Starting phenix.real_space_refine on Sat Sep 28 09:30:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxj_42766/09_2024/8uxj_42766.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxj_42766/09_2024/8uxj_42766.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxj_42766/09_2024/8uxj_42766.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxj_42766/09_2024/8uxj_42766.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxj_42766/09_2024/8uxj_42766.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uxj_42766/09_2024/8uxj_42766.cif" } resolution = 2.71 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= 0.002 sd= 0.046 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 144 5.16 5 C 42768 2.51 5 N 12060 2.21 5 O 14724 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 280 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 69696 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "B" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "C" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "D" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "E" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "F" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "G" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "H" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "I" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "J" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "K" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "L" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "M" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "N" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "O" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "P" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "Q" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "R" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "S" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "T" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "U" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "V" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "W" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "X" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "Y" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "Z" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "a" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "b" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "c" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "d" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "e" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "f" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "h" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "i" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "j" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "g" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1936 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Time building chain proxies: 29.94, per 1000 atoms: 0.43 Number of scatterers: 69696 At special positions: 0 Unit cell: (140.112, 137.61, 330.264, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 144 16.00 O 14724 8.00 N 12060 7.00 C 42768 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.02 Conformation dependent library (CDL) restraints added in 7.5 seconds 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 18000 Finding SS restraints... Secondary structure from input PDB file: 284 helices and 34 sheets defined 76.8% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.48 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: 3.957A pdb=" N VAL A 65 " --> pdb=" O SER A 61 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ALA A 99 " --> pdb=" O GLU A 95 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA A 100 " --> pdb=" O LYS A 96 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER A 101 " --> pdb=" O ALA A 97 " (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: 3.901A pdb=" N GLY A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 262 removed outlier: 3.961A pdb=" N GLU A 240 " --> pdb=" O ASP A 236 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA A 242 " --> pdb=" O ALA A 238 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLN A 245 " --> pdb=" O SER A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 272 removed outlier: 3.989A pdb=" N SER A 267 " --> pdb=" O SER A 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 36 Processing helix chain 'B' and resid 45 through 61 Processing helix chain 'B' and resid 61 through 101 removed outlier: 4.051A pdb=" N VAL B 65 " --> pdb=" O SER B 61 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA B 99 " --> pdb=" O GLU B 95 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA B 100 " --> pdb=" O LYS B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 130 Processing helix chain 'B' and resid 179 through 234 removed outlier: 4.101A pdb=" N GLY B 188 " --> pdb=" O LYS B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 262 removed outlier: 3.519A pdb=" N GLU B 240 " --> pdb=" O ASP B 236 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA B 242 " --> pdb=" O ALA B 238 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN B 245 " --> pdb=" O SER B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 270 removed outlier: 4.165A pdb=" N LEU B 269 " --> pdb=" O SER B 265 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N SER B 270 " --> pdb=" O SER B 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 265 through 270' Processing helix chain 'C' and resid 9 through 36 Processing helix chain 'C' and resid 45 through 61 Processing helix chain 'C' and resid 62 through 101 Processing helix chain 'C' and resid 106 through 130 Processing helix chain 'C' and resid 179 through 234 removed outlier: 4.090A pdb=" N GLY C 188 " --> pdb=" O LYS C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 263 removed outlier: 3.556A pdb=" N GLU C 240 " --> pdb=" O ASP C 236 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA C 242 " --> pdb=" O ALA C 238 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLN C 245 " --> pdb=" O SER C 241 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN C 263 " --> pdb=" O SER C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 272 removed outlier: 3.547A pdb=" N SER C 267 " --> pdb=" O SER C 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 36 removed outlier: 4.224A pdb=" N MET 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: 4.053A 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: 3.999A pdb=" N GLY D 188 " --> pdb=" O LYS D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 263 removed outlier: 3.957A pdb=" N GLU D 240 " --> pdb=" O ASP D 236 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA D 242 " --> pdb=" O ALA D 238 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLN D 245 " --> pdb=" O SER D 241 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLN D 263 " --> pdb=" O SER D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 270 removed outlier: 4.301A pdb=" N LEU D 269 " --> pdb=" O SER D 265 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N SER D 270 " --> pdb=" O SER D 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 265 through 270' 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 100 removed outlier: 4.061A pdb=" N VAL E 65 " --> pdb=" O SER E 61 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA E 100 " --> pdb=" O LYS E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 130 Processing helix chain 'E' and resid 179 through 234 removed outlier: 3.772A pdb=" N GLY E 188 " --> pdb=" O LYS E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 262 removed outlier: 4.140A pdb=" N GLU E 240 " --> pdb=" O ASP E 236 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA E 242 " --> pdb=" O ALA E 238 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLN E 245 " --> pdb=" O SER E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 263 through 266 Processing helix chain 'E' and resid 267 through 272 removed outlier: 3.959A pdb=" N LEU E 271 " --> pdb=" O SER E 267 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE E 272 " --> pdb=" O ILE E 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 267 through 272' 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 101 removed outlier: 4.014A pdb=" N VAL F 65 " --> pdb=" O SER F 61 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA F 99 " --> pdb=" O GLU F 95 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER F 101 " --> pdb=" O ALA F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 130 Processing helix chain 'F' and resid 166 through 170 removed outlier: 3.658A pdb=" N GLY F 170 " --> pdb=" O ALA F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 234 removed outlier: 4.063A pdb=" N GLY F 188 " --> pdb=" O LYS F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 236 through 262 removed outlier: 4.036A pdb=" N GLU F 240 " --> pdb=" O ASP F 236 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA F 242 " --> pdb=" O ALA F 238 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLN F 245 " --> pdb=" O SER F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 263 through 265 No H-bonds generated for 'chain 'F' and resid 263 through 265' Processing helix chain 'F' and resid 266 through 271 removed outlier: 4.308A pdb=" N SER F 270 " --> pdb=" O SER F 266 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU F 271 " --> pdb=" O SER F 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 266 through 271' Processing helix chain 'G' and resid 9 through 36 removed outlier: 3.508A pdb=" N MET 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 101 removed outlier: 4.128A 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: 3.946A pdb=" N GLY G 188 " --> pdb=" O LYS G 184 " (cutoff:3.500A) Processing helix chain 'G' and resid 236 through 263 removed outlier: 3.836A pdb=" N GLU G 240 " --> pdb=" O ASP G 236 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA G 242 " --> pdb=" O ALA G 238 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLN G 245 " --> pdb=" O SER G 241 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLN G 263 " --> pdb=" O SER G 259 " (cutoff:3.500A) Processing helix chain 'G' and resid 264 through 272 removed outlier: 3.534A pdb=" N SER G 267 " --> pdb=" O SER G 264 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 36 Processing helix chain 'H' and resid 45 through 61 Processing helix chain 'H' and resid 61 through 101 removed outlier: 4.245A 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 165 through 170 removed outlier: 3.830A pdb=" N GLY H 170 " --> pdb=" O ALA H 167 " (cutoff:3.500A) Processing helix chain 'H' and resid 179 through 234 removed outlier: 4.040A pdb=" N GLY H 188 " --> pdb=" O LYS H 184 " (cutoff:3.500A) Processing helix chain 'H' and resid 236 through 262 removed outlier: 3.539A pdb=" N GLU H 240 " --> pdb=" O ASP H 236 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA H 242 " --> pdb=" O ALA H 238 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN H 245 " --> pdb=" O SER H 241 " (cutoff:3.500A) Processing helix chain 'H' and resid 263 through 272 removed outlier: 4.036A pdb=" N SER H 267 " --> pdb=" O SER H 264 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU H 269 " --> pdb=" O SER H 266 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 36 removed outlier: 3.500A pdb=" N MET I 13 " --> pdb=" O ASN I 9 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 61 Processing helix chain 'I' and resid 61 through 101 removed outlier: 4.238A 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 165 through 170 removed outlier: 3.952A pdb=" N GLY I 170 " --> pdb=" O ALA I 167 " (cutoff:3.500A) Processing helix chain 'I' and resid 179 through 234 removed outlier: 3.909A pdb=" N GLY I 188 " --> pdb=" O LYS I 184 " (cutoff:3.500A) Processing helix chain 'I' and resid 236 through 262 removed outlier: 3.902A pdb=" N GLU I 240 " --> pdb=" O ASP I 236 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA I 242 " --> pdb=" O ALA I 238 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLN I 245 " --> pdb=" O SER I 241 " (cutoff:3.500A) Processing helix chain 'I' and resid 263 through 266 Processing helix chain 'I' and resid 267 through 272 removed outlier: 3.924A pdb=" N LEU I 271 " --> pdb=" O SER I 267 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE I 272 " --> pdb=" O ILE I 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 267 through 272' Processing helix chain 'J' and resid 9 through 36 Processing helix chain 'J' and resid 45 through 61 Processing helix chain 'J' and resid 61 through 101 removed outlier: 4.226A pdb=" N VAL J 65 " --> pdb=" O SER J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 106 through 130 Processing helix chain 'J' and resid 166 through 170 removed outlier: 3.829A pdb=" N GLY J 170 " --> pdb=" O ALA J 167 " (cutoff:3.500A) Processing helix chain 'J' and resid 179 through 234 removed outlier: 3.936A pdb=" N GLY J 188 " --> pdb=" O LYS J 184 " (cutoff:3.500A) Processing helix chain 'J' and resid 236 through 263 removed outlier: 4.159A pdb=" N GLU J 240 " --> pdb=" O ASP J 236 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA J 242 " --> pdb=" O ALA J 238 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLN J 245 " --> pdb=" O SER J 241 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN J 263 " --> pdb=" O SER J 259 " (cutoff:3.500A) Processing helix chain 'J' and resid 264 through 272 removed outlier: 3.943A pdb=" N SER J 267 " --> pdb=" O SER J 264 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE J 268 " --> pdb=" O SER J 265 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU J 269 " --> pdb=" O SER J 266 " (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 102 removed outlier: 4.040A pdb=" N VAL K 65 " --> pdb=" O SER K 61 " (cutoff:3.500A) removed outlier: 4.075A 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 179 through 234 removed outlier: 4.037A pdb=" N GLY K 188 " --> pdb=" O LYS K 184 " (cutoff:3.500A) Processing helix chain 'K' and resid 236 through 263 removed outlier: 3.668A pdb=" N GLU K 240 " --> pdb=" O ASP K 236 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA K 242 " --> pdb=" O ALA K 238 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLN K 245 " --> pdb=" O SER K 241 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLN K 263 " --> pdb=" O SER K 259 " (cutoff:3.500A) Processing helix chain 'K' and resid 264 through 272 removed outlier: 4.190A pdb=" N SER K 267 " --> pdb=" O SER K 264 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE K 268 " --> pdb=" O SER K 265 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU K 269 " --> pdb=" O SER K 266 " (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 62 through 102 removed outlier: 3.804A pdb=" N ASP L 102 " --> pdb=" O LEU L 98 " (cutoff:3.500A) Processing helix chain 'L' and resid 106 through 130 Processing helix chain 'L' and resid 165 through 169 Processing helix chain 'L' and resid 179 through 234 removed outlier: 3.937A pdb=" N GLY L 188 " --> pdb=" O LYS L 184 " (cutoff:3.500A) Processing helix chain 'L' and resid 236 through 263 removed outlier: 3.939A pdb=" N GLU L 240 " --> pdb=" O ASP L 236 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA L 242 " --> pdb=" O ALA L 238 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLN L 245 " --> pdb=" O SER L 241 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN L 263 " --> pdb=" O SER L 259 " (cutoff:3.500A) Processing helix chain 'L' and resid 265 through 271 removed outlier: 4.332A pdb=" N LEU L 269 " --> pdb=" O SER L 265 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N SER L 270 " --> pdb=" O SER L 266 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU L 271 " --> pdb=" O SER L 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 265 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 61 through 101 removed outlier: 4.186A pdb=" N VAL M 65 " --> pdb=" O SER M 61 " (cutoff:3.500A) Processing helix chain 'M' and resid 106 through 130 Processing helix chain 'M' and resid 166 through 170 removed outlier: 3.623A pdb=" N GLY M 170 " --> pdb=" O ALA M 167 " (cutoff:3.500A) Processing helix chain 'M' and resid 179 through 234 removed outlier: 3.895A pdb=" N GLY M 188 " --> pdb=" O LYS M 184 " (cutoff:3.500A) Processing helix chain 'M' and resid 237 through 263 removed outlier: 3.550A pdb=" N ALA M 242 " --> pdb=" O ALA M 238 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLN M 245 " --> pdb=" O SER M 241 " (cutoff:3.500A) Processing helix chain 'M' and resid 264 through 266 No H-bonds generated for 'chain 'M' and resid 264 through 266' Processing helix chain 'M' and resid 267 through 272 removed outlier: 3.886A pdb=" N LEU M 271 " --> pdb=" O SER M 267 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE M 272 " --> pdb=" O ILE M 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 