Starting phenix.real_space_refine on Thu Jan 23 07:56:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cep_45506/01_2025/9cep_45506.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cep_45506/01_2025/9cep_45506.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cep_45506/01_2025/9cep_45506.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cep_45506/01_2025/9cep_45506.map" model { file = "/net/cci-nas-00/data/ceres_data/9cep_45506/01_2025/9cep_45506.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cep_45506/01_2025/9cep_45506.cif" } resolution = 3.13 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= 0.041 sd= 0.138 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 111 5.16 5 C 43956 2.51 5 N 12469 2.21 5 O 15133 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 75 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 71669 Number of models: 1 Model: "" Number of chains: 37 Chain: "A" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1937 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "B" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1937 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "C" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1937 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "D" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1937 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "E" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1937 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "F" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1937 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "G" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1937 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "H" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1937 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "I" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1937 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "J" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1937 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "K" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1937 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "L" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1937 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "M" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1937 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "N" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1937 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "O" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1937 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "P" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1937 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "Q" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1937 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "R" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1937 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "S" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1937 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "T" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1937 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "U" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1937 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "V" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1937 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "W" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1937 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "X" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1937 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "Y" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1937 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "Z" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1937 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "a" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1937 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "b" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1937 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "c" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1937 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "d" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1937 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "e" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1937 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "f" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1937 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "g" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1937 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "h" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1937 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "i" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1937 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "j" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1937 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "k" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1937 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Time building chain proxies: 29.74, per 1000 atoms: 0.41 Number of scatterers: 71669 At special positions: 0 Unit cell: (137.61, 136.776, 337.77, 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 111 16.00 O 15133 8.00 N 12469 7.00 C 43956 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: 14.51 Conformation dependent library (CDL) restraints added in 7.4 seconds 19906 Ramachandran restraints generated. 