Starting phenix.real_space_refine on Wed Jan 22 10:21:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cej_45503/01_2025/9cej_45503.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cej_45503/01_2025/9cej_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/cci-nas-00/data/ceres_data/9cej_45503/01_2025/9cej_45503.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cej_45503/01_2025/9cej_45503.map" model { file = "/net/cci-nas-00/data/ceres_data/9cej_45503/01_2025/9cej_45503.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cej_45503/01_2025/9cej_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-5571/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: 28.95, per 1000 atoms: 0.42 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: 13.28 Conformation dependent library (CDL) restraints added in 7.3 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: 4.24 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: 25.76 Time building geometry restraints manager: 15.74 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: 0.02 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: 0.000 Normalize map: mean=0, sd=1: 14.490 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: 0.000 Extract box with map and model: 1.160 Check model and map are aligned: 0.390 Set scattering table: 0.480 Process input model: 117.410 Find NCS groups from input model: 2.260 Set up NCS constraints: 0.860 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: 0.030 Load rotamer database and sin/cos tables:11.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 149.040 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 3 poor density : 1087 time to evaluate : 5.914 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: 1.4175 time to fit residues: 2036.9410 Evaluate side-chains 679 residues out of total 7560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 678 time to evaluate : 5.838 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.122843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.109313 restraints weight = 96314.431| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.41 r_work: 0.3390 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1291 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 47.425 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 to be fit. rotamer outliers: 165 poor density : 699 time to evaluate : 5.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7807 (tm130) REVERT: B 35 THR cc_start: 0.8475 (m) cc_final: 0.8224 (p) REVERT: B 95 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7382 (mt-10) REVERT: B 126 LYS cc_start: 0.7994 (OUTLIER) cc_final: 0.7743 (tppp) REVERT: C 248 GLN cc_start: 0.8628 (OUTLIER) cc_final: 0.8193 (mt0) REVERT: D 95 GLU cc_start: 0.5689 (mm-30) cc_final: 0.5185 (mt-10) REVERT: E 256 GLN cc_start: 0.7972 (tt0) cc_final: 0.7573 (mt0) REVERT: F 253 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7425 (mt) REVERT: F 264 SER cc_start: 0.7606 (t) cc_final: 0.7325 (p) REVERT: G 220 LYS cc_start: 0.7354 (mtmt) cc_final: 0.6183 (mmtt) REVERT: H 191 ASP cc_start: 0.8160 (t0) cc_final: 0.7714 (m-30) REVERT: H 226 ASP cc_start: 0.7483 (m-30) cc_final: 0.7168 (m-30) REVERT: I 31 GLN cc_start: 0.7074 (pp30) cc_final: 0.6479 (mm-40) REVERT: J 32 ARG cc_start: 0.7376 (ttm-80) cc_final: 0.7108 (ttt180) REVERT: J 43 LYS cc_start: 0.5179 (mmmt) cc_final: 0.4656 (mmpt) REVERT: K 71 ARG cc_start: 0.7543 (ttt90) cc_final: 0.6323 (mtm110) REVERT: K 77 ASP cc_start: 0.7576 (p0) cc_final: 0.7103 (m-30) REVERT: L 253 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7974 (mm) REVERT: M 93 MET cc_start: 0.7932 (mtp) cc_final: 0.7575 (mtp) REVERT: M 145 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7825 (pttm) REVERT: M 195 GLN cc_start: 0.7032 (tt0) cc_final: 0.6538 (tm-30) REVERT: O 31 GLN cc_start: 0.7503 (OUTLIER) cc_final: 0.6902 (tm-30) REVERT: O 84 ASP cc_start: 0.7364 (m-30) cc_final: 0.6899 (t0) REVERT: O 93 MET cc_start: 0.8494 (mtp) cc_final: 0.8293 (mtp) REVERT: P 256 GLN cc_start: 0.7731 (tt0) cc_final: 0.7490 (mt0) REVERT: Q 38 LYS cc_start: 0.8256 (ptmm) cc_final: 0.7624 (pttm) REVERT: Q 132 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8470 (mtpp) REVERT: Q 220 LYS cc_start: 0.6542 (mmmt) cc_final: 0.5547 (mttp) REVERT: Q 267 SER cc_start: 0.7992 (OUTLIER) cc_final: 0.7747 (p) REVERT: R 67 ASP cc_start: 0.7480 (m-30) cc_final: 0.7094 (m-30) REVERT: R 240 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7282 (mp0) REVERT: R 263 GLN cc_start: 0.7293 (mp10) cc_final: 0.6695 (mm-40) REVERT: S 14 ILE cc_start: 0.7141 (OUTLIER) cc_final: 0.6914 (mm) REVERT: S 31 GLN cc_start: 0.7921 (OUTLIER) cc_final: 0.7045 (tp40) REVERT: V 34 ASN cc_start: 0.7840 (p0) cc_final: 0.7523 (p0) REVERT: V 88 ASP cc_start: 0.7817 (m-30) cc_final: 0.7553 (m-30) REVERT: V 123 GLN cc_start: 0.7558 (tp40) cc_final: 0.6754 (mt0) REVERT: V 173 THR cc_start: 0.8780 (m) cc_final: 0.8472 (p) REVERT: W 123 GLN cc_start: 0.7327 (tp40) cc_final: 0.6471 (mt0) REVERT: W 195 GLN cc_start: 0.8056 (mt0) cc_final: 0.7621 (mm-40) REVERT: X 151 ASN cc_start: 0.7948 (p0) cc_final: 0.7157 (t0) REVERT: X 226 ASP cc_start: 0.7618 (m-30) cc_final: 0.7269 (m-30) REVERT: N 3 LEU cc_start: 0.5749 (tp) cc_final: 0.5032 (tt) REVERT: N 31 GLN cc_start: 0.7347 (OUTLIER) cc_final: 0.7089 (mm110) REVERT: N 67 ASP cc_start: 0.7572 (m-30) cc_final: 0.7254 (m-30) REVERT: N 245 GLN cc_start: 0.6132 (pt0) cc_final: 0.5759 (tp-100) REVERT: a 62 MET cc_start: 0.7092 (OUTLIER) cc_final: 0.6631 (tpp) REVERT: a 87 THR cc_start: 0.7425 (m) cc_final: 0.6838 (p) REVERT: a 220 LYS cc_start: 0.7625 (mtmt) cc_final: 0.6524 (mmtt) REVERT: b 73 GLN cc_start: 0.6964 (mt0) cc_final: 0.6680 (mt0) REVERT: b 256 GLN cc_start: 0.7784 (OUTLIER) cc_final: 0.7240 (tm-30) REVERT: c 263 GLN cc_start: 0.8390 (mm110) cc_final: 0.7216 (tp40) REVERT: d 31 GLN cc_start: 0.7773 (OUTLIER) cc_final: 0.7417 (pt0) REVERT: d 123 GLN cc_start: 0.6000 (tp-100) cc_final: 0.5243 (mt0) REVERT: e 252 GLN cc_start: 0.8132 (mt0) cc_final: 0.7607 (mm-40) REVERT: f 62 MET cc_start: 0.6588 (mpt) cc_final: 0.6278 (mpp) REVERT: f 89 LEU cc_start: 0.6218 (OUTLIER) cc_final: 0.5779 (mp) REVERT: h 95 GLU cc_start: 0.7335 (tt0) cc_final: 0.6734 (mt-10) REVERT: i 31 GLN cc_start: 0.7239 (OUTLIER) cc_final: 0.6794 (mt0) REVERT: i 37 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.8208 (mttp) REVERT: i 175 SER cc_start: 0.8786 (m) cc_final: 0.8529 (m) REVERT: j 71 ARG cc_start: 0.7603 (ttp-110) cc_final: 0.7346 (ttp-110) REVERT: j 243 LYS cc_start: 0.7455 (ttmt) cc_final: 0.6839 (tptt) REVERT: j 263 GLN cc_start: 0.7431 (pt0) cc_final: 0.6923 (mp-120) REVERT: g 93 MET cc_start: 0.7992 (mtp) cc_final: 0.7625 (mtp) REVERT: g 106 ASN cc_start: 0.7289 (t0) cc_final: 0.5545 (p0) REVERT: g 174 THR cc_start: 0.8286 (m) cc_final: 0.8055 (p) REVERT: g 184 LYS cc_start: 0.7184 (tttp) cc_final: 0.6647 (tptt) REVERT: g 252 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7283 (mp10) outliers start: 165 outliers final: 79 residues processed: 824 average time/residue: 1.3130 time to fit residues: 1457.4908 Evaluate side-chains 731 residues out of total 7560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 632 time to evaluate : 5.762 ------------------------------------------------------------------------------- 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 37 LYS 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 99 optimal weight: 3.9990 chunk 414 optimal weight: 0.9990 chunk 916 optimal weight: 6.9990 chunk 385 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 317 optimal weight: 0.6980 chunk 3 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 849 optimal weight: 10.0000 chunk 808 optimal weight: 9.9990 chunk 724 optimal weight: 0.6980 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 123 GLN U 151 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.124111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.110618 restraints weight = 96545.842| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.39 r_work: 0.3409 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 70056 Z= 0.196 Angle : 0.451 8.202 94824 Z= 0.260 Chirality : 0.034 0.147 12204 Planarity : 0.002 0.021 12132 Dihedral : 3.791 22.165 9792 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 2.09 % Allowed : 8.27 % 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: 3.96 (0.09), residues: 9648 helix: 3.39 (0.06), residues: 7020 sheet: -2.81 (0.19), residues: 432 loop : 1.18 (0.15), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP f 49 HIS 0.004 0.001 HIS C 214 PHE 0.016 0.002 PHE P 217 ARG 0.006 0.000 ARG a 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 864 residues out of total 7560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 706 time to evaluate : 5.