267 through 272' Processing helix chain 'N' and resid 9 through 36 Processing helix chain 'N' and resid 45 through 61 Processing helix chain 'N' and resid 61 through 101 removed outlier: 4.057A 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 166 through 170 removed outlier: 3.570A pdb=" N GLY N 170 " --> pdb=" O ALA N 167 " (cutoff:3.500A) Processing helix chain 'N' and resid 179 through 234 removed outlier: 4.003A pdb=" N GLY N 188 " --> pdb=" O LYS N 184 " (cutoff:3.500A) Processing helix chain 'N' and resid 236 through 263 removed outlier: 3.569A pdb=" N GLU N 240 " --> pdb=" O ASP N 236 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA N 242 " --> pdb=" O ALA N 238 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLN N 245 " --> pdb=" O SER N 241 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN N 263 " --> pdb=" O SER N 259 " (cutoff:3.500A) Processing helix chain 'N' and resid 265 through 272 removed outlier: 4.351A pdb=" N LEU N 269 " --> pdb=" O SER N 265 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N SER N 270 " --> pdb=" O SER N 266 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU N 271 " --> pdb=" O SER N 267 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE N 272 " --> pdb=" O ILE N 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 265 through 272' Processing helix chain 'O' and resid 9 through 36 removed outlier: 3.826A pdb=" N MET O 13 " --> pdb=" O ASN O 9 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 61 Processing helix chain 'O' and resid 61 through 101 removed outlier: 4.250A pdb=" N VAL O 65 " --> pdb=" O SER O 61 " (cutoff:3.500A) Processing helix chain 'O' and resid 106 through 130 Processing helix chain 'O' and resid 165 through 170 removed outlier: 3.933A pdb=" N GLY O 170 " --> pdb=" O ALA O 167 " (cutoff:3.500A) Processing helix chain 'O' and resid 179 through 234 removed outlier: 4.077A pdb=" N GLY O 188 " --> pdb=" O LYS O 184 " (cutoff:3.500A) Processing helix chain 'O' and resid 236 through 263 removed outlier: 3.803A pdb=" N THR O 249 " --> pdb=" O GLN O 245 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLN O 263 " --> pdb=" O SER O 259 " (cutoff:3.500A) Processing helix chain 'O' and resid 264 through 272 removed outlier: 3.856A pdb=" N SER O 267 " --> pdb=" O SER O 264 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER O 270 " --> pdb=" O SER O 267 " (cutoff:3.500A) Processing helix chain 'P' and resid 9 through 36 Processing helix chain 'P' and resid 45 through 61 Processing helix chain 'P' and resid 61 through 102 removed outlier: 4.245A pdb=" N VAL P 65 " --> pdb=" O SER P 61 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASP P 102 " --> pdb=" O LEU P 98 " (cutoff:3.500A) Processing helix chain 'P' and resid 106 through 130 Processing helix chain 'P' and resid 165 through 170 removed outlier: 3.946A pdb=" N GLY P 170 " --> pdb=" O ALA P 167 " (cutoff:3.500A) Processing helix chain 'P' and resid 179 through 234 removed outlier: 3.923A pdb=" N GLY P 188 " --> pdb=" O LYS P 184 " (cutoff:3.500A) Processing helix chain 'P' and resid 236 through 263 removed outlier: 3.536A pdb=" N ALA P 242 " --> pdb=" O ALA P 238 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN P 263 " --> pdb=" O SER P 259 " (cutoff:3.500A) Processing helix chain 'P' and resid 265 through 272 removed outlier: 4.108A pdb=" N LEU P 269 " --> pdb=" O SER P 265 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N SER P 270 " --> pdb=" O SER P 266 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU P 271 " --> pdb=" O SER P 267 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N PHE P 272 " --> pdb=" O ILE P 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 265 through 272' Processing helix chain 'Q' and resid 9 through 36 removed outlier: 3.640A pdb=" N MET Q 13 " --> pdb=" O ASN Q 9 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY Q 36 " --> pdb=" O ARG Q 32 " (cutoff:3.500A) Processing helix chain 'Q' and resid 45 through 61 Processing helix chain 'Q' and resid 61 through 101 removed outlier: 4.304A pdb=" N VAL Q 65 " --> pdb=" O SER Q 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 106 through 130 Processing helix chain 'Q' and resid 165 through 170 removed outlier: 3.813A pdb=" N GLY Q 170 " --> pdb=" O ALA Q 167 " (cutoff:3.500A) Processing helix chain 'Q' and resid 179 through 234 removed outlier: 3.979A pdb=" N GLY Q 188 " --> pdb=" O LYS Q 184 " (cutoff:3.500A) Processing helix chain 'Q' and resid 236 through 263 removed outlier: 3.857A pdb=" N ALA Q 242 " --> pdb=" O ALA Q 238 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLN Q 263 " --> pdb=" O SER Q 259 " (cutoff:3.500A) Processing helix chain 'Q' and resid 264 through 272 removed outlier: 4.376A pdb=" N SER Q 267 " --> pdb=" O SER Q 264 " (cutoff:3.500A) Processing helix chain 'R' and resid 9 through 36 removed outlier: 3.653A pdb=" N MET R 13 " --> pdb=" O ASN R 9 " (cutoff:3.500A) Processing helix chain 'R' and resid 45 through 61 Processing helix chain 'R' and resid 61 through 101 removed outlier: 4.160A 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 166 through 170 removed outlier: 3.518A pdb=" N ILE R 169 " --> pdb=" O LEU R 166 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY R 170 " --> pdb=" O ALA R 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 166 through 170' Processing helix chain 'R' and resid 179 through 234 removed outlier: 3.916A pdb=" N GLY R 188 " --> pdb=" O LYS R 184 " (cutoff:3.500A) Processing helix chain 'R' and resid 236 through 263 removed outlier: 3.876A pdb=" N ALA R 242 " --> pdb=" O ALA R 238 " (cutoff:3.500A) Processing helix chain 'R' and resid 266 through 271 removed outlier: 3.780A pdb=" N SER R 270 " --> pdb=" O SER R 266 " (cutoff:3.500A) Processing helix chain 'S' and resid 9 through 36 removed outlier: 3.825A pdb=" N MET S 13 " --> pdb=" O ASN S 9 " (cutoff:3.500A) Processing helix chain 'S' and resid 45 through 61 Processing helix chain 'S' and resid 61 through 101 removed outlier: 4.317A pdb=" N VAL S 65 " --> pdb=" O SER S 61 " (cutoff:3.500A) Processing helix chain 'S' and resid 106 through 130 Processing helix chain 'S' and resid 166 through 170 removed outlier: 3.879A pdb=" N GLY S 170 " --> pdb=" O ALA S 167 " (cutoff:3.500A) Processing helix chain 'S' and resid 179 through 234 removed outlier: 3.966A pdb=" N GLY S 188 " --> pdb=" O LYS S 184 " (cutoff:3.500A) Processing helix chain 'S' and resid 236 through 263 removed outlier: 4.005A pdb=" N GLN S 263 " --> pdb=" O SER S 259 " (cutoff:3.500A) Processing helix chain 'S' and resid 264 through 266 No H-bonds generated for 'chain 'S' and resid 264 through 266' Processing helix chain 'S' and resid 267 through 272 removed outlier: 3.855A pdb=" N LEU S 271 " --> pdb=" O SER S 267 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N PHE S 272 " --> pdb=" O ILE S 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 267 through 272' Processing helix chain 'T' and resid 9 through 36 removed outlier: 3.771A pdb=" N MET T 13 " --> pdb=" O ASN T 9 " (cutoff:3.500A) Processing helix chain 'T' and resid 45 through 61 Processing helix chain 'T' and resid 61 through 101 removed outlier: 4.229A 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 165 through 170 removed outlier: 3.941A pdb=" N GLY T 170 " --> pdb=" O ALA T 167 " (cutoff:3.500A) Processing helix chain 'T' and resid 179 through 234 removed outlier: 3.914A 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: 3.805A pdb=" N ILE T 268 " --> pdb=" O SER T 265 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE T 272 " --> pdb=" O LEU T 269 " (cutoff:3.500A) Processing helix chain 'U' and resid 9 through 36 removed outlier: 3.502A pdb=" N MET U 13 " --> pdb=" O ASN U 9 " (cutoff:3.500A) Processing helix chain 'U' and resid 45 through 61 Processing helix chain 'U' and resid 61 through 101 removed outlier: 4.081A 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 166 through 170 removed outlier: 3.518A pdb=" N ILE U 169 " --> pdb=" O LEU U 166 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY U 170 " --> pdb=" O ALA U 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 166 through 170' Processing helix chain 'U' and resid 179 through 234 removed outlier: 4.016A pdb=" N GLY U 188 " --> pdb=" O LYS U 184 " (cutoff:3.500A) Processing helix chain 'U' and resid 236 through 263 removed outlier: 3.703A pdb=" N GLN U 263 " --> pdb=" O SER U 259 " (cutoff:3.500A) Processing helix chain 'U' and resid 264 through 266 No H-bonds generated for 'chain 'U' and resid 264 through 266' Processing helix chain 'U' and resid 267 through 272 removed outlier: 3.874A pdb=" N LEU U 271 " --> pdb=" O SER U 267 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N PHE U 272 " --> pdb=" O ILE U 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 267 through 272' Processing helix chain 'V' and resid 9 through 36 removed outlier: 3.508A pdb=" N MET V 13 " --> pdb=" O ASN V 9 " (cutoff:3.500A) Processing helix chain 'V' and resid 45 through 61 Processing helix chain 'V' and resid 61 through 101 removed outlier: 4.045A pdb=" N VAL V 65 " --> pdb=" O SER V 61 " (cutoff:3.500A) Processing helix chain 'V' and resid 106 through 130 Processing helix chain 'V' and resid 165 through 170 removed outlier: 3.750A pdb=" N GLY V 170 " --> pdb=" O ALA V 167 " (cutoff:3.500A) Processing helix chain 'V' and resid 179 through 234 removed outlier: 3.961A pdb=" N GLY V 188 " --> pdb=" O LYS V 184 " (cutoff:3.500A) Processing helix chain 'V' and resid 236 through 264 Processing helix chain 'V' and resid 265 through 272 Processing helix chain 'W' and resid 9 through 36 removed outlier: 3.597A pdb=" N MET W 13 " --> pdb=" O ASN W 9 " (cutoff:3.500A) Processing helix chain 'W' and resid 45 through 61 Processing helix chain 'W' and resid 61 through 102 removed outlier: 4.149A pdb=" N VAL W 65 " --> pdb=" O SER W 61 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ASP W 102 " --> pdb=" O LEU W 98 " (cutoff:3.500A) Processing helix chain 'W' and resid 106 through 130 Processing helix chain 'W' and resid 166 through 170 removed outlier: 3.850A pdb=" N GLY W 170 " --> pdb=" O ALA W 167 " (cutoff:3.500A) Processing helix chain 'W' and resid 179 through 234 removed outlier: 3.950A pdb=" N GLY W 188 " --> pdb=" O LYS W 184 " (cutoff:3.500A) Processing helix chain 'W' and resid 236 through 263 removed outlier: 3.534A pdb=" N GLN W 245 " --> pdb=" O SER W 241 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN W 263 " --> pdb=" O SER W 259 " (cutoff:3.500A) Processing helix chain 'W' and resid 264 through 272 removed outlier: 4.261A pdb=" N SER W 267 " --> pdb=" O SER W 264 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE W 268 " --> pdb=" O SER W 265 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE W 272 " --> pdb=" O LEU W 269 " (cutoff:3.500A) Processing helix chain 'X' and resid 9 through 36 removed outlier: 3.567A pdb=" N MET X 13 " --> pdb=" O ASN X 9 " (cutoff:3.500A) Processing helix chain 'X' and resid 45 through 61 Processing helix chain 'X' and resid 62 through 102 removed outlier: 4.184A pdb=" N ASP X 102 " --> pdb=" O LEU X 98 " (cutoff:3.500A) Processing helix chain 'X' and resid 106 through 130 Processing helix chain 'X' and resid 179 through 234 removed outlier: 3.731A pdb=" N GLY X 188 " --> pdb=" O LYS X 184 " (cutoff:3.500A) Processing helix chain 'X' and resid 236 through 263 removed outlier: 3.649A pdb=" N GLN X 263 " --> pdb=" O SER X 259 " (cutoff:3.500A) Processing helix chain 'X' and resid 264 through 272 removed outlier: 3.813A pdb=" N SER X 267 " --> pdb=" O SER X 264 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 36 Processing helix chain 'Y' and resid 45 through 61 Processing helix chain 'Y' and resid 61 through 101 removed outlier: 4.231A 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 179 through 234 removed outlier: 3.977A pdb=" N GLY Y 188 " --> pdb=" O LYS Y 184 " (cutoff:3.500A) Processing helix chain 'Y' and resid 236 through 263 removed outlier: 3.521A pdb=" N GLU Y 240 " --> pdb=" O ASP Y 236 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN Y 263 " --> pdb=" O SER Y 259 " (cutoff:3.500A) Processing helix chain 'Y' and resid 264 through 272 removed outlier: 4.125A pdb=" N SER Y 267 " --> pdb=" O SER Y 264 " (cutoff:3.500A) Processing helix chain 'Z' and resid 9 through 36 Processing helix chain 'Z' and resid 45 through 61 Processing helix chain 'Z' and resid 61 through 101 removed outlier: 4.242A pdb=" N VAL Z 65 " --> pdb=" O SER Z 61 " (cutoff:3.500A) Processing helix chain 'Z' and resid 106 through 131 removed outlier: 3.637A pdb=" N ALA Z 131 " --> pdb=" O ALA Z 127 " (cutoff:3.500A) Processing helix chain 'Z' and resid 166 through 170 removed outlier: 3.798A pdb=" N GLY Z 170 " --> pdb=" O ALA Z 167 " (cutoff:3.500A) Processing helix chain 'Z' and resid 179 through 234 removed outlier: 4.052A pdb=" N GLY Z 188 " --> pdb=" O LYS Z 184 " (cutoff:3.500A) Processing helix chain 'Z' and resid 236 through 263 removed outlier: 3.561A pdb=" N GLU Z 240 " --> pdb=" O ASP Z 236 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA Z 242 " --> pdb=" O ALA Z 238 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN Z 245 " --> pdb=" O SER Z 241 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN Z 263 " --> pdb=" O SER Z 259 " (cutoff:3.500A) Processing helix chain 'Z' and resid 264 through 272 removed outlier: 4.082A pdb=" N SER Z 267 " --> pdb=" O SER Z 264 " (cutoff:3.500A) Processing helix chain 'a' and resid 9 through 36 removed outlier: 3.565A pdb=" N MET a 13 " --> pdb=" O ASN a 9 " (cutoff:3.500A) Processing helix chain 'a' and resid 45 through 61 Processing helix chain 'a' and resid 61 through 101 removed outlier: 4.267A 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 166 through 170 removed outlier: 3.691A pdb=" N GLY a 170 " --> pdb=" O ALA a 167 " (cutoff:3.500A) Processing helix chain 'a' and resid 179 through 234 removed outlier: 4.001A pdb=" N GLY a 188 " --> pdb=" O LYS a 184 " (cutoff:3.500A) Processing helix chain 'a' and resid 236 through 263 removed outlier: 3.588A pdb=" N GLU a 240 " --> pdb=" O ASP a 236 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLN a 245 " --> pdb=" O SER a 241 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN a 263 " --> pdb=" O SER a 259 " (cutoff:3.500A) Processing helix chain 'a' and resid 266 through 272 removed outlier: 4.178A pdb=" N SER a 270 " --> pdb=" O SER a 266 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU a 271 " --> pdb=" O SER a 267 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE a 272 " --> pdb=" O ILE a 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 266 through 272' 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: 3.868A 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 Processing helix chain 'b' and resid 179 through 234 removed outlier: 3.927A pdb=" N GLY b 188 " --> pdb=" O LYS b 184 " (cutoff:3.500A) Processing helix chain 'b' and resid 236 through 263 removed outlier: 3.705A pdb=" N GLU b 240 " --> pdb=" O ASP b 236 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN b 245 " --> pdb=" O SER b 241 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN b 263 " --> pdb=" O SER b 259 " (cutoff:3.500A) Processing helix chain 'b' and resid 265 through 270 removed outlier: 4.304A pdb=" N LEU b 269 " --> pdb=" O SER b 265 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N SER b 270 " --> pdb=" O SER b 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 265 through 270' Processing helix chain 'c' and resid 9 through 36 removed outlier: 3.548A pdb=" N MET c 13 " --> pdb=" O ASN c 9 " (cutoff:3.500A) Processing helix chain 'c' and resid 45 through 61 Processing helix chain 'c' and resid 61 through 102 removed outlier: 4.061A pdb=" N VAL c 65 " --> pdb=" O SER c 61 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASP c 102 " --> pdb=" O LEU c 98 " (cutoff:3.500A) Processing helix chain 'c' and resid 106 through 130 Processing helix chain 'c' and resid 179 through 234 removed outlier: 3.864A pdb=" N GLY c 188 " --> pdb=" O LYS c 184 " (cutoff:3.500A) Processing helix chain 'c' and resid 236 through 263 removed outlier: 3.614A pdb=" N GLN c 263 " --> pdb=" O SER c 259 " (cutoff:3.500A) Processing helix chain 'c' and resid 264 through 272 removed outlier: 3.500A pdb=" N SER c 267 " --> pdb=" O SER c 264 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE c 268 " --> pdb=" O SER c 265 " (cutoff:3.500A) Processing helix chain 'd' and resid 9 through 36 removed outlier: 3.574A pdb=" N MET 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 102 removed outlier: 4.190A pdb=" N VAL d 65 " --> pdb=" O SER d 61 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASP d 102 " --> pdb=" O LEU d 98 " (cutoff:3.500A) Processing helix chain 'd' and resid 106 through 130 Processing helix chain 'd' and resid 179 