9953 Oldfield, 0 Emsley, 9953 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 18574 Finding SS restraints... Secondary structure from input PDB file: 254 helices and 37 sheets defined 76.3% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.17 Creating SS restraints... Processing helix chain 'A' and resid 9 through 36 Processing helix chain 'A' and resid 45 through 102 removed outlier: 4.264A pdb=" N ASN A 63 " --> pdb=" O ALA A 59 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ALA A 64 " --> pdb=" O ASN A 60 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N THR A 85 " --> pdb=" O ALA A 81 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASP A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 130 Processing helix chain 'A' and resid 165 through 169 Processing helix chain 'A' and resid 179 through 234 removed outlier: 4.798A pdb=" N GLY A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR A 189 " --> pdb=" O THR A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 263 removed outlier: 3.764A pdb=" N GLU A 240 " --> pdb=" O ASP A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 266 No H-bonds generated for 'chain 'A' and resid 264 through 266' Processing helix chain 'A' and resid 267 through 272 removed outlier: 4.037A pdb=" N LEU A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE A 272 " --> pdb=" O ILE A 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 267 through 272' Processing helix chain 'B' and resid 9 through 36 Processing helix chain 'B' and resid 45 through 101 removed outlier: 4.417A pdb=" N ASN B 63 " --> pdb=" O ALA B 59 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ALA B 64 " --> pdb=" O ASN B 60 " (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: 4.047A pdb=" N GLY B 188 " --> pdb=" O LYS B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 263 removed outlier: 4.430A pdb=" N ALA B 242 " --> pdb=" O ALA B 238 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS B 243 " --> pdb=" O LYS B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 272 removed outlier: 4.110A pdb=" N SER B 270 " --> pdb=" O SER B 266 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU B 271 " --> pdb=" O ALA B 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 36 removed outlier: 3.501A pdb=" N LEU C 13 " --> pdb=" O ASN C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 102 removed outlier: 4.548A pdb=" N ASN C 63 " --> pdb=" O ALA C 59 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ALA C 64 " --> pdb=" O ASN C 60 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASP C 102 " --> pdb=" O LEU C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 130 removed outlier: 3.604A pdb=" N PHE C 110 " --> pdb=" O ASN C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 170 removed outlier: 3.504A pdb=" N GLY C 170 " --> pdb=" O THR C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 234 removed outlier: 4.045A pdb=" N GLY C 188 " --> pdb=" O LYS C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 263 removed outlier: 3.510A pdb=" N GLU C 240 " --> pdb=" O ASP C 236 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA C 242 " --> pdb=" O ALA C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 272 removed outlier: 4.194A pdb=" N LEU C 269 " --> pdb=" O SER C 265 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER C 270 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU C 271 " --> pdb=" O ALA C 267 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE C 272 " --> pdb=" O ILE C 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 265 through 272' Processing helix chain 'D' and resid 9 through 36 removed outlier: 3.503A pdb=" N LEU D 13 " --> pdb=" O ASN D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 101 removed outlier: 4.300A pdb=" N ASN D 63 " --> pdb=" O ALA D 59 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ALA D 64 " --> pdb=" O ASN D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 130 Processing helix chain 'D' and resid 165 through 170 Processing helix chain 'D' and resid 179 through 234 removed outlier: 4.209A pdb=" N GLY D 188 " --> pdb=" O LYS D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 263 Processing helix chain 'D' and resid 266 through 272 removed outlier: 3.732A pdb=" N SER D 270 " --> pdb=" O SER D 266 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU D 271 " --> pdb=" O ALA D 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 36 Processing helix chain 'E' and resid 45 through 102 removed outlier: 4.791A pdb=" N ASN E 63 " --> pdb=" O ALA E 59 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ALA E 64 " --> pdb=" O ASN E 60 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL E 65 " --> pdb=" O SER E 61 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR E 85 " --> pdb=" O ALA E 81 " (cutoff:3.500A) removed outlier: 4.127A 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 removed outlier: 3.528A pdb=" N GLY E 170 " --> pdb=" O THR E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 234 removed outlier: 4.021A pdb=" N GLY E 188 " --> pdb=" O LYS E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 263 removed outlier: 3.893A pdb=" N ALA E 242 " --> pdb=" O ALA E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 271 removed outlier: 4.284A pdb=" N LEU E 269 " --> pdb=" O SER E 265 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER E 270 " --> pdb=" O SER E 266 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU E 271 " --> pdb=" O ALA E 