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7773 (tm130) REVERT: B 95 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7450 (mt-10) REVERT: B 126 LYS cc_start: 0.7839 (OUTLIER) cc_final: 0.7627 (tppp) REVERT: D 95 GLU cc_start: 0.6353 (mm-30) cc_final: 0.5805 (mt-10) REVERT: E 256 GLN cc_start: 0.7949 (tt0) cc_final: 0.7544 (mt0) REVERT: F 256 GLN cc_start: 0.6951 (OUTLIER) cc_final: 0.5930 (mt0) REVERT: F 264 SER cc_start: 0.7524 (t) cc_final: 0.7250 (p) REVERT: G 32 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.8157 (mtt180) REVERT: G 220 LYS cc_start: 0.7282 (mtmt) cc_final: 0.6172 (mmtt) REVERT: H 191 ASP cc_start: 0.8196 (t0) cc_final: 0.7795 (m-30) REVERT: H 226 ASP cc_start: 0.7455 (m-30) cc_final: 0.7105 (m-30) REVERT: I 31 GLN cc_start: 0.7112 (pp30) cc_final: 0.6421 (mm-40) REVERT: J 32 ARG cc_start: 0.7360 (ttm-80) cc_final: 0.7008 (ttt180) REVERT: J 43 LYS cc_start: 0.5088 (mmmt) cc_final: 0.4651 (mmpt) REVERT: K 71 ARG cc_start: 0.7519 (ttt90) cc_final: 0.6300 (mtm110) REVERT: K 77 ASP cc_start: 0.7470 (p0) cc_final: 0.7188 (m-30) REVERT: K 92 LYS cc_start: 0.8520 (mtpp) cc_final: 0.8202 (mtmt) REVERT: M 145 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7826 (pttm) REVERT: M 195 GLN cc_start: 0.7057 (tt0) cc_final: 0.6553 (tm-30) REVERT: M 243 LYS cc_start: 0.8223 (tppt) cc_final: 0.7943 (mmmm) REVERT: O 31 GLN cc_start: 0.7402 (OUTLIER) cc_final: 0.6775 (tm-30) REVERT: O 84 ASP cc_start: 0.7334 (m-30) cc_final: 0.6927 (t0) REVERT: T 8 THR cc_start: 0.8312 (t) cc_final: 0.7980 (m) REVERT: Q 38 LYS cc_start: 0.8264 (ptmm) cc_final: 0.7651 (pttm) REVERT: Q 220 LYS cc_start: 0.6416 (mmmt) cc_final: 0.5493 (mttt) REVERT: Q 267 SER cc_start: 0.8045 (OUTLIER) cc_final: 0.7730 (p) REVERT: R 67 ASP cc_start: 0.7383 (m-30) cc_final: 0.7042 (m-30) REVERT: R 240 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7234 (mp0) REVERT: R 263 GLN cc_start: 0.7332 (mp10) cc_final: 0.6680 (mm-40) REVERT: S 14 ILE cc_start: 0.7132 (OUTLIER) cc_final: 0.6904 (mm) REVERT: S 25 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7100 (mt-10) REVERT: S 95 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7212 (tt0) REVERT: S 186 MET cc_start: 0.8271 (tpt) cc_final: 0.8040 (tpp) REVERT: V 34 ASN cc_start: 0.7736 (p0) cc_final: 0.7355 (p0) REVERT: V 123 GLN cc_start: 0.7541 (tp40) cc_final: 0.6739 (mt0) REVERT: V 173 THR cc_start: 0.8791 (m) cc_final: 0.8502 (p) REVERT: V 245 GLN cc_start: 0.7685 (mm-40) cc_final: 0.7340 (mm110) REVERT: W 123 GLN cc_start: 0.7337 (tp40) cc_final: 0.6481 (mt0) REVERT: W 195 GLN cc_start: 0.8033 (mt0) cc_final: 0.7603 (mm-40) REVERT: X 93 MET cc_start: 0.8590 (ttm) cc_final: 0.7916 (mtp) REVERT: X 151 ASN cc_start: 0.8043 (p0) cc_final: 0.7190 (t0) REVERT: X 226 ASP cc_start: 0.7655 (m-30) cc_final: 0.7418 (m-30) REVERT: N 3 LEU cc_start: 0.5824 (tp) cc_final: 0.5112 (tt) REVERT: N 31 GLN cc_start: 0.7387 (OUTLIER) cc_final: 0.7091 (tt0) REVERT: N 67 ASP cc_start: 0.7541 (m-30) cc_final: 0.7190 (m-30) REVERT: N 245 GLN cc_start: 0.6057 (pt0) cc_final: 0.5803 (tp-100) REVERT: a 62 MET cc_start: 0.7099 (OUTLIER) cc_final: 0.6541 (tpp) REVERT: a 87 THR cc_start: 0.7387 (m) cc_final: 0.6799 (p) REVERT: a 220 LYS cc_start: 0.7662 (mtmt) cc_final: 0.6589 (mmtt) REVERT: b 73 GLN cc_start: 0.6983 (mt0) cc_final: 0.6737 (mt0) REVERT: b 95 GLU cc_start: 0.7146 (tp30) cc_final: 0.6501 (tt0) REVERT: b 256 GLN cc_start: 0.7825 (OUTLIER) cc_final: 0.7259 (tm-30) REVERT: c 30 GLN cc_start: 0.7173 (tp40) cc_final: 0.6868 (tp40) REVERT: c 263 GLN cc_start: 0.8357 (mm110) cc_final: 0.7249 (tp40) REVERT: d 31 GLN cc_start: 0.7746 (OUTLIER) cc_final: 0.7381 (pt0) REVERT: d 123 GLN cc_start: 0.6014 (tp-100) cc_final: 0.5264 (mt0) REVERT: e 252 GLN cc_start: 0.8117 (mt0) cc_final: 0.7592 (mm-40) REVERT: f 62 MET cc_start: 0.6655 (OUTLIER) cc_final: 0.6405 (mpp) REVERT: f 89 LEU cc_start: 0.6130 (OUTLIER) cc_final: 0.5655 (mp) REVERT: h 95 GLU cc_start: 0.7290 (tt0) cc_final: 0.6592 (mt-10) REVERT: i 31 GLN cc_start: 0.7205 (OUTLIER) cc_final: 0.6812 (mt0) REVERT: i 37 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.8202 (mttp) REVERT: i 175 SER cc_start: 0.8819 (m) cc_final: 0.8554 (m) REVERT: j 62 MET cc_start: 0.8016 (OUTLIER) cc_final: 0.7732 (mmt) REVERT: j 71 ARG cc_start: 0.7559 (ttp-110) cc_final: 0.7315 (ttp-110) REVERT: j 212 ASP cc_start: 0.7989 (m-30) cc_final: 0.7746 (m-30) REVERT: j 243 LYS cc_start: 0.7407 (ttmt) cc_final: 0.6760 (tptt) REVERT: j 263 GLN cc_start: 0.7540 (pt0) cc_final: 0.6949 (mp-120) REVERT: g 67 ASP cc_start: 0.7984 (m-30) cc_final: 0.7584 (m-30) REVERT: g 106 ASN cc_start: 0.7172 (t0) cc_final: 0.5434 (p0) REVERT: g 174 THR cc_start: 0.8345 (m) cc_final: 0.8112 (p) REVERT: g 184 LYS cc_start: 0.7023 (tttp) cc_final: 0.6469 (tptt) REVERT: g 252 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7320 (mp10) outliers start: 158 outliers final: 72 residues processed: 823 average time/residue: 1.3058 time to fit residues: 1450.4547 Evaluate side-chains 732 residues out of total 7560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 639 time to evaluate : 5.825 ------------------------------------------------------------------------------- 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 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 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 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 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 62 MET 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 37 LYS Chi-restraints excluded: chain i residue 84 ASP Chi-restraints excluded: chain i residue 103 THR Chi-restraints excluded: chain j residue 62 MET Chi-restraints excluded: chain g residue 172 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 294 optimal weight: 2.9990 chunk 401 optimal weight: 10.0000 chunk 675 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 490 optimal weight: 0.5980 chunk 713 optimal weight: 3.9990 chunk 885 optimal weight: 4.9990 chunk 883 optimal weight: 0.9980 chunk 682 optimal weight: 1.9990 chunk 148 optimal weight: 6.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 30 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 263 GLN P 7 ASN T 151 ASN R 123 GLN R 245 GLN U 151 ASN U 252 GLN V 18 ASN V 31 GLN V 151 ASN V 251 GLN V 256 GLN V 263 GLN X 130 ASN X 263 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 256 GLN j 262 ASN g 31 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.124895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.111334 restraints weight = 96402.914| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.41 r_work: 0.3416 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 70056 Z= 0.179 Angle : 0.428 8.511 94824 Z= 0.248 Chirality : 0.033 0.155 12204 Planarity : 0.002 0.019 12132 Dihedral : 3.693 21.589 9792 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 2.22 % Allowed : 9.11 % Favored : 88.66 % 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: 4.24 (0.09), residues: 9648 helix: 3.65 (0.06), residues: 7020 sheet: -2.51 (0.19), residues: 432 loop : 1.03 (0.15), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP f 49 HIS 0.004 0.001 HIS C 214 PHE 0.014 0.002 PHE P 217 ARG 0.004 0.000 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 858 residues out of total 7560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 690 time to evaluate : 5.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7751 (tm130) REVERT: B 95 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7446 (mt-10) REVERT: B 256 GLN cc_start: 0.7986 (tt0) cc_final: 0.7772 (tt0) REVERT: D 95 GLU cc_start: 0.6214 (mm-30) cc_final: 0.5723 (mt-10) REVERT: F 256 GLN cc_start: 0.6854 (OUTLIER) cc_final: 0.5500 (mp10) REVERT: F 264 SER cc_start: 0.7496 (t) cc_final: 0.7235 (p) REVERT: G 220 LYS cc_start: 0.7283 (mtmt) cc_final: 0.6208 (mmtt) REVERT: H 25 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8262 (mt-10) REVERT: H 191 ASP cc_start: 0.8171 (t0) cc_final: 0.7803 (m-30) REVERT: H 226 ASP cc_start: 0.7430 (m-30) cc_final: 0.7059 (m-30) REVERT: I 31 GLN cc_start: 0.7117 (pp30) cc_final: 0.6447 (mm-40) REVERT: J 32 ARG cc_start: 0.7364 (ttm-80) cc_final: 0.6926 (ttt180) REVERT: J 43 LYS cc_start: 0.5158 (mmmt) cc_final: 0.4610 (mmpt) REVERT: K 71 ARG cc_start: 0.7505 (ttt90) cc_final: 0.6295 (mtm110) REVERT: K 77 ASP cc_start: 0.7467 (p0) cc_final: 0.7155 (m-30) REVERT: K 92 LYS cc_start: 0.8510 (mtpp) cc_final: 0.8166 (mtmt) REVERT: M 13 MET cc_start: 0.7413 (mtp) cc_final: 0.7048 (mtt) REVERT: M 145 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7822 (pttm) REVERT: M 195 GLN cc_start: 0.7039 (tt0) cc_final: 0.6519 (tm-30) REVERT: M 243 LYS cc_start: 0.8250 (tppt) cc_final: 0.8000 (mmmm) REVERT: O 31 GLN cc_start: 0.7384 (OUTLIER) cc_final: 0.6936 (tm-30) REVERT: O 84 ASP cc_start: 0.7248 (m-30) cc_final: 0.6876 (t0) REVERT: O 231 ASN cc_start: 0.8567 (t0) cc_final: 0.8108 (t0) REVERT: T 8 THR cc_start: 0.8343 (t) cc_final: 0.8108 (m) REVERT: Q 38 LYS cc_start: 0.8253 (ptmm) cc_final: 0.7696 (pttm) REVERT: Q 123 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.7519 (tp-100) REVERT: Q 220 LYS cc_start: 0.6448 (mmmt) cc_final: 0.5541 (mttt) REVERT: Q 267 SER cc_start: 0.7997 (OUTLIER) cc_final: 0.7779 (p) REVERT: R 67 ASP cc_start: 0.7318 (m-30) cc_final: 0.7049 (m-30) REVERT: R 240 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7321 (mp0) REVERT: R 263 GLN cc_start: 0.7321 (mp10) cc_final: 0.6651 (mm-40) REVERT: S 14 ILE cc_start: 0.7118 (OUTLIER) cc_final: 0.6893 (mm) REVERT: S 25 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7103 (mt-10) REVERT: S 31 GLN cc_start: 0.7814 (OUTLIER) cc_final: 0.6983 (tp40) REVERT: S 95 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7126 (tt0) REVERT: S 186 MET cc_start: 0.8206 (tpt) cc_final: 0.7961 (tpp) REVERT: V 34 ASN cc_start: 0.7710 (p0) cc_final: 0.7349 (p0) REVERT: V 123 GLN cc_start: 0.7530 (tp40) cc_final: 0.6739 (mt0) REVERT: V 173 THR cc_start: 0.8799 (m) cc_final: 0.8508 (p) REVERT: W 95 