through 234 removed outlier: 3.763A pdb=" N GLY d 188 " --> pdb=" O LYS d 184 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU d 232 " --> pdb=" O GLY d 228 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL d 233 " --> pdb=" O VAL d 229 " (cutoff:3.500A) Processing helix chain 'd' and resid 236 through 263 removed outlier: 3.718A pdb=" N GLU d 240 " --> pdb=" O ASP d 236 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN d 245 " --> pdb=" O SER d 241 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN d 263 " --> pdb=" O SER d 259 " (cutoff:3.500A) Processing helix chain 'd' and resid 264 through 272 removed outlier: 3.723A pdb=" N SER d 267 " --> pdb=" O SER d 264 " (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: 4.044A pdb=" N VAL e 65 " --> pdb=" O SER e 61 " (cutoff:3.500A) removed outlier: 4.133A 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 165 through 170 Processing helix chain 'e' and resid 179 through 234 removed outlier: 4.354A pdb=" N GLY e 188 " --> pdb=" O LYS e 184 " (cutoff:3.500A) Processing helix chain 'e' and resid 236 through 263 removed outlier: 3.624A pdb=" N GLU e 240 " --> pdb=" O ASP e 236 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA e 242 " --> pdb=" O ALA e 238 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN e 263 " --> pdb=" O SER e 259 " (cutoff:3.500A) Processing helix chain 'e' and resid 264 through 272 removed outlier: 4.006A pdb=" N SER e 267 " --> pdb=" O SER e 264 " (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 101 removed outlier: 4.346A 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 166 through 170 removed outlier: 3.756A pdb=" N GLY f 170 " --> pdb=" O ALA f 167 " (cutoff:3.500A) Processing helix chain 'f' and resid 179 through 234 removed outlier: 3.813A pdb=" N GLY f 188 " --> pdb=" O LYS f 184 " (cutoff:3.500A) Processing helix chain 'f' and resid 236 through 264 removed outlier: 3.826A pdb=" N GLU f 240 " --> pdb=" O ASP f 236 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN f 245 " --> pdb=" O SER f 241 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER f 264 " --> pdb=" O ILE f 260 " (cutoff:3.500A) Processing helix chain 'f' and resid 266 through 272 removed outlier: 4.016A pdb=" N SER f 270 " --> pdb=" O SER f 266 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU f 271 " --> pdb=" O SER f 267 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE f 272 " --> pdb=" O ILE f 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 266 through 272' Processing helix chain 'h' and resid 9 through 36 Processing helix chain 'h' and resid 45 through 61 Processing helix chain 'h' and resid 61 through 102 removed outlier: 4.278A pdb=" N VAL h 65 " --> pdb=" O SER h 61 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASP h 102 " --> pdb=" O LEU h 98 " (cutoff:3.500A) Processing helix chain 'h' and resid 106 through 130 Processing helix chain 'h' and resid 166 through 170 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: 3.591A pdb=" N GLU h 240 " --> pdb=" O ASP h 236 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA h 242 " --> pdb=" O ALA h 238 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLN h 245 " --> pdb=" O SER h 241 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLN h 263 " --> pdb=" O SER h 259 " (cutoff:3.500A) Processing helix chain 'h' and resid 265 through 271 removed outlier: 4.219A pdb=" N LEU h 269 " --> pdb=" O SER h 265 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER h 270 " --> pdb=" O SER h 266 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU h 271 " --> pdb=" O SER h 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 265 through 271' Processing helix chain 'i' and resid 9 through 36 Processing helix chain 'i' and resid 45 through 61 Processing helix chain 'i' and resid 61 through 102 removed outlier: 3.915A pdb=" N VAL i 65 " --> pdb=" O SER i 61 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASP i 102 " --> pdb=" O LEU i 98 " (cutoff:3.500A) Processing helix chain 'i' and resid 106 through 130 Processing helix chain 'i' and resid 166 through 170 removed outlier: 3.520A pdb=" N ILE i 169 " --> pdb=" O LEU i 166 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY i 170 " --> pdb=" O ALA i 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 166 through 170' Processing helix chain 'i' and resid 179 through 234 removed outlier: 4.019A pdb=" N GLY i 188 " --> pdb=" O LYS i 184 " (cutoff:3.500A) Processing helix chain 'i' and resid 236 through 263 removed outlier: 3.653A pdb=" N GLU i 240 " --> pdb=" O ASP i 236 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA i 242 " --> pdb=" O ALA i 238 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN i 245 " --> pdb=" O SER i 241 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLN i 263 " --> pdb=" O SER i 259 " (cutoff:3.500A) Processing helix chain 'i' and resid 265 through 270 removed outlier: 4.267A pdb=" N LEU i 269 " --> pdb=" O SER i 265 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N SER i 270 " --> pdb=" O SER i 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 265 through 270' 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: 3.977A pdb=" N VAL j 65 " --> pdb=" O SER j 61 " (cutoff:3.500A) Processing helix chain 'j' and resid 106 through 130 Processing helix chain 'j' and resid 166 through 170 removed outlier: 3.614A pdb=" N ILE j 169 " --> pdb=" O LEU j 166 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY j 170 " --> pdb=" O ALA j 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 166 through 170' Processing helix chain 'j' and resid 179 through 234 removed outlier: 3.958A pdb=" N GLY j 188 " --> pdb=" O LYS j 184 " (cutoff:3.500A) Processing helix chain 'j' and resid 236 through 263 removed outlier: 3.557A pdb=" N GLU j 240 " --> pdb=" O ASP j 236 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA j 242 " --> pdb=" O ALA j 238 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLN j 263 " --> pdb=" O SER j 259 " (cutoff:3.500A) Processing helix chain 'j' and resid 264 through 266 No H-bonds generated for 'chain 'j' and resid 264 through 266' Processing helix chain 'j' and resid 267 through 272 removed outlier: 4.086A pdb=" N LEU j 271 " --> pdb=" O SER j 267 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE j 272 " --> pdb=" O ILE j 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 267 through 272' Processing helix chain 'g' and resid 9 through 36 removed outlier: 3.800A pdb=" N MET g 13 " --> pdb=" O ASN g 9 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY g 21 " --> pdb=" O GLN g 17 " (cutoff:3.500A) Processing helix chain 'g' and resid 45 through 102 removed outlier: 4.442A pdb=" N ASN g 63 " --> pdb=" O ALA g 59 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA g 64 " --> pdb=" O ALA g 60 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL g 65 " --> pdb=" O SER g 61 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR g 85 " --> pdb=" O ALA g 81 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS g 94 " --> pdb=" O LEU g 90 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU g 95 " --> pdb=" O GLY g 91 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS g 96 " --> pdb=" O LYS g 92 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASP g 102 " --> pdb=" O LEU g 98 " (cutoff:3.500A) Processing helix chain 'g' and resid 106 through 131 removed outlier: 3.583A pdb=" N GLN g 123 " --> pdb=" O SER g 119 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE g 124 " --> pdb=" O LEU g 120 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR g 129 " --> pdb=" O GLU g 125 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA g 131 " --> pdb=" O ALA g 127 " (cutoff:3.500A) Processing helix chain 'g' and resid 165 through 170 Processing helix chain 'g' and resid 179 through 234 removed outlier: 4.186A pdb=" N GLY g 188 " --> pdb=" O LYS g 184 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR g 189 " --> pdb=" O THR g 185 " (cutoff:3.500A) Processing helix chain 'g' and resid 236 through 264 removed outlier: 4.199A pdb=" N ALA g 242 " --> pdb=" O ALA g 238 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS g 243 " --> pdb=" O LYS g 239 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER g 264 " --> pdb=" O ILE g 260 " (cutoff:3.500A) Processing helix chain 'g' and resid 265 through 272 removed outlier: 4.419A pdb=" N LEU g 269 " --> pdb=" O SER g 265 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 145 through 146 Processing sheet with id=AA2, first strand: chain 'B' and resid 145 through 149 Processing sheet with id=AA3, first strand: chain 'C' and resid 145 through 149 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 149 Processing sheet with id=AA8, first strand: chain 'H' and resid 145 through 149 Processing sheet with id=AA9, first strand: chain 'I' and resid 145 through 149 Processing sheet with id=AB1, first strand: chain 'J' and resid 145 through 146 Processing sheet with id=AB2, first strand: chain 'K' and resid 145 through 149 Processing sheet with id=AB3, first strand: chain 'L' and resid 145 through 146 Processing sheet with id=AB4, first strand: chain 'M' and resid 145 through 146 Processing sheet with id=AB5, first strand: chain 'N' and resid 148 through 149 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 149 removed outlier: 3.525A pdb=" N PHE R 148 " --> pdb=" O PHE R 157 " (cutoff:3.500A) 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 149 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: 3.545A 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 149 removed outlier: 3.531A pdb=" N PHE X 148 " --> pdb=" O PHE X 157 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'Y' and resid 145 through 149 Processing sheet with id=AC8, first strand: chain 'Z' and resid 145 through 149 Processing sheet with id=AC9, first strand: chain 'a' and resid 145 through 149 Processing sheet with id=AD1, first strand: chain 'b' and resid 145 through 149 removed outlier: 3.511A pdb=" N PHE b 148 " --> pdb=" O PHE b 157 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'c' and resid 145 through 149 removed outlier: 3.589A pdb=" N PHE c 148 " --> pdb=" O PHE c 157 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'd' and resid 145 through 146 Processing sheet with id=AD4, first strand: chain 'e' and resid 145 through 146 Processing sheet with id=AD5, first strand: chain 'h' and resid 145 through 146 Processing sheet with id=AD6, first strand: chain 'j' and resid 145 through 146 Processing sheet with id=AD7, first strand: chain 'g' and resid 145 through 149 removed outlier: 3.697A pdb=" N PHE g 148 " --> pdb=" O PHE g 157 " (cutoff:3.500A) 6174 hydrogen bonds defined for protein. 18174 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: 26.15 Time building geometry restraints manager: 16.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 18509 1.33 - 1.45: 10247 1.45 - 1.57: 41012 1.57 - 1.69: 0 1.69 - 1.81: 288 Bond restraints: 70056 Sorted by residual: bond pdb=" N LEU f 90 " pdb=" CA LEU f 90 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.20e-02 6.94e+03 8.80e+00 bond pdb=" N LEU E 204 " pdb=" CA LEU E 204 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.71e+00 bond pdb=" CA ASN g 4 " pdb=" CB ASN g 4 " ideal model delta sigma weight residual 1.527 1.543 -0.016 7.60e-03 1.73e+04 4.19e+00 bond pdb=" CG1 ILE R 190 " pdb=" CD1 ILE R 190 " ideal model delta sigma weight residual 1.513 1.446 0.067 3.90e-02 6.57e+02 2.97e+00 bond pdb=" CG1 ILE i 124 " pdb=" CD1 ILE i 124 " ideal model delta sigma weight residual 1.513 1.446 0.067 3.90e-02 6.57e+02 2.97e+00 ... (remaining 70051 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 93665 2.02 - 4.05: 1011 4.05 - 6.07: 120 6.07 - 8.09: 16 8.09 - 10.12: 12 Bond angle restraints: 94824 Sorted by residual: angle pdb=" N ILE X 164 " pdb=" CA ILE X 164 " pdb=" C ILE X 164 " ideal model delta sigma weight residual 112.43 109.39 3.04 9.20e-01 1.18e+00 1.09e+01 angle pdb=" N GLN Q 31 " pdb=" CA GLN Q 31 " pdb=" CB GLN Q 31 " ideal model delta sigma weight residual 110.12 114.94 -4.82 1.47e+00 4.63e-01 1.08e+01 angle pdb=" N GLN K 31 " pdb=" CA GLN K 31 " pdb=" CB GLN K 31 " ideal model delta sigma weight residual 110.16 114.91 -4.75 1.48e+00 4.57e-01 1.03e+01 angle pdb=" CB MET h 93 " pdb=" CG MET h 93 " pdb=" SD MET h 93 " ideal model delta sigma weight residual 112.70 103.12 9.58 3.00e+00 1.11e-01 1.02e+01 angle pdb=" N GLU A 25 " pdb=" CA GLU A 25 " pdb=" CB GLU A 25 " ideal model delta sigma weight residual 110.28 115.20 -4.92 1.55e+00 4.16e-01 1.01e+01 ... (remaining 94819 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 40057 17.95 - 35.90: 2236 35.90 - 53.86: 243 53.86 - 71.81: 78 71.81 - 89.76: 82 Dihedral angle restraints: 42696 sinusoidal: 15012 harmonic: 27684 Sorted by residual: dihedral pdb=" CA THR g 103 " pdb=" C THR g 103 " pdb=" N SER g 104 " pdb=" CA SER g 104 " ideal model delta harmonic sigma weight residual 180.00 -159.12 -20.88 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA LEU Y 232 " pdb=" C LEU Y 232 " pdb=" N VAL Y 233 " pdb=" CA VAL Y 233 " ideal model delta harmonic sigma weight residual -180.00 -161.42 -18.58 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA ASP g 118 " pdb=" CB ASP g 118 " pdb=" CG ASP g 118 " pdb=" OD1 ASP g 118 " ideal model delta sinusoidal sigma weight residual -30.00 -90.33 60.33 1 2.00e+01 2.50e-03 1.21e+01 ... (remaining 42693 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 10687 0.055 - 0.111: 1385 0.111 - 0.166: 128 0.166 - 0.222: 2 0.222 - 0.277: 2 Chirality restraints: 12204 Sorted by residual: chirality pdb=" CB ILE e 86 " pdb=" CA ILE e 86 " pdb=" CG1 ILE e 86 " pdb=" CG2 ILE e 86 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CB ILE g 164 " pdb=" CA ILE g 164 " pdb=" CG1 ILE g 164 " pdb=" CG2 ILE g 164 " both_signs ideal model delta sigma weight residual False 2.64 2.87 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CG LEU W 89 " pdb=" CB LEU W 89 " pdb=" CD1 LEU W 89 " pdb=" CD2 LEU W 89 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.65e-01 ... (remaining 12201 not shown) Planarity restraints: 12132 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA e 82 " -0.011 2.00e-02 2.50e+03 2.30e-02 5.30e+00 pdb=" C ALA e 82 " 0.040 2.00e-02 2.50e+03 pdb=" O ALA e 82 " -0.015 2.00e-02 2.50e+03 pdb=" N GLY e 83 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP L 84 " 0.010 2.00e-02 2.50e+03 1.98e-02 3.93e+00 pdb=" CG ASP L 84 " -0.034 2.00e-02 2.50e+03 pdb=" OD1 ASP L 84 " 0.012 2.00e-02 2.50e+03 pdb=" OD2 ASP L 84 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP L 77 " 0.009 2.00e-02 2.50e+03 1.74e-02 3.04e+00 pdb=" CG ASP L 77 " -0.030 2.00e-02 2.50e+03 pdb=" OD1 ASP L 77 " 0.011 2.00e-02 2.50e+03 pdb=" OD2 ASP L 77 " 0.011 2.00e-02 2.50e+03 ... (remaining 12129 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 700 2.64 - 3.20: 68775 3.20 - 3.77: 112585 3.77 - 4.33: 145255 4.33 - 4.90: 246371 Nonbonded interactions: 573686 Sorted by model distance: nonbonded pdb=" O ILE C 6 " pdb=" OG SER j 246 " model vdw 2.072 3.040 nonbonded pdb=" NH2 ARG Z 71 " pdb=" OD2 ASP a 102 " model vdw 2.108 3.120 nonbonded pdb=" NH1 ARG O 121 " pdb=" O THR O 173 " model vdw 2.126 3.120 nonbonded pdb=" O ILE i 6 " pdb=" OG SER g 246 " model vdw 2.131 3.040 nonbonded pdb=" OG SER f 246 " pdb=" O ILE h 6 " model vdw 2.132 3.040 ... (remaining 573681 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 275.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.090 Extract box with map and model: 2.050 Check model and map are aligned: 0.410 Set scattering table: 0.510 Process input model: 121.890 Find NCS groups from input model: 2.240 Set up NCS constraints: 0.800 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:10.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 414.