Starting phenix.real_space_refine on Sun Sep 29 04:54:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ceo_45505/09_2024/9ceo_45505.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ceo_45505/09_2024/9ceo_45505.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ceo_45505/09_2024/9ceo_45505.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ceo_45505/09_2024/9ceo_45505.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ceo_45505/09_2024/9ceo_45505.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ceo_45505/09_2024/9ceo_45505.cif" } resolution = 2.76 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= 0.007 sd= 0.111 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 114 5.16 5 C 45030 2.51 5 N 12730 2.21 5 O 15542 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 393 residue(s): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 73416 Number of models: 1 Model: "" Number of chains: 38 Chain: "A" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "B" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "C" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "D" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "E" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "F" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "G" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "H" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "I" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "J" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "K" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "L" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "M" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "N" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "O" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "P" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "Q" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "R" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "S" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "T" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "U" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "V" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "W" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "X" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "Y" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "Z" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "a" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "b" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "c" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "d" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "e" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "f" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "g" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "h" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "i" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "j" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "k" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "l" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Time building chain proxies: 31.64, per 1000 atoms: 0.43 Number of scatterers: 73416 At special positions: 0 Unit cell: (138.444, 139.278, 335.268, 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 114 16.00 O 15542 8.00 N 12730 7.00 C 45030 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: 14.25 Conformation dependent library (CDL) restraints added in 7.7 seconds 20368 Ramachandran restraints generated. 10184 Oldfield, 0 Emsley, 10184 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 18924 Finding SS restraints... Secondary structure from input PDB file: 273 helices and 38 sheets defined 75.6% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.56 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: 4.187A 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: 4.084A pdb=" N GLY A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 263 removed outlier: 3.697A pdb=" N GLU A 240 " --> pdb=" O ASP A 236 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA A 242 " --> pdb=" O ALA A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 272 removed outlier: 3.556A pdb=" N SER A 267 " --> pdb=" O SER A 264 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE A 268 " --> pdb=" O SER A 265 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER A 270 " --> pdb=" O SER A 267 " (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: 4.177A pdb=" N VAL B 65 " --> pdb=" O SER B 61 " (cutoff:3.500A) removed outlier: 4.016A 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: 3.999A pdb=" N GLY B 188 " --> pdb=" O LYS B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 263 removed outlier: 3.533A pdb=" N GLU B 240 " --> pdb=" O ASP B 236 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA B 242 " --> pdb=" O ALA B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 272 removed outlier: 3.832A pdb=" N ILE B 268 " --> pdb=" O SER B 265 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER B 270 " --> pdb=" O SER B 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 36 Processing helix chain 'C' and resid 45 through 61 Processing helix chain 'C' and resid 61 through 101 removed outlier: 4.168A 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: 4.046A pdb=" N GLY C 188 " --> pdb=" O LYS C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 263 removed outlier: 3.844A pdb=" N GLU C 240 " --> pdb=" O ASP C 236 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA C 242 " --> pdb=" O ALA C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 270 removed outlier: 3.624A pdb=" N SER C 267 " --> pdb=" O SER C 264 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE C 268 " --> pdb=" O SER C 265 " (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 101 removed outlier: 4.117A pdb=" N VAL D 65 " --> pdb=" O SER D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 130 Processing helix chain 'D' and resid 179 through 234 removed outlier: 3.800A pdb=" N GLY D 188 " --> pdb=" O LYS D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 263 removed outlier: 4.106A pdb=" N GLU D 240 " --> pdb=" O ASP D 236 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA D 242 " --> pdb=" O ALA D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 270 removed outlier: 3.835A pdb=" N SER D 267 " --> pdb=" O SER D 264 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE D 268 " --> pdb=" O SER D 265 " (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: 4.287A 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: 4.020A pdb=" N GLY E 188 " --> pdb=" O LYS E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 263 removed outlier: 3.682A pdb=" N ALA E 242 " --> pdb=" O ALA E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 271 removed outlier: 4.173A pdb=" N SER E 270 " --> pdb=" O SER E 266 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU E 271 " --> pdb=" O SER E 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 266 through 271' Processing helix chain 'F' and resid 9 through 36 removed outlier: 3.667A pdb=" N LEU 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: 4.231A 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: 4.002A pdb=" N GLY F 188 " --> pdb=" O LYS F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 236 through 263 removed outlier: 3.617A pdb=" N GLU F 240 " --> pdb=" O ASP F 236 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA F 242 " --> pdb=" O ALA F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 264 through 270 removed outlier: 3.689A pdb=" N SER F 267 " --> pdb=" O SER F 264 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE F 268 " --> pdb=" O SER F 265 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 36 removed outlier: 3.521A pdb=" N LEU G 13 " --> pdb=" O ASN G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 61 Processing helix chain 'G' and resid 61 through 102 removed outlier: 4.127A pdb=" N VAL G 65 " --> pdb=" O SER G 61 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASP G 102 " --> pdb=" O LEU G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 130 removed outlier: 3.560A pdb=" N THR G 125 " --> pdb=" O ARG G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 179 through 234 removed outlier: 4.011A pdb=" N GLY G 188 " --> pdb=" O LYS G 184 " (cutoff:3.500A) Processing helix chain 'G' and resid 236 through 263 removed outlier: 4.093A pdb=" N ALA G 242 " --> pdb=" O ALA G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 264 through 272 removed outlier: 4.453A pdb=" N ILE G 268 " --> pdb=" O SER G 264 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LEU G 269 " --> pdb=" O SER G 265 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER G 270 " --> pdb=" O SER G 266 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU G 271 " --> pdb=" O SER G 267 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE G 272 " --> pdb=" O ILE G 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 264 through 272' Processing helix chain 'H' and resid 9 through 36 removed outlier: 3.517A pdb=" N LEU H 13 " --> pdb=" O ASN H 9 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 61 removed outlier: 3.535A pdb=" N TRP H 49 " --> pdb=" O ASN H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 101 removed outlier: 4.383A pdb=" N VAL H 65 " --> pdb=" O SER H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 130 removed outlier: 3.631A pdb=" N THR H 125 " --> pdb=" O ARG H 121 " (cutoff:3.500A) Processing helix chain 'H' and resid 179 through 234 removed outlier: 3.908A pdb=" N GLY H 188 " --> pdb=" O LYS H 184 " (cutoff:3.500A) Processing helix chain 'H' and resid 236 through 263 removed outlier: 4.036A pdb=" N ALA H 242 " --> pdb=" O ALA H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 266 through 271 removed outlier: 3.962A pdb=" N SER H 270 " --> pdb=" O SER H 266 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU H 271 " --> pdb=" O SER H 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 266 through 271' Processing helix chain 'I' and resid 9 through 36 removed outlier: 3.541A pdb=" N LEU 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 101 removed outlier: 4.409A 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: 3.850A pdb=" N GLY I 188 " --> pdb=" O LYS I 184 " (cutoff:3.500A) Processing helix chain 'I' and resid 236 through 263 removed outlier: 3.860A pdb=" N ALA I 242 " --> pdb=" O ALA I 238 " (cutoff:3.500A) Processing helix chain 'I' and resid 264 through 266 No H-bonds generated for 'chain 'I' and resid 264 through 266' Processing helix chain 'I' and resid 267 through 272 removed outlier: 3.539A pdb=" N LEU I 271 " --> pdb=" O SER I 267 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 36 removed outlier: 3.559A pdb=" N LEU J 13 " --> pdb=" O ASN J 9 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 61 Processing helix chain 'J' and resid 61 through 101 removed outlier: 4.195A 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 179 through 234 removed outlier: 3.842A pdb=" N GLY J 188 " --> pdb=" O LYS J 184 " (cutoff:3.500A) Processing helix chain 'J' and resid 236 through 264 removed outlier: 3.959A pdb=" N ALA J 242 " --> pdb=" O ALA J 238 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER J 264 " --> pdb=" O ILE J 260 " (cutoff:3.500A) Processing helix chain 'J' and resid 265 through 270 removed outlier: 3.944A pdb=" N ILE J 268 " --> pdb=" O SER J 265 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N SER J 270 " --> pdb=" O SER J 267 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 36 removed outlier: 3.562A pdb=" N LEU K 13 " --> pdb=" O ASN K 9 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 61 Processing helix chain 'K' and resid 61 through 102 removed outlier: 4.223A pdb=" N VAL K 65 " --> pdb=" O SER K 61 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASP K 102 " --> pdb=" O LEU K 98 " (cutoff:3.500A) Processing helix chain 'K' and resid 106 through 130 Processing helix chain 'K' and resid 165 through 170 Processing helix chain 'K' and resid 179 through 234 removed outlier: 3.723A pdb=" N GLY K 188 " --> pdb=" O LYS K 184 " (cutoff:3.500A) Processing helix chain 'K' and resid 236 through 263 removed outlier: 3.686A pdb=" N ALA K 242 " --> pdb=" O ALA K 238 " (cutoff:3.500A) Processing helix chain 'K' and resid 264 through 272 removed outlier: 4.097A pdb=" N SER K 267 " --> pdb=" O SER K 264 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE K 268 " --> pdb=" O SER K 265 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 36 removed outlier: 3.796A pdb=" N LEU 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 62 through 101 Processing helix chain 'L' and resid 106 through 130 Processing helix chain 'L' and resid 179 through 234 removed outlier: 3.825A pdb=" N GLY L 188 " --> pdb=" O LYS L 184 " (cutoff:3.500A) Processing helix chain 'L' and resid 236 through 263 removed outlier: 3.785A pdb=" N ALA L 242 " --> pdb=" O ALA L 238 " (cutoff:3.500A) Processing helix chain 'L' and resid 266 through 271 removed outlier: 4.317A pdb=" N SER L 270 " --> pdb=" O SER L 266 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU L 271 " --> pdb=" O SER L 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 266 through 271' Processing helix chain 'M' and resid 9 through 36 Processing helix chain 'M' and resid 45 through 61 Processing helix chain 'M' and resid 62 through 101 Processing helix chain 'M' and resid 106 through 130 Processing helix chain 'M' and resid 179 through 234 removed outlier: 3.721A pdb=" N GLY M 188 " --> pdb=" O LYS M 184 " (cutoff:3.500A) Processing helix chain 'M' and resid 236 through 263 removed outlier: 3.634A pdb=" N ALA M 242 " --> pdb=" O ALA M 238 " (cutoff:3.500A) Processing helix chain 'M' and resid 264 through 270 removed outlier: 4.134A pdb=" N SER M 267 " --> pdb=" O SER M 264 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE M 268 " --> pdb=" O SER M 265 " (cutoff:3.500A) Processing helix chain 'N' and resid 9 through 36 removed outlier: 3.734A pdb=" N LEU 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: 4.042A 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: 4.116A pdb=" N GLY N 188 " --> pdb=" O LYS N 184 " (cutoff:3.500A) Processing helix chain 'N' and resid 236 through 263 removed outlier: 3.744A pdb=" N ALA N 242 " --> pdb=" O ALA N 238 " (cutoff:3.500A) Processing helix chain 'N' and resid 266 through 271 removed outlier: 4.149A pdb=" N SER N 270 " --> pdb=" O SER N 266 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU N 271 " --> pdb=" O SER N 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 266 through 271' Processing helix chain 'O' and resid 9 through 36 removed outlier: 3.659A pdb=" N LEU 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: 4.463A 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 179 through 234 removed outlier: 3.856A