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7788 (tm-30) REVERT: W 123 GLN cc_start: 0.7330 (tp40) cc_final: 0.6466 (mt0) REVERT: W 195 GLN cc_start: 0.7997 (mt0) cc_final: 0.7528 (mm-40) REVERT: X 93 MET cc_start: 0.8606 (ttm) cc_final: 0.7819 (mtp) REVERT: X 151 ASN cc_start: 0.8004 (p0) cc_final: 0.7167 (t0) REVERT: X 226 ASP cc_start: 0.7684 (m-30) cc_final: 0.7445 (m-30) REVERT: Z 77 ASP cc_start: 0.7798 (m-30) cc_final: 0.7546 (m-30) REVERT: N 3 LEU cc_start: 0.5821 (tp) cc_final: 0.5112 (tt) REVERT: N 31 GLN cc_start: 0.7370 (OUTLIER) cc_final: 0.7117 (tt0) REVERT: N 67 ASP cc_start: 0.7524 (m-30) cc_final: 0.7157 (m-30) REVERT: N 151 ASN cc_start: 0.8433 (t0) cc_final: 0.7873 (t0) REVERT: N 245 GLN cc_start: 0.6009 (pt0) cc_final: 0.5772 (tp-100) REVERT: a 87 THR cc_start: 0.7374 (m) cc_final: 0.6781 (p) REVERT: a 220 LYS cc_start: 0.7658 (mtmt) cc_final: 0.6592 (tptt) REVERT: b 73 GLN cc_start: 0.6934 (mt0) cc_final: 0.6686 (mt0) REVERT: b 95 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6426 (tt0) REVERT: b 256 GLN cc_start: 0.7807 (OUTLIER) cc_final: 0.7286 (tm-30) REVERT: c 30 GLN cc_start: 0.7201 (tp40) cc_final: 0.6831 (tp40) REVERT: c 151 ASN cc_start: 0.7984 (p0) cc_final: 0.7699 (p0) REVERT: c 263 GLN cc_start: 0.8337 (mm110) cc_final: 0.7252 (tp40) REVERT: d 31 GLN cc_start: 0.7761 (OUTLIER) cc_final: 0.7401 (pt0) REVERT: d 123 GLN cc_start: 0.5942 (tp-100) cc_final: 0.5254 (mt0) REVERT: e 252 GLN cc_start: 0.8107 (mt0) cc_final: 0.7597 (mm-40) REVERT: f 62 MET cc_start: 0.6625 (OUTLIER) cc_final: 0.6372 (mpp) REVERT: f 89 LEU cc_start: 0.6045 (OUTLIER) cc_final: 0.5539 (mp) REVERT: h 95 GLU cc_start: 0.7307 (tt0) cc_final: 0.6529 (mt-10) REVERT: i 31 GLN cc_start: 0.7215 (OUTLIER) cc_final: 0.6865 (mt0) REVERT: i 37 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.8197 (mttp) REVERT: i 175 SER cc_start: 0.8813 (m) cc_final: 0.8518 (m) REVERT: j 62 MET cc_start: 0.8012 (OUTLIER) cc_final: 0.7704 (mmt) REVERT: j 71 ARG cc_start: 0.7551 (ttp-110) cc_final: 0.7316 (ttp-110) REVERT: j 212 ASP cc_start: 0.8070 (OUTLIER) cc_final: 0.7780 (m-30) REVERT: j 243 LYS cc_start: 0.7445 (ttmt) cc_final: 0.6844 (tptt) REVERT: j 256 GLN cc_start: 0.6523 (OUTLIER) cc_final: 0.6290 (tt0) REVERT: j 263 GLN cc_start: 0.7550 (pt0) cc_final: 0.6951 (mp-120) REVERT: g 67 ASP cc_start: 0.7946 (m-30) cc_final: 0.7525 (m-30) REVERT: g 106 ASN cc_start: 0.7106 (t0) cc_final: 0.5419 (p0) REVERT: g 184 LYS cc_start: 0.6872 (tttp) cc_final: 0.6362 (tptt) REVERT: g 252 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7287 (mp10) outliers start: 168 outliers final: 84 residues processed: 815 average time/residue: 1.3572 time to fit residues: 1487.9428 Evaluate side-chains 753 residues out of total 7560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 645 time to evaluate : 5.786 ------------------------------------------------------------------------------- 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 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 24 SER 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 173 THR 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 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 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 225 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 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 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 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 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 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 N residue 31 GLN Chi-restraints excluded: chain N residue 268 ILE 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 c residue 33 ILE 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 159 VAL Chi-restraints excluded: chain e residue 33 ILE Chi-restraints excluded: chain e residue 101 SER Chi-restraints excluded: chain f residue 62 MET 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 f residue 268 ILE Chi-restraints excluded: chain h residue 16 LEU Chi-restraints excluded: chain h residue 27 THR 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 37 LYS Chi-restraints excluded: chain i residue 98 LEU 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 j residue 212 ASP Chi-restraints excluded: chain j residue 256 GLN 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 526 optimal weight: 6.9990 chunk 901 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 283 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 853 optimal weight: 2.9990 chunk 148 optimal weight: 0.9990 chunk 210 optimal weight: 0.8980 chunk 858 optimal weight: 0.7980 chunk 144 optimal weight: 0.5980 chunk 542 optimal weight: 6.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 GLN D 256 GLN E 31 GLN E 251 GLN F 151 ASN G 151 ASN H 245 GLN J 30 GLN K 263 GLN T 151 ASN R 123 GLN R 245 GLN U 123 GLN U 151 ASN V 151 ASN V 245 GLN V 251 GLN V 263 GLN W 30 GLN ** 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 N 263 GLN a 54 ASN a 134 ASN a 231 ASN c 111 ASN d 256 GLN ** e 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 130 ASN j 9 ASN j 262 ASN g 31 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.128193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.114674 restraints weight = 96198.668| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.41 r_work: 0.3461 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 70056 Z= 0.142 Angle : 0.387 8.965 94824 Z= 0.228 Chirality : 0.031 0.146 12204 Planarity : 0.002 0.015 12132 Dihedral : 3.523 20.079 9792 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 1.92 % Allowed : 9.87 % Favored : 88.21 % 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: 4.56 (0.09), residues: 9648 helix: 3.92 (0.06), residues: 7020 sheet: -2.19 (0.19), residues: 432 loop : 0.98 (0.15), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP f 49 HIS 0.003 0.001 HIS C 214 PHE 0.015 0.001 PHE f 177 ARG 0.002 0.000 ARG G 121 *********************** 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 877 residues out of total 7560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 732 time to evaluate : 5.794 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: 0.8047 (m-30) cc_final: 0.7846 (m-30) REVERT: B 256 GLN cc_start: 0.7994 (tt0) cc_final: 0.7786 (tt0) REVERT: D 95 GLU cc_start: 0.6174 (mm-30) cc_final: 0.5663 (mt-10) REVERT: E 13 MET cc_start: 0.8638 (mtt) cc_final: 0.8378 (mtm) REVERT: F 95 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7775 (mt-10) REVERT: F 256 GLN cc_start: 0.6795 (OUTLIER) cc_final: 0.5506 (mp10) REVERT: F 264 SER cc_start: 0.7495 (t) cc_final: 0.7245 (p) REVERT: G 220 LYS cc_start: 0.7211 (mtmt) cc_final: 0.6211 (mmtt) REVERT: H 25 GLU cc_start: 0.8474 (mt-10) cc_final: 0.8246 (mt-10) REVERT: H 191 ASP cc_start: 0.8024 (t0) cc_final: 0.7709 (m-30) REVERT: H 226 ASP cc_start: 0.7333 (m-30) cc_final: 0.6970 (m-30) REVERT: I 31 GLN cc_start: 0.7109 (pp30) cc_final: 0.6410 (mm-40) REVERT: J 43 LYS cc_start: 0.5133 (mmmt) cc_final: 0.4598 (mmpt) REVERT: K 71 ARG cc_start: 0.7568 (ttt90) cc_final: 0.6379 (mtm110) REVERT: K 77 ASP cc_start: 0.7419 (p0) cc_final: 0.7057 (m-30) REVERT: M 13 MET cc_start: 0.7296 (mtp) cc_final: 0.6996 (mtt) REVERT: M 195 GLN cc_start: 0.7075 (tt0) cc_final: 0.6491 (tm-30) REVERT: M 243 LYS cc_start: 0.8180 (tppt) cc_final: 0.7968 (mmmm) REVERT: M 256 GLN cc_start: 0.7279 (tt0) cc_final: 0.7024 (tt0) REVERT: O 31 GLN cc_start: 0.7423 (OUTLIER) cc_final: 0.6820 (tm-30) REVERT: O 84 ASP cc_start: 0.7122 (m-30) cc_final: 0.6821 (t0) REVERT: O 231 ASN cc_start: 0.8478 (t0) cc_final: 0.8130 (t0) REVERT: Q 38 LYS cc_start: 0.8244 (ptmm) cc_final: 0.7736 (pttm) REVERT: Q 123 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.7529 (tp-100) REVERT: Q 220 LYS cc_start: 0.6441 (mmmt) cc_final: 0.5629 (mttt) REVERT: Q 267 SER cc_start: 0.8092 (m) cc_final: 0.7888 (p) REVERT: R 263 GLN cc_start: 0.7290 (mp10) cc_final: 0.6559 (mm-40) REVERT: S 14 ILE cc_start: 0.7107 (OUTLIER) cc_final: 0.6882 (mm) REVERT: S 25 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7091 (mt-10) REVERT: S 31 GLN cc_start: 0.7755 (OUTLIER) cc_final: 0.6999 (tp40) REVERT: S 186 MET cc_start: 0.8205 (tpt) cc_final: 0.7971 (tpp) REVERT: V 123 GLN cc_start: 0.7512 (tp40) cc_final: 0.6756 (mt0) REVERT: V 173 THR cc_start: 0.8774 (m) cc_final: 0.8479 (p) REVERT: W 123 GLN cc_start: 0.7308 (tp40) cc_final: 0.6471 (mt0) REVERT: W 195 GLN cc_start: 0.7945 (mt0) cc_final: 0.7497 (mm-40) REVERT: X 151 ASN cc_start: 0.7910 (p0) cc_final: 0.7052 (t0) REVERT: Y 123 GLN cc_start: 0.7386 (OUTLIER) cc_final: 0.7096 (mm-40) REVERT: Z 123 GLN cc_start: 0.7450 (OUTLIER) cc_final: 0.6495 (mm-40) REVERT: Z 243 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.8034 (tttp) REVERT: N 3 LEU cc_start: 0.5857 (tp) cc_final: 0.5152 (tt) REVERT: N 67 ASP cc_start: 0.7399 (m-30) cc_final: 0.7005 (m-30) REVERT: a 62 MET cc_start: 0.7402 (mmt) cc_final: 0.7119 (mmt) REVERT: a 87 THR cc_start: 0.7304 (m) cc_final: 0.6710 (p) REVERT: a 220 LYS cc_start: 0.7690 (mtmt) cc_final: 0.6678 (tptt) REVERT: b 73 GLN cc_start: 0.6805 (mt0) cc_final: 0.6568 (mt0) REVERT: b 95 GLU cc_start: 0.7046 (OUTLIER) cc_final: 0.6390 (tt0) REVERT: b 116 ASP cc_start: 0.6988 (m-30) cc_final: 0.6634 (m-30) REVERT: b 256 GLN cc_start: 0.7823 (OUTLIER) cc_final: 0.7309 (tm-30) REVERT: c 30 GLN cc_start: 0.7151 (tp40) cc_final: 