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 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 0.067 70056 Z= 0.222 Angle : 0.571 10.117 94824 Z= 0.324 Chirality : 0.036 0.277 12204 Planarity : 0.003 0.050 12132 Dihedral : 11.933 89.761 24696 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.04 % Allowed : 0.37 % Favored : 99.59 % 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: 2.76 (0.08), residues: 9648 helix: 2.42 (0.06), residues: 7056 sheet: -2.68 (0.22), residues: 360 loop : 0.81 (0.14), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP O 49 HIS 0.006 0.001 HIS Y 214 PHE 0.025 0.002 PHE b 217 ARG 0.009 0.001 ARG W 121 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1072 residues out of total 7560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1069 time to evaluate : 5.806 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7718 (mt0) cc_final: 0.7317 (tm-30) REVERT: B 126 LYS cc_start: 0.7202 (mmmm) cc_final: 0.6702 (mppt) REVERT: B 240 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7347 (mm-30) REVERT: C 67 ASP cc_start: 0.7687 (m-30) cc_final: 0.7385 (m-30) REVERT: C 125 GLU cc_start: 0.8118 (tp30) cc_final: 0.7800 (tp30) REVERT: C 191 ASP cc_start: 0.8331 (t0) cc_final: 0.8064 (t70) REVERT: E 88 ASP cc_start: 0.7740 (m-30) cc_final: 0.7400 (m-30) REVERT: G 62 MET cc_start: 0.8489 (mmt) cc_final: 0.8238 (mmt) REVERT: H 95 GLU cc_start: 0.8345 (tt0) cc_final: 0.8075 (tt0) REVERT: I 236 ASP cc_start: 0.7367 (t0) cc_final: 0.7105 (t70) REVERT: L 206 THR cc_start: 0.7713 (t) cc_final: 0.7408 (m) REVERT: M 38 LYS cc_start: 0.7274 (ptmt) cc_final: 0.6738 (pttm) REVERT: O 9 ASN cc_start: 0.8539 (t0) cc_final: 0.8209 (t0) REVERT: P 88 ASP cc_start: 0.7071 (p0) cc_final: 0.6859 (m-30) REVERT: P 118 ASP cc_start: 0.7784 (m-30) cc_final: 0.7174 (m-30) REVERT: P 263 GLN cc_start: 0.7634 (mp10) cc_final: 0.7417 (mp10) REVERT: Q 43 LYS cc_start: 0.6734 (mptt) cc_final: 0.6508 (mtpt) REVERT: R 29 VAL cc_start: 0.7820 (t) cc_final: 0.7605 (p) REVERT: R 122 ASP cc_start: 0.7193 (m-30) cc_final: 0.6882 (m-30) REVERT: R 226 ASP cc_start: 0.8340 (m-30) cc_final: 0.7991 (m-30) REVERT: R 255 VAL cc_start: 0.7680 (p) cc_final: 0.7390 (t) REVERT: T 93 MET cc_start: 0.8085 (mtp) cc_final: 0.7855 (mtp) REVERT: T 122 ASP cc_start: 0.7810 (m-30) cc_final: 0.7496 (m-30) REVERT: T 151 ASN cc_start: 0.8173 (t0) cc_final: 0.7909 (t0) REVERT: U 38 LYS cc_start: 0.7491 (ttpt) cc_final: 0.7232 (tttm) REVERT: V 77 ASP cc_start: 0.7816 (m-30) cc_final: 0.7453 (m-30) REVERT: V 151 ASN cc_start: 0.8276 (m110) cc_final: 0.7945 (t0) REVERT: W 245 GLN cc_start: 0.6779 (mp10) cc_final: 0.5752 (mm110) REVERT: X 95 GLU cc_start: 0.6462 (tt0) cc_final: 0.6133 (tt0) REVERT: X 252 GLN cc_start: 0.7310 (tp-100) cc_final: 0.6909 (mt0) REVERT: X 256 GLN cc_start: 0.6904 (tp-100) cc_final: 0.6200 (pt0) REVERT: Y 88 ASP cc_start: 0.8279 (m-30) cc_final: 0.8077 (m-30) REVERT: Y 122 ASP cc_start: 0.8643 (m-30) cc_final: 0.8422 (m-30) REVERT: Z 116 ASP cc_start: 0.7599 (m-30) cc_final: 0.7388 (m-30) REVERT: Z 256 GLN cc_start: 0.7656 (mm110) cc_final: 0.7296 (mt0) REVERT: a 95 GLU cc_start: 0.8189 (tt0) cc_final: 0.7968 (tt0) REVERT: a 240 GLU cc_start: 0.7194 (mm-30) cc_final: 0.6606 (mm-30) REVERT: b 134 ASN cc_start: 0.7680 (OUTLIER) cc_final: 0.7315 (t0) REVERT: c 95 GLU cc_start: 0.7990 (tp30) cc_final: 0.7781 (tt0) REVERT: d 256 GLN cc_start: 0.7904 (tp-100) cc_final: 0.7536 (mt0) REVERT: e 31 GLN cc_start: 0.7180 (pp30) cc_final: 0.6443 (mm110) REVERT: e 105 LEU cc_start: 0.7950 (mt) cc_final: 0.7578 (mt) REVERT: g 9 ASN cc_start: 0.7420 (t0) cc_final: 0.7212 (t0) REVERT: g 25 GLU cc_start: 0.7323 (mm-30) cc_final: 0.6493 (mt-10) REVERT: g 106 ASN cc_start: 0.3446 (t0) cc_final: 0.3142 (p0) outliers start: 3 outliers final: 5 residues processed: 1071 average time/residue: 1.5098 time to fit residues: 2152.0991 Evaluate side-chains 583 residues out of total 7560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 577 time to evaluate : 6.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 45 ASN Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain b residue 134 ASN Chi-restraints excluded: chain e residue 33 ILE Chi-restraints excluded: chain f residue 153 ASP Chi-restraints excluded: chain i residue 84 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 820 optimal weight: 4.9990 chunk 736 optimal weight: 6.9990 chunk 408 optimal weight: 5.9990 chunk 251 optimal weight: 1.9990 chunk 496 optimal weight: 8.9990 chunk 393 optimal weight: 9.9990 chunk 761 optimal weight: 2.9990 chunk 294 optimal weight: 1.9990 chunk 463 optimal weight: 10.0000 chunk 567 optimal weight: 1.9990 chunk 882 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 63 ASN B 18 ASN D 251 GLN E 70 GLN E 123 GLN E 151 ASN E 245 GLN E 252 GLN F 31 GLN F 245 GLN F 256 GLN F 263 GLN G 23 ASN G 251 GLN H 4 ASN ** H 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 134 ASN I 23 ASN I 130 ASN I 251 GLN J 9 ASN J 20 ASN J 30 GLN ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 130 ASN K 252 GLN K 262 ASN L 7 ASN L 130 ASN L 134 ASN L 199 ASN L 231 ASN M 20 ASN M 130 ASN O 4 ASN P 4 ASN P 55 GLN Q 7 ASN Q 111 ASN Q 130 ASN Q 262 ASN R 23 ASN ** S 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 111 ASN S 151 ASN T 7 ASN T 9 ASN T 63 ASN T 123 GLN U 31 GLN U 130 ASN V 30 GLN V 31 GLN V 252 GLN W 23 ASN W 30 GLN ** W 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 251 GLN X 4 ASN X 248 GLN Y 195 GLN Y 222 GLN Y 262 ASN Z 123 GLN Z 130 ASN Z 262 ASN ** a 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 199 ASN a 245 GLN b 18 ASN b 248 GLN b 263 GLN c 45 ASN c 55 GLN c 123 GLN d 30 GLN e 18 ASN f 7 ASN ** f 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 111 ASN f 245 GLN h 18 ASN ** h 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 262 ASN ** i 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 31 GLN ** i 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 73 GLN j 18 ASN g 73 GLN Total number of N/Q/H flips: 82 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 70056 Z= 0.263 Angle : 0.523 8.663 94824 Z= 0.293 Chirality : 0.036 0.209 12204 Planarity : 0.003 0.033 12132 Dihedral : 4.000 72.525 9804 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Rotamer: Outliers : 2.01 % Allowed : 7.17 % Favored : 90.82 % 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: 3.76 (0.08), residues: 9648 helix: 3.18 (0.06), residues: 6804 sheet: -2.51 (0.22), residues: 360 loop : 1.37 (0.14), residues: 2484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP O 49 HIS 0.005 0.002 HIS J 214 PHE 0.018 0.002 PHE T 110 ARG 0.008 0.001 ARG H 121 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 783 residues out of total 7560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 631 time to evaluate : 5.875 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7751 (mt0) cc_final: 0.7331 (tm-30) REVERT: B 126 LYS cc_start: 0.7237 (mmmm) cc_final: 0.6810 (mtmt) REVERT: B 240 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7471 (mm-30) REVERT: C 67 ASP cc_start: 0.7534 (m-30) cc_final: 0.7184 (m-30) REVERT: C 191 ASP cc_start: 0.8358 (t0) cc_final: 0.7956 (t0) REVERT: C 256 GLN cc_start: 0.7401 (OUTLIER) cc_final: 0.7028 (mt0) REVERT: D 212 ASP cc_start: 0.8251 (t70) cc_final: 0.7912 (m-30) REVERT: E 31 GLN cc_start: 0.7406 (tm-30) cc_final: 0.6846 (mt0) REVERT: E 88 ASP cc_start: 0.7795 (m-30) cc_final: 0.7400 (m-30) REVERT: E 95 GLU cc_start: 0.5532 (mm-30) cc_final: 0.5186 (mm-30) REVERT: F 251 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.6868 (tm-30) REVERT: F 252 GLN cc_start: 0.8350 (mm-40) cc_final: 0.7982 (mm-40) REVERT: G 240 GLU cc_start: 0.7735 (mp0) cc_final: 0.7438 (mp0) REVERT: I 236 ASP cc_start: 0.7318 (t0) cc_final: 0.7030 (t70) REVERT: K 32 ARG cc_start: 0.7237 (OUTLIER) cc_final: 0.7030 (mtt90) REVERT: K 195 GLN cc_start: 0.7964 (OUTLIER) cc_final: 0.7484 (tt0) REVERT: L 206 THR cc_start: 0.7738 (t) cc_final: 0.7452 (m) REVERT: M 38 LYS cc_start: 0.7244 (ptmt) cc_final: 0.6649 (pttm) REVERT: N 31 GLN cc_start: 0.6867 (OUTLIER) cc_final: 0.6076 (mp10) REVERT: P 88 ASP cc_start: 0.7195 (p0) cc_final: 0.6989 (m-30) REVERT: P 118 ASP cc_start: 0.7787 (m-30) cc_final: 0.7453 (m-30) REVERT: Q 43 LYS cc_start: 0.6866 (mptt) cc_final: 0.6559 (mtpt) REVERT: R 29 VAL cc_start: 0.7945 (t) cc_final: 0.7697 (p) REVERT: R 122 ASP cc_start: 0.7251 (m-30) cc_final: 0.6953 (m-30) REVERT: R 220 LYS cc_start: 0.5806 (OUTLIER) cc_final: 0.4228 (mtpt) REVERT: R 226 ASP cc_start: 0.8329 (m-30) cc_final: 0.8011 (m-30) REVERT: R 255 VAL cc_start: 0.7765 (p) cc_final: 0.7497 (t) REVERT: S 31 GLN cc_start: 0.7758 (OUTLIER) cc_final: 0.7072 (tp40) REVERT: T 31 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.7067 (tt0) REVERT: T 95 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.6797 (tm-30) REVERT: T 118 ASP cc_start: 0.7843 (m-30) cc_final: 0.7384 (m-30) REVERT: T 122 ASP cc_start: 0.7729 (m-30) cc_final: 0.7336 (m-30) REVERT: U 31 GLN cc_start: 0.7475 (OUTLIER) cc_final: 0.6362 (tp40) REVERT: U 93 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7777 (mtt) REVERT: V 77 ASP cc_start: 0.7867 (m-30) cc_final: 0.7538 (m-30) REVERT: W 245 GLN cc_start: 0.6811 (mp10) cc_final: 0.6178 (mm-40) REVERT: X 95 GLU cc_start: 0.6610 (tt0) cc_final: 0.6212 (tt0) REVERT: X 252 GLN cc_start: 0.7192 (tp-100) cc_final: 0.6861 (mt0) REVERT: X 256 GLN cc_start: 0.6907 (tp-100) cc_final: 0.6208 (pt0) REVERT: Y 88 ASP cc_start: 0.8297 (m-30) cc_final: 0.8089 (m-30) REVERT: Y 122 ASP cc_start: 0.8673 (m-30) cc_final: 0.8434 (m-30) REVERT: Z 256 GLN cc_start: 0.7685 (mm110) cc_final: 0.7332 (mt0) REVERT: Z 263 GLN cc_start: 0.7735 (mp10) cc_final: 0.7320 (mp10) REVERT: a 95 GLU cc_start: 0.8241 (tt0) cc_final: 0.8040 (tt0) REVERT: a 240 GLU cc_start: 0.7222 (mm-30) cc_final: 0.6778 (mm-30) REVERT: a 262 ASN cc_start: 0.7131 (t0) cc_final: 0.6859 (m-40) REVERT: c 93 MET cc_start: 0.8353 (ttm) cc_final: 0.8149 (mtp) REVERT: c 256 GLN cc_start: 0.7388 (OUTLIER) cc_final: 0.6516 (tm-30) REVERT: d 256 GLN cc_start: 0.7903 (tp-100) cc_final: 0.7540 (mt0) REVERT: e 31 GLN cc_start: 0.7286 (pp30) cc_final: 0.6383 (mm110) REVERT: e 105 LEU cc_start: 0.8043 (mt) cc_final: 0.7661 (mt) REVERT: f 95 GLU cc_start: 0.5848 (tp30) cc_final: 0.5528 (tt0) REVERT: h 71 ARG cc_start: 0.7700 (ttm110) cc_final: 0.7424 (ttp-110) REVERT: h 144 THR cc_start: 0.8628 (t) cc_final: 0.8267 (m) REVERT: g 25 GLU cc_start: 0.7290 (mm-30) cc_final: 0.6354 (mt-10) REVERT: g 145 LYS cc_start: 0.7869 (OUTLIER) cc_final: 0.7498 (ptmm) outliers start: 152 outliers final: 64 residues processed: 744 average time/residue: 1.3703 time to fit residues: 1366.6973 Evaluate side-chains 623 residues out of total 7560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 546 time to evaluate : 5.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 256 GLN Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain F residue 31 GLN Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 251 GLN Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain H residue 30 GLN Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 239 LYS Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain J residue 77 ASP Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain K residue 32 ARG Chi-restraints excluded: chain K residue 195 GLN Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain L residue 30 GLN Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain L residue 191 ASP Chi-restraints excluded: chain L residue 223 ASP Chi-restraints excluded: chain N residue 31 GLN Chi-restraints excluded: chain O residue 123 GLN Chi-restraints excluded: chain P residue 122 ASP Chi-restraints excluded: chain Q residue 243 LYS Chi-restraints excluded: chain R residue 61 SER Chi-restraints excluded: chain R residue 220 LYS Chi-restraints excluded: chain S residue 31 GLN Chi-restraints excluded: chain S residue 178 THR Chi-restraints excluded: chain T residue 27 THR Chi-restraints excluded: chain T residue 31 GLN Chi-restraints excluded: chain T residue 77 ASP Chi-restraints excluded: chain T residue 95 GLU Chi-restraints excluded: chain U residue 16 LEU Chi-restraints excluded: chain U residue 31 GLN Chi-restraints excluded: chain U residue 93 MET Chi-restraints excluded: chain V residue 27 THR Chi-restraints excluded: chain W residue 56 SER Chi-restraints excluded: chain W residue 159 VAL Chi-restraints excluded: chain X residue 269 LEU Chi-restraints excluded: chain Z residue 264 SER Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain b residue 84 ASP Chi-restraints excluded: chain b residue 179 THR Chi-restraints excluded: chain c residue 147 THR Chi-restraints excluded: chain c residue 159 VAL Chi-restraints excluded: chain c residue 233 VAL Chi-restraints excluded: chain c residue 256 GLN Chi-restraints excluded: chain e residue 117 PHE Chi-restraints excluded: chain e residue 147 THR Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain e residue 187 ILE Chi-restraints excluded: chain f residue 101 SER Chi-restraints excluded: chain f residue 174 THR Chi-restraints excluded: chain h residue 172 THR Chi-restraints excluded: chain i residue 136 VAL Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain g residue 5 SER Chi-restraints excluded: chain g residue 145 LYS Chi-restraints excluded: chain g residue 159 VAL Chi-restraints excluded: chain g residue 172 THR Chi-restraints excluded: chain g residue 207 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 490 optimal weight: 0.3980 chunk 273 optimal weight: 6.9990 chunk 734 optimal weight: 5.9990 chunk 601 optimal weight: 6.9990 chunk 243 optimal weight: 7.9990 chunk 884 optimal weight: 6.9990 chunk 955 optimal weight: 0.9990 chunk 787 optimal weight: 5.9990 chunk 876 optimal weight: 0.9990 chunk 301 optimal weight: 1.9990 chunk 709 optimal weight: 5.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 34 ASN ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 4 ASN C 7 ASN D 130 ASN E 123 GLN E 130 ASN F 31 GLN F 256 GLN F 263 GLN ** H 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 30 GLN ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 20 ASN L 199 ASN M 123 GLN O 4 ASN O 199 ASN Q 70 GLN R 263 GLN ** S 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 248 GLN T 123 GLN U 18 ASN U 130 ASN U 262 ASN ** V 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 123 GLN W 55 GLN Y 151 ASN Z 130 ASN Z 151 ASN a 20 ASN a 245 GLN b 245 GLN c 45 ASN c 55 GLN c 195 GLN ** f 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 54 ASN f 63 ASN ** i 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 7 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 70056 Z= 0.218 Angle : 0.464 7.690 94824 Z= 0.264 Chirality : 0.034 0.187 12204 Planarity : 0.002 0.044 12132 Dihedral : 3.743 25.204 9794 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 2.14 % Allowed : 8.44 % Favored : 89.42 % 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: 4.02 (0.08), residues: 9648 helix: 3.45 (0.06), residues: 6804 sheet: -2.26 (0.23), residues: 360 loop : 1.17 (0.14), residues: 2484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 49 HIS 0.004 0.001 HIS J 214 PHE 0.014 0.002 PHE b 117 ARG 0.006 0.001 ARG g 121 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 763 residues out of total 7560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 601 time to evaluate : 5.818 Fit side-chains REVERT: A 13 MET cc_start: 0.7958 (mtm) cc_final: 0.7743 (mtm) REVERT: A 31 GLN cc_start: 0.7736 (mt0) cc_final: 0.7325 (tm-30) REVERT: B 126 LYS cc_start: 0.7228 (mmmm) cc_final: 0.6845 (mtmt) REVERT: B 240 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7353 (mm-30) REVERT: B 252 GLN cc_start: 0.7680 (OUTLIER) cc_final: 0.6836 (mp10) REVERT: C 67 ASP cc_start: 0.7489 (m-30) cc_final: 0.7135 (m-30) REVERT: C 191 ASP cc_start: 0.8330 (t0) cc_final: 0.7986 (t0) REVERT: C 256 GLN cc_start: 0.7386 (OUTLIER) cc_final: 0.7105 (mt0) REVERT: D 20 ASN cc_start: 0.8312 (m110) cc_final: 0.7895 (m110) REVERT: D 212 ASP cc_start: 0.8236 (t70) cc_final: 0.7891 (m-30) REVERT: E 31 GLN cc_start: 0.7286 (tm-30) cc_final: 0.6772 (mt0) REVERT: E 88 ASP cc_start: 0.7801 (m-30) cc_final: 0.7415 (m-30) REVERT: E 220 LYS cc_start: 0.6880 (OUTLIER) cc_final: 0.6630 (mmtt) REVERT: F 251 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.6719 (tm-30) REVERT: F 252 GLN cc_start: 0.8465 (mm-40) cc_final: 0.8057 (mm-40) REVERT: I 236 ASP cc_start: 0.7326 (t0) cc_final: 0.7089 (t70) REVERT: K 195 GLN cc_start: 0.7979 (OUTLIER) cc_final: 0.7508 (tt0) REVERT: L 95 GLU cc_start: 0.7537 (tm-30) cc_final: 0.6545 (tt0) REVERT: L 206 THR cc_start: 0.7780 (t) cc_final: 0.7493 (m) REVERT: M 38 LYS cc_start: 0.7232 (ptmt) cc_final: 0.6650 (pttm) REVERT: P 245 GLN cc_start: 0.7639 (OUTLIER) cc_final: 0.6306 (mp10) REVERT: Q 43 LYS cc_start: 0.6898 (mptt) cc_final: 0.6556 (mtpt) REVERT: Q 263 GLN cc_start: 0.7957 (mp10) cc_final: 0.6729 (pp30) REVERT: R 29 VAL cc_start: 0.7928 (t) cc_final: 0.7688 (p) REVERT: R 122 ASP cc_start: 0.7221 (m-30) cc_final: 0.6924 (m-30) REVERT: R 226 ASP cc_start: 0.8277 (m-30) cc_final: 0.7970 (m-30) REVERT: R 255 VAL cc_start: 0.7761 (p) cc_final: 0.7528 (t) REVERT: S 256 GLN cc_start: 0.7949 (tt0) cc_final: 0.7732 (mt0) REVERT: T 31 GLN cc_start: 0.7817 (OUTLIER) cc_final: 0.7012 (tt0) REVERT: T 95 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.6704 (tm-30) REVERT: T 118 ASP cc_start: 0.7852 (m-30) cc_final: 0.7314 (m-30) REVERT: T 122 ASP cc_start: 0.7638 (m-30) cc_final: 0.7244 (m-30) REVERT: U 31 GLN cc_start: 0.7421 (OUTLIER) cc_final: 0.6740 (tp-100) REVERT: U 93 MET cc_start: 0.7933 (OUTLIER) cc_final: 0.7568 (mtt) REVERT: V 77 ASP cc_start: 0.7851 (m-30) cc_final: 0.7487 (m-30) REVERT: W 245 GLN cc_start: 0.6909 (mp10) cc_final: 0.6359 (mm-40) REVERT: X 95 GLU cc_start: 0.6519 (tt0) cc_final: 0.6197 (tt0) REVERT: X 252 GLN cc_start: 0.7152 (tp-100) cc_final: 0.6801 (mt0) REVERT: X 256 GLN cc_start: 0.6933 (tp-100) cc_final: 0.6115 (pt0) REVERT: Y 88 ASP cc_start: 0.8294 (m-30) cc_final: 0.8085 (m-30) REVERT: Y 122 ASP cc_start: 0.8671 (m-30) cc_final: 0.8451 (m-30) REVERT: Z 116 ASP cc_start: 0.7570 (m-30) cc_final: 0.7355 (m-30) REVERT: Z 256 GLN cc_start: 0.7686 (mm110) cc_final: 0.7333 (mt0) REVERT: a 151 ASN cc_start: 0.8347 (t0) cc_final: 0.7907 (t0) REVERT: a 240 GLU cc_start: 0.7277 (mm-30) cc_final: 0.6895 (mm-30) REVERT: a 262 ASN cc_start: 0.7250 (t0) cc_final: 0.6998 (m-40) REVERT: b 32 ARG cc_start: 0.7425 (OUTLIER) cc_final: 0.6260 (ttp-170) REVERT: c 93 MET cc_start: 0.8335 (ttm) cc_final: 0.8119 (mtp) REVERT: d 31 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7561 (tm-30) REVERT: d 256 GLN cc_start: 0.7908 (tp-100) cc_final: 0.7539 (mt0) REVERT: e 31 GLN cc_start: 0.7216 (pp30) cc_final: 0.6231 (mm110) REVERT: e 105 LEU cc_start: 0.8016 (mt) cc_final: 0.7648 (mt) REVERT: f 95 GLU cc_start: 0.5841 (tp30) cc_final: 0.5551 (tt0) REVERT: h 144 THR cc_start: 0.8624 (t) cc_final: 0.8271 (m) REVERT: g 25 GLU cc_start: 0.7244 (mm-30) cc_final: 0.6291 (mt-10) outliers start: 162 outliers final: 71 residues processed: 715 average time/residue: 1.3273 time to fit residues: 1279.0378 Evaluate side-chains 631 residues out of total 7560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 548 time to evaluate : 5.