pdb=" N GLY O 188 " --> pdb=" O LYS O 184 " (cutoff:3.500A) Processing helix chain 'O' and resid 236 through 264 removed outlier: 3.807A pdb=" N GLU O 240 " --> pdb=" O ASP O 236 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA O 242 " --> pdb=" O ALA O 238 " (cutoff:3.500A) Processing helix chain 'O' and resid 265 through 272 removed outlier: 3.630A pdb=" N ILE O 268 " --> pdb=" O SER O 265 " (cutoff:3.500A) Processing helix chain 'P' and resid 9 through 36 removed outlier: 3.740A pdb=" N LEU 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 101 removed outlier: 4.309A pdb=" N VAL P 65 " --> pdb=" O SER P 61 " (cutoff:3.500A) Processing helix chain 'P' and resid 106 through 130 Processing helix chain 'P' and resid 179 through 234 removed outlier: 3.886A pdb=" N GLY P 188 " --> pdb=" O LYS P 184 " (cutoff:3.500A) Processing helix chain 'P' and resid 236 through 264 removed outlier: 3.841A pdb=" N ALA P 242 " --> pdb=" O ALA P 238 " (cutoff:3.500A) Processing helix chain 'P' and resid 265 through 272 removed outlier: 3.642A pdb=" N ILE P 268 " --> pdb=" O SER P 265 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER P 270 " --> pdb=" O SER P 267 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE P 272 " --> pdb=" O LEU P 269 " (cutoff:3.500A) Processing helix chain 'Q' and resid 9 through 36 removed outlier: 3.517A pdb=" N LEU 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 62 through 101 Processing helix chain 'Q' and resid 106 through 130 Processing helix chain 'Q' and resid 179 through 234 removed outlier: 3.816A pdb=" N GLY Q 188 " --> pdb=" O LYS Q 184 " (cutoff:3.500A) Processing helix chain 'Q' and resid 236 through 264 removed outlier: 3.710A pdb=" N ALA Q 242 " --> pdb=" O ALA Q 238 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER Q 264 " --> pdb=" O ILE Q 260 " (cutoff:3.500A) Processing helix chain 'Q' and resid 265 through 272 removed outlier: 3.636A pdb=" N ILE Q 268 " --> pdb=" O SER Q 265 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER Q 270 " --> pdb=" O SER Q 267 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE Q 272 " --> pdb=" O LEU Q 269 " (cutoff:3.500A) Processing helix chain 'R' and resid 9 through 36 removed outlier: 3.647A pdb=" N LEU 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: 4.310A 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 179 through 234 removed outlier: 3.888A pdb=" N GLY R 188 " --> pdb=" O LYS R 184 " (cutoff:3.500A) Processing helix chain 'R' and resid 236 through 264 removed outlier: 3.623A pdb=" N ALA R 242 " --> pdb=" O ALA R 238 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER R 264 " --> pdb=" O ILE R 260 " (cutoff:3.500A) Processing helix chain 'R' and resid 265 through 270 removed outlier: 3.690A pdb=" N ILE R 268 " --> pdb=" O SER R 265 " (cutoff:3.500A) Processing helix chain 'S' and resid 9 through 36 removed outlier: 3.562A pdb=" N LEU 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: 4.238A pdb=" N VAL S 65 " --> pdb=" O SER S 61 " (cutoff:3.500A) removed outlier: 4.102A 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 179 through 234 removed outlier: 3.925A pdb=" N GLY S 188 " --> pdb=" O LYS S 184 " (cutoff:3.500A) Processing helix chain 'S' and resid 236 through 263 removed outlier: 3.764A pdb=" N GLU S 240 " --> pdb=" O ASP S 236 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA S 242 " --> pdb=" O ALA S 238 " (cutoff:3.500A) Processing helix chain 'S' and resid 264 through 272 removed outlier: 3.563A pdb=" N ILE S 268 " --> pdb=" O SER S 265 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER S 270 " --> pdb=" O SER S 267 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE S 272 " --> pdb=" O LEU S 269 " (cutoff:3.500A) Processing helix chain 'T' and resid 9 through 36 removed outlier: 3.554A pdb=" N LEU 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 101 removed outlier: 4.306A pdb=" N VAL T 65 " --> pdb=" O SER T 61 " (cutoff:3.500A) Processing helix chain 'T' and resid 106 through 130 Processing helix chain 'T' and resid 179 through 234 removed outlier: 3.969A pdb=" N GLY T 188 " --> pdb=" O LYS T 184 " (cutoff:3.500A) Processing helix chain 'T' and resid 236 through 264 Processing helix chain 'T' and resid 265 through 272 removed outlier: 3.930A pdb=" N ILE T 268 " --> pdb=" O SER T 265 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER T 270 " --> pdb=" O SER T 267 " (cutoff:3.500A) Processing helix chain 'U' and resid 9 through 36 removed outlier: 3.638A pdb=" N LEU 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: 4.108A pdb=" N VAL U 65 " --> pdb=" O SER U 61 " (cutoff:3.500A) Processing helix chain 'U' and resid 106 through 130 Processing helix chain 'U' and resid 179 through 234 removed outlier: 3.866A pdb=" N GLY U 188 " --> pdb=" O LYS U 184 " (cutoff:3.500A) Processing helix chain 'U' and resid 236 through 264 removed outlier: 3.682A pdb=" N ALA U 242 " --> pdb=" O ALA U 238 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER U 264 " --> pdb=" O ILE U 260 " (cutoff:3.500A) Processing helix chain 'U' and resid 265 through 272 removed outlier: 3.914A pdb=" N ILE U 268 " --> pdb=" O SER U 265 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER U 270 " --> pdb=" O SER U 267 " (cutoff:3.500A) Processing helix chain 'V' and resid 9 through 36 removed outlier: 3.920A pdb=" N LEU 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 165 through 170 removed outlier: 3.525A pdb=" N LEU V 169 " --> pdb=" O LEU V 166 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY V 170 " --> pdb=" O GLY V 167 " (cutoff:3.500A) Processing helix chain 'V' and resid 179 through 234 removed outlier: 4.045A pdb=" N GLY V 188 " --> pdb=" O LYS V 184 " (cutoff:3.500A) Processing helix chain 'V' and resid 236 through 263 removed outlier: 3.554A pdb=" N GLU V 240 " --> pdb=" O ASP V 236 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA V 242 " --> pdb=" O ALA V 238 " (cutoff:3.500A) Processing helix chain 'V' and resid 264 through 272 removed outlier: 3.785A pdb=" N ILE V 268 " --> pdb=" O SER V 265 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER V 270 " --> pdb=" O SER V 267 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE V 272 " --> pdb=" O LEU V 269 " (cutoff:3.500A) Processing helix chain 'W' and resid 9 through 36 Processing helix chain 'W' and resid 45 through 61 Processing helix chain 'W' and resid 61 through 101 removed outlier: 4.233A 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 179 through 234 removed outlier: 4.014A pdb=" N GLY W 188 " --> pdb=" O LYS W 184 " (cutoff:3.500A) Processing helix chain 'W' and resid 236 through 264 removed outlier: 3.521A pdb=" N GLU W 240 " --> pdb=" O ASP W 236 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA W 242 " --> pdb=" O ALA W 238 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER W 264 " --> pdb=" O ILE W 260 " (cutoff:3.500A) Processing helix chain 'W' and resid 265 through 272 removed outlier: 3.810A pdb=" N ILE W 268 " --> pdb=" O SER W 265 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER W 270 " --> pdb=" O SER W 267 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE W 272 " --> pdb=" O LEU W 269 " (cutoff:3.500A) 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 101 removed outlier: 4.076A pdb=" N VAL X 65 " --> pdb=" O SER X 61 " (cutoff:3.500A) Processing helix chain 'X' and resid 106 through 130 Processing helix chain 'X' and resid 179 through 234 removed outlier: 3.839A pdb=" N GLY X 188 " --> pdb=" O LYS X 184 " (cutoff:3.500A) Processing helix chain 'X' and resid 236 through 264 removed outlier: 3.587A pdb=" N GLU X 240 " --> pdb=" O ASP X 236 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALA X 242 " --> pdb=" O ALA X 238 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER X 264 " --> pdb=" O ILE X 260 " (cutoff:3.500A) Processing helix chain 'X' and resid 265 through 270 removed outlier: 4.041A pdb=" N ILE X 268 " --> pdb=" O SER X 265 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER X 270 " --> pdb=" O SER X 267 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 36 removed outlier: 3.622A pdb=" N LEU Y 13 " --> pdb=" O ASN Y 9 " (cutoff:3.500A) Processing helix chain 'Y' and resid 45 through 61 Processing helix chain 'Y' and resid 61 through 101 removed outlier: 4.159A 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 Processing helix chain 'Y' and resid 179 through 234 removed outlier: 3.896A pdb=" N GLY Y 188 " --> pdb=" O LYS Y 184 " (cutoff:3.500A) Processing helix chain 'Y' and resid 236 through 263 removed outlier: 3.620A pdb=" N GLU Y 240 " --> pdb=" O ASP Y 236 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA Y 242 " --> pdb=" O ALA Y 238 " (cutoff:3.500A) Processing helix chain 'Y' and resid 264 through 270 removed outlier: 3.687A pdb=" N SER Y 267 " --> pdb=" O SER Y 264 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE Y 268 " --> pdb=" O SER Y 265 " (cutoff:3.500A) Processing helix chain 'Z' and resid 9 through 36 removed outlier: 3.682A pdb=" N LEU Z 13 " --> pdb=" O ASN Z 9 " (cutoff:3.500A) Processing helix chain 'Z' and resid 45 through 61 Processing helix chain 'Z' and resid 61 through 101 removed outlier: 4.046A pdb=" N VAL Z 65 " --> pdb=" O SER Z 61 " (cutoff:3.500A) Processing helix chain 'Z' and resid 106 through 130 Processing helix chain 'Z' and resid 179 through 234 removed outlier: 3.794A pdb=" N GLY Z 188 " --> pdb=" O LYS Z 184 " (cutoff:3.500A) Processing helix chain 'Z' and resid 236 through 263 removed outlier: 3.701A pdb=" N GLU Z 240 " --> pdb=" O ASP Z 236 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA Z 242 " --> pdb=" O ALA Z 238 " (cutoff:3.500A) Processing helix chain 'Z' and resid 264 through 272 removed outlier: 3.633A pdb=" N SER Z 267 " --> pdb=" O SER Z 264 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE Z 268 " --> pdb=" O SER Z 265 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER Z 270 " --> pdb=" O SER Z 267 " (cutoff:3.500A) Processing helix chain 'a' and resid 9 through 36 removed outlier: 3.726A pdb=" N LEU 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: 4.214A 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: 3.961A pdb=" N GLY a 188 " --> pdb=" O LYS a 184 " (cutoff:3.500A) Processing helix chain 'a' and resid 236 through 263 removed outlier: 3.615A pdb=" N GLU a 240 " --> pdb=" O ASP a 236 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA a 242 " --> pdb=" O ALA a 238 " (cutoff:3.500A) Processing helix chain 'a' and resid 264 through 272 removed outlier: 3.690A pdb=" N ILE a 268 " --> pdb=" O SER a 265 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER a 270 " --> pdb=" O SER a 267 " (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 101 removed outlier: 4.093A 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 165 through 170 removed outlier: 3.699A pdb=" N GLY b 170 " --> pdb=" O GLY b 167 " (cutoff:3.500A) Processing helix chain 'b' and resid 179 through 234 removed outlier: 4.105A pdb=" N GLY b 188 " --> pdb=" O LYS b 184 " (cutoff:3.500A) Processing helix chain 'b' and resid 236 through 263 removed outlier: 3.702A pdb=" N GLU b 240 " --> pdb=" O ASP b 236 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA b 242 " --> pdb=" O ALA b 238 " (cutoff:3.500A) Processing helix chain 'b' and resid 264 through 272 removed outlier: 3.506A pdb=" N SER b 267 " --> pdb=" O SER b 264 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE b 268 " --> pdb=" O SER b 265 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER b 270 " --> pdb=" O SER b 267 " (cutoff:3.500A) Processing helix chain 'c' and resid 9 through 36 Processing helix chain 'c' and resid 45 through 61 Processing helix chain 'c' and resid 61 through 101 removed outlier: 4.154A 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: 3.998A pdb=" N GLY c 188 " --> pdb=" O LYS c 184 " (cutoff:3.500A) Processing helix chain 'c' and resid 236 through 263 removed outlier: 3.592A pdb=" N GLU c 240 " --> pdb=" O ASP c 236 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA c 242 " --> pdb=" O ALA c 238 " (cutoff:3.500A) Processing helix chain 'c' and resid 264 through 272 removed outlier: 3.526A pdb=" N SER c 267 " --> pdb=" O SER c 264 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE c 268 " --> pdb=" O SER c 265 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER c 270 " --> pdb=" O SER c 267 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE c 272 " --> pdb=" O LEU c 269 " (cutoff:3.500A) Processing helix chain 'd' and resid 9 through 36 removed outlier: 3.551A pdb=" N LEU d 13 " --> pdb=" O ASN d 9 " (cutoff:3.500A) Processing helix chain 'd' and resid 45 through 61 Processing helix chain 'd' and resid 61 through 101 removed outlier: 4.104A pdb=" N VAL d 65 " --> pdb=" O SER d 61 " (cutoff:3.500A) Processing helix chain 'd' and resid 106 through 130 Processing helix chain 'd' and resid 165 through 170 removed outlier: 3.568A pdb=" N LEU d 169 " --> pdb=" O LEU d 166 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY d 170 " --> pdb=" O GLY d 167 " (cutoff:3.500A) Processing helix chain 'd' and resid 179 through 234 removed outlier: 4.090A pdb=" N GLY d 188 " --> pdb=" O LYS d 184 " (cutoff:3.500A) Processing helix chain 'd' and resid 236 through 263 removed outlier: 3.989A pdb=" N ALA d 242 " --> pdb=" O ALA d 238 " (cutoff:3.500A) Processing helix chain 'd' and resid 264 through 272 removed outlier: 3.644A pdb=" N SER d 267 " --> pdb=" O SER d 264 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE d 268 " --> pdb=" O SER d 265 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER d 270 " --> pdb=" O SER d 267 " (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 102 removed outlier: 3.987A pdb=" N VAL e 65 " --> pdb=" O SER e 61 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ASP e 102 " --> pdb=" O LEU e 98 " (cutoff:3.500A) Processing helix chain 'e' and resid 106 through 130 Processing helix chain 'e' and resid 179 through 234 removed outlier: 3.737A pdb=" N GLY e 188 " --> pdb=" O LYS e 184 " (cutoff:3.500A) Processing helix chain 'e' and resid 236 through 263 removed outlier: 3.599A pdb=" N GLU e 240 " --> pdb=" O ASP e 236 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA e 242 " --> pdb=" O ALA e 238 " (cutoff:3.500A) Processing helix chain 'e' and resid 264 through 272 removed outlier: 3.777A pdb=" N ILE e 268 " --> pdb=" O SER e 265 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER e 270 " --> pdb=" O SER e 267 " (cutoff:3.500A) Processing helix chain 'f' and resid 9 through 36 Processing helix chain 'f' and resid 45 through 61 Processing helix chain 'f' and resid 61 through 102 removed outlier: 4.218A pdb=" N VAL f 65 " --> pdb=" O SER f 61 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASP f 102 " --> pdb=" O LEU f 98 " (cutoff:3.500A) Processing helix chain 'f' and