0.6823 (tp40) REVERT: c 151 ASN cc_start: 0.7930 (OUTLIER) cc_final: 0.7618 (p0) REVERT: c 263 GLN cc_start: 0.8275 (mm110) cc_final: 0.7270 (tp40) REVERT: d 31 GLN cc_start: 0.7695 (OUTLIER) cc_final: 0.7333 (pt0) REVERT: d 123 GLN cc_start: 0.5950 (tp-100) cc_final: 0.5261 (mt0) REVERT: e 252 GLN cc_start: 0.8043 (mt0) cc_final: 0.7516 (mm-40) REVERT: f 16 LEU cc_start: 0.6215 (OUTLIER) cc_final: 0.5717 (tt) REVERT: f 62 MET cc_start: 0.6551 (OUTLIER) cc_final: 0.6333 (mpp) REVERT: f 268 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7420 (mp) REVERT: h 27 THR cc_start: 0.8997 (OUTLIER) cc_final: 0.8725 (p) REVERT: h 95 GLU cc_start: 0.7277 (tt0) cc_final: 0.6481 (mt-10) REVERT: i 31 GLN cc_start: 0.7254 (OUTLIER) cc_final: 0.6929 (mt0) REVERT: i 37 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.8217 (mttp) REVERT: j 67 ASP cc_start: 0.6469 (m-30) cc_final: 0.6047 (m-30) REVERT: j 71 ARG cc_start: 0.7498 (OUTLIER) cc_final: 0.7280 (ttp-110) REVERT: j 212 ASP cc_start: 0.8172 (OUTLIER) cc_final: 0.7917 (m-30) REVERT: j 243 LYS cc_start: 0.7414 (ttmt) cc_final: 0.6810 (tptt) REVERT: j 263 GLN cc_start: 0.7595 (pt0) cc_final: 0.6955 (mm-40) REVERT: g 184 LYS cc_start: 0.6641 (tttp) cc_final: 0.6192 (mmtt) REVERT: g 252 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7330 (mp10) outliers start: 145 outliers final: 63 residues processed: 838 average time/residue: 1.2884 time to fit residues: 1462.7156 Evaluate side-chains 741 residues out of total 7560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 656 time to evaluate : 5.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 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 V residue 159 VAL Chi-restraints excluded: chain V residue 246 SER 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 123 GLN 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 Z residue 243 LYS 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 151 ASN 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 159 VAL Chi-restraints excluded: chain e residue 33 ILE Chi-restraints excluded: chain f residue 16 LEU Chi-restraints excluded: chain f residue 62 MET 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 f residue 268 ILE Chi-restraints excluded: chain h residue 16 LEU Chi-restraints excluded: chain h residue 27 THR 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 37 LYS Chi-restraints excluded: chain i residue 98 LEU Chi-restraints excluded: chain i residue 103 THR Chi-restraints excluded: chain i residue 265 SER Chi-restraints excluded: chain j residue 71 ARG Chi-restraints excluded: chain j residue 212 ASP 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 465 optimal weight: 1.9990 chunk 456 optimal weight: 0.9980 chunk 97 optimal weight: 6.9990 chunk 542 optimal weight: 0.9990 chunk 822 optimal weight: 7.9990 chunk 368 optimal weight: 0.5980 chunk 174 optimal weight: 7.9990 chunk 828 optimal weight: 3.9990 chunk 671 optimal weight: 5.9990 chunk 654 optimal weight: 0.8980 chunk 731 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 GLN D 256 GLN E 31 GLN F 31 GLN F 151 ASN F 262 ASN H 245 GLN K 18 ASN K 134 ASN ** T 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 123 GLN R 245 GLN U 123 GLN U 151 ASN U 252 GLN 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 151 ASN N 263 GLN a 134 ASN a 231 ASN d 256 GLN ** e 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 73 GLN h 18 ASN g 31 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.127405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.113870 restraints weight = 95730.332| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.40 r_work: 0.3449 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1784 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= 0.156 Angle : 0.396 9.279 94824 Z= 0.232 Chirality : 0.032 0.172 12204 Planarity : 0.002 0.015 12132 Dihedral : 3.513 19.856 9792 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 1.92 % Allowed : 10.71 % Favored : 87.37 % 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: 4.58 (0.09), residues: 9648 helix: 3.94 (0.06), residues: 7020 sheet: -1.97 (0.20), residues: 432 loop : 0.91 (0.15), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP f 49 HIS 0.003 0.001 HIS C 214 PHE 0.015 0.001 PHE f 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 840 residues out of total 7560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 695 time to evaluate : 5.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7935 (OUTLIER) cc_final: 0.7683 (tm130) REVERT: B 191 ASP cc_start: 0.8064 (m-30) cc_final: 0.7856 (m-30) REVERT: B 256 GLN cc_start: 0.8000 (tt0) cc_final: 0.7778 (tt0) REVERT: D 95 GLU cc_start: 0.6160 (mm-30) cc_final: 0.5667 (mt-10) REVERT: E 13 MET cc_start: 0.8664 (mtt) cc_final: 0.8407 (mtm) REVERT: F 256 GLN cc_start: 0.6795 (OUTLIER) cc_final: 0.5573 (mp10) REVERT: F 264 SER cc_start: 0.7491 (t) cc_final: 0.7238 (p) REVERT: G 220 LYS cc_start: 0.7152 (mtmt) cc_final: 0.6202 (mmtt) REVERT: H 25 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8228 (mt-10) REVERT: H 191 ASP cc_start: 0.7998 (t0) cc_final: 0.7684 (m-30) REVERT: H 226 ASP cc_start: 0.7376 (OUTLIER) cc_final: 0.7005 (m-30) REVERT: I 31 GLN cc_start: 0.7098 (pp30) cc_final: 0.6441 (mm-40) REVERT: J 43 LYS cc_start: 0.5157 (mmmt) cc_final: 0.4594 (mmpt) REVERT: K 71 ARG cc_start: 0.7553 (ttt90) cc_final: 0.6394 (mtm110) REVERT: K 77 ASP cc_start: 0.7432 (p0) cc_final: 0.7074 (m-30) REVERT: K 92 LYS cc_start: 0.8472 (mtpp) cc_final: 0.8107 (mtmt) REVERT: M 13 MET cc_start: 0.7321 (mtp) cc_final: 0.7021 (mtt) REVERT: M 195 GLN cc_start: 0.7087 (tt0) cc_final: 0.6491 (tm-30) REVERT: M 243 LYS cc_start: 0.8214 (tppt) cc_final: 0.8003 (mmmm) REVERT: M 256 GLN cc_start: 0.7219 (tt0) cc_final: 0.6990 (tt0) REVERT: O 31 GLN cc_start: 0.7473 (OUTLIER) cc_final: 0.6873 (tm-30) REVERT: O 84 ASP cc_start: 0.7099 (m-30) cc_final: 0.6815 (t0) REVERT: O 231 ASN cc_start: 0.8509 (t0) cc_final: 0.8161 (t0) REVERT: Q 38 LYS cc_start: 0.8253 (ptmm) cc_final: 0.7741 (pttm) REVERT: Q 123 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7527 (tp-100) REVERT: Q 220 LYS cc_start: 0.6418 (mmmt) cc_final: 0.5578 (mttt) REVERT: R 191 ASP cc_start: 0.8278 (m-30) cc_final: 0.8061 (m-30) REVERT: R 240 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7317 (mp0) REVERT: R 263 GLN cc_start: 0.7330 (mt0) cc_final: 0.6581 (mm-40) REVERT: S 14 ILE cc_start: 0.7128 (OUTLIER) cc_final: 0.6902 (mm) REVERT: S 25 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7115 (mt-10) REVERT: S 31 GLN cc_start: 0.7796 (OUTLIER) cc_final: 0.6994 (tp40) REVERT: S 95 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.6778 (tt0) REVERT: S 186 MET cc_start: 0.8226 (tpt) cc_final: 0.7958 (tpp) REVERT: V 123 GLN cc_start: 0.7486 (tp40) cc_final: 0.6719 (mt0) REVERT: V 173 THR cc_start: 0.8790 (m) cc_final: 0.8501 (p) REVERT: W 123 GLN cc_start: 0.7315 (tp40) cc_final: 0.6486 (mt0) REVERT: W 195 GLN cc_start: 0.7954 (mt0) cc_final: 0.7492 (mm-40) REVERT: X 151 ASN cc_start: 0.7907 (p0) cc_final: 0.7102 (t0) REVERT: Y 123 GLN cc_start: 0.7406 (OUTLIER) cc_final: 0.7116 (mm-40) REVERT: Z 123 GLN cc_start: 0.7461 (OUTLIER) cc_final: 0.6530 (mm-40) REVERT: Z 243 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.8039 (tttp) REVERT: a 87 THR cc_start: 0.7357 (m) cc_final: 0.6783 (p) REVERT: a 220 LYS cc_start: 0.7688 (mtmt) cc_final: 0.6704 (tptt) REVERT: b 95 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.6436 (tt0) REVERT: b 116 ASP cc_start: 0.6979 (m-30) cc_final: 0.6667 (m-30) REVERT: b 256 GLN cc_start: 0.7828 (OUTLIER) cc_final: 0.7318 (tm-30) REVERT: c 30 GLN cc_start: 0.7177 (tp40) cc_final: 0.6854 (tp40) REVERT: c 232 LEU cc_start: 0.7248 (OUTLIER) cc_final: 0.7018 (tp) REVERT: c 263 GLN cc_start: 0.8279 (mm110) cc_final: 0.7364 (tp40) REVERT: d 31 GLN cc_start: 0.7713 (OUTLIER) cc_final: 0.7361 (pt0) REVERT: d 123 GLN cc_start: 0.5950 (tp-100) cc_final: 0.5256 (mt0) REVERT: e 252 GLN cc_start: 0.8035 (mt0) cc_final: 0.7503 (mm-40) REVERT: f 13 MET cc_start: 0.6729 (OUTLIER) cc_final: 0.6522 (ptp) REVERT: f 16 LEU cc_start: 0.6250 (OUTLIER) cc_final: 0.5789 (tt) REVERT: f 62 MET cc_start: 0.6591 (OUTLIER) cc_final: 0.6369 (mpp) REVERT: h 27 THR cc_start: 0.8991 (OUTLIER) cc_final: 0.8725 (p) REVERT: h 95 GLU cc_start: 0.7255 (tt0) cc_final: 0.6453 (mt-10) REVERT: i 31 GLN cc_start: 0.7192 (OUTLIER) cc_final: 0.6926 (mt0) REVERT: i 37 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.8227 (mttp) REVERT: j 38 LYS cc_start: 0.7833 (pttt) cc_final: 0.7532 (ttpp) REVERT: j 67 ASP cc_start: 0.6433 (m-30) cc_final: 0.6027 (m-30) REVERT: j 71 ARG cc_start: 0.7455 (ttp-110) cc_final: 0.7219 (ttp-110) REVERT: j 212 ASP cc_start: 0.8171 (OUTLIER) cc_final: 0.7930 (m-30) REVERT: j 243 LYS cc_start: 0.7459 (ttmt) cc_final: 0.6843 (tptt) REVERT: j 263 GLN cc_start: 0.7635 (pt0) cc_final: 0.6901 (mp-120) REVERT: g 67 ASP cc_start: 0.8018 (m-30) cc_final: 0.7642 (m-30) REVERT: g 184 LYS cc_start: 0.6629 (tttp) cc_final: 0.6180 (mmtt) REVERT: g 252 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7299 (mp10) outliers start: 145 outliers final: 69 residues processed: 802 average time/residue: 1.2899 time to fit residues: 1398.1286 Evaluate side-chains 740 residues out of total 7560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 646 time to evaluate : 5.793 ------------------------------------------------------------------------------- 