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 252 GLN Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 256 GLN Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 220 LYS Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 251 GLN Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain H residue 30 GLN Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 239 LYS Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain J residue 77 ASP Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain K residue 8 THR Chi-restraints excluded: chain K residue 88 ASP Chi-restraints excluded: chain K residue 195 GLN Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain L residue 30 GLN Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 191 ASP Chi-restraints excluded: chain L residue 223 ASP Chi-restraints excluded: chain O residue 123 GLN Chi-restraints excluded: chain O residue 172 THR Chi-restraints excluded: chain O residue 186 MET Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 243 LYS Chi-restraints excluded: chain P residue 245 GLN Chi-restraints excluded: chain R residue 61 SER Chi-restraints excluded: chain T residue 27 THR Chi-restraints excluded: chain T residue 31 GLN Chi-restraints excluded: chain T residue 88 ASP Chi-restraints excluded: chain T residue 95 GLU Chi-restraints excluded: chain U residue 31 GLN Chi-restraints excluded: chain U residue 93 MET Chi-restraints excluded: chain V residue 27 THR Chi-restraints excluded: chain V residue 84 ASP Chi-restraints excluded: chain V residue 246 SER Chi-restraints excluded: chain W residue 56 SER Chi-restraints excluded: chain W residue 159 VAL Chi-restraints excluded: chain Z residue 264 SER Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain b residue 32 ARG Chi-restraints excluded: chain b residue 101 SER Chi-restraints excluded: chain b residue 226 ASP Chi-restraints excluded: chain c residue 101 SER Chi-restraints excluded: chain c residue 147 THR Chi-restraints excluded: chain c residue 159 VAL Chi-restraints excluded: chain c residue 233 VAL Chi-restraints excluded: chain d residue 31 GLN Chi-restraints excluded: chain d residue 258 LEU Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain e residue 187 ILE Chi-restraints excluded: chain f residue 101 SER Chi-restraints excluded: chain f residue 153 ASP Chi-restraints excluded: chain f residue 174 THR Chi-restraints excluded: chain h residue 109 SER Chi-restraints excluded: chain h residue 172 THR Chi-restraints excluded: chain i residue 136 VAL Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 136 VAL Chi-restraints excluded: chain g residue 14 ILE Chi-restraints excluded: chain g residue 138 ILE Chi-restraints excluded: chain g residue 159 VAL Chi-restraints excluded: chain g residue 174 THR Chi-restraints excluded: chain g residue 207 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 873 optimal weight: 1.9990 chunk 664 optimal weight: 0.9990 chunk 458 optimal weight: 0.4980 chunk 97 optimal weight: 8.9990 chunk 422 optimal weight: 5.9990 chunk 593 optimal weight: 9.9990 chunk 887 optimal weight: 0.9980 chunk 939 optimal weight: 2.9990 chunk 463 optimal weight: 1.9990 chunk 841 optimal weight: 3.9990 chunk 253 optimal weight: 10.0000 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 GLN D 23 ASN F 31 GLN ** F 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 263 GLN H 45 ASN I 195 GLN I 199 ASN J 30 GLN ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 55 GLN L 199 ASN P 130 ASN ** S 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 123 GLN U 31 GLN U 130 ASN ** V 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 123 GLN V 252 GLN ** W 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 151 ASN a 245 GLN b 245 GLN ** f 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 70056 Z= 0.167 Angle : 0.415 9.213 94824 Z= 0.239 Chirality : 0.032 0.178 12204 Planarity : 0.002 0.042 12132 Dihedral : 3.559 27.715 9794 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Rotamer: Outliers : 2.02 % Allowed : 9.47 % Favored : 88.51 % 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: 4.34 (0.08), residues: 9648 helix: 3.75 (0.06), residues: 6804 sheet: -2.06 (0.24), residues: 360 loop : 1.10 (0.14), residues: 2484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Q 49 HIS 0.004 0.001 HIS J 214 PHE 0.016 0.001 PHE b 117 ARG 0.009 0.000 ARG A 121 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 791 residues out of total 7560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 638 time to evaluate : 5.925 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7717 (mt0) cc_final: 0.7278 (tm-30) REVERT: B 126 LYS cc_start: 0.7154 (mmmm) cc_final: 0.6730 (mtmt) REVERT: B 240 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7287 (mm-30) REVERT: B 252 GLN cc_start: 0.7705 (OUTLIER) cc_final: 0.6884 (mp10) REVERT: C 67 ASP cc_start: 0.7561 (m-30) cc_final: 0.7238 (m-30) REVERT: C 191 ASP cc_start: 0.8305 (t0) cc_final: 0.7981 (t0) REVERT: D 20 ASN cc_start: 0.8250 (m110) cc_final: 0.7814 (m110) REVERT: D 212 ASP cc_start: 0.8186 (t70) cc_final: 0.7815 (m-30) REVERT: E 31 GLN cc_start: 0.7259 (tm-30) cc_final: 0.6717 (mt0) REVERT: E 88 ASP cc_start: 0.7835 (m-30) cc_final: 0.7443 (m-30) REVERT: E 95 GLU cc_start: 0.6090 (mm-30) cc_final: 0.5834 (mm-30) REVERT: E 177 PHE cc_start: 0.7391 (p90) cc_final: 0.7007 (p90) REVERT: F 67 ASP cc_start: 0.7714 (m-30) cc_final: 0.7485 (m-30) REVERT: H 98 LEU cc_start: 0.6774 (OUTLIER) cc_final: 0.6322 (tt) REVERT: I 236 ASP cc_start: 0.7344 (t0) cc_final: 0.7066 (t70) REVERT: J 45 ASN cc_start: 0.8687 (t0) cc_final: 0.8407 (t0) REVERT: J 77 ASP cc_start: 0.8473 (OUTLIER) cc_final: 0.8105 (m-30) REVERT: K 195 GLN cc_start: 0.7948 (OUTLIER) cc_final: 0.7488 (tt0) REVERT: K 243 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7651 (mmtt) REVERT: L 95 GLU cc_start: 0.7495 (tm-30) cc_final: 0.6510 (tt0) REVERT: L 206 THR cc_start: 0.7812 (t) cc_final: 0.7485 (m) REVERT: M 38 LYS cc_start: 0.7172 (ptmt) cc_final: 0.6596 (pttm) REVERT: N 31 GLN cc_start: 0.6503 (OUTLIER) cc_final: 0.6280 (mp10) REVERT: P 9 ASN cc_start: 0.7761 (t0) cc_final: 0.7312 (t0) REVERT: P 118 ASP cc_start: 0.7783 (m-30) cc_final: 0.7252 (m-30) REVERT: P 245 GLN cc_start: 0.7534 (OUTLIER) cc_final: 0.6276 (mp10) REVERT: Q 43 LYS cc_start: 0.6837 (mptt) cc_final: 0.6490 (mtpt) REVERT: Q 93 MET cc_start: 0.6290 (mtp) cc_final: 0.6023 (mtm) REVERT: Q 176 THR cc_start: 0.8124 (t) cc_final: 0.7781 (m) REVERT: R 122 ASP cc_start: 0.7234 (m-30) cc_final: 0.6929 (m-30) REVERT: R 220 LYS cc_start: 0.5764 (OUTLIER) cc_final: 0.4071 (mtpt) REVERT: R 226 ASP cc_start: 0.8205 (m-30) cc_final: 0.7881 (m-30) REVERT: R 255 VAL cc_start: 0.7666 (p) cc_final: 0.7427 (t) REVERT: S 256 GLN cc_start: 0.7998 (tt0) cc_final: 0.7753 (mt0) REVERT: T 95 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.6544 (tm-30) REVERT: T 118 ASP cc_start: 0.7860 (m-30) cc_final: 0.7444 (m-30) REVERT: T 122 ASP cc_start: 0.7574 (m-30) cc_final: 0.7198 (m-30) REVERT: T 245 GLN cc_start: 0.7220 (OUTLIER) cc_final: 0.6913 (mp10) REVERT: U 93 MET cc_start: 0.7749 (OUTLIER) cc_final: 0.7348 (mtt) REVERT: V 77 ASP cc_start: 0.7825 (m-30) cc_final: 0.7488 (m-30) REVERT: X 90 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7392 (tp) REVERT: X 95 GLU cc_start: 0.6464 (tt0) cc_final: 0.6108 (tt0) REVERT: X 252 GLN cc_start: 0.7251 (tp-100) cc_final: 0.6840 (mt0) REVERT: Y 122 ASP cc_start: 0.8648 (m-30) cc_final: 0.8389 (m-30) REVERT: Z 116 ASP cc_start: 0.7516 (m-30) cc_final: 0.7083 (m-30) REVERT: Z 256 GLN cc_start: 0.7665 (mm110) cc_final: 0.7311 (mt0) REVERT: a 151 ASN cc_start: 0.8325 (t0) cc_final: 0.7862 (t0) REVERT: a 239 LYS cc_start: 0.7574 (OUTLIER) cc_final: 0.7264 (ptpt) REVERT: b 32 ARG cc_start: 0.7234 (OUTLIER) cc_final: 0.6066 (ttp-170) REVERT: b 105 LEU cc_start: 0.6671 (OUTLIER) cc_final: 0.6454 (pp) REVERT: c 93 MET cc_start: 0.8286 (ttm) cc_final: 0.8067 (mtp) REVERT: c 195 GLN cc_start: 0.7537 (OUTLIER) cc_final: 0.6762 (mm110) REVERT: d 31 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.7509 (tm-30) REVERT: d 245 GLN cc_start: 0.7724 (OUTLIER) cc_final: 0.6926 (mt0) REVERT: d 256 GLN cc_start: 0.7941 (tp-100) cc_final: 0.7523 (mt0) REVERT: e 31 GLN cc_start: 0.7192 (pp30) cc_final: 0.6126 (mm-40) REVERT: e 105 LEU cc_start: 0.8019 (mt) cc_final: 0.7627 (mt) REVERT: h 144 THR cc_start: 0.8608 (t) cc_final: 0.8252 (m) REVERT: h 263 GLN cc_start: 0.7969 (mm-40) cc_final: 0.7699 (mm110) REVERT: i 84 ASP cc_start: 0.6692 (t0) cc_final: 0.6076 (t0) REVERT: j 191 ASP cc_start: 0.7316 (t0) cc_final: 0.7098 (m-30) REVERT: g 25 GLU cc_start: 0.7268 (mm-30) cc_final: 0.6293 (mt-10) outliers start: 153 outliers final: 59 residues processed: 753 average time/residue: 1.2749 time to fit residues: 1308.6900 Evaluate side-chains 644 residues out of total 7560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 567 time to evaluate : 6.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 252 GLN Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain H residue 30 GLN Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain J residue 77 ASP Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain K residue 195 GLN Chi-restraints excluded: chain K residue 243 LYS Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 221 LEU Chi-restraints excluded: chain N residue 31 GLN Chi-restraints excluded: chain O residue 186 MET Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 186 MET Chi-restraints excluded: chain P residue 243 LYS Chi-restraints excluded: chain P residue 245 GLN Chi-restraints excluded: chain Q residue 31 GLN Chi-restraints excluded: chain Q residue 243 LYS Chi-restraints excluded: chain R residue 220 LYS Chi-restraints excluded: chain T residue 77 ASP Chi-restraints excluded: chain T residue 95 GLU Chi-restraints excluded: chain T residue 245 GLN Chi-restraints excluded: chain U residue 16 LEU Chi-restraints excluded: chain U residue 93 MET Chi-restraints excluded: chain V residue 27 THR Chi-restraints excluded: chain V residue 84 ASP Chi-restraints excluded: chain V residue 246 SER Chi-restraints excluded: chain W residue 159 VAL Chi-restraints excluded: chain X residue 90 LEU Chi-restraints excluded: chain Z residue 232 LEU Chi-restraints excluded: chain a residue 239 LYS Chi-restraints excluded: chain b residue 29 VAL Chi-restraints excluded: chain b residue 32 ARG Chi-restraints excluded: chain b residue 101 SER Chi-restraints excluded: chain b residue 105 LEU Chi-restraints excluded: chain b residue 226 ASP Chi-restraints excluded: chain c residue 101 SER Chi-restraints excluded: chain c residue 147 THR Chi-restraints excluded: chain c residue 159 VAL Chi-restraints excluded: chain c residue 195 GLN Chi-restraints excluded: chain c residue 233 VAL Chi-restraints excluded: chain d residue 31 GLN Chi-restraints excluded: chain d residue 142 SER Chi-restraints excluded: chain d residue 245 GLN Chi-restraints excluded: chain d residue 258 LEU Chi-restraints excluded: chain e residue 65 VAL Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain e residue 187 ILE Chi-restraints excluded: chain f residue 101 SER Chi-restraints excluded: chain f residue 153 ASP Chi-restraints excluded: chain f residue 174 THR Chi-restraints excluded: chain h residue 172 THR Chi-restraints excluded: chain i residue 136 VAL Chi-restraints excluded: chain j residue 136 VAL Chi-restraints excluded: chain g residue 69 LEU Chi-restraints excluded: chain g residue 159 VAL Chi-restraints excluded: chain g residue 174 THR Chi-restraints excluded: chain g residue 179 THR Chi-restraints excluded: chain g residue 207 SER Chi-restraints excluded: chain g residue 269 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 782 optimal weight: 3.9990 chunk 533 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 699 optimal weight: 3.9990 chunk 387 optimal weight: 2.9990 chunk 801 optimal weight: 2.9990 chunk 649 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 479 optimal weight: 9.9990 chunk 843 optimal weight: 10.0000 chunk 237 optimal weight: 7.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 GLN ** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 ASN E 34 ASN F 31 GLN ** F 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 263 GLN I 231 ASN J 30 GLN ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 199 ASN M 4 ASN O 130 ASN P 130 ASN ** Q 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 231 ASN R 263 GLN ** S 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 262 ASN T 123 GLN U 130 ASN ** V 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 151 ASN Z 151 ASN ** a 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 245 GLN ** b 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 245 GLN e 73 GLN ** f 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 7 ASN i 18 ASN ** i 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 262 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 70056 Z= 0.234 Angle : 0.458 8.646 94824 Z= 0.259 Chirality : 0.034 0.296 12204 Planarity : 0.002 0.030 12132 Dihedral : 3.635 18.067 9792 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 2.22 % Allowed : 10.32 % Favored : 87.46 % 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: 4.17 (0.08), residues: 9648 helix: 3.63 (0.06), residues: 6804 sheet: -1.93 (0.24), residues: 360 loop : 0.96 (0.13), residues: 2484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 49 HIS 0.005 0.001 HIS J 214 PHE 0.020 0.002 PHE Q 117 ARG 0.006 0.000 ARG A 121 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 751 residues out of total 7560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 583 time to evaluate : 5.879 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7744 (mt0) cc_final: 0.7344 (tm-30) REVERT: B 126 LYS cc_start: 0.7250 (mmmm) cc_final: 0.6775 (mtmt) REVERT: B 240 GLU cc_start: 0.7675 (mm-30) cc_final: 0.7331 (mm-30) REVERT: B 252 GLN cc_start: 0.7703 (OUTLIER) cc_final: 0.6855 (mp10) REVERT: C 67 ASP cc_start: 0.7515 (m-30) cc_final: 0.7161 (m-30) REVERT: C 191 ASP cc_start: 0.8343 (t0) cc_final: 0.8024 (t0) REVERT: D 20 ASN cc_start: 0.8310 (m110) cc_final: 0.7837 (m110) REVERT: D 212 ASP cc_start: 0.8200 (t70) cc_final: 0.7808 (m-30) REVERT: E 31 GLN cc_start: 0.7293 (tm-30) cc_final: 0.6864 (mt0) REVERT: E 88 ASP cc_start: 0.7847 (m-30) cc_final: 0.7451 (m-30) REVERT: E 94 LYS cc_start: 0.8050 (tttm) cc_final: 0.7844 (tmmm) REVERT: E 95 GLU cc_start: 0.6314 (mm-30) cc_final: 0.6039 (mm-30) REVERT: E 220 LYS cc_start: 0.6872 (OUTLIER) cc_final: 0.6616 (mmtt) REVERT: H 98 LEU cc_start: 0.6744 (OUTLIER) cc_final: 0.6366 (tt) REVERT: I 236 ASP cc_start: 0.7328 (t0) cc_final: 0.7080 (t70) REVERT: J 45 ASN cc_start: 0.8734 (t0) cc_final: 0.8407 (t0) REVERT: K 195 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.7511 (tt0) REVERT: K 243 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7676 (mmtt) REVERT: L 206 THR cc_start: 0.7875 (t) cc_final: 0.7560 (m) REVERT: M 38 LYS cc_start: 0.7195 (ptmt) cc_final: 0.6629 (pttm) REVERT: N 31 GLN cc_start: 0.6528 (OUTLIER) cc_final: 0.6172 (mp10) REVERT: P 9 ASN cc_start: 0.7787 (t0) cc_final: 0.7352 (t0) REVERT: P 245 GLN cc_start: 0.7605 (OUTLIER) cc_final: 0.6254 (mp10) REVERT: Q 43 LYS cc_start: 0.6889 (mptt) cc_final: 0.6462 (mtpt) REVERT: Q 93 MET cc_start: 0.6407 (mtp) cc_final: 0.6182 (mtm) REVERT: Q 176 THR cc_start: 0.8179 (t) cc_final: 0.7759 (m) REVERT: R 29 VAL cc_start: 