resid 106 through 130 Processing helix chain 'f' and resid 179 through 234 removed outlier: 4.008A pdb=" N GLY f 188 " --> pdb=" O LYS f 184 " (cutoff:3.500A) Processing helix chain 'f' and resid 236 through 263 removed outlier: 3.805A pdb=" N GLU f 240 " --> pdb=" O ASP f 236 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA f 242 " --> pdb=" O ALA f 238 " (cutoff:3.500A) Processing helix chain 'f' and resid 264 through 272 removed outlier: 3.783A pdb=" N ILE f 268 " --> pdb=" O SER f 265 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER f 270 " --> pdb=" O SER f 267 " (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: 4.220A 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 179 through 234 removed outlier: 4.085A pdb=" N GLY g 188 " --> pdb=" O LYS g 184 " (cutoff:3.500A) Processing helix chain 'g' and resid 236 through 263 removed outlier: 3.523A pdb=" N GLU g 240 " --> pdb=" O ASP g 236 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA g 242 " --> pdb=" O ALA g 238 " (cutoff:3.500A) Processing helix chain 'g' and resid 264 through 272 removed outlier: 3.833A pdb=" N ILE g 268 " --> pdb=" O SER g 265 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER g 270 " --> pdb=" O SER g 267 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE g 272 " --> pdb=" O LEU g 269 " (cutoff:3.500A) Processing helix chain 'h' and resid 9 through 36 removed outlier: 3.563A pdb=" N LEU h 13 " --> pdb=" O ASN h 9 " (cutoff:3.500A) Processing helix chain 'h' and resid 45 through 61 Processing helix chain 'h' and resid 61 through 101 removed outlier: 4.146A 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 179 through 234 removed outlier: 3.994A pdb=" N GLY h 188 " --> pdb=" O LYS h 184 " (cutoff:3.500A) Processing helix chain 'h' and resid 236 through 263 removed outlier: 3.550A pdb=" N GLU h 240 " --> pdb=" O ASP h 236 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA h 242 " --> pdb=" O ALA h 238 " (cutoff:3.500A) Processing helix chain 'h' and resid 264 through 270 removed outlier: 3.502A pdb=" N SER h 267 " --> pdb=" O SER h 264 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE h 268 " --> pdb=" O SER h 265 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER h 270 " --> pdb=" O SER h 267 " (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: 4.143A 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: 3.754A pdb=" N GLY i 188 " --> pdb=" O LYS i 184 " (cutoff:3.500A) Processing helix chain 'i' and resid 236 through 264 removed outlier: 3.592A pdb=" N GLU i 240 " --> pdb=" O ASP i 236 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA i 242 " --> pdb=" O ALA i 238 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N SER i 264 " --> pdb=" O ILE i 260 " (cutoff:3.500A) Processing helix chain 'i' and resid 265 through 272 removed outlier: 3.756A pdb=" N ILE i 268 " --> pdb=" O SER i 265 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER i 270 " --> pdb=" O SER i 267 " (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 101 removed outlier: 4.125A 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 179 through 234 removed outlier: 3.996A pdb=" N GLY j 188 " --> pdb=" O LYS j 184 " (cutoff:3.500A) Processing helix chain 'j' and resid 236 through 263 removed outlier: 3.538A pdb=" N GLU j 240 " --> pdb=" O ASP j 236 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA j 242 " --> pdb=" O ALA j 238 " (cutoff:3.500A) Processing helix chain 'j' and resid 264 through 272 removed outlier: 3.770A pdb=" N ILE j 268 " --> pdb=" O SER j 265 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER j 270 " --> pdb=" O SER j 267 " (cutoff:3.500A) Processing helix chain 'k' and resid 9 through 36 Processing helix chain 'k' and resid 45 through 61 Processing helix chain 'k' and resid 61 through 101 removed outlier: 4.176A pdb=" N VAL k 65 " --> pdb=" O SER k 61 " (cutoff:3.500A) Processing helix chain 'k' and resid 106 through 130 Processing helix chain 'k' and resid 179 through 234 removed outlier: 4.085A pdb=" N GLY k 188 " --> pdb=" O LYS k 184 " (cutoff:3.500A) Processing helix chain 'k' and resid 236 through 263 removed outlier: 3.982A pdb=" N ALA k 242 " --> pdb=" O ALA k 238 " (cutoff:3.500A) Processing helix chain 'k' and resid 264 through 272 removed outlier: 3.757A pdb=" N ILE k 268 " --> pdb=" O SER k 265 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER k 270 " --> pdb=" O SER k 267 " (cutoff:3.500A) Processing helix chain 'l' and resid 9 through 36 Processing helix chain 'l' and resid 45 through 61 Processing helix chain 'l' and resid 61 through 101 removed outlier: 4.124A 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: 3.989A pdb=" N GLY l 188 " --> pdb=" O LYS l 184 " (cutoff:3.500A) Processing helix chain 'l' and resid 236 through 263 removed outlier: 3.519A pdb=" N GLU l 240 " --> pdb=" O ASP l 236 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA l 242 " --> pdb=" O ALA l 238 " (cutoff:3.500A) Processing helix chain 'l' and resid 264 through 272 removed outlier: 3.824A pdb=" N ILE l 268 " --> pdb=" O SER l 265 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 145 through 149 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 146 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 Processing sheet with id=AA7, first strand: chain 'G' and resid 145 through 146 Processing sheet with id=AA8, first strand: chain 'H' and resid 145 through 146 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 149 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 'N' and resid 145 through 146 Processing sheet with id=AB6, first strand: chain 'O' and resid 145 through 149 Processing sheet with id=AB7, first strand: chain 'P' 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 146 Processing sheet with id=AC1, first strand: chain 'S' and resid 145 through 149 Processing sheet with id=AC2, first strand: chain 'T' and resid 145 through 146 Processing sheet with id=AC3, first strand: chain 'U' and resid 145 through 149 Processing sheet with id=AC4, first strand: chain 'V' and resid 145 through 149 removed outlier: 3.537A pdb=" N PHE V 148 " --> pdb=" O PHE V 157 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'W' and resid 145 through 146 Processing sheet with id=AC6, first strand: chain 'X' and resid 145 through 146 Processing sheet with id=AC7, first strand: chain 'Y' and resid 148 through 149 Processing sheet with id=AC8, first strand: chain 'Z' and resid 145 through 146 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 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 'g' and resid 145 through 146 Processing sheet with id=AD7, first strand: chain 'h' and resid 145 through 146 Processing sheet with id=AD8, first strand: chain 'i' and resid 145 through 149 Processing sheet with id=AD9, first strand: chain 'j' and resid 145 through 146 Processing sheet with id=AE1, first strand: chain 'k' and resid 145 through 149 Processing sheet with id=AE2, first strand: chain 'l' and resid 145 through 149 6565 hydrogen bonds defined for protein. 19359 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: 26.25 Time building geometry restraints manager: 16.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 16747 1.33 - 1.45: 13478 1.45 - 1.57: 43343 1.57 - 1.69: 0 1.69 - 1.81: 228 Bond restraints: 73796 Sorted by residual: bond pdb=" CG1 ILE X 124 " pdb=" CD1 ILE X 124 " ideal model delta sigma weight residual 1.513 1.447 0.066 3.90e-02 6.57e+02 2.85e+00 bond pdb=" N GLN T 17 " pdb=" CA GLN T 17 " ideal model delta sigma weight residual 1.459 1.479 -0.020 1.20e-02 6.94e+03 2.67e+00 bond pdb=" CG1 ILE a 190 " pdb=" CD1 ILE a 190 " ideal model delta sigma weight residual 1.513 1.453 0.060 3.90e-02 6.57e+02 2.40e+00 bond pdb=" CG1 ILE U 124 " pdb=" CD1 ILE U 124 " ideal model delta sigma weight residual 1.513 1.457 0.056 3.90e-02 6.57e+02 2.07e+00 bond pdb=" CG ASP X 77 " pdb=" OD1 ASP X 77 " ideal model delta sigma weight residual 1.249 1.222 0.027 1.90e-02 2.77e+03 1.99e+00 ... (remaining 73791 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 98643 2.24 - 4.48: 1066 4.48 - 6.72: 131 6.72 - 8.96: 20 8.96 - 11.21: 4 Bond angle restraints: 99864 Sorted by residual: angle pdb=" CB MET U 93 " pdb=" CG MET U 93 " pdb=" SD MET U 93 " ideal model delta sigma weight residual 112.70 101.49 11.21 3.00e+00 1.11e-01 1.40e+01 angle pdb=" CA MET U 93 " pdb=" CB MET U 93 " pdb=" CG MET U 93 " ideal model delta sigma weight residual 114.10 121.44 -7.34 2.00e+00 2.50e-01 1.35e+01 angle pdb=" C ASP K 122 " pdb=" N GLN K 123 " pdb=" CA GLN K 123 " ideal model delta sigma weight residual 121.58 114.63 6.95 1.95e+00 2.63e-01 1.27e+01 angle pdb=" CB MET d 93 " pdb=" CG MET d 93 " pdb=" SD MET d 93 " ideal model delta sigma weight residual 112.70 102.32 10.38 3.00e+00 1.11e-01 1.20e+01 angle pdb=" N GLN I 31 " pdb=" CA GLN I 31 " pdb=" CB GLN I 31 " ideal model delta sigma weight residual 110.16 115.14 -4.98 1.48e+00 4.57e-01 1.13e+01 ... (remaining 99859 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 41810 18.00 - 35.99: 2566 35.99 - 53.99: 355 53.99 - 71.99: 98 71.99 - 89.98: 87 Dihedral angle restraints: 44916 sinusoidal: 15770 harmonic: 29146 Sorted by residual: dihedral pdb=" CA GLN i 263 " pdb=" C GLN i 263 " pdb=" N SER i 264 " pdb=" CA SER i 264 " ideal model delta harmonic sigma weight residual -180.00 -159.58 -20.42 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA ASN Z 45 " pdb=" C ASN Z 45 " pdb=" N GLY Z 46 " pdb=" CA GLY Z 46 " ideal model delta harmonic sigma weight residual -180.00 -160.78 -19.22 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA GLN k 263 " pdb=" C GLN k 263 " pdb=" N SER k 264 " pdb=" CA SER k 264 " ideal model delta harmonic sigma weight residual -180.00 -160.84 -19.16 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 44913 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 11201 0.055 - 0.109: 1474 0.109 - 0.164: 162 0.164 - 0.218: 6 0.218 - 0.273: 1 Chirality restraints: 12844 Sorted by residual: chirality pdb=" CA GLN T 17 " pdb=" N GLN T 17 " pdb=" C GLN T 17 " pdb=" CB GLN T 17 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CG LEU I 26 " pdb=" CB LEU I 26 " pdb=" CD1 LEU I 26 " pdb=" CD2 LEU I 26 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 8.44e-01 chirality pdb=" CB ILE K 124 " pdb=" CA ILE K 124 " pdb=" CG1 ILE K 124 " pdb=" CG2 ILE K 124 " 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 12841 not shown) Planarity restraints: 12768 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG i 121 " -0.179 9.50e-02 1.11e+02 8.04e-02 4.32e+00 pdb=" NE ARG i 121 " 0.014 2.00e-02 2.50e+03 pdb=" CZ ARG i 121 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG i 121 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG i 121 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN L 134 " -0.010 2.00e-02 2.50e+03 1.96e-02 3.84e+00 pdb=" C ASN L 134 " 0.034 2.00e-02 2.50e+03 pdb=" O ASN L 134 " -0.013 2.00e-02 2.50e+03 pdb=" N GLY L 135 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN Z 134 " -0.008 2.00e-02 2.50e+03 1.68e-02 2.82e+00 pdb=" C ASN Z 134 " 0.029 2.00e-02 2.50e+03 pdb=" O ASN Z 134 " -0.011 2.00e-02 2.50e+03 pdb=" N GLY Z 135 " -0.010 2.00e-02 2.50e+03 ... (remaining 12765 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 1004 2.68 - 3.23: 76687 3.23 - 3.79: 117309 3.79 - 4.34: 154482 4.34 - 4.90: 255402 Nonbonded interactions: 604884 Sorted by model distance: nonbonded pdb=" OG SER A 5 " pdb=" OD2 ASP B 234 " model vdw 2.121 3.040 nonbonded pdb=" NH1 ARG D 121 " pdb=" O ALA D 173 " model vdw 2.141 3.120 nonbonded pdb=" O GLN J 31 " pdb=" OG1 THR J 35 " model vdw 2.145 3.040 nonbonded pdb=" NE2 GLN P 73 " pdb=" OD1 ASP P 212 " model vdw 2.156 3.120 nonbonded pdb=" OG1 THR K 206 " pdb=" OD1 ASP N 116 " model vdw 2.158 3.040 ... (remaining 604879 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 10.840 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: 0.060 Extract box with map and model: 2.450 Check model and map are aligned: 0.440 Set scattering table: 0.540 Process input model: 126.380 Find NCS groups from input model: 2.860 Set up NCS constraints: 0.630 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 154.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 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 0.066 73796 Z= 0.202 Angle : 0.650 11.205 99864 Z= 0.378 Chirality : 0.036 0.273 12844 Planarity : 0.004 0.080 12768 Dihedral : 12.758 89.981 25992 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.70 % Favored : 98.16 % Rotamer: Outliers : 0.03 % Allowed : 0.29 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.07), residues: 10184 helix: 0.11 (0.04), residues: 7524 sheet: -3.76 (0.18), residues: 380 loop : 1.28 (0.15), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP a 49 HIS 0.004 0.001 HIS h 214 PHE 0.028 0.002 PHE g 117 ARG 0.012 0.001 ARG d 121 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20368 Ramachandran restraints generated. 10184 Oldfield, 0 Emsley, 10184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20368 Ramachandran restraints generated. 10184 Oldfield, 0 Emsley, 10184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1062 residues out of total 7980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1060 time to evaluate : 6.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.8341 (mt-10) cc_final: 0.8108 (mt-10) REVERT: I 84 ASP cc_start: 0.6876 (m-30) cc_final: 0.6628 (m-30) REVERT: J 84 ASP cc_start: 0.8250 (m-30) cc_final: 0.7853 (m-30) REVERT: K 93 MET cc_start: 0.7220 (mtp) cc_final: 0.6939 (mtp) REVERT: L 4 ASN cc_start: 0.6630 (t0) cc_final: 0.6236 (t0) REVERT: M 38 LYS cc_start: 0.8046 (tptt) cc_final: 0.7797 (tptp) REVERT: N 208 SER cc_start: 0.8246 (t) cc_final: 0.7968 (p) REVERT: P 77 ASP cc_start: 0.8035 (m-30) cc_final: 0.7822 (m-30) REVERT: P 130 ASN cc_start: 0.7792 (m110) cc_final: 0.7458 (m110) REVERT: Q 126 LYS cc_start: 0.7765 (ttmt) cc_final: 0.7281 (tttt) REVERT: R 240 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7431 (mm-30) REVERT: T 77 ASP cc_start: 0.7397 (m-30) cc_final: 0.7193 (m-30) REVERT: T 151 ASN cc_start: 0.8432 (t0) cc_final: 0.8200 (t0) REVERT: U 124 ILE cc_start: 0.7722 (mt) cc_final: 0.7448 (mt) REVERT: V 130 ASN cc_start: 0.7620 (m110) cc_final: 0.7168 (m110) REVERT: X 62 MET cc_start: 0.9099 (mmt) cc_final: 0.8893 (mmt) REVERT: b 29 VAL cc_start: 0.8099 (t) cc_final: 0.7822 (p) REVERT: f 28 GLN cc_start: 0.8195 (mm110) cc_final: 0.7989 (mp10) REVERT: g 67 ASP cc_start: 0.8175 (m-30) cc_final: 0.7959 (m-30) REVERT: h 88 ASP cc_start: 0.8461 (m-30) cc_final: 0.8181 (m-30) REVERT: i 252 GLN cc_start: 0.8514 (mm110) cc_final: 0.8232 (mm-40) REVERT: k 140 ASP cc_start: 0.8043 (t0) cc_final: 0.7606 (m-30) REVERT: l 77 ASP cc_start: 0.7942 (m-30) cc_final: 0.7722 (m-30) outliers start: 2 outliers final: 1 residues processed: 1062 average time/residue: 1.4459 time to fit residues: 2048.2524 Evaluate side-chains 586 residues out of total 7980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 585 time to evaluate : 6.