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 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 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 H residue 16 LEU 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 8 THR Chi-restraints excluded: chain K residue 253 LEU Chi-restraints excluded: chain L residue 267 SER Chi-restraints excluded: chain M residue 8 THR 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 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 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 33 ILE Chi-restraints excluded: chain U residue 84 ASP 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 123 GLN 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 Z residue 243 LYS 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 159 VAL Chi-restraints excluded: chain c residue 232 LEU 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 13 MET Chi-restraints excluded: chain f residue 16 LEU Chi-restraints excluded: chain f residue 62 MET 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 27 THR 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 37 LYS Chi-restraints excluded: chain i residue 98 LEU Chi-restraints excluded: chain i residue 103 THR Chi-restraints excluded: chain i residue 265 SER Chi-restraints excluded: chain j residue 212 ASP 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 544 optimal weight: 4.9990 chunk 535 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 chunk 615 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 829 optimal weight: 1.9990 chunk 843 optimal weight: 0.9990 chunk 234 optimal weight: 3.9990 chunk 911 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 825 optimal weight: 8.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 31 GLN F 151 ASN H 245 GLN K 134 ASN L 20 ASN ** T 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 123 GLN R 245 GLN U 123 GLN U 151 ASN V 151 ASN V 245 GLN V 251 GLN V 263 GLN W 199 ASN ** X 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 263 GLN Z 31 GLN Z 151 ASN N 151 ASN N 263 GLN a 134 ASN a 231 ASN a 256 GLN d 256 GLN f 73 GLN g 31 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.125110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.111535 restraints weight = 96123.169| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.40 r_work: 0.3419 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 70056 Z= 0.184 Angle : 0.422 9.601 94824 Z= 0.244 Chirality : 0.033 0.268 12204 Planarity : 0.002 0.016 12132 Dihedral : 3.588 19.924 9792 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 2.17 % Allowed : 10.93 % Favored : 86.90 % 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: 4.46 (0.08), residues: 9648 helix: 3.85 (0.06), residues: 7020 sheet: -1.84 (0.20), residues: 432 loop : 0.83 (0.15), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP f 49 HIS 0.004 0.002 HIS h 214 PHE 0.017 0.002 PHE f 177 ARG 0.003 0.000 ARG T 121 *********************** 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 827 residues out of total 7560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 663 time to evaluate : 5.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7755 (tm130) REVERT: B 256 GLN cc_start: 0.8037 (tt0) cc_final: 0.7794 (tt0) REVERT: C 31 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7649 (tt0) REVERT: D 95 GLU cc_start: 0.6199 (mm-30) cc_final: 0.5722 (mt-10) REVERT: E 13 MET cc_start: 0.8705 (mtt) cc_final: 0.8441 (mtm) REVERT: F 256 GLN cc_start: 0.6787 (OUTLIER) cc_final: 0.5511 (mp10) REVERT: F 264 SER cc_start: 0.7515 (t) cc_final: 0.7244 (p) REVERT: G 220 LYS cc_start: 0.7187 (mtmt) cc_final: 0.6198 (mmtt) REVERT: H 25 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8281 (mt-10) REVERT: H 191 ASP cc_start: 0.8095 (t0) cc_final: 0.7748 (m-30) REVERT: H 226 ASP cc_start: 0.7406 (OUTLIER) cc_final: 0.7012 (m-30) REVERT: I 31 GLN cc_start: 0.7146 (pp30) cc_final: 0.6459 (mm-40) REVERT: J 43 LYS cc_start: 0.5196 (mmmt) cc_final: 0.4600 (mmpt) REVERT: K 71 ARG cc_start: 0.7513 (ttt90) cc_final: 0.6285 (mtm110) REVERT: K 77 ASP cc_start: 0.7471 (p0) cc_final: 0.7147 (m-30) REVERT: K 92 LYS cc_start: 0.8504 (mtpp) cc_final: 0.8143 (mtmt) REVERT: L 253 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7910 (mm) REVERT: M 13 MET cc_start: 0.7389 (mtp) cc_final: 0.7074 (mtt) REVERT: M 195 GLN cc_start: 0.7108 (tt0) cc_final: 0.6506 (tm-30) REVERT: M 243 LYS cc_start: 0.8261 (tppt) cc_final: 0.8040 (mmmm) REVERT: M 256 GLN cc_start: 0.7283 (tt0) cc_final: 0.7016 (tt0) REVERT: O 31 GLN cc_start: 0.7537 (OUTLIER) cc_final: 0.6934 (tm-30) REVERT: O 84 ASP cc_start: 0.7132 (m-30) cc_final: 0.6835 (t0) REVERT: O 116 ASP cc_start: 0.6548 (m-30) cc_final: 0.6289 (m-30) REVERT: O 231 ASN cc_start: 0.8591 (t0) cc_final: 0.8201 (t0) REVERT: Q 38 LYS cc_start: 0.8262 (ptmm) cc_final: 0.7716 (pttm) REVERT: Q 62 MET cc_start: 0.8730 (mtt) cc_final: 0.8350 (mtt) REVERT: Q 123 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.7539 (tp-100) REVERT: Q 220 LYS cc_start: 0.6537 (mmmt) cc_final: 0.5617 (mttt) REVERT: R 67 ASP cc_start: 0.7349 (m-30) cc_final: 0.7059 (m-30) REVERT: R 92 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8404 (mttm) REVERT: R 191 ASP cc_start: 0.8312 (m-30) cc_final: 0.8080 (m-30) REVERT: R 240 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7384 (mp0) REVERT: S 14 ILE cc_start: 0.7117 (OUTLIER) cc_final: 0.6867 (mm) REVERT: S 25 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7103 (mt-10) REVERT: S 31 GLN cc_start: 0.7821 (OUTLIER) cc_final: 0.6995 (tp40) REVERT: S 95 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.6799 (tt0) REVERT: S 186 MET cc_start: 0.8236 (tpt) cc_final: 0.7969 (tpp) REVERT: V 123 GLN cc_start: 0.7509 (tp40) cc_final: 0.6725 (mt0) REVERT: V 173 THR cc_start: 0.8810 (m) cc_final: 0.8531 (p) REVERT: W 95 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7827 (tm-30) REVERT: W 123 GLN cc_start: 0.7354 (tp40) cc_final: 0.6504 (mt0) REVERT: W 195 GLN cc_start: 0.7999 (mt0) cc_final: 0.7540 (mm-40) REVERT: X 151 ASN cc_start: 0.7993 (p0) cc_final: 0.7231 (t0) REVERT: Y 123 GLN cc_start: 0.7489 (OUTLIER) cc_final: 0.7176 (mm-40) REVERT: Z 123 GLN cc_start: 0.7511 (OUTLIER) cc_final: 0.6635 (tm-30) REVERT: Z 243 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.8060 (tttp) REVERT: N 67 ASP cc_start: 0.7523 (m-30) cc_final: 0.7174 (m-30) REVERT: a 62 MET cc_start: 0.7477 (mmt) cc_final: 0.6932 (mmt) REVERT: a 87 THR cc_start: 0.7414 (m) cc_final: 0.6843 (p) REVERT: a 220 LYS cc_start: 0.7687 (mtmt) cc_final: 0.6678 (tptt) REVERT: b 95 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.6489 (tt0) REVERT: b 256 GLN cc_start: 0.7814 (OUTLIER) cc_final: 0.7310 (tm-30) REVERT: c 30 GLN cc_start: 0.7258 (tp40) cc_final: 0.6904 (tp40) REVERT: c 263 GLN cc_start: 0.8280 (mm110) cc_final: 0.7364 (tp40) REVERT: d 31 GLN cc_start: 0.7763 (OUTLIER) cc_final: 0.7403 (pt0) REVERT: d 123 GLN cc_start: 0.5889 (tp-100) cc_final: 0.5214 (mt0) REVERT: e 252 GLN cc_start: 0.8059 (mt0) cc_final: 0.7534 (mm-40) REVERT: f 13 MET cc_start: 0.6781 (ptp) cc_final: 0.6547 (ptp) REVERT: f 16 LEU cc_start: 0.6306 (OUTLIER) cc_final: 0.5904 (tt) REVERT: f 62 MET cc_start: 0.6680 (OUTLIER) cc_final: 0.6413 (mpp) REVERT: h 95 GLU cc_start: 0.7322 (tt0) cc_final: 0.6518 (mt-10) REVERT: i 31 GLN cc_start: 0.7189 (OUTLIER) cc_final: 0.6910 (mt0) REVERT: i 37 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.8221 (mttp) REVERT: j 32 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.5502 (mpp80) REVERT: j 38 LYS cc_start: 0.7862 (pttt) cc_final: 0.7625 (ttpp) REVERT: j 71 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.7240 (ttp-110) REVERT: j 243 LYS cc_start: 0.7529 (ttmt) cc_final: 0.6841 (tptt) REVERT: j 263 GLN cc_start: 0.7672 (pt0) cc_final: 0.6962 (mp-120) REVERT: g 67 ASP cc_start: 0.7971 (m-30) cc_final: 0.7548 (m-30) REVERT: g 184 LYS cc_start: 0.6629 (tttp) cc_final: 0.6215 (mmtt) REVERT: g 252 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7314 (mp10) outliers start: 164 outliers final: 86 residues processed: 780 average time/residue: 1.3974 time to fit residues: 1480.7642 Evaluate side-chains 752 residues out of total 7560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 639 time to evaluate : 5.774 ------------------------------------------------------------------------------- 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 169 ILE Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 155 SER 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 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 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 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 77 ASP 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 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 8 THR 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 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 92 LYS 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 95 GLU 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 V residue 159 VAL Chi-restraints excluded: chain W residue 6 ILE Chi-restraints excluded: chain W residue 56 SER 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 123 GLN 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 Z residue 243 LYS 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 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 