0.7938 (t) cc_final: 0.7680 (p) REVERT: R 67 ASP cc_start: 0.7489 (m-30) cc_final: 0.6991 (t0) REVERT: R 122 ASP cc_start: 0.7242 (m-30) cc_final: 0.6969 (m-30) REVERT: R 220 LYS cc_start: 0.5844 (OUTLIER) cc_final: 0.4116 (mtpt) REVERT: R 226 ASP cc_start: 0.8264 (m-30) cc_final: 0.7951 (m-30) REVERT: R 255 VAL cc_start: 0.7787 (p) cc_final: 0.7552 (t) REVERT: S 256 GLN cc_start: 0.8071 (tt0) cc_final: 0.7737 (mt0) REVERT: T 95 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.6824 (tm-30) REVERT: T 118 ASP cc_start: 0.7851 (m-30) cc_final: 0.7434 (m-30) REVERT: T 122 ASP cc_start: 0.7567 (m-30) cc_final: 0.7178 (m-30) REVERT: T 212 ASP cc_start: 0.7830 (OUTLIER) cc_final: 0.7580 (m-30) REVERT: T 245 GLN cc_start: 0.7248 (OUTLIER) cc_final: 0.6951 (mp10) REVERT: U 93 MET cc_start: 0.7977 (OUTLIER) cc_final: 0.7618 (mtt) REVERT: V 77 ASP cc_start: 0.7895 (m-30) cc_final: 0.7533 (m-30) REVERT: X 90 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7412 (tp) REVERT: X 95 GLU cc_start: 0.6420 (tt0) cc_final: 0.6090 (tt0) REVERT: Z 116 ASP cc_start: 0.7549 (m-30) cc_final: 0.7123 (m-30) REVERT: Z 256 GLN cc_start: 0.7678 (mm110) cc_final: 0.7324 (mt0) REVERT: a 151 ASN cc_start: 0.8328 (t0) cc_final: 0.7865 (t0) REVERT: a 240 GLU cc_start: 0.7234 (mm-30) cc_final: 0.6973 (mm-30) REVERT: b 32 ARG cc_start: 0.7311 (OUTLIER) cc_final: 0.6073 (ttp-170) REVERT: c 93 MET cc_start: 0.8352 (ttm) cc_final: 0.8128 (mtp) REVERT: c 195 GLN cc_start: 0.7541 (OUTLIER) cc_final: 0.6763 (mm110) REVERT: d 31 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7560 (tm-30) REVERT: d 245 GLN cc_start: 0.7773 (OUTLIER) cc_final: 0.6954 (mt0) REVERT: d 256 GLN cc_start: 0.7956 (tp-100) cc_final: 0.7525 (mt0) REVERT: e 31 GLN cc_start: 0.7225 (pp30) cc_final: 0.6145 (mm110) REVERT: e 105 LEU cc_start: 0.7977 (mt) cc_final: 0.7610 (mt) REVERT: f 95 GLU cc_start: 0.5836 (tp30) cc_final: 0.5622 (tt0) REVERT: f 263 GLN cc_start: 0.7149 (tp-100) cc_final: 0.6529 (mt0) REVERT: h 144 THR cc_start: 0.8558 (t) cc_final: 0.8219 (m) REVERT: h 263 GLN cc_start: 0.8021 (mm-40) cc_final: 0.7772 (mm110) REVERT: j 191 ASP cc_start: 0.7379 (t0) cc_final: 0.7153 (m-30) REVERT: g 25 GLU cc_start: 0.7313 (mm-30) cc_final: 0.6358 (mt-10) REVERT: g 123 GLN cc_start: 0.4458 (mp10) cc_final: 0.3844 (mm-40) outliers start: 168 outliers final: 81 residues processed: 705 average time/residue: 1.3195 time to fit residues: 1255.7155 Evaluate side-chains 654 residues out of total 7560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 556 time to evaluate : 5.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 252 GLN Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 220 LYS Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain F residue 31 GLN Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain H residue 30 GLN Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain J residue 77 ASP Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain J residue 151 ASN Chi-restraints excluded: chain K residue 8 THR Chi-restraints excluded: chain K residue 195 GLN Chi-restraints excluded: chain K residue 243 LYS Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 256 GLN Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain L residue 30 GLN Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 191 ASP Chi-restraints excluded: chain L residue 221 LEU Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain N residue 31 GLN Chi-restraints excluded: chain O residue 123 GLN Chi-restraints excluded: chain O residue 172 THR Chi-restraints excluded: chain O residue 186 MET Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 243 LYS Chi-restraints excluded: chain P residue 245 GLN Chi-restraints excluded: chain P residue 267 SER Chi-restraints excluded: chain Q residue 31 GLN Chi-restraints excluded: chain Q residue 243 LYS Chi-restraints excluded: chain R residue 61 SER Chi-restraints excluded: chain R residue 220 LYS Chi-restraints excluded: chain T residue 77 ASP Chi-restraints excluded: chain T residue 95 GLU Chi-restraints excluded: chain T residue 212 ASP Chi-restraints excluded: chain T residue 245 GLN Chi-restraints excluded: chain U residue 16 LEU Chi-restraints excluded: chain U residue 93 MET Chi-restraints excluded: chain V residue 27 THR Chi-restraints excluded: chain V residue 84 ASP Chi-restraints excluded: chain V residue 246 SER Chi-restraints excluded: chain W residue 56 SER Chi-restraints excluded: chain W residue 159 VAL Chi-restraints excluded: chain X residue 90 LEU Chi-restraints excluded: chain X residue 269 LEU Chi-restraints excluded: chain Z residue 232 LEU Chi-restraints excluded: chain Z residue 264 SER Chi-restraints excluded: chain b residue 32 ARG Chi-restraints excluded: chain b residue 101 SER Chi-restraints excluded: chain b residue 226 ASP Chi-restraints excluded: chain c residue 45 ASN Chi-restraints excluded: chain c residue 86 ILE Chi-restraints excluded: chain c residue 101 SER Chi-restraints excluded: chain c residue 147 THR Chi-restraints excluded: chain c residue 159 VAL Chi-restraints excluded: chain c residue 195 GLN Chi-restraints excluded: chain c residue 233 VAL Chi-restraints excluded: chain d residue 31 GLN Chi-restraints excluded: chain d residue 142 SER Chi-restraints excluded: chain d residue 245 GLN Chi-restraints excluded: chain e residue 65 VAL Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain e residue 187 ILE Chi-restraints excluded: chain e residue 204 LEU Chi-restraints excluded: chain f residue 101 SER Chi-restraints excluded: chain f residue 153 ASP Chi-restraints excluded: chain f residue 173 THR Chi-restraints excluded: chain f residue 174 THR Chi-restraints excluded: chain h residue 109 SER Chi-restraints excluded: chain h residue 172 THR Chi-restraints excluded: chain i residue 136 VAL Chi-restraints excluded: chain j residue 136 VAL Chi-restraints excluded: chain g residue 5 SER Chi-restraints excluded: chain g residue 14 ILE Chi-restraints excluded: chain g residue 159 VAL Chi-restraints excluded: chain g residue 174 THR Chi-restraints excluded: chain g residue 207 SER Chi-restraints excluded: chain g residue 269 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 316 optimal weight: 6.9990 chunk 846 optimal weight: 0.8980 chunk 185 optimal weight: 0.8980 chunk 551 optimal weight: 3.9990 chunk 231 optimal weight: 9.9990 chunk 940 optimal weight: 2.9990 chunk 780 optimal weight: 6.9990 chunk 435 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 311 optimal weight: 4.9990 chunk 493 optimal weight: 0.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 ASN F 31 GLN ** F 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 263 GLN I 199 ASN J 30 GLN ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 199 ASN ** Q 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 231 ASN ** S 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 123 GLN U 130 ASN ** V 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 123 GLN ** W 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 30 GLN Z 151 ASN Z 231 ASN ** a 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 245 GLN ** b 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 245 GLN d 73 GLN e 73 GLN ** f 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 63 ASN g 256 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 70056 Z= 0.167 Angle : 0.413 9.970 94824 Z= 0.238 Chirality : 0.032 0.178 12204 Planarity : 0.002 0.030 12132 Dihedral : 3.502 18.686 9792 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 1.96 % Allowed : 10.91 % Favored : 87.13 % 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: 4.41 (0.08), residues: 9648 helix: 3.84 (0.06), residues: 6804 sheet: -1.73 (0.24), residues: 360 loop : 0.93 (0.14), residues: 2484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Q 49 HIS 0.004 0.001 HIS J 214 PHE 0.017 0.001 PHE R 110 ARG 0.009 0.000 ARG L 121 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 768 residues out of total 7560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 620 time to evaluate : 5.860 Fit side-chains REVERT: A 31 GLN cc_start: 0.7698 (mt0) cc_final: 0.7299 (tm-30) REVERT: B 126 LYS cc_start: 0.7209 (mmmm) cc_final: 0.6734 (mtmt) REVERT: B 240 GLU cc_start: 0.7643 (mm-30) cc_final: 0.7296 (mm-30) REVERT: B 252 GLN cc_start: 0.7665 (OUTLIER) cc_final: 0.6852 (mp10) REVERT: C 67 ASP cc_start: 0.7566 (m-30) cc_final: 0.7243 (m-30) REVERT: C 191 ASP cc_start: 0.8311 (t0) cc_final: 0.7998 (t0) REVERT: D 20 ASN cc_start: 0.8270 (m110) cc_final: 0.7809 (m110) REVERT: D 212 ASP cc_start: 0.8187 (t70) cc_final: 0.7813 (m-30) REVERT: E 31 GLN cc_start: 0.7281 (tm-30) cc_final: 0.6790 (mt0) REVERT: E 84 ASP cc_start: 0.6728 (OUTLIER) cc_final: 0.6414 (m-30) REVERT: E 88 ASP cc_start: 0.7836 (m-30) cc_final: 0.7446 (m-30) REVERT: E 95 GLU cc_start: 0.6183 (mm-30) cc_final: 0.5873 (mm-30) REVERT: E 177 PHE cc_start: 0.7256 (p90) cc_final: 0.6925 (p90) REVERT: E 220 LYS cc_start: 0.6869 (OUTLIER) cc_final: 0.6562 (mmtt) REVERT: F 32 ARG cc_start: 0.7302 (OUTLIER) cc_final: 0.6866 (ttm170) REVERT: F 67 ASP cc_start: 0.7724 (m-30) cc_final: 0.7523 (m-30) REVERT: H 98 LEU cc_start: 0.6655 (OUTLIER) cc_final: 0.6267 (tt) REVERT: I 236 ASP cc_start: 0.7314 (t0) cc_final: 0.7050 (t70) REVERT: J 45 ASN cc_start: 0.8644 (t0) cc_final: 0.8280 (t0) REVERT: J 77 ASP cc_start: 0.8474 (OUTLIER) cc_final: 0.8112 (m-30) REVERT: K 32 ARG cc_start: 0.7051 (OUTLIER) cc_final: 0.6841 (mtt90) REVERT: K 195 GLN cc_start: 0.7937 (OUTLIER) cc_final: 0.7479 (tt0) REVERT: K 243 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7664 (mmtt) REVERT: L 95 GLU cc_start: 0.7392 (tm-30) cc_final: 0.6346 (tt0) REVERT: L 206 THR cc_start: 0.7802 (t) cc_final: 0.7476 (m) REVERT: M 38 LYS cc_start: 0.7197 (ptmt) cc_final: 0.6675 (pttm) REVERT: P 9 ASN cc_start: 0.7831 (t0) cc_final: 0.7401 (t0) REVERT: P 245 GLN cc_start: 0.7515 (OUTLIER) cc_final: 0.6192 (mp10) REVERT: Q 43 LYS cc_start: 0.6864 (mptt) cc_final: 0.6417 (mtpt) REVERT: Q 176 THR cc_start: 0.8175 (t) cc_final: 0.7813 (m) REVERT: R 122 ASP cc_start: 0.7201 (m-30) cc_final: 0.6904 (m-30) REVERT: R 226 ASP cc_start: 0.8214 (m-30) cc_final: 0.7916 (m-30) REVERT: R 255 VAL cc_start: 0.7714 (p) cc_final: 0.7498 (t) REVERT: S 256 GLN cc_start: 0.8073 (tt0) cc_final: 0.7743 (mt0) REVERT: T 95 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.6618 (tm-30) REVERT: T 118 ASP cc_start: 0.7782 (m-30) cc_final: 0.7346 (m-30) REVERT: T 122 ASP cc_start: 0.7573 (m-30) cc_final: 0.7178 (m-30) REVERT: T 212 ASP cc_start: 0.7825 (OUTLIER) cc_final: 0.7589 (m-30) REVERT: T 245 GLN cc_start: 0.7218 (OUTLIER) cc_final: 0.6934 (mp10) REVERT: V 77 ASP cc_start: 0.7828 (m-30) cc_final: 0.7501 (m-30) REVERT: X 95 GLU cc_start: 0.6573 (tt0) cc_final: 0.6261 (tt0) REVERT: X 252 GLN cc_start: 0.7102 (tm-30) cc_final: 0.6665 (mt0) REVERT: Y 122 ASP cc_start: 0.8642 (m-30) cc_final: 0.8427 (m-30) REVERT: Z 116 ASP cc_start: 0.7530 (m-30) cc_final: 0.7082 (m-30) REVERT: Z 256 GLN cc_start: 0.7668 (mm110) cc_final: 0.7314 (mt0) REVERT: a 151 ASN cc_start: 0.8352 (t0) cc_final: 0.7876 (t0) REVERT: a 262 ASN cc_start: 0.7303 (t0) cc_final: 0.7053 (m-40) REVERT: b 62 MET cc_start: 0.8270 (mmt) cc_final: 0.7718 (mmt) REVERT: b 240 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7686 (mm-30) REVERT: c 93 MET cc_start: 0.8345 (ttm) cc_final: 0.8127 (mtp) REVERT: c 195 GLN cc_start: 0.7528 (OUTLIER) cc_final: 0.6771 (mm110) REVERT: d 31 GLN cc_start: 0.7901 (OUTLIER) cc_final: 0.7503 (tm-30) REVERT: d 245 GLN cc_start: 0.7743 (OUTLIER) cc_final: 0.6924 (mt0) REVERT: d 256 GLN cc_start: 0.7949 (tp-100) cc_final: 0.7500 (mt0) REVERT: e 105 LEU cc_start: 0.8030 (mt) cc_final: 0.7665 (mt) REVERT: f 95 GLU cc_start: 0.5859 (tp30) cc_final: 0.5638 (tt0) REVERT: f 263 GLN cc_start: 0.7140 (tp-100) cc_final: 0.6486 (mt0) REVERT: h 144 THR cc_start: 0.8564 (t) cc_final: 0.8220 (m) REVERT: h 263 GLN cc_start: 0.7934 (mm-40) cc_final: 0.7693 (mm110) REVERT: i 84 ASP cc_start: 0.6708 (t0) cc_final: 0.6025 (t0) REVERT: j 191 ASP cc_start: 0.7352 (t0) cc_final: 0.7121 (m-30) REVERT: g 25 GLU cc_start: 0.7292 (mm-30) cc_final: 0.6326 (mt-10) REVERT: g 123 GLN cc_start: 0.4511 (mp10) cc_final: 0.3884 (mm-40) outliers start: 148 outliers final: 72 residues processed: 729 average time/residue: 1.2785 time to fit residues: 1270.0664 Evaluate side-chains 653 residues out of total 7560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 565 time to evaluate : 5.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 252 GLN Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 220 LYS Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain F residue 32 ARG Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain H residue 30 GLN Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain J residue 77 ASP Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain J residue 151 ASN Chi-restraints excluded: chain K residue 32 ARG Chi-restraints excluded: chain K residue 88 ASP Chi-restraints excluded: chain K residue 195 GLN Chi-restraints excluded: chain K residue 243 LYS Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 256 GLN Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain L residue 30 GLN Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 191 ASP Chi-restraints excluded: chain L residue 221 LEU Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain O residue 172 THR Chi-restraints excluded: chain O residue 186 MET Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 243 LYS Chi-restraints excluded: chain P residue 245 GLN Chi-restraints excluded: chain P residue 267 SER Chi-restraints excluded: chain Q residue 243 LYS Chi-restraints excluded: chain R residue 61 SER Chi-restraints excluded: chain T residue 65 VAL Chi-restraints excluded: chain T residue 77 ASP Chi-restraints excluded: chain T residue 88 ASP Chi-restraints excluded: chain T residue 95 GLU Chi-restraints excluded: chain T residue 212 ASP Chi-restraints excluded: chain T residue 245 GLN Chi-restraints excluded: chain U residue 16 LEU Chi-restraints excluded: chain V residue 27 THR Chi-restraints excluded: chain V residue 84 ASP Chi-restraints excluded: chain V residue 124 ILE Chi-restraints excluded: chain V residue 246 SER Chi-restraints excluded: chain W residue 159 VAL Chi-restraints excluded: chain Y residue 233 VAL Chi-restraints excluded: chain Z residue 232 LEU Chi-restraints excluded: chain Z residue 264 SER Chi-restraints excluded: chain a residue 45 ASN Chi-restraints excluded: chain b residue 29 VAL Chi-restraints excluded: chain b residue 101 SER Chi-restraints excluded: chain b residue 226 ASP Chi-restraints excluded: chain c residue 45 ASN Chi-restraints excluded: chain c residue 101 SER Chi-restraints excluded: chain c residue 147 THR Chi-restraints excluded: chain c residue 159 VAL Chi-restraints excluded: chain c residue 195 GLN Chi-restraints excluded: chain c residue 231 ASN Chi-restraints excluded: chain c residue 233 VAL Chi-restraints excluded: chain d residue 31 GLN Chi-restraints excluded: chain d residue 142 SER Chi-restraints excluded: chain d residue 245 GLN Chi-restraints excluded: chain e residue 65 VAL Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain e residue 187 ILE Chi-restraints excluded: chain e residue 260 ILE Chi-restraints excluded: chain f residue 101 SER Chi-restraints excluded: chain f residue 153 ASP Chi-restraints excluded: chain f residue 174 THR Chi-restraints excluded: chain h residue 109 SER Chi-restraints excluded: chain h residue 172 THR Chi-restraints excluded: chain i residue 136 VAL Chi-restraints excluded: chain g residue 14 ILE Chi-restraints excluded: chain g residue 174 THR Chi-restraints excluded: chain g residue 207 SER Chi-restraints excluded: chain g residue 269 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 906 optimal weight: 0.5980 chunk 106 optimal weight: 0.9980 chunk 535 optimal weight: 2.9990 chunk 686 optimal weight: 5.9990 chunk 532 optimal weight: 0.7980 chunk 791 optimal weight: 2.9990 chunk 525 optimal weight: 6.9990 chunk 936 optimal weight: 4.9990 chunk 586 optimal weight: 3.9990 chunk 571 optimal weight: 7.9990 chunk 432 optimal weight: 10.0000 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 ASN F 31 GLN ** F 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 263 GLN J 30 GLN P 130 ASN ** Q 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 231 ASN ** S 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 123 GLN U 130 ASN ** V 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 123 GLN W 30 GLN W 34 ASN ** W 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 151 ASN a 45 ASN a 245 GLN ** b 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 245 GLN e 73 GLN ** f 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 70056 Z= 0.187 Angle : 0.424 9.935 94824 Z= 0.243 Chirality : 0.033 0.193 12204 Planarity : 0.002 