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 186 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1026 random chunks: chunk 866 optimal weight: 3.9990 chunk 777 optimal weight: 4.9990 chunk 431 optimal weight: 9.9990 chunk 265 optimal weight: 2.9990 chunk 524 optimal weight: 2.9990 chunk 415 optimal weight: 0.6980 chunk 804 optimal weight: 0.6980 chunk 311 optimal weight: 0.0870 chunk 488 optimal weight: 9.9990 chunk 598 optimal weight: 0.8980 chunk 931 optimal weight: 7.9990 overall best weight: 1.0760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 ASN B 18 ASN B 30 GLN C 28 GLN C 130 ASN C 134 ASN D 231 ASN E 30 GLN F 134 ASN ** G 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 251 GLN H 45 ASN H 123 GLN I 28 GLN I 34 ASN I 45 ASN I 54 ASN I 252 GLN J 23 ASN J 28 GLN J 263 GLN L 263 GLN M 28 GLN M 54 ASN N 45 ASN N 54 ASN ** N 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 20 ASN O 23 ASN ** O 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 123 GLN O 151 ASN O 251 GLN P 111 ASN P 123 GLN ** P 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 252 GLN Q 256 GLN R 106 ASN R 248 GLN R 262 ASN S 7 ASN ** S 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 31 GLN ** S 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 17 GLN T 30 GLN T 54 ASN ** U 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 151 ASN U 263 GLN V 123 GLN V 231 ASN ** W 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 134 ASN W 151 ASN W 263 GLN X 28 GLN X 73 GLN Y 7 ASN Y 123 GLN Z 63 ASN a 4 ASN ** a 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 7 ASN b 130 ASN c 18 ASN c 28 GLN c 30 GLN c 123 GLN d 18 ASN d 28 GLN d 30 GLN d 130 ASN d 263 GLN e 18 ASN e 28 GLN f 73 GLN g 30 GLN g 263 GLN ** h 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 130 ASN i 195 GLN i 199 ASN j 256 GLN l 18 ASN Total number of N/Q/H flips: 76 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 73796 Z= 0.172 Angle : 0.480 11.437 99864 Z= 0.271 Chirality : 0.033 0.270 12844 Planarity : 0.003 0.033 12768 Dihedral : 3.934 37.941 10339 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Rotamer: Outliers : 2.03 % Allowed : 6.92 % Favored : 91.05 % 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: 3.70 (0.08), residues: 10184 helix: 3.06 (0.05), residues: 7334 sheet: -3.53 (0.18), residues: 380 loop : 1.67 (0.14), residues: 2470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP a 49 HIS 0.003 0.001 HIS h 214 PHE 0.027 0.002 PHE X 117 ARG 0.007 0.001 ARG a 121 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20368 Ramachandran restraints generated. 10184 Oldfield, 0 Emsley, 10184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20368 Ramachandran restraints generated. 10184 Oldfield, 0 Emsley, 10184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 847 residues out of total 7980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 685 time to evaluate : 6.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 252 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.8403 (mt0) REVERT: J 84 ASP cc_start: 0.8231 (m-30) cc_final: 0.7870 (m-30) REVERT: K 62 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.8255 (mtt) REVERT: L 56 SER cc_start: 0.8648 (OUTLIER) cc_final: 0.8366 (m) REVERT: O 151 ASN cc_start: 0.7945 (t0) cc_final: 0.7399 (t0) REVERT: P 77 ASP cc_start: 0.8044 (m-30) cc_final: 0.7831 (m-30) REVERT: Q 126 LYS cc_start: 0.7941 (ttmt) cc_final: 0.7351 (tttt) REVERT: Q 189 THR cc_start: 0.7944 (p) cc_final: 0.7630 (p) REVERT: R 240 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7447 (mm-30) REVERT: S 25 GLU cc_start: 0.7988 (mp0) cc_final: 0.7787 (mm-30) REVERT: S 62 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.7845 (mtp) REVERT: T 245 GLN cc_start: 0.7744 (mp10) cc_final: 0.7458 (mp10) REVERT: V 130 ASN cc_start: 0.7557 (m110) cc_final: 0.7194 (m110) REVERT: W 134 ASN cc_start: 0.8333 (OUTLIER) cc_final: 0.8070 (t0) REVERT: X 30 GLN cc_start: 0.7980 (mt0) cc_final: 0.7584 (tm-30) REVERT: X 164 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8223 (mp) REVERT: Y 263 GLN cc_start: 0.7689 (mt0) cc_final: 0.7249 (tp40) REVERT: Y 268 ILE cc_start: 0.8712 (pt) cc_final: 0.8454 (pt) REVERT: a 226 ASP cc_start: 0.8406 (m-30) cc_final: 0.8172 (m-30) REVERT: b 29 VAL cc_start: 0.8284 (t) cc_final: 0.8021 (p) REVERT: b 171 LEU cc_start: 0.8187 (tp) cc_final: 0.7955 (mt) REVERT: f 26 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8161 (tt) REVERT: g 67 ASP cc_start: 0.8222 (m-30) cc_final: 0.7987 (m-30) REVERT: h 88 ASP cc_start: 0.8446 (m-30) cc_final: 0.8143 (m-30) REVERT: i 252 GLN cc_start: 0.8493 (mm110) cc_final: 0.8235 (mm-40) REVERT: k 140 ASP cc_start: 0.8091 (t0) cc_final: 0.7716 (m-30) REVERT: l 77 ASP cc_start: 0.7996 (m-30) cc_final: 0.7761 (m-30) REVERT: l 256 GLN cc_start: 0.7859 (OUTLIER) cc_final: 0.7214 (tt0) outliers start: 162 outliers final: 49 residues processed: 804 average time/residue: 1.2547 time to fit residues: 1396.1051 Evaluate side-chains 608 residues out of total 7980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 551 time to evaluate : 6.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 256 GLN Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain F residue 155 SER Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain I residue 129 SER Chi-restraints excluded: chain I residue 185 THR Chi-restraints excluded: chain I residue 252 GLN Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain K residue 62 MET Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 208 SER Chi-restraints excluded: chain K residue 253 LEU Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain L residue 125 THR Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 191 ASP Chi-restraints excluded: chain L residue 268 ILE Chi-restraints excluded: chain M residue 269 LEU Chi-restraints excluded: chain N residue 138 ILE Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain S residue 62 MET Chi-restraints excluded: chain T residue 68 SER Chi-restraints excluded: chain U residue 268 ILE Chi-restraints excluded: chain V residue 256 GLN Chi-restraints excluded: chain W residue 31 GLN Chi-restraints excluded: chain W residue 134 ASN Chi-restraints excluded: chain X residue 147 SER Chi-restraints excluded: chain X residue 159 VAL Chi-restraints excluded: chain X residue 164 LEU Chi-restraints excluded: chain X residue 226 ASP Chi-restraints excluded: chain Y residue 26 LEU Chi-restraints excluded: chain Y residue 56 SER Chi-restraints excluded: chain Z residue 56 SER Chi-restraints excluded: chain Z residue 213 THR Chi-restraints excluded: chain a residue 17 GLN Chi-restraints excluded: chain d residue 95 GLU Chi-restraints excluded: chain d residue 152 SER Chi-restraints excluded: chain d residue 252 GLN Chi-restraints excluded: chain f residue 26 LEU Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 125 THR Chi-restraints excluded: chain f residue 172 THR Chi-restraints excluded: chain h residue 10 SER Chi-restraints excluded: chain i residue 3 LEU Chi-restraints excluded: chain j residue 84 ASP Chi-restraints excluded: chain k residue 256 GLN Chi-restraints excluded: chain l residue 256 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1026 random chunks: chunk 517 optimal weight: 5.9990 chunk 289 optimal weight: 1.9990 chunk 775 optimal weight: 0.9980 chunk 634 optimal weight: 10.0000 chunk 257 optimal weight: 5.9990 chunk 933 optimal weight: 7.9990 chunk 1008 optimal weight: 0.8980 chunk 831 optimal weight: 0.9990 chunk 925 optimal weight: 4.9990 chunk 318 optimal weight: 0.9990 chunk 748 optimal weight: 4.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 18 ASN D 195 GLN E 30 GLN F 20 ASN ** G 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 262 ASN H 123 GLN I 28 GLN I 34 ASN I 252 GLN J 28 GLN J 262 ASN L 28 GLN L 263 GLN M 28 GLN ** N 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 30 GLN P 123 GLN ** P 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 251 GLN Q 23 ASN Q 199 ASN S 45 ASN ** S 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 248 GLN U 263 GLN ** V 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 123 GLN ** W 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 263 GLN Z 31 GLN ** a 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 195 GLN c 7 ASN c 28 GLN e 45 ASN h 34 ASN h 256 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 73796 Z= 0.166 Angle : 0.440 10.992 99864 Z= 0.249 Chirality : 0.032 0.248 12844 Planarity : 0.002 0.029 12768 Dihedral : 3.724 17.698 10336 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 2.16 % Allowed : 8.51 % Favored : 89.34 % 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: 4.50 (0.08), residues: 10184 helix: 3.78 (0.05), residues: 7334 sheet: -3.26 (0.17), residues: 380 loop : 1.50 (0.14), residues: 2470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP a 49 HIS 0.003 0.001 HIS h 214 PHE 0.025 0.001 PHE X 117 ARG 0.006 0.000 ARG I 32 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20368 Ramachandran restraints generated. 10184 Oldfield, 0 Emsley, 10184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20368 Ramachandran restraints generated. 10184 Oldfield, 0 Emsley, 10184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 800 residues out of total 7980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 628 time to evaluate : 6.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 84 ASP cc_start: 0.8221 (m-30) cc_final: 0.7840 (m-30) REVERT: L 56 SER cc_start: 0.8623 (OUTLIER) cc_final: 0.8365 (m) REVERT: O 151 ASN cc_start: 0.7973 (t0) cc_final: 0.7553 (t0) REVERT: P 77 ASP cc_start: 0.8027 (m-30) cc_final: 0.7826 (m-30) REVERT: Q 126 LYS cc_start: 0.7987 (ttmt) cc_final: 0.7389 (tttt) REVERT: Q 189 THR cc_start: 0.7853 (p) cc_final: 0.7608 (p) REVERT: R 95 GLU cc_start: 0.8933 (tt0) cc_final: 0.8662 (tt0) REVERT: S 32 ARG cc_start: 0.8097 (ttp-110) cc_final: 0.7893 (ttm170) REVERT: S 45 ASN cc_start: 0.8651 (OUTLIER) cc_final: 0.8191 (t0) REVERT: S 62 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.7862 (mtp) REVERT: S 240 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.6833 (mp0) REVERT: T 93 MET cc_start: 0.8262 (mtt) cc_final: 0.7876 (mtt) REVERT: T 130 ASN cc_start: 0.7918 (m110) cc_final: 0.7588 (m-40) REVERT: T 245 GLN cc_start: 0.7785 (mp10) cc_final: 0.7391 (mp10) REVERT: V 130 ASN cc_start: 0.7548 (m110) cc_final: 0.7128 (m110) REVERT: X 30 GLN cc_start: 0.8024 (mt0) cc_final: 0.7612 (tm-30) REVERT: X 62 MET cc_start: 0.9029 (mmt) cc_final: 0.8814 (mmt) REVERT: Y 212 ASP cc_start: 0.8225 (OUTLIER) cc_final: 0.7907 (m-30) REVERT: Y 263 GLN cc_start: 0.7667 (mt0) cc_final: 0.7220 (tp40) REVERT: Y 268 ILE cc_start: 0.8670 (pt) cc_final: 0.8404 (pt) REVERT: Z 69 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7788 (mm) REVERT: a 94 LYS cc_start: 0.7671 (OUTLIER) cc_final: 0.7064 (tmmt) REVERT: b 29 VAL cc_start: 0.8359 (t) cc_final: 0.8108 (p) REVERT: b 30 GLN cc_start: 0.7740 (OUTLIER) cc_final: 0.7536 (tt0) REVERT: b 184 LYS cc_start: 0.5955 (tppt) cc_final: 0.5518 (tppt) REVERT: f 26 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8243 (tt) REVERT: g 67 ASP cc_start: 0.8291 (m-30) cc_final: 0.8038 (m-30) REVERT: h 88 ASP cc_start: 0.8442 (m-30) cc_final: 0.8143 (m-30) REVERT: h 263 GLN cc_start: 0.7596 (mt0) cc_final: 0.7186 (tt0) REVERT: i 252 GLN cc_start: 0.8499 (mm110) cc_final: 0.8257 (mm-40) REVERT: k 140 ASP cc_start: 0.8095 (t0) cc_final: 0.7724 (m-30) REVERT: l 77 ASP cc_start: 0.7993 (m-30) cc_final: 0.7743 (m-30) REVERT: l 256 GLN cc_start: 0.7788 (OUTLIER) cc_final: 0.7208 (tt0) outliers start: 172 outliers final: 69 residues processed: 757 average time/residue: 1.2364 time to fit residues: 1297.4276 Evaluate side-chains 631 residues out of total 7980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 552 time to evaluate : 6.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 256 GLN Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 268 ILE Chi-restraints excluded: chain F residue 155 SER Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 114 LYS Chi-restraints excluded: chain I residue 129 SER Chi-restraints excluded: chain I residue 185 THR Chi-restraints excluded: chain I residue 272 PHE Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain K residue 186 MET Chi-restraints excluded: chain K residue 208 SER Chi-restraints excluded: chain K residue 253 LEU Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain L residue 125 THR Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 191 ASP Chi-restraints excluded: chain L residue 268 ILE Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain P residue 269 LEU Chi-restraints excluded: chain R residue 35 THR Chi-restraints excluded: chain S residue 45 ASN Chi-restraints excluded: chain S residue 62 MET Chi-restraints excluded: chain S residue 240 GLU Chi-restraints excluded: chain U residue 194 LEU Chi-restraints excluded: chain U residue 268 ILE Chi-restraints excluded: chain V residue 253 LEU Chi-restraints excluded: chain V residue 256 GLN Chi-restraints excluded: chain V residue 269 LEU Chi-restraints excluded: chain W residue 31 GLN Chi-restraints excluded: chain W residue 232 LEU Chi-restraints excluded: chain X residue 147 SER Chi-restraints excluded: chain X residue 159 VAL Chi-restraints excluded: chain Y residue 26 LEU Chi-restraints excluded: chain Y residue 56 SER Chi-restraints excluded: chain Y residue 69 LEU Chi-restraints excluded: chain Y residue 212 ASP Chi-restraints excluded: chain Z residue 56 SER Chi-restraints excluded: chain Z residue 69 LEU Chi-restraints excluded: chain Z residue 147 SER Chi-restraints excluded: chain Z residue 213 THR Chi-restraints excluded: chain a residue 17 GLN Chi-restraints excluded: chain a residue 92 LYS Chi-restraints excluded: chain a residue 94 LYS Chi-restraints excluded: chain a residue 245 GLN Chi-restraints excluded: chain b residue 26 LEU Chi-restraints excluded: chain b residue 30 GLN Chi-restraints excluded: chain b residue 123 GLN Chi-restraints excluded: chain b residue 125 THR Chi-restraints excluded: chain d residue 5 SER Chi-restraints excluded: chain d residue 152 SER Chi-restraints excluded: chain e residue 114 LYS Chi-restraints excluded: chain e residue 126 LYS Chi-restraints excluded: chain f residue 26 LEU Chi-restraints excluded: chain f residue 28 GLN Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 125 THR Chi-restraints excluded: chain f residue 172 THR Chi-restraints excluded: chain g residue 267 SER Chi-restraints excluded: chain h residue 10 SER Chi-restraints excluded: chain i residue 3 LEU Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain j residue 84 ASP Chi-restraints excluded: chain l residue 198 THR Chi-restraints excluded: chain l residue 256 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1026 random chunks: chunk 922 optimal weight: 0.9990 chunk 701 optimal weight: 6.9990 chunk 484 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 445 optimal weight: 4.9990 chunk 626 optimal weight: 8.9990 chunk 936 optimal weight: 0.9980 chunk 991 optimal weight: 4.9990 chunk 489 optimal weight: 0.0570 chunk 887 optimal weight: 0.8980 chunk 267 optimal weight: 1.9990 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN B 4 ASN D 130 ASN D 195 GLN D 199 ASN E 30 GLN E 54 ASN F 4 ASN G 134 ASN H 123 GLN I 28 GLN I 55 GLN I 262 ASN K 123 GLN K 263 GLN L 263 GLN M 28 GLN N 262 ASN ** O 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 123 GLN ** P 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 123 GLN U 263 GLN ** V 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 123 GLN W 263 GLN ** a 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 28 GLN h 34 ASN i 262 ASN j 55 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 73796 Z= 0.137 Angle : 0.405 10.889 99864 Z= 0.232 Chirality : 0.031 0.214 12844 Planarity : 0.002 0.019 12768 Dihedral : 3.576 16.196 10336 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 2.02 % Allowed : 9.67 % Favored : 88.31 % 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: 4.81 (0.08), residues: 10184 helix: 4.09 (0.05), residues: 7296 sheet: -2.90 (0.18), residues: 380 loop : 1.34 (0.14), residues: 2508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP a 49 HIS 0.002 0.001 HIS h 214 PHE 0.023 0.001 PHE X 117 ARG 0.003 0.000 ARG a 121 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20368 Ramachandran restraints generated. 