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 62 MET 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 37 LYS Chi-restraints excluded: chain i residue 98 LEU Chi-restraints excluded: chain i residue 103 THR Chi-restraints excluded: chain j residue 32 ARG Chi-restraints excluded: chain j residue 71 ARG Chi-restraints excluded: chain g residue 89 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 912 optimal weight: 0.9990 chunk 218 optimal weight: 2.9990 chunk 454 optimal weight: 4.9990 chunk 760 optimal weight: 9.9990 chunk 117 optimal weight: 1.9990 chunk 502 optimal weight: 0.9990 chunk 498 optimal weight: 0.6980 chunk 611 optimal weight: 2.9990 chunk 522 optimal weight: 0.7980 chunk 800 optimal weight: 0.9980 chunk 263 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN D 256 GLN E 31 GLN E 251 GLN F 31 GLN F 151 ASN H 245 GLN K 134 ASN K 263 GLN M 55 GLN ** T 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 123 GLN U 123 GLN U 151 ASN U 252 GLN 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 151 ASN a 134 ASN a 231 ASN a 256 GLN d 256 GLN ** e 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 73 GLN j 73 GLN g 31 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.128056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.114538 restraints weight = 96008.809| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.41 r_work: 0.3459 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 70056 Z= 0.145 Angle : 0.391 9.850 94824 Z= 0.229 Chirality : 0.031 0.308 12204 Planarity : 0.002 0.019 12132 Dihedral : 3.472 19.341 9792 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 1.71 % Allowed : 11.48 % Favored : 86.81 % 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: 4.67 (0.09), residues: 9648 helix: 4.01 (0.06), residues: 7020 sheet: -1.65 (0.21), residues: 432 loop : 0.85 (0.15), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP f 49 HIS 0.003 0.001 HIS C 214 PHE 0.017 0.001 PHE f 177 ARG 0.005 0.000 ARG T 121 *********************** 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 819 residues out of total 7560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 690 time to evaluate : 5.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 256 GLN cc_start: 0.7985 (tt0) cc_final: 0.7783 (tt0) REVERT: D 95 GLU cc_start: 0.6171 (mm-30) cc_final: 0.5712 (mt-10) REVERT: E 13 MET cc_start: 0.8644 (mtt) cc_final: 0.8392 (mtm) REVERT: F 256 GLN cc_start: 0.6750 (OUTLIER) cc_final: 0.5545 (mp10) REVERT: F 264 SER cc_start: 0.7522 (t) cc_final: 0.7245 (p) REVERT: G 220 LYS cc_start: 0.7140 (mtmt) cc_final: 0.6224 (mmtt) REVERT: H 25 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8232 (mt-10) REVERT: H 191 ASP cc_start: 0.8010 (t0) cc_final: 0.7693 (m-30) REVERT: H 226 ASP cc_start: 0.7335 (OUTLIER) cc_final: 0.6964 (m-30) REVERT: I 31 GLN cc_start: 0.7057 (pp30) cc_final: 0.6392 (mm-40) REVERT: J 43 LYS cc_start: 0.5128 (mmmt) cc_final: 0.4560 (mmpt) REVERT: K 71 ARG cc_start: 0.7557 (ttt90) cc_final: 0.6379 (mtm110) REVERT: K 77 ASP cc_start: 0.7441 (p0) cc_final: 0.7081 (m-30) REVERT: K 92 LYS cc_start: 0.8458 (mtpp) cc_final: 0.8092 (mtmt) REVERT: M 13 MET cc_start: 0.7317 (mtp) cc_final: 0.7053 (mtt) REVERT: M 195 GLN cc_start: 0.7065 (tt0) cc_final: 0.6473 (tm-30) REVERT: M 256 GLN cc_start: 0.7233 (tt0) cc_final: 0.7001 (tt0) REVERT: O 84 ASP cc_start: 0.7029 (m-30) cc_final: 0.6789 (t0) REVERT: O 116 ASP cc_start: 0.6531 (m-30) cc_final: 0.6272 (m-30) REVERT: O 231 ASN cc_start: 0.8489 (t0) cc_final: 0.8146 (t0) REVERT: Q 38 LYS cc_start: 0.8258 (ptmm) cc_final: 0.7743 (pttm) REVERT: Q 62 MET cc_start: 0.8665 (mtt) cc_final: 0.8344 (mtt) REVERT: Q 123 GLN cc_start: 0.8350 (OUTLIER) cc_final: 0.7491 (tm-30) REVERT: Q 220 LYS cc_start: 0.6442 (mmmt) cc_final: 0.5604 (mttt) REVERT: R 92 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8354 (mttm) REVERT: R 191 ASP cc_start: 0.8248 (m-30) cc_final: 0.8036 (m-30) REVERT: R 240 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7380 (mp0) REVERT: S 14 ILE cc_start: 0.7087 (OUTLIER) cc_final: 0.6835 (mm) REVERT: S 25 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7099 (mt-10) REVERT: S 95 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.6723 (tt0) REVERT: S 186 MET cc_start: 0.8225 (tpt) cc_final: 0.7989 (tpp) REVERT: V 123 GLN cc_start: 0.7494 (tp40) cc_final: 0.6737 (mt0) REVERT: V 173 THR cc_start: 0.8767 (m) cc_final: 0.8489 (p) REVERT: W 123 GLN cc_start: 0.7316 (tp40) cc_final: 0.6476 (mt0) REVERT: W 195 GLN cc_start: 0.7943 (mt0) cc_final: 0.7487 (mm-40) REVERT: X 151 ASN cc_start: 0.7896 (p0) cc_final: 0.7102 (t0) REVERT: X 226 ASP cc_start: 0.7703 (m-30) cc_final: 0.7441 (m-30) REVERT: Y 123 GLN cc_start: 0.7348 (OUTLIER) cc_final: 0.7070 (mm-40) REVERT: Z 38 LYS cc_start: 0.8063 (mtmm) cc_final: 0.7745 (mtmm) REVERT: Z 123 GLN cc_start: 0.7460 (OUTLIER) cc_final: 0.6485 (mm-40) REVERT: Z 243 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.8007 (tttp) REVERT: a 62 MET cc_start: 0.7440 (mmt) cc_final: 0.6856 (mmt) REVERT: a 87 THR cc_start: 0.7307 (m) cc_final: 0.6715 (p) REVERT: a 220 LYS cc_start: 0.7727 (mtmt) cc_final: 0.6733 (tptt) REVERT: b 95 GLU cc_start: 0.7026 (OUTLIER) cc_final: 0.6379 (tt0) REVERT: b 116 ASP cc_start: 0.6976 (m-30) cc_final: 0.6626 (m-30) REVERT: b 256 GLN cc_start: 0.7810 (OUTLIER) cc_final: 0.7305 (tm-30) REVERT: c 25 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7647 (mt-10) REVERT: c 30 GLN cc_start: 0.7227 (tp40) cc_final: 0.6899 (tp40) REVERT: c 263 GLN cc_start: 0.8247 (mm110) cc_final: 0.7352 (tp40) REVERT: d 31 GLN cc_start: 0.7697 (OUTLIER) cc_final: 0.7352 (pt0) REVERT: d 123 GLN cc_start: 0.5903 (tp-100) cc_final: 0.5239 (mt0) REVERT: e 66 LYS cc_start: 0.6397 (mmtp) cc_final: 0.6148 (mmtp) REVERT: e 125 GLU cc_start: 0.6604 (tp30) cc_final: 0.6260 (mm-30) REVERT: e 252 GLN cc_start: 0.8038 (mt0) cc_final: 0.7519 (mm-40) REVERT: f 13 MET cc_start: 0.6730 (OUTLIER) cc_final: 0.6516 (ptp) REVERT: f 16 LEU cc_start: 0.6310 (OUTLIER) cc_final: 0.5727 (tt) REVERT: f 62 MET cc_start: 0.6608 (OUTLIER) cc_final: 0.6371 (mpp) REVERT: f 88 ASP cc_start: 0.6061 (m-30) cc_final: 0.5820 (m-30) REVERT: f 263 GLN cc_start: 0.7259 (tm-30) cc_final: 0.6769 (tt0) REVERT: f 268 ILE cc_start: 0.8267 (pp) cc_final: 0.8035 (mp) REVERT: h 95 GLU cc_start: 0.7238 (tt0) cc_final: 0.6517 (mt-10) REVERT: i 31 GLN cc_start: 0.7207 (OUTLIER) cc_final: 0.6965 (mt0) REVERT: i 37 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8217 (mttp) REVERT: j 67 ASP cc_start: 0.6513 (m-30) cc_final: 0.6098 (m-30) REVERT: j 71 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.7128 (ttp-110) REVERT: j 212 ASP cc_start: 0.8036 (OUTLIER) cc_final: 0.7808 (m-30) REVERT: j 243 LYS cc_start: 0.7415 (ttmt) cc_final: 0.7016 (tmtt) REVERT: j 263 GLN cc_start: 0.7665 (pt0) cc_final: 0.6985 (mp-120) REVERT: g 67 ASP cc_start: 0.8025 (m-30) cc_final: 0.7651 (m-30) REVERT: g 184 LYS cc_start: 0.6591 (tttp) cc_final: 0.6189 (mmtt) REVERT: g 252 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7327 (mp10) outliers start: 129 outliers final: 78 residues processed: 785 average time/residue: 1.2958 time to fit residues: 1376.6294 Evaluate side-chains 753 residues out of total 7560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 652 time to evaluate : 5.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 155 SER 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 124 ILE 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 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 84 ASP Chi-restraints excluded: chain K residue 253 LEU Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain L residue 267 SER Chi-restraints excluded: chain M residue 8 THR 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 R residue 92 LYS 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 95 GLU Chi-restraints excluded: chain S residue 159 VAL Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 33 ILE 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 247 LEU 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 123 GLN 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 Z residue 243 LYS 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 25 GLU 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 159 VAL Chi-restraints excluded: chain e residue 33 ILE Chi-restraints excluded: chain e residue 101 SER Chi-restraints excluded: chain f residue 13 MET Chi-restraints excluded: chain f residue 16 LEU Chi-restraints excluded: chain f residue 62 MET 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 37 LYS Chi-restraints excluded: chain i residue 98 LEU Chi-restraints excluded: chain i residue 103 THR Chi-restraints excluded: chain i residue 265 SER Chi-restraints excluded: chain j residue 71 ARG Chi-restraints excluded: chain j residue 212 ASP Chi-restraints excluded: chain g residue 89 LEU 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 758 optimal weight: 0.9990 chunk 467 optimal weight: 0.9980 chunk 861 optimal weight: 8.9990 chunk 69 optimal weight: 0.9990 chunk 468 optimal weight: 2.9990 chunk 781 optimal weight: 6.9990 chunk 643 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 768 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 GLN D 256 GLN E 31 GLN E 251 GLN F 31 GLN F 151 ASN ** G 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 151 ASN H 245 GLN K 45 ASN K 134 ASN M 55 GLN ** T 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 123 GLN U 123 GLN U 151 ASN V 151 ASN V 263 GLN ** X 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 263 GLN Z 31 GLN Z 151 ASN N 151 ASN a 134 ASN a 231 ASN a 256 GLN c 9 ASN d 256 GLN ** e 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 73 GLN j 73 GLN g 31 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.128052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.114501 restraints weight = 96060.422| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.41 r_work: 0.3459 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 70056 Z= 0.151 Angle : 0.397 10.064 94824 Z= 0.232 Chirality : 0.032 0.353 12204 Planarity : 0.002 0.017 12132 Dihedral : 3.463 18.633 9792 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 1.71 % Allowed : 11.80 % Favored : 86.49 % 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: 4.66 (0.09), residues: 9648 helix: 4.00 (0.06), residues: 7020 sheet: -1.53 (0.21), residues: 432 loop : 0.82 (0.15), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP f 49 HIS 0.003 0.001 HIS C 214 PHE 0.019 0.001 PHE P 110 ARG 0.005 0.000 ARG T 121 *********************** 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 791 residues out of total 7560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 662 time to evaluate : 5.