0.029 12132 Dihedral : 3.512 17.949 9792 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 2.06 % Allowed : 11.47 % Favored : 86.47 % 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: 4.36 (0.08), residues: 9648 helix: 3.80 (0.06), residues: 6804 sheet: -1.64 (0.24), residues: 360 loop : 0.88 (0.13), residues: 2484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Q 49 HIS 0.004 0.001 HIS J 214 PHE 0.019 0.001 PHE Q 117 ARG 0.009 0.000 ARG L 121 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 747 residues out of total 7560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 591 time to evaluate : 6.247 Fit side-chains REVERT: A 31 GLN cc_start: 0.7697 (mt0) cc_final: 0.7319 (tm-30) REVERT: B 126 LYS cc_start: 0.7228 (mmmm) cc_final: 0.6749 (mtmt) REVERT: B 240 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7302 (mm-30) REVERT: B 252 GLN cc_start: 0.7658 (OUTLIER) cc_final: 0.6845 (mp10) REVERT: C 67 ASP cc_start: 0.7577 (m-30) cc_final: 0.7247 (m-30) REVERT: C 191 ASP cc_start: 0.8293 (t0) cc_final: 0.7977 (t0) REVERT: D 20 ASN cc_start: 0.8342 (m110) cc_final: 0.7890 (m110) REVERT: D 212 ASP cc_start: 0.8177 (t70) cc_final: 0.7780 (m-30) REVERT: E 31 GLN cc_start: 0.7305 (tm-30) cc_final: 0.6833 (mt0) REVERT: E 84 ASP cc_start: 0.6751 (OUTLIER) cc_final: 0.6435 (m-30) REVERT: E 88 ASP cc_start: 0.7850 (m-30) cc_final: 0.7467 (m-30) REVERT: E 220 LYS cc_start: 0.6863 (OUTLIER) cc_final: 0.6560 (mmtt) REVERT: G 240 GLU cc_start: 0.7841 (mp0) cc_final: 0.7618 (mp0) REVERT: H 98 LEU cc_start: 0.6618 (OUTLIER) cc_final: 0.6263 (tt) REVERT: I 236 ASP cc_start: 0.7318 (t0) cc_final: 0.7061 (t70) REVERT: J 45 ASN cc_start: 0.8642 (t0) cc_final: 0.8283 (t0) REVERT: K 32 ARG cc_start: 0.7065 (OUTLIER) cc_final: 0.6853 (mtt90) REVERT: K 195 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7484 (tt0) REVERT: K 243 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7665 (mmtt) REVERT: L 95 GLU cc_start: 0.7403 (tm-30) cc_final: 0.6367 (tt0) REVERT: L 206 THR cc_start: 0.7849 (t) cc_final: 0.7527 (m) REVERT: M 38 LYS cc_start: 0.7207 (ptmt) cc_final: 0.6689 (pttm) REVERT: P 9 ASN cc_start: 0.7899 (t0) cc_final: 0.7456 (t0) REVERT: P 245 GLN cc_start: 0.7529 (OUTLIER) cc_final: 0.6191 (mp10) REVERT: Q 43 LYS cc_start: 0.6802 (mptt) cc_final: 0.6348 (mtpt) REVERT: Q 176 THR cc_start: 0.8224 (t) cc_final: 0.7838 (m) REVERT: R 29 VAL cc_start: 0.7864 (t) cc_final: 0.7597 (p) REVERT: R 122 ASP cc_start: 0.7273 (m-30) cc_final: 0.6993 (m-30) REVERT: R 226 ASP cc_start: 0.8231 (m-30) cc_final: 0.7935 (m-30) REVERT: R 255 VAL cc_start: 0.7734 (p) cc_final: 0.7509 (t) REVERT: S 31 GLN cc_start: 0.7584 (OUTLIER) cc_final: 0.7059 (tp40) REVERT: S 263 GLN cc_start: 0.7778 (OUTLIER) cc_final: 0.7240 (mp10) REVERT: T 95 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.6800 (tm-30) REVERT: T 118 ASP cc_start: 0.7786 (m-30) cc_final: 0.7365 (m-30) REVERT: T 122 ASP cc_start: 0.7532 (m-30) cc_final: 0.7166 (m-30) REVERT: T 212 ASP cc_start: 0.7829 (OUTLIER) cc_final: 0.7594 (m-30) REVERT: T 245 GLN cc_start: 0.7222 (OUTLIER) cc_final: 0.6938 (mp10) REVERT: V 77 ASP cc_start: 0.7850 (m-30) cc_final: 0.7520 (m-30) REVERT: X 95 GLU cc_start: 0.6471 (tt0) cc_final: 0.6128 (tt0) REVERT: X 252 GLN cc_start: 0.7167 (tm-30) cc_final: 0.6673 (mt0) REVERT: Y 122 ASP cc_start: 0.8715 (m-30) cc_final: 0.8496 (m-30) REVERT: Z 116 ASP cc_start: 0.7534 (m-30) cc_final: 0.7095 (m-30) REVERT: Z 256 GLN cc_start: 0.7670 (mm110) cc_final: 0.7312 (mt0) REVERT: a 151 ASN cc_start: 0.8360 (t0) cc_final: 0.7867 (t0) REVERT: b 32 ARG cc_start: 0.7255 (OUTLIER) cc_final: 0.7037 (ttt180) REVERT: c 93 MET cc_start: 0.8334 (ttm) cc_final: 0.8114 (mtp) REVERT: c 195 GLN cc_start: 0.7492 (OUTLIER) cc_final: 0.6763 (mm110) REVERT: d 245 GLN cc_start: 0.7758 (OUTLIER) cc_final: 0.6934 (mt0) REVERT: d 256 GLN cc_start: 0.7960 (tp-100) cc_final: 0.7519 (mt0) REVERT: e 105 LEU cc_start: 0.8032 (mt) cc_final: 0.7666 (mt) REVERT: f 95 GLU cc_start: 0.5960 (tp30) cc_final: 0.5623 (tt0) REVERT: f 263 GLN cc_start: 0.7244 (tp-100) cc_final: 0.6596 (mt0) REVERT: h 144 THR cc_start: 0.8520 (t) cc_final: 0.8180 (m) REVERT: h 263 GLN cc_start: 0.7945 (mm-40) cc_final: 0.7744 (mm110) REVERT: i 84 ASP cc_start: 0.6692 (t0) cc_final: 0.6079 (t0) REVERT: j 191 ASP cc_start: 0.7357 (t0) cc_final: 0.7129 (m-30) REVERT: g 25 GLU cc_start: 0.7357 (mm-30) cc_final: 0.6413 (mt-10) REVERT: g 164 ILE cc_start: 0.7040 (OUTLIER) cc_final: 0.6832 (pt) outliers start: 156 outliers final: 87 residues processed: 710 average time/residue: 1.3243 time to fit residues: 1273.3890 Evaluate side-chains 666 residues out of total 7560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 562 time to evaluate : 5.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 252 GLN Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 220 LYS Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain F residue 31 GLN Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain H residue 30 GLN Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain J residue 77 ASP Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain J residue 151 ASN Chi-restraints excluded: chain K residue 32 ARG Chi-restraints excluded: chain K residue 88 ASP Chi-restraints excluded: chain K residue 195 GLN Chi-restraints excluded: chain K residue 243 LYS Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 256 GLN Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 30 GLN Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 191 ASP Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain O residue 172 THR Chi-restraints excluded: chain O residue 186 MET Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 186 MET Chi-restraints excluded: chain P residue 243 LYS Chi-restraints excluded: chain P residue 245 GLN Chi-restraints excluded: chain P residue 267 SER Chi-restraints excluded: chain Q residue 243 LYS Chi-restraints excluded: chain R residue 61 SER Chi-restraints excluded: chain S residue 31 GLN Chi-restraints excluded: chain S residue 263 GLN Chi-restraints excluded: chain T residue 65 VAL Chi-restraints excluded: chain T residue 77 ASP Chi-restraints excluded: chain T residue 88 ASP Chi-restraints excluded: chain T residue 95 GLU Chi-restraints excluded: chain T residue 212 ASP Chi-restraints excluded: chain T residue 245 GLN Chi-restraints excluded: chain U residue 16 LEU Chi-restraints excluded: chain U residue 106 ASN Chi-restraints excluded: chain V residue 27 THR Chi-restraints excluded: chain V residue 84 ASP Chi-restraints excluded: chain V residue 124 ILE Chi-restraints excluded: chain V residue 198 THR Chi-restraints excluded: chain V residue 246 SER Chi-restraints excluded: chain W residue 56 SER Chi-restraints excluded: chain W residue 159 VAL Chi-restraints excluded: chain X residue 269 LEU Chi-restraints excluded: chain Y residue 233 VAL Chi-restraints excluded: chain Z residue 232 LEU Chi-restraints excluded: chain Z residue 264 SER Chi-restraints excluded: chain b residue 29 VAL Chi-restraints excluded: chain b residue 32 ARG Chi-restraints excluded: chain b residue 101 SER Chi-restraints excluded: chain b residue 226 ASP Chi-restraints excluded: chain c residue 45 ASN Chi-restraints excluded: chain c residue 101 SER Chi-restraints excluded: chain c residue 147 THR Chi-restraints excluded: chain c residue 159 VAL Chi-restraints excluded: chain c residue 195 GLN Chi-restraints excluded: chain c residue 231 ASN Chi-restraints excluded: chain c residue 233 VAL Chi-restraints excluded: chain d residue 142 SER Chi-restraints excluded: chain d residue 245 GLN Chi-restraints excluded: chain d residue 258 LEU Chi-restraints excluded: chain e residue 31 GLN Chi-restraints excluded: chain e residue 65 VAL Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain e residue 179 THR Chi-restraints excluded: chain e residue 187 ILE Chi-restraints excluded: chain f residue 101 SER Chi-restraints excluded: chain f residue 174 THR Chi-restraints excluded: chain f residue 179 THR Chi-restraints excluded: chain h residue 109 SER Chi-restraints excluded: chain h residue 172 THR Chi-restraints excluded: chain i residue 136 VAL Chi-restraints excluded: chain g residue 14 ILE Chi-restraints excluded: chain g residue 69 LEU Chi-restraints excluded: chain g residue 164 ILE Chi-restraints excluded: chain g residue 174 THR Chi-restraints excluded: chain g residue 207 SER Chi-restraints excluded: chain g residue 269 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 579 optimal weight: 3.9990 chunk 374 optimal weight: 6.9990 chunk 559 optimal weight: 5.9990 chunk 282 optimal weight: 0.6980 chunk 184 optimal weight: 4.9990 chunk 181 optimal weight: 0.7980 chunk 595 optimal weight: 7.9990 chunk 638 optimal weight: 6.9990 chunk 463 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 736 optimal weight: 4.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 231 ASN F 263 GLN I 199 ASN J 30 GLN ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 55 GLN ** Q 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 231 ASN R 262 ASN ** S 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 123 GLN T 123 GLN V 30 GLN V 123 GLN W 34 ASN ** W 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 151 ASN a 245 GLN ** b 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 245 GLN c 55 GLN d 106 ASN e 73 GLN ** f 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 231 ASN ** g 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 70056 Z= 0.281 Angle : 0.497 11.000 94824 Z= 0.279 Chirality : 0.036 0.217 12204 Planarity : 0.002 0.036 12132 Dihedral : 3.752 17.834 9792 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.98 % Allowed : 11.77 % Favored : 86.24 % 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: 3.71 (0.08), residues: 9648 helix: 3.31 (0.06), residues: 7020 sheet: -1.66 (0.24), residues: 360 loop : 0.31 (0.14), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Q 49 HIS 0.005 0.002 HIS J 214 PHE 0.018 0.002 PHE R 110 ARG 0.008 0.001 ARG L 121 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 716 residues out of total 7560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 566 time to evaluate : 5.902 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7820 (mt0) cc_final: 0.7391 (tm-30) REVERT: B 126 LYS cc_start: 0.7322 (mmmm) cc_final: 0.6886 (mtmt) REVERT: B 240 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7333 (mm-30) REVERT: C 67 ASP cc_start: 0.7607 (m-30) cc_final: 0.7238 (m-30) REVERT: C 191 ASP cc_start: 0.8341 (t0) cc_final: 0.8043 (t0) REVERT: D 212 ASP cc_start: 0.8218 (t70) cc_final: 0.7804 (m-30) REVERT: E 31 GLN cc_start: 0.7338 (tm-30) cc_final: 0.6777 (mt0) REVERT: E 88 ASP cc_start: 0.7849 (m-30) cc_final: 0.7453 (m-30) REVERT: H 98 LEU cc_start: 0.6691 (OUTLIER) cc_final: 0.6355 (tt) REVERT: H 149 LEU cc_start: 0.7448 (OUTLIER) cc_final: 0.6992 (mp) REVERT: I 236 ASP cc_start: 0.7278 (t0) cc_final: 0.7061 (t70) REVERT: J 45 ASN cc_start: 0.8720 (t0) cc_final: 0.8401 (t0) REVERT: K 92 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7646 (mtpt) REVERT: K 195 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.7495 (tt0) REVERT: K 243 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7678 (mmtt) REVERT: L 206 THR cc_start: 0.7867 (t) cc_final: 0.7573 (m) REVERT: M 38 LYS cc_start: 0.7241 (ptmt) cc_final: 0.6659 (pttm) REVERT: N 31 GLN cc_start: 0.6610 (OUTLIER) cc_final: 0.6225 (mp10) REVERT: O 269 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7728 (mm) REVERT: P 9 ASN cc_start: 0.7903 (t0) cc_final: 0.7471 (t0) REVERT: P 245 GLN cc_start: 0.7618 (OUTLIER) cc_final: 0.6157 (mp10) REVERT: Q 31 GLN cc_start: 0.6520 (OUTLIER) cc_final: 0.5250 (mp10) REVERT: Q 43 LYS cc_start: 0.6755 (mptt) cc_final: 0.6353 (mtpt) REVERT: Q 176 THR cc_start: 0.8341 (t) cc_final: 0.7896 (m) REVERT: Q 263 GLN cc_start: 0.8022 (mp10) cc_final: 0.6668 (pp30) REVERT: R 29 VAL cc_start: 0.8019 (t) cc_final: 0.7769 (p) REVERT: R 122 ASP cc_start: 0.7352 (m-30) cc_final: 0.7101 (m-30) REVERT: R 226 ASP cc_start: 0.8305 (m-30) cc_final: 0.8034 (m-30) REVERT: R 255 VAL cc_start: 0.7814 (p) cc_final: 0.7595 (t) REVERT: T 118 ASP cc_start: 0.7983 (m-30) cc_final: 0.7545 (m-30) REVERT: T 122 ASP cc_start: 0.7506 (m-30) cc_final: 0.7121 (m-30) REVERT: T 212 ASP cc_start: 0.7874 (OUTLIER) cc_final: 0.7609 (m-30) REVERT: V 4 ASN cc_start: 0.7244 (t0) cc_final: 0.7020 (t0) REVERT: V 77 ASP cc_start: 0.7888 (m-30) cc_final: 0.7541 (m-30) REVERT: X 93 MET cc_start: 0.7693 (mtp) cc_final: 0.7085 (mtm) REVERT: X 95 GLU cc_start: 0.6803 (tt0) cc_final: 0.6477 (tt0) REVERT: Z 116 ASP cc_start: 0.7638 (m-30) cc_final: 0.7251 (m-30) REVERT: Z 256 GLN cc_start: 0.7673 (mm110) cc_final: 0.7336 (mt0) REVERT: a 151 ASN cc_start: 0.8351 (t0) cc_final: 0.7836 (t0) REVERT: a 240 GLU cc_start: 0.7255 (mm-30) cc_final: 0.7013 (mm-30) REVERT: b 32 ARG cc_start: 0.7282 (OUTLIER) cc_final: 0.7023 (ttt180) REVERT: c 93 MET cc_start: 0.8440 (ttm) cc_final: 0.8211 (mtp) REVERT: c 195 GLN cc_start: 0.7578 (OUTLIER) cc_final: 0.6816 (mm110) REVERT: d 142 SER cc_start: 0.8806 (OUTLIER) cc_final: 0.8390 (m) REVERT: d 245 GLN cc_start: 0.7817 (OUTLIER) cc_final: 0.6970 (mt0) REVERT: d 256 GLN cc_start: 0.7970 (tp-100) cc_final: 0.7527 (mt0) REVERT: e 31 GLN cc_start: 0.7483 (OUTLIER) cc_final: 0.6211 (mm110) REVERT: e 105 LEU cc_start: 0.7923 (mt) cc_final: 0.7569 (mt) REVERT: f 95 GLU cc_start: 0.5949 (tp30) cc_final: 0.5643 (tt0) REVERT: f 263 GLN cc_start: 0.7375 (tp-100) cc_final: 0.6875 (mt0) REVERT: h 71 ARG cc_start: 0.7649 (ttm110) cc_final: 0.7344 (ttp-110) REVERT: h 144 THR cc_start: 0.8506 (t) cc_final: 0.8191 (m) REVERT: h 263 GLN cc_start: 0.8062 (mm-40) cc_final: 0.7809 (mm110) REVERT: i 30 GLN cc_start: 0.6696 (tt0) cc_final: 0.6426 (mt0) REVERT: i 84 ASP cc_start: 0.6817 (t0) cc_final: 0.6231 (t0) REVERT: i 95 GLU cc_start: 0.7798 (tt0) cc_final: 0.7304 (mt-10) REVERT: g 164 ILE cc_start: 0.7069 (OUTLIER) cc_final: 0.6831 (pt) outliers start: 150 outliers final: 84 residues processed: 682 average time/residue: 1.4367 time to fit residues: 1319.2885 Evaluate side-chains 641 residues out of total 7560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 541 time to evaluate : 5.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain H residue 30 GLN Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain J residue 77 ASP Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain J residue 151 ASN Chi-restraints excluded: chain K residue 8 THR Chi-restraints excluded: chain K residue 92 LYS Chi-restraints excluded: chain K residue 195 GLN Chi-restraints excluded: chain K residue 243 LYS Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 256 GLN Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 30 GLN Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 173 THR Chi-restraints excluded: chain L residue 221 LEU Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain N residue 31 GLN Chi-restraints excluded: chain O residue 172 THR Chi-restraints excluded: chain O residue 186 MET Chi-restraints excluded: chain O residue 269 LEU Chi-restraints excluded: chain P residue 6 ILE Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 243 LYS Chi-restraints excluded: chain P residue 245 GLN Chi-restraints excluded: chain P residue 267 SER Chi-restraints excluded: chain Q residue 31 GLN Chi-restraints excluded: chain Q residue 243 LYS Chi-restraints excluded: chain R residue 61 SER Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain T residue 65 VAL Chi-restraints excluded: chain T residue 77 ASP Chi-restraints excluded: chain T residue 95 GLU Chi-restraints excluded: chain T residue 212 ASP Chi-restraints excluded: chain U residue 16 LEU Chi-restraints excluded: chain V residue 27 THR Chi-restraints excluded: chain V residue 84 ASP Chi-restraints excluded: chain V residue 198 THR Chi-restraints excluded: chain V residue 246 SER Chi-restraints excluded: chain W residue 56 SER Chi-restraints excluded: chain W residue 159 VAL Chi-restraints excluded: chain X residue 269 LEU Chi-restraints excluded: chain Y residue 233 VAL Chi-restraints excluded: chain Z residue 264 SER Chi-restraints excluded: chain a residue 245 GLN Chi-restraints excluded: chain b residue 32 ARG Chi-restraints excluded: chain b residue 101 SER Chi-restraints excluded: chain b residue 226 ASP Chi-restraints excluded: chain c residue 101 SER Chi-restraints excluded: chain c residue 147 THR Chi-restraints excluded: chain c residue 159 VAL Chi-restraints excluded: chain c residue 195 GLN Chi-restraints excluded: chain c residue 233 VAL Chi-restraints excluded: chain d residue 142 SER Chi-restraints excluded: chain d residue 245 GLN Chi-restraints excluded: chain d residue 258 LEU Chi-restraints excluded: chain e residue 31 GLN Chi-restraints excluded: chain e residue 65 VAL Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain e residue 187 ILE Chi-restraints excluded: chain e residue 204 LEU Chi-restraints excluded: chain f residue 101 SER Chi-restraints excluded: chain f residue 153 ASP Chi-restraints excluded: chain f residue 174 THR Chi-restraints excluded: chain f residue 179 THR Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 109 SER Chi-restraints excluded: chain h residue 172 THR Chi-restraints excluded: chain i residue 136 VAL Chi-restraints excluded: chain g residue 5 SER Chi-restraints excluded: chain g residue 14 ILE Chi-restraints excluded: chain g residue 164 ILE Chi-restraints excluded: chain g residue 207 SER Chi-restraints excluded: chain g residue 269 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 852 optimal weight: 7.9990 chunk 897 optimal weight: 1.9990 chunk 818 optimal weight: 1.9990 chunk 873 optimal weight: 0.9980 chunk 525 optimal weight: 0.8980 chunk 380 optimal weight: 8.9990 chunk 685 optimal weight: 0.5980 chunk 267 optimal weight: 0.9990 chunk 788 optimal weight: 0.7980 chunk 825 optimal weight: 7.9990 chunk 869 optimal weight: 6.