVERT: a 220 LYS cc_start: 0.7931 (mtmt) cc_final: 0.7042 (tptt) REVERT: b 73 GLN cc_start: 0.6975 (mt0) cc_final: 0.6757 (mt0) REVERT: b 95 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.6758 (tt0) REVERT: b 116 ASP cc_start: 0.7168 (m-30) cc_final: 0.6797 (m-30) REVERT: b 256 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.7645 (tm-30) REVERT: c 30 GLN cc_start: 0.7720 (tp40) cc_final: 0.7462 (tp40) REVERT: c 263 GLN cc_start: 0.8346 (mm110) cc_final: 0.7543 (tp40) REVERT: d 31 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7542 (pt0) REVERT: d 123 GLN cc_start: 0.5959 (tp-100) cc_final: 0.5425 (mt0) REVERT: e 125 GLU cc_start: 0.6901 (tp30) cc_final: 0.6599 (mm-30) REVERT: e 252 GLN cc_start: 0.8358 (mt0) cc_final: 0.8018 (mm-40) REVERT: f 16 LEU cc_start: 0.7011 (OUTLIER) cc_final: 0.6569 (tt) REVERT: h 95 GLU cc_start: 0.7391 (tt0) cc_final: 0.6618 (mt-10) REVERT: j 67 ASP cc_start: 0.6877 (m-30) cc_final: 0.6480 (m-30) REVERT: j 212 ASP cc_start: 0.8194 (m-30) cc_final: 0.7897 (m-30) REVERT: j 243 LYS cc_start: 0.7786 (ttmt) cc_final: 0.7186 (tptt) REVERT: j 263 GLN cc_start: 0.7726 (pt0) cc_final: 0.7230 (mp-120) REVERT: g 67 ASP cc_start: 0.8068 (m-30) cc_final: 0.7695 (m-30) REVERT: g 93 MET cc_start: 0.7991 (mtp) cc_final: 0.7747 (mtp) REVERT: g 106 ASN cc_start: 0.7206 (t0) cc_final: 0.5453 (p0) REVERT: g 184 LYS cc_start: 0.6664 (tttp) cc_final: 0.6265 (mmtt) REVERT: g 191 ASP cc_start: 0.7812 (m-30) cc_final: 0.7472 (m-30) REVERT: g 252 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7467 (mp10) outliers start: 108 outliers final: 77 residues processed: 724 average time/residue: 1.3278 time to fit residues: 1292.3264 Evaluate side-chains 719 residues out of total 7560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 627 time to evaluate : 5.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain C residue 5 SER Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain D residue 30 GLN Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 126 LYS Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 256 GLN Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 226 ASP Chi-restraints excluded: chain I residue 56 SER Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain I residue 264 SER Chi-restraints excluded: chain J residue 31 GLN Chi-restraints excluded: chain J residue 116 ASP Chi-restraints excluded: chain K residue 253 LEU Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain L residue 225 LEU Chi-restraints excluded: chain L residue 253 LEU Chi-restraints excluded: chain L residue 267 SER Chi-restraints excluded: chain M residue 88 ASP Chi-restraints excluded: chain M residue 253 LEU Chi-restraints excluded: chain M residue 259 SER Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain O residue 267 SER Chi-restraints excluded: chain P residue 208 SER Chi-restraints excluded: chain P residue 259 SER Chi-restraints excluded: chain T residue 105 LEU Chi-restraints excluded: chain T residue 223 ASP Chi-restraints excluded: chain Q residue 123 GLN Chi-restraints excluded: chain S residue 14 ILE Chi-restraints excluded: chain S residue 25 GLU Chi-restraints excluded: chain S residue 31 GLN Chi-restraints excluded: chain S residue 51 THR Chi-restraints excluded: chain S residue 65 VAL Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 159 VAL Chi-restraints excluded: chain U residue 87 THR Chi-restraints excluded: chain V residue 159 VAL Chi-restraints excluded: chain W residue 6 ILE Chi-restraints excluded: chain W residue 56 SER Chi-restraints excluded: chain X residue 29 VAL Chi-restraints excluded: chain X residue 249 THR Chi-restraints excluded: chain X residue 253 LEU Chi-restraints excluded: chain Y residue 29 VAL Chi-restraints excluded: chain Y residue 232 LEU Chi-restraints excluded: chain Y residue 233 VAL Chi-restraints excluded: chain Z residue 27 THR Chi-restraints excluded: chain Z residue 123 GLN Chi-restraints excluded: chain Z residue 232 LEU Chi-restraints excluded: chain a residue 179 THR Chi-restraints excluded: chain b residue 95 GLU Chi-restraints excluded: chain b residue 256 GLN Chi-restraints excluded: chain b residue 264 SER Chi-restraints excluded: chain c residue 33 ILE Chi-restraints excluded: chain c residue 158 THR Chi-restraints excluded: chain c residue 159 VAL Chi-restraints excluded: chain c residue 253 LEU Chi-restraints excluded: chain d residue 4 ASN Chi-restraints excluded: chain d residue 31 GLN Chi-restraints excluded: chain d residue 101 SER Chi-restraints excluded: chain d residue 129 THR Chi-restraints excluded: chain d residue 159 VAL Chi-restraints excluded: chain e residue 33 ILE Chi-restraints excluded: chain e residue 101 SER Chi-restraints excluded: chain f residue 16 LEU Chi-restraints excluded: chain f residue 107 THR Chi-restraints excluded: chain f residue 124 ILE Chi-restraints excluded: chain f residue 164 ILE Chi-restraints excluded: chain f residue 189 THR Chi-restraints excluded: chain h residue 16 LEU Chi-restraints excluded: chain h residue 116 ASP Chi-restraints excluded: chain h residue 198 THR Chi-restraints excluded: chain i residue 98 LEU Chi-restraints excluded: chain i residue 103 THR Chi-restraints excluded: chain g residue 89 LEU Chi-restraints excluded: chain g residue 172 THR Chi-restraints excluded: chain g residue 252 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 612 optimal weight: 4.9990 chunk 821 optimal weight: 0.9980 chunk 236 optimal weight: 0.9980 chunk 711 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 214 optimal weight: 9.9990 chunk 772 optimal weight: 5.9990 chunk 323 optimal weight: 4.9990 chunk 793 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 142 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 ASN D 256 GLN E 31 GLN E 251 GLN F 151 ASN ** G 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 245 GLN K 134 ASN M 55 GLN P 256 GLN ** T 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 123 GLN U 151 ASN V 151 ASN V 245 GLN V 251 GLN V 263 GLN ** X 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 263 GLN Z 31 GLN Z 151 ASN N 31 GLN a 134 ASN a 231 ASN d 256 GLN ** f 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 151 ASN g 31 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.125195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.111640 restraints weight = 96260.483| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.40 r_work: 0.3420 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 70056 Z= 0.178 Angle : 0.427 10.198 94824 Z= 0.247 Chirality : 0.033 0.276 12204 Planarity : 0.002 0.058 12132 Dihedral : 3.588 19.823 9792 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 1.53 % Allowed : 12.33 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.44 (0.08), residues: 9648 helix: 3.85 (0.06), residues: 7020 sheet: -1.50 (0.22), residues: 432 loop : 0.66 (0.15), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP f 49 HIS 0.004 0.001 HIS G 214 PHE 0.020 0.002 PHE P 110 ARG 0.015 0.000 ARG j 71 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22285.40 seconds wall clock time: 384 minutes 53.64 seconds (23093.64 seconds total)