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 256 GLN cc_start: 0.7998 (tt0) cc_final: 0.7786 (tt0) REVERT: D 30 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7850 (mt0) REVERT: D 95 GLU cc_start: 0.6364 (mm-30) cc_final: 0.5863 (mt-10) REVERT: E 13 MET cc_start: 0.8662 (mtt) cc_final: 0.8378 (mtm) REVERT: F 256 GLN cc_start: 0.6752 (OUTLIER) cc_final: 0.5543 (mp10) REVERT: F 264 SER cc_start: 0.7558 (t) cc_final: 0.7288 (p) REVERT: G 220 LYS cc_start: 0.7159 (mtmt) cc_final: 0.6256 (mmtt) REVERT: H 191 ASP cc_start: 0.7988 (t0) cc_final: 0.7690 (m-30) REVERT: H 226 ASP cc_start: 0.7291 (OUTLIER) cc_final: 0.6924 (m-30) REVERT: I 31 GLN cc_start: 0.7065 (pp30) cc_final: 0.6396 (mm-40) REVERT: J 43 LYS cc_start: 0.5149 (mmmt) cc_final: 0.4557 (mmpt) REVERT: K 71 ARG cc_start: 0.7546 (ttt90) cc_final: 0.6371 (mtm110) REVERT: K 77 ASP cc_start: 0.7444 (p0) cc_final: 0.7061 (m-30) REVERT: K 92 LYS cc_start: 0.8460 (mtpp) cc_final: 0.8096 (mtmt) REVERT: M 13 MET cc_start: 0.7334 (mtp) cc_final: 0.7067 (mtt) REVERT: M 62 MET cc_start: 0.7686 (mmt) cc_final: 0.7279 (mtt) REVERT: M 195 GLN cc_start: 0.7067 (tt0) cc_final: 0.6480 (tm-30) REVERT: M 256 GLN cc_start: 0.7217 (tt0) cc_final: 0.6976 (tt0) REVERT: O 84 ASP cc_start: 0.7051 (m-30) cc_final: 0.6832 (t0) REVERT: O 116 ASP cc_start: 0.6554 (m-30) cc_final: 0.6299 (m-30) REVERT: O 231 ASN cc_start: 0.8482 (t0) cc_final: 0.8152 (t0) REVERT: P 225 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7831 (mp) REVERT: Q 38 LYS cc_start: 0.8234 (ptmm) cc_final: 0.7716 (pttm) REVERT: Q 62 MET cc_start: 0.8661 (mtt) cc_final: 0.8350 (mtt) REVERT: Q 123 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.7505 (tm-30) REVERT: Q 220 LYS cc_start: 0.6486 (mmmt) cc_final: 0.5646 (mttt) REVERT: R 92 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8350 (mttm) REVERT: R 191 ASP cc_start: 0.8240 (m-30) cc_final: 0.8029 (m-30) REVERT: R 240 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7399 (mp0) REVERT: R 245 GLN cc_start: 0.6653 (pt0) cc_final: 0.6382 (pt0) REVERT: S 14 ILE cc_start: 0.7101 (OUTLIER) cc_final: 0.6852 (mm) REVERT: S 25 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7100 (mt-10) REVERT: S 31 GLN cc_start: 0.7734 (OUTLIER) cc_final: 0.6964 (tp40) REVERT: S 95 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.6715 (tt0) REVERT: S 186 MET cc_start: 0.8222 (tpt) cc_final: 0.7983 (tpp) REVERT: V 123 GLN cc_start: 0.7515 (tp40) cc_final: 0.6749 (mt0) REVERT: V 173 THR cc_start: 0.8792 (m) cc_final: 0.8511 (p) REVERT: W 123 GLN cc_start: 0.7318 (tp40) cc_final: 0.6476 (mt0) REVERT: W 195 GLN cc_start: 0.7952 (mt0) cc_final: 0.7171 (mm-40) REVERT: W 198 THR cc_start: 0.8274 (m) cc_final: 0.7931 (p) REVERT: X 151 ASN cc_start: 0.7906 (p0) cc_final: 0.7136 (t0) REVERT: X 226 ASP cc_start: 0.7680 (m-30) cc_final: 0.7412 (m-30) REVERT: Y 123 GLN cc_start: 0.7415 (OUTLIER) cc_final: 0.7120 (mm-40) REVERT: Z 123 GLN cc_start: 0.7463 (OUTLIER) cc_final: 0.6483 (mm-40) REVERT: Z 243 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.8016 (tttp) REVERT: a 62 MET cc_start: 0.7441 (mmt) cc_final: 0.6833 (mmt) REVERT: a 87 THR cc_start: 0.7319 (m) cc_final: 0.6730 (p) REVERT: a 220 LYS cc_start: 0.7731 (mtmt) cc_final: 0.6761 (tptt) REVERT: b 95 GLU cc_start: 0.7022 (OUTLIER) cc_final: 0.6433 (tt0) REVERT: b 116 ASP cc_start: 0.6974 (m-30) cc_final: 0.6662 (m-30) REVERT: b 256 GLN cc_start: 0.7774 (OUTLIER) cc_final: 0.7270 (tm-30) REVERT: c 30 GLN cc_start: 0.7230 (tp40) cc_final: 0.6916 (tp40) REVERT: c 263 GLN cc_start: 0.8243 (mm110) cc_final: 0.7421 (tp40) REVERT: d 31 GLN cc_start: 0.7665 (OUTLIER) cc_final: 0.7322 (pt0) REVERT: d 123 GLN cc_start: 0.5890 (tp-100) cc_final: 0.5226 (mt0) REVERT: e 66 LYS cc_start: 0.6375 (mmtp) cc_final: 0.6156 (mmtp) REVERT: e 125 GLU cc_start: 0.6647 (tp30) cc_final: 0.6297 (mm-30) REVERT: e 252 GLN cc_start: 0.8032 (mt0) cc_final: 0.7508 (mm-40) REVERT: f 13 MET cc_start: 0.6756 (OUTLIER) cc_final: 0.6537 (ptp) REVERT: f 16 LEU cc_start: 0.6326 (OUTLIER) cc_final: 0.5732 (tt) REVERT: f 62 MET cc_start: 0.6612 (OUTLIER) cc_final: 0.6345 (mpp) REVERT: f 88 ASP cc_start: 0.6036 (m-30) cc_final: 0.5829 (m-30) REVERT: f 263 GLN cc_start: 0.7379 (tm-30) cc_final: 0.6913 (tt0) REVERT: h 95 GLU cc_start: 0.7240 (tt0) cc_final: 0.6520 (mt-10) REVERT: i 31 GLN cc_start: 0.7201 (OUTLIER) cc_final: 0.6899 (mt0) REVERT: i 37 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.8226 (mttp) REVERT: j 67 ASP cc_start: 0.6458 (m-30) cc_final: 0.6047 (m-30) REVERT: j 71 ARG cc_start: 0.7434 (OUTLIER) cc_final: 0.7112 (ttp-110) REVERT: j 212 ASP cc_start: 0.8024 (OUTLIER) cc_final: 0.7767 (m-30) REVERT: j 243 LYS cc_start: 0.7426 (ttmt) cc_final: 0.7020 (tmtt) REVERT: j 263 GLN cc_start: 0.7708 (pt0) cc_final: 0.7104 (mp-120) REVERT: g 67 ASP cc_start: 0.8049 (m-30) cc_final: 0.7682 (m-30) REVERT: g 184 LYS cc_start: 0.6618 (tttp) cc_final: 0.6222 (mmtt) REVERT: g 252 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7301 (mp10) outliers start: 129 outliers final: 82 residues processed: 759 average time/residue: 1.3004 time to fit residues: 1333.8043 Evaluate side-chains 749 residues out of total 7560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 642 time to evaluate : 5.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 155 SER 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 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 124 ILE 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 267 SER Chi-restraints excluded: chain M residue 8 THR 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 225 LEU 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 92 LYS 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 95 GLU Chi-restraints excluded: chain S residue 159 VAL Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 33 ILE 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 247 LEU 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 123 GLN 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 Z residue 243 LYS Chi-restraints excluded: chain a residue 179 THR Chi-restraints excluded: chain a residue 218 VAL 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 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 80 LEU Chi-restraints excluded: chain e residue 101 SER Chi-restraints excluded: chain f residue 13 MET Chi-restraints excluded: chain f residue 16 LEU Chi-restraints excluded: chain f residue 33 ILE Chi-restraints excluded: chain f residue 62 MET 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 i residue 31 GLN Chi-restraints excluded: chain i residue 37 LYS Chi-restraints excluded: chain i residue 98 LEU Chi-restraints excluded: chain i residue 103 THR Chi-restraints excluded: chain i residue 265 SER Chi-restraints excluded: chain j residue 71 ARG Chi-restraints excluded: chain j residue 212 ASP 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 795 optimal weight: 5.9990 chunk 430 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 246 optimal weight: 3.9990 chunk 465 optimal weight: 0.9990 chunk 193 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 488 optimal weight: 2.9990 chunk 758 optimal weight: 1.9990 chunk 541 optimal weight: 7.9990 chunk 354 optimal weight: 2.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 GLN D 256 GLN E 31 GLN E 251 GLN F 31 GLN F 151 ASN ** G 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 245 GLN K 45 ASN K 134 ASN M 55 GLN O 20 ASN ** T 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 123 GLN U 151 ASN U 252 GLN 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 151 ASN a 134 ASN a 231 ASN a 256 GLN d 256 GLN ** e 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 31 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.127277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.113697 restraints weight = 95873.377| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.41 r_work: 0.3447 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 70056 Z= 0.161 Angle : 0.406 10.188 94824 Z= 0.236 Chirality : 0.032 0.355 12204 Planarity : 0.002 0.017 12132 Dihedral : 3.483 18.597 9792 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 1.57 % Allowed : 12.00 % Favored : 86.43 % 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: 4.62 (0.09), residues: 9648 helix: 3.97 (0.06), residues: 7020 sheet: -1.49 (0.21), residues: 432 loop : 0.80 (0.15), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP f 49 HIS 0.003 0.001 HIS C 214 PHE 0.018 0.001 PHE f 177 ARG 0.004 0.000 ARG T 121 ********************** 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 767 residues out of total 7560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 648 time to evaluate : 5.