10184 Oldfield, 0 Emsley, 10184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20368 Ramachandran restraints generated. 10184 Oldfield, 0 Emsley, 10184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 834 residues out of total 7980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 673 time to evaluate : 6.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 5 SER cc_start: 0.8539 (t) cc_final: 0.8276 (p) REVERT: D 195 GLN cc_start: 0.7478 (OUTLIER) cc_final: 0.7157 (tt0) REVERT: F 67 ASP cc_start: 0.8206 (m-30) cc_final: 0.8003 (m-30) REVERT: J 84 ASP cc_start: 0.8075 (m-30) cc_final: 0.7799 (m-30) REVERT: L 186 MET cc_start: 0.7996 (tpp) cc_final: 0.7725 (tpp) REVERT: O 151 ASN cc_start: 0.7951 (t0) cc_final: 0.7513 (t0) REVERT: O 245 GLN cc_start: 0.6254 (pt0) cc_final: 0.5535 (tp40) REVERT: P 77 ASP cc_start: 0.7938 (m-30) cc_final: 0.7733 (m-30) REVERT: Q 126 LYS cc_start: 0.7999 (ttmt) cc_final: 0.7343 (tttt) REVERT: R 62 MET cc_start: 0.8596 (mtt) cc_final: 0.8292 (mtt) REVERT: R 95 GLU cc_start: 0.8866 (tt0) cc_final: 0.8619 (tt0) REVERT: R 191 ASP cc_start: 0.7630 (m-30) cc_final: 0.7421 (m-30) REVERT: R 240 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7561 (mm-30) REVERT: S 32 ARG cc_start: 0.8091 (ttp-110) cc_final: 0.7808 (ttm170) REVERT: S 62 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7780 (mtp) REVERT: T 130 ASN cc_start: 0.7828 (m110) cc_final: 0.7514 (m-40) REVERT: T 245 GLN cc_start: 0.7770 (mp10) cc_final: 0.7484 (mp10) REVERT: V 130 ASN cc_start: 0.7512 (m110) cc_final: 0.7053 (m110) REVERT: X 30 GLN cc_start: 0.7944 (mt0) cc_final: 0.7549 (tm-30) REVERT: X 84 ASP cc_start: 0.8278 (p0) cc_final: 0.7885 (m-30) REVERT: Y 212 ASP cc_start: 0.8197 (OUTLIER) cc_final: 0.7857 (m-30) REVERT: Y 263 GLN cc_start: 0.7651 (mt0) cc_final: 0.7259 (tp40) REVERT: Y 268 ILE cc_start: 0.8654 (pt) cc_final: 0.8362 (pt) REVERT: a 13 LEU cc_start: 0.7177 (mt) cc_final: 0.6911 (mt) REVERT: a 94 LYS cc_start: 0.7667 (OUTLIER) cc_final: 0.7030 (tmmt) REVERT: b 29 VAL cc_start: 0.8246 (t) cc_final: 0.8001 (p) REVERT: c 191 ASP cc_start: 0.8119 (t0) cc_final: 0.7808 (m-30) REVERT: f 26 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8292 (tt) REVERT: g 67 ASP cc_start: 0.8268 (m-30) cc_final: 0.8035 (m-30) REVERT: h 88 ASP cc_start: 0.8403 (m-30) cc_final: 0.8088 (m-30) REVERT: h 263 GLN cc_start: 0.7536 (mt0) cc_final: 0.7151 (tt0) REVERT: i 252 GLN cc_start: 0.8532 (mm110) cc_final: 0.8297 (mm-40) REVERT: j 62 MET cc_start: 0.8622 (mmt) cc_final: 0.8286 (mmt) REVERT: k 140 ASP cc_start: 0.8061 (t0) cc_final: 0.7677 (m-30) REVERT: k 251 GLN cc_start: 0.9131 (tt0) cc_final: 0.8889 (tt0) REVERT: l 77 ASP cc_start: 0.7913 (m-30) cc_final: 0.7667 (m-30) outliers start: 161 outliers final: 60 residues processed: 791 average time/residue: 1.2527 time to fit residues: 1376.8929 Evaluate side-chains 635 residues out of total 7980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 570 time to evaluate : 6.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain B residue 256 GLN Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 195 GLN Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 155 SER Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain I residue 129 SER Chi-restraints excluded: chain I residue 253 LEU Chi-restraints excluded: chain I residue 272 PHE Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 186 MET Chi-restraints excluded: chain K residue 208 SER Chi-restraints excluded: chain K residue 253 LEU Chi-restraints excluded: chain L residue 16 LEU Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain L residue 125 THR Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 191 ASP Chi-restraints excluded: chain M residue 263 GLN Chi-restraints excluded: chain M residue 269 LEU Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain O residue 149 LEU Chi-restraints excluded: chain P residue 269 LEU Chi-restraints excluded: chain R residue 5 SER Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain S residue 62 MET Chi-restraints excluded: chain U residue 194 LEU Chi-restraints excluded: chain U residue 268 ILE Chi-restraints excluded: chain V residue 109 SER Chi-restraints excluded: chain V residue 256 GLN Chi-restraints excluded: chain V residue 268 ILE Chi-restraints excluded: chain W residue 31 GLN Chi-restraints excluded: chain X residue 159 VAL Chi-restraints excluded: chain X residue 226 ASP Chi-restraints excluded: chain Y residue 56 SER Chi-restraints excluded: chain Y residue 69 LEU Chi-restraints excluded: chain Y residue 212 ASP Chi-restraints excluded: chain Z residue 56 SER Chi-restraints excluded: chain a residue 17 GLN Chi-restraints excluded: chain a residue 94 LYS Chi-restraints excluded: chain a residue 179 THR Chi-restraints excluded: chain a residue 245 GLN Chi-restraints excluded: chain a residue 270 SER Chi-restraints excluded: chain b residue 26 LEU Chi-restraints excluded: chain b residue 123 GLN Chi-restraints excluded: chain d residue 95 GLU Chi-restraints excluded: chain d residue 152 SER Chi-restraints excluded: chain d residue 174 THR Chi-restraints excluded: chain e residue 114 LYS Chi-restraints excluded: chain f residue 26 LEU Chi-restraints excluded: chain f residue 28 GLN Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 125 THR Chi-restraints excluded: chain f residue 172 THR Chi-restraints excluded: chain h residue 10 SER Chi-restraints excluded: chain i residue 3 LEU Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 119 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1026 random chunks: chunk 825 optimal weight: 6.9990 chunk 562 optimal weight: 2.9990 chunk 14 optimal weight: 8.9990 chunk 738 optimal weight: 1.9990 chunk 409 optimal weight: 1.9990 chunk 846 optimal weight: 0.6980 chunk 685 optimal weight: 8.9990 chunk 1 optimal weight: 0.8980 chunk 506 optimal weight: 0.9990 chunk 890 optimal weight: 10.0000 chunk 250 optimal weight: 6.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 GLN E 30 GLN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 262 ASN H 30 GLN H 123 GLN I 9 ASN I 28 GLN I 34 ASN K 263 GLN L 28 GLN L 263 GLN M 28 GLN O 18 ASN ** O 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 231 ASN P 31 GLN P 111 ASN P 123 GLN P 130 ASN ** P 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 262 ASN ** R 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 73 GLN ** S 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 151 ASN U 263 GLN ** V 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 123 GLN V 263 GLN W 263 GLN X 34 ASN Z 31 GLN ** a 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 111 ASN b 130 ASN c 28 GLN e 262 ASN e 263 GLN f 231 ASN h 34 ASN h 256 GLN j 30 GLN k 18 ASN k 130 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 73796 Z= 0.169 Angle : 0.431 11.510 99864 Z= 0.243 Chirality : 0.032 0.285 12844 Planarity : 0.002 0.024 12768 Dihedral : 3.577 15.249 10336 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 2.36 % Allowed : 10.16 % Favored : 87.48 % 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: 4.87 (0.08), residues: 10184 helix: 4.10 (0.05), residues: 7334 sheet: -2.65 (0.18), residues: 380 loop : 1.36 (0.14), residues: 2470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP a 49 HIS 0.004 0.001 HIS h 214 PHE 0.020 0.001 PHE X 117 ARG 0.004 0.000 ARG I 32 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20368 Ramachandran restraints generated. 10184 Oldfield, 0 Emsley, 10184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20368 Ramachandran restraints generated. 10184 Oldfield, 0 Emsley, 10184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 787 residues out of total 7980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 599 time to evaluate : 6.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 105 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8436 (mp) REVERT: B 263 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.7265 (mp10) REVERT: D 236 ASP cc_start: 0.6040 (OUTLIER) cc_final: 0.5515 (t70) REVERT: I 32 ARG cc_start: 0.8316 (mtm-85) cc_final: 0.8112 (ttp-170) REVERT: J 84 ASP cc_start: 0.8125 (m-30) cc_final: 0.7832 (m-30) REVERT: M 118 ASP cc_start: 0.6877 (OUTLIER) cc_final: 0.6480 (m-30) REVERT: O 151 ASN cc_start: 0.7975 (t0) cc_final: 0.7546 (t0) REVERT: P 77 ASP cc_start: 0.8016 (m-30) cc_final: 0.7809 (m-30) REVERT: Q 95 GLU cc_start: 0.5604 (OUTLIER) cc_final: 0.4317 (mp0) REVERT: Q 126 LYS cc_start: 0.8089 (ttmt) cc_final: 0.7339 (tttt) REVERT: R 62 MET cc_start: 0.8665 (mtt) cc_final: 0.8375 (mtt) REVERT: R 191 ASP cc_start: 0.7797 (m-30) cc_final: 0.7526 (m-30) REVERT: R 240 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7655 (mm-30) REVERT: S 32 ARG cc_start: 0.8142 (ttp-110) cc_final: 0.7905 (ttm170) REVERT: S 240 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.7060 (mp0) REVERT: T 245 GLN cc_start: 0.7789 (mp10) cc_final: 0.7441 (mp10) REVERT: V 130 ASN cc_start: 0.7585 (m110) cc_final: 0.7131 (m110) REVERT: X 30 GLN cc_start: 0.8095 (mt0) cc_final: 0.7715 (tm130) REVERT: X 84 ASP cc_start: 0.8321 (p0) cc_final: 0.7934 (m-30) REVERT: Y 26 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8312 (tp) REVERT: Y 212 ASP cc_start: 0.8200 (OUTLIER) cc_final: 0.7853 (m-30) REVERT: Y 263 GLN cc_start: 0.7758 (mt0) cc_final: 0.7345 (tp40) REVERT: Y 268 ILE cc_start: 0.8626 (pt) cc_final: 0.8363 (pt) REVERT: a 13 LEU cc_start: 0.7211 (mt) cc_final: 0.6953 (mt) REVERT: a 116 ASP cc_start: 0.6606 (m-30) cc_final: 0.6237 (m-30) REVERT: b 29 VAL cc_start: 0.8410 (t) cc_final: 0.8170 (p) REVERT: d 263 GLN cc_start: 0.7206 (OUTLIER) cc_final: 0.6855 (mp10) REVERT: f 26 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8282 (tt) REVERT: g 67 ASP cc_start: 0.8280 (m-30) cc_final: 0.8031 (m-30) REVERT: h 88 ASP cc_start: 0.8425 (m-30) cc_final: 0.8097 (m-30) REVERT: h 262 ASN cc_start: 0.7195 (m-40) cc_final: 0.6967 (m-40) REVERT: h 263 GLN cc_start: 0.7525 (mt0) cc_final: 0.7111 (tt0) REVERT: i 252 GLN cc_start: 0.8514 (mm110) cc_final: 0.8276 (mm-40) REVERT: k 140 ASP cc_start: 0.8091 (t0) cc_final: 0.7704 (m-30) REVERT: k 256 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.7710 (tt0) REVERT: l 77 ASP cc_start: 0.7999 (m-30) cc_final: 0.7796 (m-30) outliers start: 188 outliers final: 91 residues processed: 742 average time/residue: 1.2908 time to fit residues: 1322.4763 Evaluate side-chains 648 residues out of total 7980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 546 time to evaluate : 6.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain B residue 263 GLN Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 268 ILE Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 155 SER Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 38 LYS Chi-restraints excluded: chain I residue 129 SER Chi-restraints excluded: chain I residue 253 LEU Chi-restraints excluded: chain I residue 272 PHE Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 186 MET Chi-restraints excluded: chain K residue 208 SER Chi-restraints excluded: chain K residue 253 LEU Chi-restraints excluded: chain K residue 268 ILE Chi-restraints excluded: chain L residue 16 LEU Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain L residue 125 THR Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 191 ASP Chi-restraints excluded: chain L residue 268 ILE Chi-restraints excluded: chain M residue 118 ASP Chi-restraints excluded: chain M residue 263 GLN Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 179 THR Chi-restraints excluded: chain N residue 272 PHE Chi-restraints excluded: chain O residue 149 LEU Chi-restraints excluded: chain P residue 7 ASN Chi-restraints excluded: chain P residue 269 LEU Chi-restraints excluded: chain Q residue 95 GLU Chi-restraints excluded: chain R residue 5 SER Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain S residue 240 GLU Chi-restraints excluded: chain T residue 68 SER Chi-restraints excluded: chain U residue 194 LEU Chi-restraints excluded: chain U residue 268 ILE Chi-restraints excluded: chain V residue 69 LEU Chi-restraints excluded: chain V residue 109 SER Chi-restraints excluded: chain V residue 256 GLN Chi-restraints excluded: chain V residue 268 ILE Chi-restraints excluded: chain W residue 31 GLN Chi-restraints excluded: chain W residue 268 ILE Chi-restraints excluded: chain X residue 34 ASN Chi-restraints excluded: chain X residue 147 SER Chi-restraints excluded: chain X residue 159 VAL Chi-restraints excluded: chain Y residue 26 LEU Chi-restraints excluded: chain Y residue 56 SER Chi-restraints excluded: chain Y residue 69 LEU Chi-restraints excluded: chain Y residue 212 ASP Chi-restraints excluded: chain Z residue 56 SER Chi-restraints excluded: chain Z residue 69 LEU Chi-restraints excluded: chain Z residue 147 SER Chi-restraints excluded: chain Z residue 213 THR Chi-restraints excluded: chain a residue 17 GLN Chi-restraints excluded: chain a residue 84 ASP Chi-restraints excluded: chain a residue 179 THR Chi-restraints excluded: chain a residue 245 GLN Chi-restraints