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 265 through 271' Processing helix chain 'F' and resid 9 through 36 Processing helix chain 'F' and resid 45 through 101 removed outlier: 4.465A pdb=" N ASN F 63 " --> pdb=" O ALA F 59 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ALA F 64 " --> pdb=" O ASN F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 130 removed outlier: 3.615A pdb=" N THR F 125 " --> pdb=" O ARG F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 170 Processing helix chain 'F' and resid 179 through 234 removed outlier: 4.255A pdb=" N GLY F 188 " --> pdb=" O LYS F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 236 through 263 Processing helix chain 'F' and resid 266 through 272 removed outlier: 4.417A pdb=" N SER F 270 " --> pdb=" O SER F 266 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU F 271 " --> pdb=" O ALA F 267 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 36 removed outlier: 3.590A pdb=" N LEU G 13 " --> pdb=" O ASN G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 102 removed outlier: 4.534A pdb=" N ASN G 63 " --> pdb=" O ALA G 59 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ALA G 64 " --> pdb=" O ASN G 60 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ASP G 102 " --> pdb=" O LEU G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 130 Processing helix chain 'G' and resid 165 through 170 Processing helix chain 'G' and resid 179 through 234 removed outlier: 4.198A pdb=" N GLY G 188 " --> pdb=" O LYS G 184 " (cutoff:3.500A) Processing helix chain 'G' and resid 236 through 263 removed outlier: 3.517A pdb=" N GLU G 240 " --> pdb=" O ASP G 236 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA G 242 " --> pdb=" O ALA G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 264 through 272 removed outlier: 3.539A pdb=" N ALA 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 102 removed outlier: 4.350A pdb=" N ASN H 63 " --> pdb=" O ALA H 59 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ALA H 64 " --> pdb=" O ASN H 60 " (cutoff:3.500A) removed outlier: 3.902A 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 165 through 170 Processing helix chain 'H' and resid 179 through 234 removed outlier: 4.279A pdb=" N GLY H 188 " --> pdb=" O LYS H 184 " (cutoff:3.500A) Processing helix chain 'H' and resid 236 through 264 removed outlier: 3.566A pdb=" N GLU H 240 " --> pdb=" O ASP H 236 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA H 242 " --> pdb=" O ALA H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 266 through 272 removed outlier: 3.920A pdb=" N PHE H 272 " --> pdb=" O ILE H 268 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 36 removed outlier: 3.559A pdb=" N LEU I 13 " --> pdb=" O ASN I 9 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 101 removed outlier: 4.463A pdb=" N ASN I 63 " --> pdb=" O ALA I 59 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ALA I 64 " --> pdb=" O ASN I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 130 Processing helix chain 'I' and resid 165 through 170 Processing helix chain 'I' and resid 179 through 234 removed outlier: 3.966A pdb=" N GLY I 188 " --> pdb=" O LYS I 184 " (cutoff:3.500A) Processing helix chain 'I' and resid 236 through 263 removed outlier: 3.916A pdb=" N GLU I 240 " --> pdb=" O ASP I 236 " (cutoff:3.500A) Processing helix chain 'I' and resid 265 through 271 removed outlier: 4.372A pdb=" N LEU I 269 " --> pdb=" O SER I 265 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N SER I 270 " --> pdb=" O SER I 266 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU I 271 " --> pdb=" O ALA I 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 265 through 271' Processing helix chain 'J' and resid 9 through 36 Processing helix chain 'J' and resid 45 through 101 removed outlier: 4.847A pdb=" N ASN J 63 " --> pdb=" O ALA J 59 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N ALA J 64 " --> pdb=" O ASN J 60 " (cutoff:3.500A) removed outlier: 4.033A 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 165 through 170 removed outlier: 3.753A pdb=" N GLY J 170 " --> pdb=" O THR J 167 " (cutoff:3.500A) Processing helix chain 'J' and resid 179 through 234 removed outlier: 4.275A pdb=" N GLY J 188 " --> pdb=" O LYS J 184 " (cutoff:3.500A) Processing helix chain 'J' and resid 236 through 263 removed outlier: 3.706A pdb=" N GLU J 240 " --> pdb=" O ASP J 236 " (cutoff:3.500A) Processing helix chain 'J' and resid 266 through 271 removed outlier: 4.279A pdb=" N SER J 270 " --> pdb=" O SER J 266 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU J 271 " --> pdb=" O ALA J 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 266 through 271' Processing helix chain 'K' and resid 10 through 36 Processing helix chain 'K' and resid 45 through 101 removed outlier: 4.803A pdb=" N ASN K 63 " --> pdb=" O ALA K 59 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ALA K 64 " --> pdb=" O ASN K 60 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N VAL K 65 " --> pdb=" O SER K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 106 through 130 Processing helix chain 'K' and resid 165 through 170 removed outlier: 3.550A pdb=" N GLY K 170 " --> pdb=" O THR K 167 " (cutoff:3.500A) Processing helix chain 'K' and resid 179 through 234 removed outlier: 4.360A pdb=" N GLY K 188 " --> pdb=" O LYS K 184 " (cutoff:3.500A) Processing helix chain 'K' and resid 236 through 263 Processing helix chain 'K' and resid 266 through 272 removed outlier: 3.778A pdb=" N SER K 270 " --> pdb=" O SER K 