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7942 (OUTLIER) cc_final: 0.7392 (tm130) REVERT: A 126 LYS cc_start: 0.7354 (OUTLIER) cc_final: 0.6802 (ttpp) REVERT: B 256 GLN cc_start: 0.7994 (tt0) cc_final: 0.7778 (tt0) REVERT: D 95 GLU cc_start: 0.6393 (mm-30) cc_final: 0.5901 (mt-10) REVERT: E 13 MET cc_start: 0.8664 (mtt) cc_final: 0.8414 (mtm) REVERT: F 256 GLN cc_start: 0.6761 (OUTLIER) cc_final: 0.5529 (mp10) REVERT: F 264 SER cc_start: 0.7556 (t) cc_final: 0.7284 (p) REVERT: G 220 LYS cc_start: 0.7168 (mtmt) cc_final: 0.6267 (mmtt) REVERT: H 191 ASP cc_start: 0.8014 (t0) cc_final: 0.7698 (m-30) REVERT: H 226 ASP cc_start: 0.7381 (OUTLIER) cc_final: 0.7012 (m-30) REVERT: I 31 GLN cc_start: 0.7074 (pp30) cc_final: 0.6413 (mm-40) REVERT: J 43 LYS cc_start: 0.5161 (mmmt) cc_final: 0.4557 (mmpt) REVERT: K 71 ARG cc_start: 0.7583 (ttt90) cc_final: 0.6376 (mtm110) REVERT: K 77 ASP cc_start: 0.7435 (p0) cc_final: 0.7066 (m-30) REVERT: K 92 LYS cc_start: 0.8468 (mtpp) cc_final: 0.8104 (mtmt) REVERT: M 13 MET cc_start: 0.7331 (mtp) cc_final: 0.7069 (mtt) REVERT: M 62 MET cc_start: 0.7733 (mmt) cc_final: 0.7317 (mtt) REVERT: M 195 GLN cc_start: 0.7085 (tt0) cc_final: 0.6497 (tm-30) REVERT: M 256 GLN cc_start: 0.7220 (tt0) cc_final: 0.6972 (tt0) REVERT: O 84 ASP cc_start: 0.7047 (m-30) cc_final: 0.6816 (t0) REVERT: O 116 ASP cc_start: 0.6569 (m-30) cc_final: 0.6311 (m-30) REVERT: O 231 ASN cc_start: 0.8520 (t0) cc_final: 0.8183 (t0) REVERT: P 225 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7827 (mp) REVERT: Q 38 LYS cc_start: 0.8233 (ptmm) cc_final: 0.7715 (pttm) REVERT: Q 62 MET cc_start: 0.8693 (mtt) cc_final: 0.8350 (mtt) REVERT: Q 123 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.7520 (tm-30) REVERT: Q 220 LYS cc_start: 0.6501 (mmmt) cc_final: 0.5641 (mttt) REVERT: R 67 ASP cc_start: 0.7241 (m-30) cc_final: 0.7017 (m-30) REVERT: R 92 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8369 (mttm) REVERT: R 186 MET cc_start: 0.9102 (tpt) cc_final: 0.8549 (tpp) REVERT: R 191 ASP cc_start: 0.8255 (m-30) cc_final: 0.8049 (m-30) REVERT: R 240 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7412 (mp0) REVERT: R 245 GLN cc_start: 0.6685 (pt0) cc_final: 0.6427 (pt0) REVERT: S 14 ILE cc_start: 0.7103 (OUTLIER) cc_final: 0.6853 (mm) REVERT: S 31 GLN cc_start: 0.7780 (OUTLIER) cc_final: 0.6960 (tp40) REVERT: S 95 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.6711 (tt0) REVERT: S 186 MET cc_start: 0.8224 (tpt) cc_final: 0.7965 (tpp) REVERT: V 123 GLN cc_start: 0.7505 (tp40) cc_final: 0.6726 (mt0) REVERT: V 173 THR cc_start: 0.8771 (m) cc_final: 0.8491 (p) REVERT: W 123 GLN cc_start: 0.7324 (tp40) cc_final: 0.6483 (mt0) REVERT: W 195 GLN cc_start: 0.7971 (mt0) cc_final: 0.7505 (mm-40) REVERT: X 151 ASN cc_start: 0.7938 (p0) cc_final: 0.7178 (t0) REVERT: X 226 ASP cc_start: 0.7689 (m-30) cc_final: 0.7418 (m-30) REVERT: Y 123 GLN cc_start: 0.7388 (OUTLIER) cc_final: 0.7087 (mm-40) REVERT: Z 123 GLN cc_start: 0.7490 (OUTLIER) cc_final: 0.6535 (mm-40) REVERT: Z 243 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.8020 (tttp) REVERT: N 151 ASN cc_start: 0.8251 (t0) cc_final: 0.7883 (t0) REVERT: a 62 MET cc_start: 0.7456 (mmt) cc_final: 0.6846 (mmt) REVERT: a 87 THR cc_start: 0.7345 (m) cc_final: 0.6756 (p) REVERT: a 220 LYS cc_start: 0.7734 (mtmt) cc_final: 0.6753 (tptt) REVERT: b 95 GLU cc_start: 0.7087 (OUTLIER) cc_final: 0.6447 (tt0) REVERT: b 116 ASP cc_start: 0.6987 (m-30) cc_final: 0.6649 (m-30) REVERT: b 256 GLN cc_start: 0.7775 (OUTLIER) cc_final: 0.7274 (tm-30) REVERT: c 30 GLN cc_start: 0.7259 (tp40) cc_final: 0.6931 (tp40) REVERT: c 263 GLN cc_start: 0.8238 (mm110) cc_final: 0.7416 (tp40) REVERT: d 31 GLN cc_start: 0.7711 (OUTLIER) cc_final: 0.7359 (pt0) REVERT: d 123 GLN cc_start: 0.5853 (tp-100) cc_final: 0.5185 (mt0) REVERT: e 66 LYS cc_start: 0.6378 (mmtp) cc_final: 0.6132 (mmtp) REVERT: e 125 GLU cc_start: 0.6683 (tp30) cc_final: 0.6337 (mm-30) REVERT: e 252 GLN cc_start: 0.8049 (mt0) cc_final: 0.7516 (mm-40) REVERT: f 13 MET cc_start: 0.6772 (OUTLIER) cc_final: 0.6534 (ptp) REVERT: f 16 LEU cc_start: 0.6308 (OUTLIER) cc_final: 0.5794 (tt) REVERT: f 62 MET cc_start: 0.6622 (OUTLIER) cc_final: 0.6358 (mpp) REVERT: f 263 GLN cc_start: 0.7365 (tm-30) cc_final: 0.6916 (tt0) REVERT: h 95 GLU cc_start: 0.7245 (tt0) cc_final: 0.6541 (mt-10) REVERT: i 31 GLN cc_start: 0.7236 (OUTLIER) cc_final: 0.6769 (mt0) REVERT: i 37 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.8217 (mttp) REVERT: j 67 ASP cc_start: 0.6470 (m-30) cc_final: 0.6060 (m-30) REVERT: j 71 ARG cc_start: 0.7409 (OUTLIER) cc_final: 0.7089 (ttp-110) REVERT: j 212 ASP cc_start: 0.8009 (OUTLIER) cc_final: 0.7780 (m-30) REVERT: j 243 LYS cc_start: 0.7438 (ttmt) cc_final: 0.7036 (tmtt) REVERT: j 263 GLN cc_start: 0.7719 (pt0) cc_final: 0.7110 (mp-120) REVERT: g 184 LYS cc_start: 0.6612 (tttp) cc_final: 0.6236 (mmtt) REVERT: g 252 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7311 (mp10) outliers start: 119 outliers final: 83 residues processed: 737 average time/residue: 1.2830 time to fit residues: 1279.1947 Evaluate side-chains 741 residues out of total 7560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 633 time to evaluate : 5.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 126 LYS Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 155 SER 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 124 ILE 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 M residue 8 THR 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 225 LEU 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 92 LYS Chi-restraints excluded: chain R residue 240 GLU Chi-restraints excluded: chain S residue 14 ILE 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 95 GLU Chi-restraints excluded: chain S residue 159 VAL Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 33 ILE 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 247 LEU 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 123 GLN 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 Z residue 243 LYS Chi-restraints excluded: chain a residue 179 THR Chi-restraints excluded: chain a residue 218 VAL 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 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 80 LEU Chi-restraints excluded: chain e residue 101 SER Chi-restraints excluded: chain f residue 13 MET Chi-restraints excluded: chain f residue 16 LEU Chi-restraints excluded: chain f residue 33 ILE Chi-restraints excluded: chain f residue 62 MET 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 i residue 31 GLN Chi-restraints excluded: chain i residue 33 ILE Chi-restraints excluded: chain i residue 37 LYS Chi-restraints excluded: chain i residue 98 LEU Chi-restraints excluded: chain i residue 103 THR Chi-restraints excluded: chain i residue 265 SER Chi-restraints excluded: chain j residue 71 ARG Chi-restraints excluded: chain j residue 212 ASP 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 666 optimal weight: 5.9990 chunk 352 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 34 optimal weight: 9.9990 chunk 423 optimal weight: 8.9990 chunk 739 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 671 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 302 optimal weight: 3.9990 chunk 633 optimal weight: 8.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 45 ASN K 134 ASN M 55 GLN O 31 GLN P 256 GLN ** T 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 123 GLN U 151 ASN V 151 ASN V 251 GLN ** X 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 263 GLN Y 123 GLN Z 31 GLN Z 151 ASN a 134 ASN ** a 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 256 GLN d 18 ASN d 256 GLN ** f 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 251 GLN g 31 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.122961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.109476 restraints weight = 96299.760| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.39 r_work: 0.3393 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1896 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= 0.223 Angle : 0.458 10.165 94824 Z= 0.263 Chirality : 0.034 0.380 12204 Planarity : 0.002 0.021 12132 Dihedral : 3.682 19.386 9792 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 1.60 % Allowed : 12.02 % 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: 4.33 (0.08), residues: 9648 helix: 3.75 (0.06), residues: 7020 sheet: -1.53 (0.21), residues: 432 loop : 0.69 (0.15), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP f 49 HIS 0.005 0.002 HIS G 214 PHE 0.019 0.002 PHE f 177 ARG 0.004 0.000 ARG T 121 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 37337.22 seconds wall clock time: 642 minutes 24.67 seconds (38544.67 seconds total)