excluded: chain a residue 270 SER Chi-restraints excluded: chain b residue 26 LEU Chi-restraints excluded: chain b residue 84 ASP Chi-restraints excluded: chain b residue 123 GLN Chi-restraints excluded: chain b residue 125 THR Chi-restraints excluded: chain c residue 268 ILE Chi-restraints excluded: chain d residue 5 SER Chi-restraints excluded: chain d residue 95 GLU Chi-restraints excluded: chain d residue 152 SER Chi-restraints excluded: chain d residue 174 THR Chi-restraints excluded: chain d residue 263 GLN Chi-restraints excluded: chain e residue 114 LYS Chi-restraints excluded: chain e residue 165 THR Chi-restraints excluded: chain e residue 215 LEU Chi-restraints excluded: chain e residue 263 GLN Chi-restraints excluded: chain f residue 26 LEU Chi-restraints excluded: chain f residue 28 GLN Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 125 THR Chi-restraints excluded: chain f residue 172 THR Chi-restraints excluded: chain g residue 124 ILE Chi-restraints excluded: chain g residue 267 SER Chi-restraints excluded: chain h residue 10 SER Chi-restraints excluded: chain h residue 198 THR Chi-restraints excluded: chain i residue 3 LEU Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 119 SER Chi-restraints excluded: chain k residue 256 GLN Chi-restraints excluded: chain l residue 198 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1026 random chunks: chunk 333 optimal weight: 1.9990 chunk 893 optimal weight: 4.9990 chunk 196 optimal weight: 5.9990 chunk 582 optimal weight: 1.9990 chunk 244 optimal weight: 2.9990 chunk 992 optimal weight: 3.9990 chunk 824 optimal weight: 8.9990 chunk 459 optimal weight: 8.9990 chunk 82 optimal weight: 2.9990 chunk 328 optimal weight: 6.9990 chunk 521 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 ASN E 30 GLN G 20 ASN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 262 ASN H 30 GLN H 123 GLN I 28 GLN I 34 ASN K 263 GLN L 263 GLN M 28 GLN N 30 GLN N 31 GLN ** N 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 123 GLN ** P 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 231 ASN ** P 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 130 ASN ** R 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 73 GLN U 263 GLN ** V 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 123 GLN Z 31 GLN Z 199 ASN ** a 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 130 ASN b 195 GLN c 23 ASN c 28 GLN e 263 GLN f 130 ASN g 18 ASN h 34 ASN h 256 GLN j 28 GLN j 256 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 73796 Z= 0.260 Angle : 0.499 11.590 99864 Z= 0.278 Chirality : 0.035 0.314 12844 Planarity : 0.002 0.032 12768 Dihedral : 3.778 18.801 10336 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.46 % Allowed : 10.60 % Favored : 86.94 % 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 (0.08), residues: 10184 helix: 3.94 (0.05), residues: 7296 sheet: -2.92 (0.16), residues: 456 loop : 1.22 (0.14), residues: 2432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP a 49 HIS 0.005 0.002 HIS l 214 PHE 0.025 0.002 PHE X 117 ARG 0.004 0.000 ARG V 71 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20368 Ramachandran restraints generated. 10184 Oldfield, 0 Emsley, 10184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20368 Ramachandran restraints generated. 10184 Oldfield, 0 Emsley, 10184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 756 residues out of total 7980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 560 time to evaluate : 6.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 105 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8439 (mp) REVERT: B 263 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.7332 (mp10) REVERT: D 86 ILE cc_start: 0.8442 (mm) cc_final: 0.8166 (mt) REVERT: I 272 PHE cc_start: 0.7743 (OUTLIER) cc_final: 0.7520 (m-80) REVERT: J 84 ASP cc_start: 0.8329 (m-30) cc_final: 0.7942 (m-30) REVERT: K 4 ASN cc_start: 0.7276 (t0) cc_final: 0.7070 (t0) REVERT: L 186 MET cc_start: 0.8101 (tpp) cc_final: 0.7868 (tpp) REVERT: O 151 ASN cc_start: 0.7991 (t0) cc_final: 0.7522 (t0) REVERT: Q 95 GLU cc_start: 0.5514 (OUTLIER) cc_final: 0.4285 (mp0) REVERT: R 62 MET cc_start: 0.8820 (mtt) cc_final: 0.8484 (mtt) REVERT: R 240 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7474 (mm-30) REVERT: S 32 ARG cc_start: 0.8055 (ttp-110) cc_final: 0.7834 (ttp-170) REVERT: S 240 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7150 (mp0) REVERT: T 93 MET cc_start: 0.8307 (mtt) cc_final: 0.7922 (mtt) REVERT: T 245 GLN cc_start: 0.7858 (mp10) cc_final: 0.7410 (mp10) REVERT: V 130 ASN cc_start: 0.7771 (m110) cc_final: 0.7276 (m110) REVERT: X 30 GLN cc_start: 0.8037 (mt0) cc_final: 0.7723 (tm130) REVERT: X 84 ASP cc_start: 0.8379 (p0) cc_final: 0.7979 (m-30) REVERT: X 245 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.8404 (mt0) REVERT: Y 26 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8302 (tp) REVERT: Y 134 ASN cc_start: 0.8324 (t0) cc_final: 0.8106 (t0) REVERT: Y 263 GLN cc_start: 0.7882 (mt0) cc_final: 0.7418 (tp40) REVERT: Y 268 ILE cc_start: 0.8671 (OUTLIER) cc_final: 0.8444 (pt) REVERT: a 246 SER cc_start: 0.8410 (m) cc_final: 0.8133 (p) REVERT: b 29 VAL cc_start: 0.8608 (t) cc_final: 0.8386 (p) REVERT: e 114 LYS cc_start: 0.7771 (OUTLIER) cc_final: 0.7451 (mmmt) REVERT: f 26 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8227 (tt) REVERT: g 67 ASP cc_start: 0.8346 (m-30) cc_final: 0.8083 (m-30) REVERT: k 251 GLN cc_start: 0.9149 (tt0) cc_final: 0.8931 (tt0) REVERT: k 256 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7684 (tt0) REVERT: l 77 ASP cc_start: 0.8170 (m-30) cc_final: 0.7924 (m-30) outliers start: 196 outliers final: 101 residues processed: 708 average time/residue: 1.3389 time to fit residues: 1305.4340 Evaluate side-chains 624 residues out of total 7980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 512 time to evaluate : 6.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 256 GLN Chi-restraints excluded: chain B residue 263 GLN Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 268 ILE Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 155 SER Chi-restraints excluded: chain F residue 270 SER Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 38 LYS Chi-restraints excluded: chain I residue 129 SER Chi-restraints excluded: chain I residue 185 THR Chi-restraints excluded: chain I residue 253 LEU Chi-restraints excluded: chain I residue 272 PHE Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain K residue 186 MET Chi-restraints excluded: chain K residue 208 SER Chi-restraints excluded: chain K residue 253 LEU Chi-restraints excluded: chain K residue 268 ILE Chi-restraints excluded: chain L residue 6 ILE Chi-restraints excluded: chain L residue 16 LEU Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain L residue 125 THR Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 268 ILE Chi-restraints excluded: chain M residue 247 LEU Chi-restraints excluded: chain M residue 263 GLN Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 272 PHE Chi-restraints excluded: chain O residue 149 LEU Chi-restraints excluded: chain P residue 7 ASN Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain P residue 179 THR Chi-restraints excluded: chain Q residue 95 GLU Chi-restraints excluded: chain R residue 5 SER Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 35 THR Chi-restraints excluded: chain R residue 116 ASP Chi-restraints excluded: chain S residue 240 GLU Chi-restraints excluded: chain T residue 68 SER Chi-restraints excluded: chain U residue 194 LEU Chi-restraints excluded: chain U residue 268 ILE Chi-restraints excluded: chain V residue 69 LEU Chi-restraints excluded: chain V residue 109 SER Chi-restraints excluded: chain V residue 256 GLN Chi-restraints excluded: chain V residue 268 ILE Chi-restraints excluded: chain W residue 31 GLN Chi-restraints excluded: chain W residue 268 ILE Chi-restraints excluded: chain X residue 34 ASN Chi-restraints excluded: chain X residue 147 SER Chi-restraints excluded: chain X residue 159 VAL Chi-restraints excluded: chain X residue 245 GLN Chi-restraints excluded: chain Y residue 26 LEU Chi-restraints excluded: chain Y residue 56 SER Chi-restraints excluded: chain Y residue 69 LEU Chi-restraints excluded: chain Y residue 268 ILE Chi-restraints excluded: chain Z residue 56 SER Chi-restraints excluded: chain Z residue 69 LEU Chi-restraints excluded: chain Z residue 147 SER Chi-restraints excluded: chain Z residue 213 THR Chi-restraints excluded: chain a residue 17 GLN Chi-restraints excluded: chain a residue 55 GLN Chi-restraints excluded: chain a residue 84 ASP Chi-restraints excluded: chain a residue 179 THR Chi-restraints excluded: chain a residue 245 GLN Chi-restraints excluded: chain a residue 270 SER Chi-restraints excluded: chain b residue 26 LEU Chi-restraints excluded: chain b residue 123 GLN Chi-restraints excluded: chain b residue 125 THR Chi-restraints excluded: chain c residue 268 ILE Chi-restraints excluded: chain d residue 5 SER Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain d residue 95 GLU Chi-restraints excluded: chain d residue 152 SER Chi-restraints excluded: chain d residue 174 THR Chi-restraints excluded: chain d residue 252 GLN Chi-restraints excluded: chain e residue 98 LEU Chi-restraints excluded: chain e residue 114 LYS Chi-restraints excluded: chain e residue 165 THR Chi-restraints excluded: chain f residue 26 LEU Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 125 THR Chi-restraints excluded: chain f residue 172 THR Chi-restraints excluded: chain f residue 176 SER Chi-restraints excluded: chain g residue 124 ILE Chi-restraints excluded: chain g residue 267 SER Chi-restraints excluded: chain g residue 268 ILE Chi-restraints excluded: chain h residue 10 SER Chi-restraints excluded: chain h residue 198 THR Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 119 SER Chi-restraints excluded: chain j residue 268 ILE Chi-restraints excluded: chain k residue 256 GLN Chi-restraints excluded: chain l residue 198 THR Chi-restraints excluded: chain l residue 247 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1026 random chunks: chunk 957 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 565 optimal weight: 3.9990 chunk 724 optimal weight: 0.9980 chunk 561 optimal weight: 3.9990 chunk 835 optimal weight: 2.9990 chunk 554 optimal weight: 9.9990 chunk 988 optimal weight: 5.9990 chunk 618 optimal weight: 0.6980 chunk 602 optimal weight: 1.9990 chunk 456 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 30 GLN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 123 GLN I 28 GLN I 34 ASN K 18 ASN K 263 GLN M 28 GLN ** N 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 262 ASN P 123 GLN P 231 ASN ** P 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 134 ASN ** S 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 73 GLN U 263 GLN V 30 GLN ** V 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 31 GLN c 28 GLN h 34 ASN j 263 GLN l 256 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 73796 Z= 0.161 Angle : 0.428 12.255 99864 Z= 0.243 Chirality : 0.032 0.282 12844 Planarity : 0.002 0.020 12768 Dihedral : 3.601 15.613 10336 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 1.90 % Allowed : 11.50 % Favored : 86.59 % 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: 4.84 (0.08), residues: 10184 helix: 4.14 (0.05), residues: 7334 sheet: -2.74 (0.17), residues: 456 loop : 1.27 (0.15), residues: 2394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP a 49 HIS 0.003 0.001 HIS h 214 PHE 0.023 0.001 PHE X 117 ARG 0.004 0.000 ARG H 121 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20368 Ramachandran restraints generated. 10184 Oldfield, 0 Emsley, 10184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20368 Ramachandran restraints generated. 10184 Oldfield, 0 Emsley, 10184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 729 residues out of total 7980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 577 time to evaluate : 6.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 86 ILE cc_start: 0.8393 (mm) cc_final: 0.8162 (mt) REVERT: F 3 LEU cc_start: 0.6530 (OUTLIER) cc_final: 0.6224 (mt) REVERT: F 67 ASP cc_start: 0.8228 (m-30) cc_final: 0.8017 (m-30) REVERT: J 84 ASP cc_start: 0.8236 (m-30) cc_final: 0.7952 (m-30) REVERT: O 151 ASN cc_start: 0.8010 (t0) cc_final: 0.7617 (t0) REVERT: Q 95 GLU cc_start: 0.5513 (OUTLIER) cc_final: 0.4247 (mp0) REVERT: Q 126 LYS cc_start: 0.8145 (ttmt) cc_final: 0.7289 (tttt) REVERT: R 62 MET cc_start: 0.8724 (mtt) cc_final: 0.8461 (mtt) REVERT: R 240 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7590 (mm-30) REVERT: S 32 ARG cc_start: 0.8048 (ttp-110) cc_final: 0.7780 (ttm170) REVERT: T 245 GLN cc_start: 0.7808 (mp10) cc_final: 0.7388 (mp10) REVERT: V 130 ASN cc_start: 0.7563 (m110) cc_final: 0.7032 (m110) REVERT: V 269 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7440 (tp) REVERT: X 30 GLN cc_start: 0.8071 (mt0) cc_final: 0.7714 (tm130) REVERT: X 84 ASP cc_start: 0.8366 (p0) cc_final: 0.7870 (m-30) REVERT: X 124 ILE cc_start: 0.7421 (OUTLIER) cc_final: 0.7159 (mt) REVERT: Y 212 ASP cc_start: 0.8166 (m-30) cc_final: 0.7875 (m-30) REVERT: Y 263 GLN cc_start: 0.7723 (mt0) cc_final: 0.7348 (tp40) REVERT: Y 268 ILE cc_start: 0.8674 (pt) cc_final: 0.8408 (pt) REVERT: a 116 ASP cc_start: 0.6410 (m-30) cc_final: 0.6020 (m-30) REVERT: a 226 ASP cc_start: 0.8421 (m-30) cc_final: 0.8216 (m-30) REVERT: b 29 VAL cc_start: 0.8451 (t) cc_final: 0.8213 (p) REVERT: b 184 LYS cc_start: 0.6526 (tppt) cc_final: 0.6044 (tttt) REVERT: f 26 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8304 (tt) REVERT: f 31 GLN cc_start: 0.8259 (mt0) cc_final: 0.8040 (mt0) REVERT: g 67 ASP cc_start: 0.8264 (m-30) cc_final: 0.8006 (m-30) REVERT: h 88 ASP cc_start: 0.8518 (m-30) cc_final: 0.8193 (m-30) REVERT: h 263 GLN cc_start: 0.7643 (mt0) cc_final: 0.7251 (tt0) REVERT: i 252 GLN cc_start: 0.8556 (mm110) cc_final: 0.8330 (mm-40) REVERT: k 62 MET cc_start: 0.8808 (mmt) cc_final: 0.8496 (mtp) REVERT: k 140 ASP cc_start: 0.8113 (t0) cc_final: 0.7729 (m-30) REVERT: k 251 GLN cc_start: 0.9198 (tt0) cc_final: 0.8970 (tt0) REVERT: k 256 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7689 (tt0) REVERT: l 77 ASP cc_start: 0.8079 (m-30) cc_final: 0.7855 (m-30) outliers start: 152 outliers final: 90 residues processed: 704 average time/residue: 1.2806 time to fit residues: 1248.6636 Evaluate side-chains 630 residues out of total 7980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 534 time to evaluate : 6.