266 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 36 removed outlier: 3.940A pdb=" N LEU L 13 " --> pdb=" O ASN L 9 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 101 removed outlier: 4.737A pdb=" N ASN L 63 " --> pdb=" O ALA L 59 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ALA L 64 " --> pdb=" O ASN L 60 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL L 65 " --> pdb=" O SER L 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 106 through 130 Processing helix chain 'L' and resid 179 through 234 removed outlier: 3.829A pdb=" N GLY L 188 " --> pdb=" O LYS L 184 " (cutoff:3.500A) Processing helix chain 'L' and resid 236 through 263 Processing helix chain 'L' and resid 264 through 272 removed outlier: 3.740A pdb=" N ALA L 267 " --> pdb=" O SER L 264 " (cutoff:3.500A) Processing helix chain 'M' and resid 9 through 36 Processing helix chain 'M' and resid 45 through 101 removed outlier: 4.452A pdb=" N ASN M 63 " --> pdb=" O ALA M 59 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ALA M 64 " --> pdb=" O ASN M 60 " (cutoff:3.500A) Processing helix chain 'M' and resid 106 through 130 Processing helix chain 'M' and resid 165 through 170 Processing helix chain 'M' and resid 179 through 234 removed outlier: 3.884A pdb=" N GLY M 188 " --> pdb=" O LYS M 184 " (cutoff:3.500A) Processing helix chain 'M' and resid 236 through 263 Processing helix chain 'M' and resid 264 through 272 removed outlier: 3.779A pdb=" N ALA M 267 " --> pdb=" O SER M 264 " (cutoff:3.500A) Processing helix chain 'N' and resid 9 through 36 removed outlier: 3.526A pdb=" N LEU N 13 " --> pdb=" O ASN N 9 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 101 removed outlier: 4.434A pdb=" N ASN N 63 " --> pdb=" O ALA N 59 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ALA N 64 " --> pdb=" O ASN N 60 " (cutoff:3.500A) Processing helix chain 'N' and resid 106 through 131 removed outlier: 3.670A pdb=" N ALA N 131 " --> pdb=" O ALA N 127 " (cutoff:3.500A) Processing helix chain 'N' and resid 179 through 234 removed outlier: 4.176A pdb=" N GLY N 188 " --> pdb=" O LYS N 184 " (cutoff:3.500A) Processing helix chain 'N' and resid 236 through 263 Processing helix chain 'N' and resid 264 through 272 removed outlier: 3.791A pdb=" N ALA N 267 " --> pdb=" O SER N 264 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 36 removed outlier: 3.607A pdb=" N LEU O 13 " --> pdb=" O ASN O 9 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 101 removed outlier: 4.502A pdb=" N ASN O 63 " --> pdb=" O ALA O 59 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ALA O 64 " --> pdb=" O ASN O 60 " (cutoff:3.500A) removed outlier: 4.102A 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 Processing helix chain 'O' and resid 179 through 234 removed outlier: 3.977A pdb=" N GLY O 188 " --> pdb=" O LYS O 184 " (cutoff:3.500A) Processing helix chain 'O' and resid 236 through 264 Processing helix chain 'O' and resid 266 through 271 removed outlier: 4.230A pdb=" N SER O 270 " --> pdb=" O SER O 266 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LEU O 271 " --> pdb=" O ALA O 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 266 through 271' Processing helix chain 'P' and resid 9 through 36 removed outlier: 3.691A pdb=" N LEU P 13 " --> pdb=" O ASN P 9 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 101 removed outlier: 4.500A pdb=" N ASN P 63 " --> pdb=" O ALA P 59 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ALA P 64 " --> pdb=" O ASN P 60 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL P 65 " --> pdb=" O SER P 61 " (cutoff:3.500A) Processing helix chain 'P' and resid 106 through 130 Processing helix chain 'P' and resid 165 through 170 removed outlier: 3.558A pdb=" N GLY P 170 " --> pdb=" O THR P 167 " (cutoff:3.500A) Processing helix chain 'P' and resid 179 through 234 removed outlier: 4.027A pdb=" N GLY P 188 " --> pdb=" O LYS P 184 " (cutoff:3.500A) Processing helix chain 'P' and resid 236 through 264 Processing helix chain 'P' and resid 267 through 272 removed outlier: 4.051A pdb=" N LEU P 271 " --> pdb=" O ALA P 267 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N PHE P 272 " --> pdb=" O ILE P 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 267 through 272' Processing helix chain 'Q' and resid 9 through 36 Processing helix chain 'Q' and resid 45 through 101 removed outlier: 4.108A pdb=" N ASN Q 63 " --> pdb=" O ALA Q 59 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ALA Q 64 " --> pdb=" O ASN Q 60 " (cutoff:3.500A) Processing helix chain 'Q' and resid 106 through 130 Processing helix chain 'Q' and resid 165 through 170 Processing helix chain 'Q' and resid 179 through 234 removed outlier: 3.834A pdb=" N GLY Q 188 " --> pdb=" O LYS Q 184 " (cutoff:3.500A) Processing helix chain 'Q' and resid 236 through 263 Processing helix chain 'Q' and resid 264 through 272 removed outlier: 4.132A pdb=" N ALA Q 267 " --> pdb=" O SER Q 264 " (cutoff:3.500A) Processing helix chain 'R' and resid 9 through 36 removed outlier: 3.550A pdb=" N LEU R 13 " --> pdb=" O ASN R 9 " (cutoff:3.500A) Processing helix chain 'R' and resid 45 through 102 removed outlier: 4.418A pdb=" N ASN R 63 " --> pdb=" O ALA R 59 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ALA R 64 " --> pdb=" O ASN R 60 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N VAL R 65 " --> pdb=" O SER R 61 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR R 85 " --> pdb=" O ALA R 81 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASP R 102 " --> pdb=" O LEU R 98 " (cutoff:3.500A) Processing helix chain 'R' and resid 106 through 130 Processing helix chain 'R' and resid 165 through 170 removed outlier: 3.591A pdb=" N GLY R 170 " --> pdb=" O THR R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 179 through 234 removed outlier: 4.262A pdb=" N GLY R 188 " --> pdb=" O LYS R 184 " (cutoff:3.500A) Processing helix chain 'R' and resid 236 through 264 removed outlier: 3.912A pdb=" N GLU R 240 " --> pdb=" O ASP R 236 " (cutoff:3.500A) Processing helix chain 'R' and resid 266 through 272 removed outlier: 4.257A pdb=" N SER R 270 " --> pdb=" O SER R 266 " (cutoff:3.500A) Processing helix chain 'S' and resid 9 through 36 removed outlier: 3.588A pdb=" N LEU S 13 " --> pdb=" O ASN S 9 " (cutoff:3.500A) Processing helix chain 'S' and resid 45 through 101 removed outlier: 4.432A pdb=" N ASN S 63 " --> pdb=" O ALA S 59 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ALA S 64 " --> pdb=" O ASN S 60 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL S 65 " --> pdb=" O SER S 61 " (cutoff:3.500A) Processing helix chain 'S' and resid 106 through 131 removed outlier: 3.605A pdb=" N ALA S 131 " --> pdb=" O ALA S 127 " (cutoff:3.500A) Processing helix chain 'S' and resid 165 through 170 Processing helix chain 'S' and resid 179 through 234 removed outlier: 4.062A pdb=" N GLY S 188 " --> pdb=" O LYS S 184 " (cutoff:3.500A) Processing helix chain 'S' and resid 236 through 264 Processing helix chain 'S' and resid 266 through 272 removed outlier: 4.426A pdb=" N SER S 270 " --> pdb=" O SER S 266 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU S 271 " --> pdb=" O ALA S 267 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N PHE S 272 " --> pdb=" O ILE S 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 266 through 272' Processing helix chain 'T' and resid 9 through 36 removed outlier: 3.502A pdb=" N LEU T 13 " --> pdb=" O ASN T 9 " (cutoff:3.500A) Processing helix chain 'T' and resid 45 through 101 removed outlier: 4.479A pdb=" N ASN T 63 " --> pdb=" O ALA T 59 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ALA T 64 " --> pdb=" O ASN T 60 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL T 65 " --> pdb=" O SER T 61 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N THR T 85 " --> pdb=" O ALA T 81 " (cutoff:3.500A) Processing helix chain 'T' and resid 106 through 131 removed outlier: 3.789A pdb=" N ALA T 131 " --> pdb=" O ALA T 127 " (cutoff:3.500A) Processing helix chain 'T' and resid 179 through 234 removed outlier: 4.323A 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 Processing helix chain 'U' and resid 9 through 36 removed outlier: 3.804A pdb=" N LEU U 13 " --> pdb=" O ASN U 9 " (cutoff:3.500A) Processing helix chain 'U' and resid 45 through 101 removed outlier: 4.210A pdb=" N ASN U 63 " --> pdb=" O ALA U 59 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ALA U 64 " --> pdb=" O ASN U 60 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR U 85 " --> pdb=" O ALA U 81 " (cutoff:3.500A) Processing helix chain 'U' and resid 106 through 131 removed outlier: 3.600A pdb=" N THR U 125 " --> pdb=" O ARG U 121 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA U 131 " --> pdb=" O ALA U 127 " (cutoff:3.500A) Processing helix chain 'U' and resid 165 through 169 Processing helix chain 'U' and resid 179 through 234 removed outlier: 4.436A pdb=" N GLY U 188 " --> pdb=" O LYS U 184 " (cutoff:3.500A) Processing helix chain 'U' and resid 236 through 264 Processing helix chain 'U' and resid 266 through 272 removed outlier: 3.930A pdb=" N SER U 270 " --> pdb=" O SER U 266 " (cutoff:3.500A) Processing helix chain 'V' and resid 9 through 36 removed outlier: 3.567A pdb=" N LEU V 13 " --> pdb=" O ASN V 9 " (cutoff:3.500A) Processing helix chain 'V' and resid 45 through 102 removed outlier: 4.475A pdb=" N ASN V 63 " --> pdb=" O ALA V 59 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ALA V 64 " --> pdb=" O ASN V 60 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL V 65 " --> pdb=" O SER V 61 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASP V 102 " --> pdb=" O LEU V 98 " (cutoff:3.500A) Processing helix chain 'V' and resid 106 through 131 removed outlier: 3.599A pdb=" N ALA V 131 " --> pdb=" O ALA V 127 " (cutoff:3.500A) Processing helix chain 'V' and resid 165 through 169 Processing helix chain 'V' and resid 179 through 234 removed outlier: 4.181A pdb=" N GLY V 188 " --> pdb=" O LYS V 184 " (cutoff:3.500A) Processing helix chain 'V' and resid 236 through 263 removed outlier: 3.586A pdb=" N GLU V 240 " --> pdb=" O ASP V 236 " (cutoff:3.500A) Processing helix chain 'V' and resid 264 through 272 removed outlier: 3.535A pdb=" N PHE V 272 " --> pdb=" O LEU V 269 " (cutoff:3.500A) Processing helix chain 'W' and resid 9 through 36 Processing helix chain 'W' and resid 45 through 101 removed outlier: 4.422A pdb=" N ASN W 63 " --> pdb=" O ALA W 59 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ALA W 64 " --> pdb=" O ASN W 60 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL W 65 " --> pdb=" O SER W 61 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR W 85 " --> pdb=" O ALA W 81 " (cutoff:3.500A) Processing helix chain 'W' and resid 106 through 131 removed outlier: 3.726A pdb=" N ALA W 131 " --> pdb=" O ALA W 127 " (cutoff:3.500A) Processing helix chain 'W' and resid 165 through 169 Processing helix chain 'W' and resid 179 through 234 removed outlier: 4.229A pdb=" N GLY W 188 " --> pdb=" O LYS W 184 " (cutoff:3.500A) Processing helix chain 