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 31 GLN F 134 ASN F 263 GLN J 30 GLN L 199 ASN ** Q 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 231 ASN S 55 GLN T 123 GLN U 130 ASN V 123 GLN ** W 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 195 GLN Z 151 ASN ** a 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 245 GLN ** c 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 106 ASN e 73 GLN ** f 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 9 ASN ** g 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 70056 Z= 0.148 Angle : 0.407 11.012 94824 Z= 0.234 Chirality : 0.032 0.193 12204 Planarity : 0.002 0.029 12132 Dihedral : 3.434 17.183 9792 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 1.35 % Allowed : 12.61 % Favored : 86.04 % 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: 4.49 (0.09), residues: 9648 helix: 3.93 (0.06), residues: 6804 sheet: -1.44 (0.25), residues: 360 loop : 0.79 (0.14), residues: 2484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP Q 49 HIS 0.003 0.001 HIS J 214 PHE 0.016 0.001 PHE b 117 ARG 0.008 0.000 ARG L 121 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 745 residues out of total 7560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 643 time to evaluate : 5.857 Fit side-chains REVERT: A 31 GLN cc_start: 0.7639 (mt0) cc_final: 0.7267 (tm-30) REVERT: B 126 LYS cc_start: 0.7198 (mmmm) cc_final: 0.6784 (mtmt) REVERT: B 240 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7267 (mm-30) REVERT: C 30 GLN cc_start: 0.7447 (mt0) cc_final: 0.7187 (mt0) REVERT: C 67 ASP cc_start: 0.7537 (m-30) cc_final: 0.7206 (m-30) REVERT: C 191 ASP cc_start: 0.8286 (t0) cc_final: 0.7969 (t0) REVERT: D 20 ASN cc_start: 0.8376 (m110) cc_final: 0.7878 (m110) REVERT: D 212 ASP cc_start: 0.8160 (t70) cc_final: 0.7783 (m-30) REVERT: E 31 GLN cc_start: 0.7210 (tm-30) cc_final: 0.6704 (mt0) REVERT: E 88 ASP cc_start: 0.7818 (m-30) cc_final: 0.7430 (m-30) REVERT: E 177 PHE cc_start: 0.7106 (p90) cc_final: 0.6846 (p90) REVERT: G 240 GLU cc_start: 0.7765 (mp0) cc_final: 0.7563 (mp0) REVERT: J 45 ASN cc_start: 0.8599 (t0) cc_final: 0.8229 (t0) REVERT: K 195 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7553 (tt0) REVERT: K 243 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7591 (mmtt) REVERT: L 95 GLU cc_start: 0.7314 (tm-30) cc_final: 0.6203 (tt0) REVERT: L 206 THR cc_start: 0.7860 (t) cc_final: 0.7515 (m) REVERT: M 38 LYS cc_start: 0.7155 (ptmt) cc_final: 0.6636 (pttm) REVERT: O 9 ASN cc_start: 0.8753 (t0) cc_final: 0.8396 (t0) REVERT: P 9 ASN cc_start: 0.7913 (t0) cc_final: 0.7479 (t0) REVERT: P 25 GLU cc_start: 0.7855 (tt0) cc_final: 0.7570 (mm-30) REVERT: P 245 GLN cc_start: 0.7471 (OUTLIER) cc_final: 0.6234 (mp10) REVERT: Q 176 THR cc_start: 0.8181 (t) cc_final: 0.7862 (m) REVERT: Q 263 GLN cc_start: 0.7935 (mp10) cc_final: 0.6649 (pp30) REVERT: R 29 VAL cc_start: 0.7805 (t) cc_final: 0.7531 (p) REVERT: R 122 ASP cc_start: 0.7219 (m-30) cc_final: 0.6938 (m-30) REVERT: R 226 ASP cc_start: 0.8136 (m-30) cc_final: 0.7844 (m-30) REVERT: R 255 VAL cc_start: 0.7653 (p) cc_final: 0.7438 (t) REVERT: T 118 ASP cc_start: 0.7718 (m-30) cc_final: 0.7321 (m-30) REVERT: T 122 ASP cc_start: 0.7583 (m-30) cc_final: 0.7252 (m-30) REVERT: T 212 ASP cc_start: 0.7751 (OUTLIER) cc_final: 0.7513 (m-30) REVERT: V 77 ASP cc_start: 0.7762 (m-30) cc_final: 0.7483 (m-30) REVERT: X 93 MET cc_start: 0.7487 (mtp) cc_final: 0.7050 (mtm) REVERT: X 252 GLN cc_start: 0.7080 (tm-30) cc_final: 0.6626 (mt0) REVERT: Z 116 ASP cc_start: 0.7399 (m-30) cc_final: 0.6986 (m-30) REVERT: Z 256 GLN cc_start: 0.7641 (mm110) cc_final: 0.7278 (mt0) REVERT: a 151 ASN cc_start: 0.8315 (t0) cc_final: 0.7858 (t0) REVERT: a 262 ASN cc_start: 0.7388 (t0) cc_final: 0.7171 (m-40) REVERT: b 62 MET cc_start: 0.8222 (mmt) cc_final: 0.7943 (mmt) REVERT: c 93 MET cc_start: 0.8326 (ttm) cc_final: 0.8115 (mtp) REVERT: d 31 GLN cc_start: 0.7903 (OUTLIER) cc_final: 0.7692 (tt0) REVERT: d 245 GLN cc_start: 0.7755 (OUTLIER) cc_final: 0.6891 (mt0) REVERT: e 105 LEU cc_start: 0.8024 (mt) cc_final: 0.7680 (mt) REVERT: f 95 GLU cc_start: 0.5938 (tp30) cc_final: 0.5592 (tt0) REVERT: f 263 GLN cc_start: 0.7227 (tp-100) cc_final: 0.6667 (mt0) REVERT: h 144 THR cc_start: 0.8521 (t) cc_final: 0.8191 (m) REVERT: j 31 GLN cc_start: 0.7610 (mt0) cc_final: 0.7112 (tm130) REVERT: j 191 ASP cc_start: 0.7331 (t0) cc_final: 0.7127 (m-30) REVERT: g 69 LEU cc_start: 0.6933 (OUTLIER) cc_final: 0.6546 (mt) REVERT: g 164 ILE cc_start: 0.7077 (OUTLIER) cc_final: 0.6870 (pt) outliers start: 102 outliers final: 49 residues processed: 721 average time/residue: 1.2640 time to fit residues: 1243.3535 Evaluate side-chains 629 residues out of total 7560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 572 time to evaluate : 5.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain H residue 30 GLN Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain K residue 195 GLN Chi-restraints excluded: chain K residue 243 LYS Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 191 ASP Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain O residue 172 THR Chi-restraints excluded: chain O residue 186 MET Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 245 GLN Chi-restraints excluded: chain Q residue 243 LYS Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain T residue 65 VAL Chi-restraints excluded: chain T residue 212 ASP Chi-restraints excluded: chain U residue 16 LEU Chi-restraints excluded: chain W residue 56 SER Chi-restraints excluded: chain W residue 159 VAL Chi-restraints excluded: chain Y residue 233 VAL Chi-restraints excluded: chain Z residue 264 SER Chi-restraints excluded: chain b residue 29 VAL Chi-restraints excluded: chain b residue 101 SER Chi-restraints excluded: chain c residue 101 SER Chi-restraints excluded: chain c residue 147 THR Chi-restraints excluded: chain c residue 159 VAL Chi-restraints excluded: chain c residue 233 VAL Chi-restraints excluded: chain d residue 31 GLN Chi-restraints excluded: chain d residue 142 SER Chi-restraints excluded: chain d residue 245 GLN Chi-restraints excluded: chain e residue 65 VAL Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain e residue 187 ILE Chi-restraints excluded: chain f residue 101 SER Chi-restraints excluded: chain f residue 174 THR Chi-restraints excluded: chain f residue 179 THR Chi-restraints excluded: chain h residue 109 SER Chi-restraints excluded: chain h residue 172 THR Chi-restraints excluded: chain i residue 136 VAL Chi-restraints excluded: chain g residue 14 ILE Chi-restraints excluded: chain g residue 69 LEU Chi-restraints excluded: chain g residue 164 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 573 optimal weight: 9.9990 chunk 923 optimal weight: 5.9990 chunk 563 optimal weight: 0.1980 chunk 437 optimal weight: 3.9990 chunk 641 optimal weight: 10.0000 chunk 968 optimal weight: 6.9990 chunk 891 optimal weight: 0.6980 chunk 771 optimal weight: 0.9990 chunk 80 optimal weight: 10.0000 chunk 595 optimal weight: 7.9990 chunk 472 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 ASN E 231 ASN F 31 GLN F 231 ASN I 195 GLN J 30 GLN L 18 ASN L 199 ASN M 30 GLN ** Q 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 251 GLN T 123 GLN U 130 ASN ** V 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 34 ASN ** W 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 263 GLN Z 151 ASN a 245 GLN ** b 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 245 GLN ** c 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 263 GLN e 73 GLN ** f 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 70056 Z= 0.173 Angle : 0.426 11.508 94824 Z= 0.242 Chirality : 0.032 0.198 12204 Planarity : 0.002 0.033 12132 Dihedral : 3.435 16.303 9792 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 1.07 % Allowed : 13.52 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.45 (0.08), residues: 9648 helix: 3.90 (0.06), residues: 6804 sheet: -1.38 (0.25), residues: 360 loop : 0.77 (0.13), residues: 2484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Q 49 HIS 0.004 0.001 HIS J 214 PHE 0.019 0.001 PHE E 117 ARG 0.008 0.000 ARG L 121 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 7560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 583 time to evaluate : 5.925 Fit side-chains REVERT: A 31 GLN cc_start: 0.7715 (mt0) cc_final: 0.7318 (tm-30) REVERT: B 126 LYS cc_start: 0.7200 (mmmm) cc_final: 0.6770 (mtmt) REVERT: B 240 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7282 (mm-30) REVERT: C 67 ASP cc_start: 0.7556 (m-30) cc_final: 0.7220 (m-30) REVERT: C 191 ASP cc_start: 0.8266 (t0) cc_final: 0.7966 (t0) REVERT: D 20 ASN cc_start: 0.8349 (m110) cc_final: 0.7873 (m110) REVERT: D 212 ASP cc_start: 0.8170 (t70) cc_final: 0.7765 (m-30) REVERT: E 31 GLN cc_start: 0.7275 (tm-30) cc_final: 0.6701 (mt0) REVERT: E 88 ASP cc_start: 0.7827 (m-30) cc_final: 0.7455 (m-30) REVERT: I 236 ASP cc_start: 0.7293 (t0) cc_final: 0.7003 (t70) REVERT: J 45 ASN cc_start: 0.8599 (t0) cc_final: 0.8254 (t0) REVERT: K 195 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.7462 (tt0) REVERT: L 95 GLU cc_start: 0.7315 (tm-30) cc_final: 0.6237 (tt0) REVERT: L 206 THR cc_start: 0.7897 (t) cc_final: 0.7557 (m) REVERT: M 38 LYS cc_start: 0.7131 (ptmt) cc_final: 0.6628 (pttm) REVERT: P 9 ASN cc_start: 0.7893 (t0) cc_final: 0.7434 (t0) REVERT: P 245 GLN cc_start: 0.7505 (OUTLIER) cc_final: 0.6252 (mp10) REVERT: Q 31 GLN cc_start: 0.6343 (OUTLIER) cc_final: 0.5049 (mp10) REVERT: Q 176 THR cc_start: 0.8185 (t) cc_final: 0.7850 (m) REVERT: Q 263 GLN cc_start: 0.8002 (mp10) cc_final: 0.6693 (pp30) REVERT: R 29 VAL cc_start: 0.7844 (t) cc_final: 0.7525 (p) REVERT: R 122 ASP cc_start: 0.7249 (m-30) cc_final: 0.6972 (m-30) REVERT: R 226 ASP cc_start: 0.8190 (m-30) cc_final: 0.7905 (m-30) REVERT: R 255 VAL cc_start: 0.7708 (p) cc_final: 0.7489 (t) REVERT: S 31 GLN cc_start: 0.7630 (OUTLIER) cc_final: 0.7068 (tp40) REVERT: T 118 ASP cc_start: 0.7774 (m-30) cc_final: 0.7373 (m-30) REVERT: T 122 ASP cc_start: 0.7487 (m-30) cc_final: 0.7116 (m-30) REVERT: T 123 GLN cc_start: 0.8159 (OUTLIER) cc_final: 0.7795 (mt0) REVERT: T 212 ASP cc_start: 0.7802 (OUTLIER) cc_final: 0.7569 (m-30) REVERT: V 77 ASP cc_start: 0.7824 (m-30) cc_final: 0.7503 (m-30) REVERT: X 93 MET cc_start: 0.7584 (mtp) cc_final: 0.7040 (mtm) REVERT: X 95 GLU cc_start: 0.6635 (tt0) cc_final: 0.6278 (tt0) REVERT: X 252 GLN cc_start: 0.7042 (tm-30) cc_final: 0.6608 (mt0) REVERT: Z 116 ASP cc_start: 0.7442 (m-30) cc_final: 0.7015 (m-30) REVERT: Z 256 GLN cc_start: 0.7574 (mm110) cc_final: 0.7179 (mt0) REVERT: a 151 ASN cc_start: 0.8341 (t0) cc_final: 0.7870 (t0) REVERT: a 262 ASN cc_start: 0.7380 (t0) cc_final: 0.7147 (m-40) REVERT: c 195 GLN cc_start: 0.7503 (OUTLIER) cc_final: 0.6770 (mm110) REVERT: d 31 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7764 (tt0) REVERT: d 245 GLN cc_start: 0.7749 (OUTLIER) cc_final: 0.6924 (mt0) REVERT: d 256 GLN cc_start: 0.7782 (mm-40) cc_final: 0.7467 (mt0) REVERT: e 105 LEU cc_start: 0.8022 (mt) cc_final: 0.7674 (mt) REVERT: f 95 GLU cc_start: 0.5971 (tp30) cc_final: 0.5624 (tt0) REVERT: f 263 GLN cc_start: 0.7322 (tp-100) cc_final: 0.6984 (tp-100) REVERT: h 144 THR cc_start: 0.8516 (t) cc_final: 0.8185 (m) REVERT: i 84 ASP cc_start: 0.6735 (t0) cc_final: 0.5917 (t0) REVERT: j 31 GLN cc_start: 0.7594 (mt0) cc_final: 0.7117 (tm130) REVERT: j 191 ASP cc_start: 0.7329 (t0) cc_final: 0.7125 (m-30) REVERT: g 164 ILE cc_start: 0.7125 (OUTLIER) cc_final: 0.6909 (pt) outliers start: 81 outliers final: 53 residues processed: 650 average time/residue: 1.3351 time to fit residues: 1172.0962 Evaluate side-chains 626 residues out of total 7560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 563 time to evaluate : 5.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain H residue 30 GLN Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain K residue 195 GLN Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 30 GLN Chi-restraints excluded: chain L residue 191 ASP Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain O residue 172 THR Chi-restraints excluded: chain O residue 186 MET Chi-restraints excluded: chain O residue 253 LEU Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 245 GLN Chi-restraints excluded: chain Q residue 31 GLN Chi-restraints excluded: chain Q residue 243 LYS Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain S residue 31 GLN Chi-restraints excluded: chain T residue 65 VAL Chi-restraints excluded: chain T residue 123 GLN Chi-restraints excluded: chain T residue 212 ASP Chi-restraints excluded: chain U residue 16 LEU Chi-restraints excluded: chain V residue 124 ILE Chi-restraints excluded: chain W residue 159 VAL Chi-restraints excluded: chain Y residue 233 VAL Chi-restraints excluded: chain Z residue 232 LEU Chi-restraints excluded: chain b residue 29 VAL Chi-restraints excluded: chain b residue 32 ARG Chi-restraints excluded: chain b residue 101 SER Chi-restraints excluded: chain c residue 101 SER Chi-restraints excluded: chain c residue 147 THR Chi-restraints excluded: chain c residue 159 VAL Chi-restraints excluded: chain c residue 195 GLN Chi-restraints excluded: chain c residue 233 VAL Chi-restraints excluded: chain d residue 31 GLN Chi-restraints excluded: chain d residue 142 SER Chi-restraints excluded: chain d residue 245 GLN Chi-restraints excluded: chain e residue 65 VAL Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain e residue 187 ILE Chi-restraints excluded: chain e residue 260 ILE Chi-restraints excluded: chain f residue 101 SER Chi-restraints excluded: chain f residue 174 THR Chi-restraints excluded: chain f residue 179 THR Chi-restraints excluded: chain h residue 109 SER Chi-restraints excluded: chain h residue 172 THR Chi-restraints excluded: chain i residue 136 VAL Chi-restraints excluded: chain g residue 14 ILE Chi-restraints excluded: chain g residue 69 LEU Chi-restraints excluded: chain g residue 164 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 972 random chunks: chunk 612 optimal weight: 8.9990 chunk 821 optimal weight: 5.9990 chunk 236 optimal weight: 9.9990 chunk 711 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 214 optimal weight: 4.9990 chunk 772 optimal weight: 2.9990 chunk 323 optimal weight: 0.9990 chunk 793 optimal weight: 6.9990 chunk 97 optimal weight: 9.9990 chunk 142 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 ASN F 31 GLN F 231 ASN J 30 GLN ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 30 GLN ** Q 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 123 GLN ** V 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 34 ASN ** W 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 263 GLN Z 151 ASN ** a 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 245 GLN d 106 ASN ** f 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 263 GLN g 9 ASN ** g 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.120194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.109845 restraints weight = 111171.860| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 1.57 r_work: 0.3466 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 70056 Z= 0.277 Angle : 0.501 12.204 94824 Z= 0.280 Chirality : 0.036 0.208 12204 Planarity : 0.002 0.057 12132 Dihedral : 3.695 16.974 9792 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 1.27 % Allowed : 13.37 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.78 (0.08), residues: 9648 helix: 3.38 (0.06), residues: 7020 sheet: -1.45 (0.25), residues: 360 loop : 0.23 (0.14), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP Q 49 HIS 0.005 0.002 HIS h 214 PHE 0.019 0.002 PHE E 117 ARG 0.013 0.001 ARG T 121 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21115.27 seconds wall clock time: 365 minutes 23.13 seconds (21923.13 seconds total)