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 256 GLN Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 268 ILE Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 155 SER Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain G residue 186 MET Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain I residue 129 SER Chi-restraints excluded: chain I residue 253 LEU Chi-restraints excluded: chain I residue 272 PHE Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain J residue 253 LEU Chi-restraints excluded: chain J residue 272 PHE Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 186 MET Chi-restraints excluded: chain K residue 208 SER Chi-restraints excluded: chain K residue 253 LEU Chi-restraints excluded: chain K residue 268 ILE Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain L residue 125 THR Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain M residue 247 LEU Chi-restraints excluded: chain M residue 263 GLN Chi-restraints excluded: chain M residue 268 ILE Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 272 PHE Chi-restraints excluded: chain O residue 149 LEU Chi-restraints excluded: chain P residue 179 THR Chi-restraints excluded: chain Q residue 95 GLU Chi-restraints excluded: chain Q residue 134 ASN Chi-restraints excluded: chain R residue 5 SER Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 116 ASP Chi-restraints excluded: chain T residue 68 SER Chi-restraints excluded: chain U residue 194 LEU Chi-restraints excluded: chain U residue 268 ILE Chi-restraints excluded: chain V residue 69 LEU Chi-restraints excluded: chain V residue 109 SER Chi-restraints excluded: chain V residue 256 GLN Chi-restraints excluded: chain V residue 268 ILE Chi-restraints excluded: chain V residue 269 LEU Chi-restraints excluded: chain W residue 31 GLN Chi-restraints excluded: chain W residue 268 ILE Chi-restraints excluded: chain X residue 34 ASN Chi-restraints excluded: chain X residue 124 ILE Chi-restraints excluded: chain X residue 147 SER Chi-restraints excluded: chain X residue 159 VAL Chi-restraints excluded: chain X residue 226 ASP Chi-restraints excluded: chain Y residue 56 SER Chi-restraints excluded: chain Y residue 69 LEU Chi-restraints excluded: chain Z residue 56 SER Chi-restraints excluded: chain Z residue 69 LEU Chi-restraints excluded: chain Z residue 147 SER Chi-restraints excluded: chain Z residue 213 THR Chi-restraints excluded: chain a residue 17 GLN Chi-restraints excluded: chain a residue 55 GLN Chi-restraints excluded: chain a residue 179 THR Chi-restraints excluded: chain a residue 245 GLN Chi-restraints excluded: chain a residue 270 SER Chi-restraints excluded: chain b residue 26 LEU Chi-restraints excluded: chain c residue 103 THR Chi-restraints excluded: chain c residue 268 ILE Chi-restraints excluded: chain d residue 5 SER Chi-restraints excluded: chain d residue 95 GLU Chi-restraints excluded: chain d residue 152 SER Chi-restraints excluded: chain d residue 174 THR Chi-restraints excluded: chain d residue 252 GLN Chi-restraints excluded: chain e residue 165 THR Chi-restraints excluded: chain e residue 215 LEU Chi-restraints excluded: chain f residue 26 LEU Chi-restraints excluded: chain f residue 28 GLN Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 125 THR Chi-restraints excluded: chain f residue 172 THR Chi-restraints excluded: chain f residue 174 THR Chi-restraints excluded: chain g residue 124 ILE Chi-restraints excluded: chain h residue 10 SER Chi-restraints excluded: chain h residue 198 THR Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 119 SER Chi-restraints excluded: chain k residue 174 THR Chi-restraints excluded: chain k residue 256 GLN Chi-restraints excluded: chain l residue 198 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1026 random chunks: chunk 611 optimal weight: 6.9990 chunk 394 optimal weight: 0.9980 chunk 590 optimal weight: 2.9990 chunk 297 optimal weight: 10.0000 chunk 194 optimal weight: 0.8980 chunk 191 optimal weight: 2.9990 chunk 628 optimal weight: 3.9990 chunk 673 optimal weight: 0.8980 chunk 488 optimal weight: 0.9990 chunk 92 optimal weight: 10.0000 chunk 777 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 GLN E 30 GLN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 262 ASN ** H 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 123 GLN I 28 GLN I 34 ASN K 263 GLN M 28 GLN ** O 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 123 GLN ** P 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 134 ASN R 251 GLN S 31 GLN ** S 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 263 GLN ** V 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 34 ASN Z 31 GLN Z 123 GLN b 130 ASN b 195 GLN c 28 GLN e 34 ASN h 256 GLN j 263 GLN l 256 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 73796 Z= 0.151 Angle : 0.423 12.734 99864 Z= 0.239 Chirality : 0.032 0.341 12844 Planarity : 0.002 0.024 12768 Dihedral : 3.525 15.373 10336 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 1.98 % Allowed : 11.77 % Favored : 86.25 % 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: 4.93 (0.08), residues: 10184 helix: 4.21 (0.05), residues: 7334 sheet: -2.59 (0.17), residues: 456 loop : 1.29 (0.15), residues: 2394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP a 49 HIS 0.003 0.001 HIS h 214 PHE 0.024 0.001 PHE L 117 ARG 0.005 0.000 ARG I 32 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20368 Ramachandran restraints generated. 10184 Oldfield, 0 Emsley, 10184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20368 Ramachandran restraints generated. 10184 Oldfield, 0 Emsley, 10184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 735 residues out of total 7980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 577 time to evaluate : 6.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 ASN cc_start: 0.8393 (OUTLIER) cc_final: 0.8101 (m-40) REVERT: F 3 LEU cc_start: 0.6523 (OUTLIER) cc_final: 0.6184 (mt) REVERT: F 67 ASP cc_start: 0.8237 (m-30) cc_final: 0.8018 (m-30) REVERT: G 191 ASP cc_start: 0.7946 (m-30) cc_final: 0.7728 (m-30) REVERT: J 84 ASP cc_start: 0.8149 (m-30) cc_final: 0.7853 (m-30) REVERT: O 151 ASN cc_start: 0.7999 (t0) cc_final: 0.7566 (t0) REVERT: Q 95 GLU cc_start: 0.5728 (OUTLIER) cc_final: 0.4414 (mp0) REVERT: Q 126 LYS cc_start: 0.8167 (ttmt) cc_final: 0.7344 (tttt) REVERT: R 95 GLU cc_start: 0.8843 (tt0) cc_final: 0.8588 (tt0) REVERT: R 240 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7558 (mm-30) REVERT: S 240 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7207 (mp0) REVERT: T 245 GLN cc_start: 0.7772 (mp10) cc_final: 0.7377 (mp10) REVERT: T 263 GLN cc_start: 0.8227 (mt0) cc_final: 0.7974 (mt0) REVERT: V 236 ASP cc_start: 0.7793 (t0) cc_final: 0.7417 (t70) REVERT: V 269 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7419 (tp) REVERT: X 30 GLN cc_start: 0.8118 (mt0) cc_final: 0.7706 (tm-30) REVERT: X 84 ASP cc_start: 0.8386 (p0) cc_final: 0.7823 (m-30) REVERT: X 124 ILE cc_start: 0.7417 (OUTLIER) cc_final: 0.7153 (mt) REVERT: Y 26 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8247 (tp) REVERT: Y 212 ASP cc_start: 0.8126 (m-30) cc_final: 0.7839 (m-30) REVERT: Y 263 GLN cc_start: 0.7690 (mt0) cc_final: 0.7374 (tp40) REVERT: Y 268 ILE cc_start: 0.8615 (pt) cc_final: 0.8371 (pt) REVERT: a 116 ASP cc_start: 0.6450 (m-30) cc_final: 0.6130 (m-30) REVERT: b 29 VAL cc_start: 0.8425 (t) cc_final: 0.8195 (p) REVERT: b 184 LYS cc_start: 0.6374 (tppt) cc_final: 0.5965 (tppt) REVERT: e 263 GLN cc_start: 0.7797 (OUTLIER) cc_final: 0.7036 (mp10) REVERT: f 26 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8303 (tt) REVERT: f 95 GLU cc_start: 0.7811 (tp30) cc_final: 0.7309 (mt-10) REVERT: g 67 ASP cc_start: 0.8241 (m-30) cc_final: 0.8004 (m-30) REVERT: h 88 ASP cc_start: 0.8465 (m-30) cc_final: 0.8147 (m-30) REVERT: h 263 GLN cc_start: 0.7550 (mt0) cc_final: 0.7165 (tt0) REVERT: i 252 GLN cc_start: 0.8552 (mm110) cc_final: 0.8328 (mm-40) REVERT: k 62 MET cc_start: 0.8752 (mmt) cc_final: 0.8457 (mtp) REVERT: k 140 ASP cc_start: 0.8075 (t0) cc_final: 0.7685 (m-30) REVERT: k 256 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7704 (tt0) REVERT: l 77 ASP cc_start: 0.8019 (m-30) cc_final: 0.7728 (m-30) outliers start: 158 outliers final: 92 residues processed: 706 average time/residue: 1.2377 time to fit residues: 1217.4833 Evaluate side-chains 648 residues out of total 7980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 546 time to evaluate : 6.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 256 GLN Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 268 ILE Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 155 SER Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain G residue 186 MET Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain I residue 129 SER Chi-restraints excluded: chain I residue 253 LEU Chi-restraints excluded: chain I residue 272 PHE Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain J residue 272 PHE Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 186 MET Chi-restraints excluded: chain K residue 208 SER Chi-restraints excluded: chain K residue 253 LEU Chi-restraints excluded: chain L residue 6 ILE Chi-restraints excluded: chain L residue 16 LEU Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain L residue 125 THR Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 268 ILE Chi-restraints excluded: chain M residue 247 LEU Chi-restraints excluded: chain M residue 263 GLN Chi-restraints excluded: chain N residue 28 GLN Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 272 PHE Chi-restraints excluded: chain O residue 149 LEU Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain P residue 179 THR Chi-restraints excluded: chain Q residue 95 GLU Chi-restraints excluded: chain Q residue 134 ASN Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 116 ASP Chi-restraints excluded: chain S residue 240 GLU Chi-restraints excluded: chain T residue 68 SER Chi-restraints excluded: chain U residue 194 LEU Chi-restraints excluded: chain U residue 268 ILE Chi-restraints excluded: chain V residue 69 LEU Chi-restraints excluded: chain V residue 109 SER Chi-restraints excluded: chain V residue 256 GLN Chi-restraints excluded: chain V residue 268 ILE Chi-restraints excluded: chain V residue 269 LEU Chi-restraints excluded: chain W residue 31 GLN Chi-restraints excluded: chain W residue 268 ILE Chi-restraints excluded: chain X residue 34 ASN Chi-restraints excluded: chain X residue 124 ILE Chi-restraints excluded: chain X residue 159 VAL Chi-restraints excluded: chain X residue 226 ASP Chi-restraints excluded: chain Y residue 26 LEU Chi-restraints excluded: chain Y residue 56 SER Chi-restraints excluded: chain Y residue 69 LEU Chi-restraints excluded: chain Z residue 56 SER Chi-restraints excluded: chain Z residue 69 LEU Chi-restraints excluded: chain Z residue 147 SER Chi-restraints excluded: chain Z residue 179 THR Chi-restraints excluded: chain Z residue 213 THR Chi-restraints excluded: chain a residue 17 GLN Chi-restraints excluded: chain a residue 55 GLN Chi-restraints excluded: chain a residue 179 THR Chi-restraints excluded: chain a residue 245 GLN Chi-restraints excluded: chain a residue 270 SER Chi-restraints excluded: chain b residue 26 LEU Chi-restraints excluded: chain b residue 143 THR Chi-restraints excluded: chain c residue 103 THR Chi-restraints excluded: chain c residue 268 ILE Chi-restraints excluded: chain d residue 5 SER Chi-restraints excluded: chain d residue 95 GLU Chi-restraints excluded: chain d residue 152 SER Chi-restraints excluded: chain d residue 174 THR Chi-restraints excluded: chain e residue 34 ASN Chi-restraints excluded: chain e residue 165 THR Chi-restraints excluded: chain e residue 215 LEU Chi-restraints excluded: chain e residue 263 GLN Chi-restraints excluded: chain f residue 26 LEU Chi-restraints excluded: chain f residue 28 GLN Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 125 THR Chi-restraints excluded: chain f residue 172 THR Chi-restraints excluded: chain f residue 174 THR Chi-restraints excluded: chain f residue 176 SER Chi-restraints excluded: chain g residue 124 ILE Chi-restraints excluded: chain g residue 267 SER Chi-restraints excluded: chain h residue 10 SER Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 119 SER Chi-restraints excluded: chain k residue 174 THR Chi-restraints excluded: chain k residue 256 GLN Chi-restraints excluded: chain l residue 198 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1026 random chunks: chunk 899 optimal weight: 1.9990 chunk 947 optimal weight: 0.9980 chunk 864 optimal weight: 8.9990 chunk 921 optimal weight: 4.9990 chunk 554 optimal weight: 5.9990 chunk 401 optimal weight: 0.6980 chunk 723 optimal weight: 5.9990 chunk 282 optimal weight: 8.9990 chunk 832 optimal weight: 6.9990 chunk 871 optimal weight: 4.9990 chunk 918 optimal weight: 9.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 30 GLN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 20 ASN ** H 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 123 GLN I 34 ASN K 263 GLN L 151 ASN M 28 GLN N 31 GLN ** N 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 123 GLN P 231 ASN ** P 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 73 GLN U 263 GLN ** V 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 123 GLN W 263 GLN b 195 GLN c 28 GLN c 263 GLN e 34 ASN h 34 ASN h 256 GLN j 263 GLN l 130 ASN l 256 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 73796 Z= 0.272 Angle : 0.515 12.318 99864 Z= 0.285 Chirality : 0.036 0.370 12844 Planarity : 0.002 0.032 12768 Dihedral : 3.768 17.763 10336 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.89 % Allowed : 11.99 % Favored : 86.12 % 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: 4.50 (0.08), residues: 10184 helix: 3.90 (0.05), residues: 7334 sheet: -2.65 (0.17), residues: 456 loop : 1.11 (0.14), residues: 2394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP a 49 HIS 0.005 0.002 HIS l 214 PHE 0.024 0.002 PHE X 117 ARG 0.007 0.000 ARG I 32 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20368 Ramachandran restraints generated. 10184 Oldfield, 0 Emsley, 10184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20368 Ramachandran restraints generated. 10184 Oldfield, 0 Emsley, 10184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 7980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 537 time to evaluate : 6.