'W' and resid 236 through 264 removed outlier: 3.529A pdb=" N SER W 264 " --> pdb=" O ILE W 260 " (cutoff:3.500A) Processing helix chain 'W' and resid 265 through 272 Processing helix chain 'X' and resid 9 through 36 removed outlier: 3.673A pdb=" N LEU X 13 " --> pdb=" O ASN X 9 " (cutoff:3.500A) Processing helix chain 'X' and resid 45 through 101 removed outlier: 4.217A pdb=" N ASN X 63 " --> pdb=" O ALA X 59 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ALA X 64 " --> pdb=" O ASN X 60 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N THR X 85 " --> pdb=" O ALA X 81 " (cutoff:3.500A) Processing helix chain 'X' and resid 106 through 130 Processing helix chain 'X' and resid 165 through 170 removed outlier: 3.591A pdb=" N GLY X 170 " --> pdb=" O THR X 167 " (cutoff:3.500A) Processing helix chain 'X' and resid 179 through 234 removed outlier: 4.406A pdb=" N GLY X 188 " --> pdb=" O LYS X 184 " (cutoff:3.500A) Processing helix chain 'X' and resid 236 through 264 Processing helix chain 'X' and resid 265 through 272 removed outlier: 4.003A pdb=" N PHE X 272 " --> pdb=" O LEU X 269 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 36 removed outlier: 3.526A pdb=" N LEU Y 13 " --> pdb=" O ASN Y 9 " (cutoff:3.500A) Processing helix chain 'Y' and resid 45 through 101 removed outlier: 4.361A pdb=" N ASN Y 63 " --> pdb=" O ALA Y 59 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ALA Y 64 " --> pdb=" O ASN Y 60 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL Y 65 " --> pdb=" O SER Y 61 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N THR Y 85 " --> pdb=" O ALA Y 81 " (cutoff:3.500A) Processing helix chain 'Y' and resid 106 through 131 removed outlier: 3.590A pdb=" N ALA Y 131 " --> pdb=" O ALA Y 127 " (cutoff:3.500A) Processing helix chain 'Y' and resid 179 through 234 removed outlier: 4.026A pdb=" N GLY Y 188 " --> pdb=" O LYS Y 184 " (cutoff:3.500A) Processing helix chain 'Y' and resid 236 through 264 removed outlier: 3.668A pdb=" N GLU Y 240 " --> pdb=" O ASP Y 236 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER Y 264 " --> pdb=" O ILE Y 260 " (cutoff:3.500A) Processing helix chain 'Y' and resid 265 through 272 Processing helix chain 'Z' and resid 9 through 36 removed outlier: 3.625A pdb=" N LEU Z 13 " --> pdb=" O ASN Z 9 " (cutoff:3.500A) Processing helix chain 'Z' and resid 45 through 101 removed outlier: 4.380A pdb=" N ASN Z 63 " --> pdb=" O ALA Z 59 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ALA Z 64 " --> pdb=" O ASN Z 60 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL Z 65 " --> pdb=" O SER Z 61 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N THR Z 85 " --> pdb=" O ALA Z 81 " (cutoff:3.500A) Processing helix chain 'Z' and resid 106 through 131 Processing helix chain 'Z' and resid 179 through 234 removed outlier: 4.105A pdb=" N GLY Z 188 " --> pdb=" O LYS Z 184 " (cutoff:3.500A) Processing helix chain 'Z' and resid 236 through 263 Processing helix chain 'Z' and resid 266 through 272 removed outlier: 4.109A pdb=" N SER Z 270 " --> pdb=" O SER Z 266 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU Z 271 " --> pdb=" O ALA Z 267 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N PHE Z 272 " --> pdb=" O ILE Z 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 266 through 272' Processing helix chain 'a' and resid 9 through 36 removed outlier: 3.677A pdb=" N LEU a 13 " --> pdb=" O ASN a 9 " (cutoff:3.500A) Processing helix chain 'a' and resid 45 through 101 removed outlier: 4.155A pdb=" N ASN a 63 " --> pdb=" O ALA a 59 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ALA a 64 " --> pdb=" O ASN a 60 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N THR a 85 " --> pdb=" O ALA a 81 " (cutoff:3.500A) Processing helix chain 'a' and resid 106 through 131 removed outlier: 3.534A pdb=" N ALA a 131 " --> pdb=" O ALA a 127 " (cutoff:3.500A) Processing helix chain 'a' and resid 179 through 234 removed outlier: 3.843A pdb=" N GLY a 188 " --> pdb=" O LYS a 184 " (cutoff:3.500A) Processing helix chain 'a' and resid 236 through 264 removed outlier: 3.906A pdb=" N ALA a 242 " --> pdb=" O ALA a 238 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER a 264 " --> pdb=" O ILE a 260 " (cutoff:3.500A) Processing helix chain 'a' and resid 267 through 272 removed outlier: 3.903A pdb=" N LEU a 271 " --> pdb=" O ALA a 267 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N PHE a 272 " --> pdb=" O ILE a 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 267 through 272' Processing helix chain 'b' and resid 9 through 36 Processing helix chain 'b' and resid 45 through 101 removed outlier: 4.878A pdb=" N ASN b 63 " --> pdb=" O ALA b 59 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ALA b 64 " --> pdb=" O ASN b 60 " (cutoff:3.500A) removed outlier: 4.191A 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 169 Processing helix chain 'b' and resid 179 through 234 removed outlier: 4.187A pdb=" N GLY b 188 " --> pdb=" O LYS b 184 " (cutoff:3.500A) Processing helix chain 'b' and resid 236 through 263 removed outlier: 3.543A pdb=" N GLU b 240 " --> pdb=" O ASP b 236 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA b 242 " --> pdb=" O ALA b 238 " (cutoff:3.500A) Processing helix chain 'b' and resid 266 through 272 removed outlier: 4.130A pdb=" N SER b 270 " --> pdb=" O SER b 266 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU b 271 " --> pdb=" O ALA b 267 " (cutoff:3.500A) Processing helix chain 'c' and resid 9 through 36 Processing helix chain 'c' and resid 