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 ASN cc_start: 0.8574 (OUTLIER) cc_final: 0.8271 (m-40) REVERT: B 263 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.7326 (mp10) REVERT: H 114 LYS cc_start: 0.7016 (ptmm) cc_final: 0.6808 (mtpm) REVERT: I 272 PHE cc_start: 0.7655 (OUTLIER) cc_final: 0.7383 (m-80) REVERT: J 84 ASP cc_start: 0.8339 (m-30) cc_final: 0.7939 (m-30) REVERT: O 151 ASN cc_start: 0.8038 (t0) cc_final: 0.7542 (t0) REVERT: Q 95 GLU cc_start: 0.5711 (OUTLIER) cc_final: 0.4406 (mp0) REVERT: R 240 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7517 (mm-30) REVERT: S 240 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7067 (mp0) REVERT: T 245 GLN cc_start: 0.7858 (mp10) cc_final: 0.7419 (mp10) REVERT: X 30 GLN cc_start: 0.8043 (mt0) cc_final: 0.7767 (tm-30) REVERT: X 34 ASN cc_start: 0.8486 (OUTLIER) cc_final: 0.8210 (p0) REVERT: X 84 ASP cc_start: 0.8449 (p0) cc_final: 0.7979 (m-30) REVERT: X 245 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.8428 (mt0) REVERT: Y 26 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8247 (tp) REVERT: Y 134 ASN cc_start: 0.8287 (t0) cc_final: 0.8052 (t0) REVERT: a 55 GLN cc_start: 0.7447 (OUTLIER) cc_final: 0.6334 (mp10) REVERT: b 29 VAL cc_start: 0.8582 (t) cc_final: 0.8364 (p) REVERT: e 263 GLN cc_start: 0.8025 (OUTLIER) cc_final: 0.7727 (mp10) REVERT: f 26 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8232 (tt) REVERT: g 67 ASP cc_start: 0.8349 (m-30) cc_final: 0.8077 (m-30) REVERT: h 263 GLN cc_start: 0.7677 (mt0) cc_final: 0.7427 (mt0) REVERT: i 252 GLN cc_start: 0.8569 (mm110) cc_final: 0.8345 (mm-40) REVERT: k 256 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.7689 (tt0) REVERT: l 77 ASP cc_start: 0.8180 (m-30) cc_final: 0.7920 (m-30) outliers start: 151 outliers final: 94 residues processed: 660 average time/residue: 1.3251 time to fit residues: 1205.4362 Evaluate side-chains 621 residues out of total 7980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 515 time to evaluate : 6.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 256 GLN Chi-restraints excluded: chain B residue 263 GLN Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 268 ILE Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 155 SER Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain I residue 38 LYS Chi-restraints excluded: chain I residue 129 SER Chi-restraints excluded: chain I residue 185 THR Chi-restraints excluded: chain I residue 253 LEU Chi-restraints excluded: chain I residue 272 PHE Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain J residue 272 PHE Chi-restraints excluded: chain K residue 186 MET Chi-restraints excluded: chain K residue 208 SER Chi-restraints excluded: chain K residue 253 LEU Chi-restraints excluded: chain K residue 268 ILE Chi-restraints excluded: chain L residue 6 ILE Chi-restraints excluded: chain L residue 16 LEU Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain L residue 125 THR Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 268 ILE Chi-restraints excluded: chain M residue 247 LEU Chi-restraints excluded: chain M residue 263 GLN Chi-restraints excluded: chain N residue 28 GLN Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 272 PHE Chi-restraints excluded: chain O residue 149 LEU Chi-restraints excluded: chain P residue 7 ASN Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain P residue 179 THR Chi-restraints excluded: chain Q residue 95 GLU Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 116 ASP Chi-restraints excluded: chain S residue 240 GLU Chi-restraints excluded: chain T residue 68 SER Chi-restraints excluded: chain U residue 89 LEU Chi-restraints excluded: chain U residue 194 LEU Chi-restraints excluded: chain U residue 268 ILE Chi-restraints excluded: chain V residue 69 LEU Chi-restraints excluded: chain V residue 109 SER Chi-restraints excluded: chain V residue 256 GLN Chi-restraints excluded: chain V residue 268 ILE Chi-restraints excluded: chain W residue 31 GLN Chi-restraints excluded: chain W residue 268 ILE Chi-restraints excluded: chain X residue 34 ASN Chi-restraints excluded: chain X residue 159 VAL Chi-restraints excluded: chain X residue 245 GLN Chi-restraints excluded: chain Y residue 26 LEU Chi-restraints excluded: chain Y residue 56 SER Chi-restraints excluded: chain Y residue 69 LEU Chi-restraints excluded: chain Z residue 56 SER Chi-restraints excluded: chain Z residue 69 LEU Chi-restraints excluded: chain Z residue 147 SER Chi-restraints excluded: chain Z residue 179 THR Chi-restraints excluded: chain Z residue 213 THR Chi-restraints excluded: chain a residue 17 GLN Chi-restraints excluded: chain a residue 55 GLN Chi-restraints excluded: chain a residue 84 ASP Chi-restraints excluded: chain a residue 179 THR Chi-restraints excluded: chain a residue 245 GLN Chi-restraints excluded: chain a residue 270 SER Chi-restraints excluded: chain b residue 26 LEU Chi-restraints excluded: chain b residue 125 THR Chi-restraints excluded: chain b residue 143 THR Chi-restraints excluded: chain c residue 103 THR Chi-restraints excluded: chain c residue 268 ILE Chi-restraints excluded: chain d residue 5 SER Chi-restraints excluded: chain d residue 95 GLU Chi-restraints excluded: chain d residue 152 SER Chi-restraints excluded: chain d residue 174 THR Chi-restraints excluded: chain d residue 252 GLN Chi-restraints excluded: chain e residue 165 THR Chi-restraints excluded: chain e residue 263 GLN Chi-restraints excluded: chain f residue 26 LEU Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 125 THR Chi-restraints excluded: chain f residue 172 THR Chi-restraints excluded: chain f residue 174 THR Chi-restraints excluded: chain f residue 176 SER Chi-restraints excluded: chain g residue 124 ILE Chi-restraints excluded: chain g residue 267 SER Chi-restraints excluded: chain h residue 10 SER Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 119 SER Chi-restraints excluded: chain j residue 268 ILE Chi-restraints excluded: chain k residue 174 THR Chi-restraints excluded: chain k residue 256 GLN Chi-restraints excluded: chain l residue 198 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1026 random chunks: chunk 605 optimal weight: 1.9990 chunk 974 optimal weight: 0.9980 chunk 594 optimal weight: 9.9990 chunk 462 optimal weight: 5.9990 chunk 677 optimal weight: 1.9990 chunk 1022 optimal weight: 0.7980 chunk 940 optimal weight: 0.7980 chunk 813 optimal weight: 0.0870 chunk 84 optimal weight: 0.8980 chunk 628 optimal weight: 3.9990 chunk 499 optimal weight: 0.6980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 30 GLN E 30 GLN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 30 GLN ** H 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 123 GLN H 263 GLN I 34 ASN J 28 GLN K 263 GLN M 28 GLN ** O 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 123 GLN P 231 ASN ** P 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 134 ASN T 31 GLN T 73 GLN ** U 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 263 GLN ** V 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 263 GLN b 130 ASN b 195 GLN c 28 GLN e 34 ASN h 34 ASN h 256 GLN j 263 GLN l 256 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 73796 Z= 0.142 Angle : 0.425 12.601 99864 Z= 0.241 Chirality : 0.032 0.369 12844 Planarity : 0.002 0.022 12768 Dihedral : 3.530 15.114 10336 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 1.23 % Allowed : 12.68 % Favored : 86.09 % 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: 4.94 (0.08), residues: 10184 helix: 4.23 (0.05), residues: 7334 sheet: -2.47 (0.17), residues: 456 loop : 1.22 (0.15), residues: 2394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP a 49 HIS 0.002 0.001 HIS h 214 PHE 0.027 0.001 PHE N 117 ARG 0.005 0.000 ARG I 32 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20368 Ramachandran restraints generated. 10184 Oldfield, 0 Emsley, 10184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20368 Ramachandran restraints generated. 10184 Oldfield, 0 Emsley, 10184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 7980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 579 time to evaluate : 6.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 ASN cc_start: 0.8372 (OUTLIER) cc_final: 0.8091 (m-40) REVERT: D 236 ASP cc_start: 0.5879 (OUTLIER) cc_final: 0.5318 (t70) REVERT: F 3 LEU cc_start: 0.6445 (OUTLIER) cc_final: 0.6139 (mt) REVERT: G 191 ASP cc_start: 0.7933 (m-30) cc_final: 0.7697 (m-30) REVERT: O 151 ASN cc_start: 0.8019 (t0) cc_final: 0.7630 (t0) REVERT: Q 95 GLU cc_start: 0.5664 (OUTLIER) cc_final: 0.4362 (mp0) REVERT: Q 126 LYS cc_start: 0.8117 (ttmt) cc_final: 0.7384 (tttt) REVERT: Q 179 THR cc_start: 0.7771 (m) cc_final: 0.7457 (p) REVERT: R 95 GLU cc_start: 0.8828 (tt0) cc_final: 0.8574 (tt0) REVERT: R 116 ASP cc_start: 0.6887 (OUTLIER) cc_final: 0.6510 (t0) REVERT: R 190 ILE cc_start: 0.8889 (mm) cc_final: 0.8475 (mm) REVERT: R 240 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7560 (mm-30) REVERT: S 240 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7219 (mp0) REVERT: T 263 GLN cc_start: 0.8301 (mt0) cc_final: 0.8035 (mt0) REVERT: U 101 SER cc_start: 0.7657 (t) cc_final: 0.7318 (m) REVERT: X 30 GLN cc_start: 0.8107 (mt0) cc_final: 0.7703 (tm-30) REVERT: X 84 ASP cc_start: 0.8395 (p0) cc_final: 0.7779 (m-30) REVERT: X 124 ILE cc_start: 0.7408 (OUTLIER) cc_final: 0.7157 (mt) REVERT: Y 26 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8305 (tp) REVERT: Y 212 ASP cc_start: 0.8128 (m-30) cc_final: 0.7836 (m-30) REVERT: Y 268 ILE cc_start: 0.8599 (pt) cc_final: 0.8359 (pt) REVERT: a 116 ASP cc_start: 0.6295 (m-30) cc_final: 0.5911 (m-30) REVERT: b 29 VAL cc_start: 0.8352 (t) cc_final: 0.8119 (p) REVERT: e 263 GLN cc_start: 0.7740 (tp40) cc_final: 0.7036 (mp10) REVERT: f 31 GLN cc_start: 0.8197 (mt0) cc_final: 0.7959 (mt0) REVERT: f 95 GLU cc_start: 0.7802 (tp30) cc_final: 0.7234 (mt-10) REVERT: g 67 ASP cc_start: 0.8247 (m-30) cc_final: 0.7996 (m-30) REVERT: h 88 ASP cc_start: 0.8502 (m-30) cc_final: 0.8176 (m-30) REVERT: h 263 GLN cc_start: 0.7531 (mt0) cc_final: 0.7214 (tt0) REVERT: i 252 GLN cc_start: 0.8570 (mm110) cc_final: 0.8343 (mm-40) REVERT: k 62 MET cc_start: 0.8721 (mmt) cc_final: 0.8469 (mtp) REVERT: k 140 ASP cc_start: 0.8079 (t0) cc_final: 0.7705 (m-30) REVERT: k 256 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.7686 (tt0) REVERT: l 77 ASP cc_start: 0.7976 (m-30) cc_final: 0.7723 (m-30) REVERT: l 84 ASP cc_start: 0.7251 (m-30) cc_final: 0.6755 (m-30) outliers start: 98 outliers final: 63 residues processed: 657 average time/residue: 1.2881 time to fit residues: 1169.6963 Evaluate side-chains 615 residues out of total 7980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 543 time to evaluate : 6.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain B residue 256 GLN Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain I residue 185 THR Chi-restraints excluded: chain I residue 253 LEU Chi-restraints excluded: chain I residue 272 PHE Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 272 PHE Chi-restraints excluded: chain K residue 186 MET Chi-restraints excluded: chain K residue 208 SER Chi-restraints excluded: chain K residue 253 LEU Chi-restraints excluded: chain L residue 16 LEU Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain L residue 125 THR Chi-restraints excluded: chain M residue 263 GLN Chi-restraints excluded: chain N residue 28 GLN Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 272 PHE Chi-restraints excluded: chain O residue 149 LEU Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain P residue 179 THR Chi-restraints excluded: chain Q residue 95 GLU Chi-restraints excluded: chain Q residue 134 ASN Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 116 ASP Chi-restraints excluded: chain S residue 240 GLU Chi-restraints excluded: chain T residue 68 SER Chi-restraints excluded: chain U residue 194 LEU Chi-restraints excluded: chain U residue 268 ILE Chi-restraints excluded: chain V residue 69 LEU Chi-restraints excluded: chain V residue 256 GLN Chi-restraints excluded: chain V residue 268 ILE Chi-restraints excluded: chain W residue 31 GLN Chi-restraints excluded: chain X residue 34 ASN Chi-restraints excluded: chain X residue 124 ILE Chi-restraints excluded: chain X residue 159 VAL Chi-restraints excluded: chain X residue 226 ASP Chi-restraints excluded: chain Y residue 26 LEU Chi-restraints excluded: chain Y residue 56 SER Chi-restraints excluded: chain Y residue 69 LEU Chi-restraints excluded: chain Z residue 56 SER Chi-restraints excluded: chain Z residue 69 LEU Chi-restraints excluded: chain Z residue 147 SER Chi-restraints excluded: chain a residue 17 GLN Chi-restraints excluded: chain a residue 55 GLN Chi-restraints excluded: chain a residue 245 GLN Chi-restraints excluded: chain a residue 270 SER Chi-restraints excluded: chain b residue 26 LEU Chi-restraints excluded: chain d residue 95 GLU Chi-restraints excluded: chain d residue 174 THR Chi-restraints excluded: chain d residue 252 GLN Chi-restraints excluded: chain e residue 165 THR Chi-restraints excluded: chain f residue 28 GLN Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 174 THR Chi-restraints excluded: chain g residue 124 ILE Chi-restraints excluded: chain g residue 267 SER Chi-restraints excluded: chain h residue 10 SER Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain k residue 174 THR Chi-restraints excluded: chain k residue 256 GLN Chi-restraints excluded: chain l residue 198 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1026 random chunks: chunk 646 optimal weight: 0.8980 chunk 867 optimal weight: 2.9990 chunk 249 optimal weight: 3.9990 chunk 750 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 chunk 226 optimal weight: 5.9990 chunk 815 optimal weight: 0.6980 chunk 341 optimal weight: 5.9990 chunk 837 optimal weight: 7.9990 chunk 103 optimal weight: 0.9980 chunk 150 optimal weight: 9.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- 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** E 30 GLN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 123 GLN I 34 ASN J 28 GLN K 263 GLN L 31 GLN ** L 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 123 GLN ** P 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 134 ASN ** U 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 263 GLN ** V 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 263 GLN X 214 HIS b 130 ASN b 195 GLN c 28 GLN ** g 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 34 ASN h 256 GLN j 263 GLN l 256 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.119176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.103080 restraints weight = 110498.081| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.44 r_work: 0.3344 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.127 73796 Z= 0.183 Angle : 0.530 59.198 99864 Z= 0.298 Chirality : 0.033 0.548 12844 Planarity : 0.002 0.103 12768 Dihedral : 3.559 43.503 10336 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.01 % Allowed : 0.73 % Favored : 99.26 % Rotamer: Outliers : 1.28 % Allowed : 12.81 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 4.92 (0.08), residues: 10184 helix: 4.21 (0.05), residues: 7334 sheet: -2.44 (0.17), residues: 456 loop : 1.21 (0.15), residues: 2394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP a 49 HIS 0.002 0.001 HIS h 214 PHE 0.038 0.001 PHE Q 133 ARG 0.011 0.000 ARG U 121 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21941.85 seconds wall clock time: 379 minutes 52.36 seconds (22792.36 seconds total)