45 through 101 removed outlier: 4.689A pdb=" N ASN c 63 " --> pdb=" O ALA c 59 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ALA c 64 " --> pdb=" O ASN c 60 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N VAL c 65 " --> pdb=" O SER c 61 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N THR c 85 " --> pdb=" O ALA c 81 " (cutoff:3.500A) Processing helix chain 'c' and resid 106 through 131 removed outlier: 3.609A pdb=" N ALA c 131 " --> pdb=" O ALA c 127 " (cutoff:3.500A) Processing helix chain 'c' and resid 165 through 169 Processing helix chain 'c' and resid 179 through 234 removed outlier: 4.354A pdb=" N GLY c 188 " --> pdb=" O LYS c 184 " (cutoff:3.500A) Processing helix chain 'c' and resid 236 through 263 removed outlier: 3.618A pdb=" N GLU c 240 " --> pdb=" O ASP c 236 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ALA c 242 " --> pdb=" O ALA c 238 " (cutoff:3.500A) Processing helix chain 'c' and resid 266 through 272 removed outlier: 4.115A pdb=" N SER c 270 " --> pdb=" O SER c 266 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LEU c 271 " --> pdb=" O ALA c 267 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE c 272 " --> pdb=" O ILE c 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 266 through 272' Processing helix chain 'd' and resid 9 through 36 removed outlier: 3.658A pdb=" N LEU d 13 " --> pdb=" O ASN d 9 " (cutoff:3.500A) Processing helix chain 'd' and resid 45 through 101 removed outlier: 4.588A pdb=" N ASN d 63 " --> pdb=" O ALA d 59 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ALA d 64 " --> pdb=" O ASN d 60 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N VAL d 65 " --> pdb=" O SER d 61 " (cutoff:3.500A) Processing helix chain 'd' and resid 106 through 131 removed outlier: 3.696A pdb=" N ALA d 131 " --> pdb=" O ALA d 127 " (cutoff:3.500A) Processing helix chain 'd' and resid 179 through 234 removed outlier: 4.076A pdb=" N GLY d 188 " --> pdb=" O LYS d 184 " (cutoff:3.500A) Processing helix chain 'd' and resid 236 through 263 removed outlier: 3.585A pdb=" N GLU d 240 " --> pdb=" O ASP d 236 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA d 242 " --> pdb=" O ALA d 238 " (cutoff:3.500A) Processing helix chain 'd' and resid 266 through 272 removed outlier: 4.369A pdb=" N SER d 270 " --> pdb=" O SER d 266 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LEU d 271 " --> pdb=" O ALA d 267 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N PHE d 272 " --> pdb=" O ILE d 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 266 through 272' Processing helix chain 'e' and resid 9 through 36 Processing helix chain 'e' and resid 45 through 101 removed outlier: 4.358A pdb=" N ASN e 63 " --> pdb=" O ALA e 59 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ALA e 64 " --> pdb=" O ASN e 60 " (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: 4.184A pdb=" N GLY e 188 " --> pdb=" O LYS e 184 " (cutoff:3.500A) Processing helix chain 'e' and resid 236 through 263 removed outlier: 3.841A pdb=" N GLU e 240 " --> pdb=" O ASP e 236 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA e 242 " --> pdb=" O ALA e 238 " (cutoff:3.500A) Processing helix chain 'e' and resid 266 through 272 removed outlier: 4.213A pdb=" N SER e 270 " --> pdb=" O SER e 266 " (cutoff:3.500A) Processing helix chain 'f' and resid 9 through 36 Processing helix chain 'f' and resid 45 through 102 removed outlier: 4.548A pdb=" N ASN f 63 " --> pdb=" O ALA f 59 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ALA f 64 " --> pdb=" O ASN f 60 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N THR f 85 " --> pdb=" O ALA f 81 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASP f 102 " --> pdb=" O LEU f 98 " (cutoff:3.500A) Processing helix chain 'f' and resid 106 through 130 Processing helix chain 'f' and resid 165 through 170 Processing helix chain 'f' and resid 179 through 234 removed outlier: 4.183A pdb=" N GLY f 188 " --> pdb=" O LYS f 184 " (cutoff:3.500A) Processing helix chain 'f' and resid 236 through 263 removed outlier: 3.985A pdb=" N ALA f 242 " --> pdb=" O ALA f 238 " (cutoff:3.500A) Processing helix chain 'f' and resid 264 through 266 No H-bonds generated for 'chain 'f' and resid 264 through 266' Processing helix chain 'f' and resid 267 through 272 removed outlier: 3.966A pdb=" N LEU f 271 " --> pdb=" O ALA f 267 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N PHE f 272 " --> pdb=" O ILE f 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 267 through 272' Processing helix chain 'g' and resid 9 through 36 Processing helix chain 'g' and resid 45 through 101 removed outlier: 4.451A pdb=" N ASN g 63 " --> pdb=" O ALA g 59 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ALA g 64 " --> pdb=" O ASN g 60 " (cutoff:3.500A) Processing helix chain 'g' and resid 106 through 131 removed outlier: 3.634A pdb=" N THR g 125 " --> pdb=" O ARG g 121 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA g 131 " --> pdb=" O ALA g 127 " (cutoff:3.500A) Processing helix chain 'g' and resid 165 through 169 Processing helix chain 'g' and resid 179 through 234 removed outlier: 4.157A pdb=" N GLY g 188 " --> pdb=" O LYS g 184 " (cutoff:3.500A) Processing helix chain 'g' and resid 236 through 263 removed outlier: 3.588A pdb=" N GLU g 240 " --> pdb=" O ASP g 236 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA g 242 " --> pdb=" O ALA g 238 " (cutoff:3.500A) Processing helix chain 'g' and resid 266 through 272 removed outlier: 4.200A pdb=" N SER g 270 " --> pdb=" O SER g 266 " (cutoff:3.500A) Processing helix chain 'h' and resid 9 through 36 removed outlier: 3.930A pdb=" N LEU h 13 " --> pdb=" O ASN h 9 " (cutoff:3.500A) Processing helix chain 'h' and resid 45 through 101 removed outlier: 4.294A pdb=" N ASN h 63 " --> pdb=" O ALA h 59 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ALA h 64 " --> pdb=" O ASN h 60 " (cutoff:3.500A) Processing helix chain 'h' and resid 106 through 130 Processing helix chain 'h' and resid 179 through 234 removed outlier: 4.127A pdb=" N GLY h 188 " --> pdb=" O LYS h 184 " (cutoff:3.500A) Processing helix chain 'h' and resid 236 through 263 removed outlier: 4.182A pdb=" N ALA h 242 " --> pdb=" O ALA h 238 " (cutoff:3.500A) Processing helix chain 'h' and resid 264 through 266 No H-bonds generated for 'chain 'h' and resid 264 through 266' Processing helix chain 'h' and resid 267 through 272 removed outlier: 4.163A pdb=" N LEU h 271 " --> pdb=" O ALA h 267 " (cutoff:3.500A) Processing helix chain 'i' and resid 9 through 36 Processing helix chain 'i' and resid 45 through 102 removed outlier: 4.345A pdb=" N ASN i 63 " --> pdb=" O ALA i 59 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ALA i 64 " --> pdb=" O ASN i 60 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASP i 102 " --> pdb=" O LEU i 98 " (cutoff:3.500A) Processing helix chain 'i' and resid 106 through 130 removed outlier: 3.648A pdb=" N THR i 125 " --> pdb=" O ARG i 121 " (cutoff:3.500A) Processing helix chain 'i' and resid 166 through 170 Processing helix chain 'i' and resid 179 through 234 removed outlier: 4.233A pdb=" N GLY i 188 " --> pdb=" O LYS i 184 " (cutoff:3.500A) Processing helix chain 'i' and resid 236 through 263 removed outlier: 3.544A pdb=" N GLU i 240 " --> pdb=" O ASP i 236 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA i 242 " --> pdb=" O ALA i 238 " (cutoff:3.500A) Processing helix chain 'i' and resid 266 through 271 removed outlier: 4.246A pdb=" N SER i 270 " --> pdb=" O SER i 266 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEU i 271 " --> pdb=" O ALA i 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 266 through 271' Processing helix chain 'j' and resid 9 through 36 Processing helix chain 'j' and resid 45 through 101 removed outlier: 4.414A pdb=" N ASN j 63 " --> pdb=" O ALA j 59 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ALA j 64 " --> pdb=" O ASN j 60 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N THR j 85 " --> pdb=" O ALA j 81 " (cutoff:3.500A) Processing helix chain 'j' and resid 106 through 130 Processing helix chain 'j' and resid 165 through 170 Processing helix chain 'j' and resid 179 through 234 removed outlier: 4.266A pdb=" N GLY j 188 " --> pdb=" O LYS j 184 " (cutoff:3.500A) Processing helix chain 'j' and resid 236 through 263 Processing helix chain 'j' and resid 265 through 270 removed outlier: 4.100A pdb=" N LEU j 269 " --> pdb=" O SER j 265 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N SER j 270 " --> pdb=" O SER j 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 265 through 270' Processing helix chain 'k' and resid 9 through 36 Processing helix chain 'k' and resid 45 through 101 removed outlier: 4.383A pdb=" N ASN k 63 " --> pdb=" O ALA k 59 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ALA k 64 " --> pdb=" O ASN k 60 " (cutoff:3.500A) Processing helix chain 'k' and resid 106 through 130 Processing helix chain 'k' and resid 165 through 170 Processing helix chain 'k' and resid 179 through 234 removed outlier: 4.092A pdb=" N GLY k 188 " --> pdb=" O LYS k 184 " (cutoff:3.500A) Processing helix chain 'k' and resid 236 through 263 removed outlier: 4.260A pdb=" N ALA k 242 " --> pdb=" O ALA k 238 " (cutoff:3.500A) Processing helix chain 'k' and resid 265 through 272 removed outlier: 4.249A pdb=" N LEU k 269 " --> pdb=" O SER k 265 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER k 270 " --> pdb=" O SER k 266 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU k 271 " --> pdb=" O ALA k 267 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE k 272 " --> pdb=" O ILE k 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 265 through 272' Processing sheet with id=AA1, first strand: chain 'A' and resid 145 through 149 Processing sheet with id=AA2, first strand: chain 'B' and resid 145 through 149 Processing sheet with id=AA3, first strand: chain 'C' and resid 145 through 149 Processing sheet with id=AA4, first strand: chain 'D' and resid 145 through 149 Processing sheet with id=AA5, first strand: chain 'E' and resid 145 through 149 Processing sheet with id=AA6, first strand: chain 'F' and resid 145 through 149 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 149 Processing sheet with id=AB2, first strand: chain 'K' and resid 145 through 149 Processing sheet with id=AB3, first strand: chain 'L' and resid 145 through 149 Processing sheet with id=AB4, first strand: chain 'M' and resid 145 through 149 Processing sheet with id=AB5, first strand: chain 'N' and resid 145 through 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 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 Processing sheet with id=AC5, first strand: chain 'W' and resid 145 through 149 Processing sheet with id=AC6, first strand: chain 'X' and resid 145 through 149 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 Processing sheet with id=AD2, first strand: chain 'c' and resid 145 through 149 Processing sheet with id=AD3, first strand: chain 'd' and resid 145 through 149 Processing sheet with id=AD4, first strand: chain 'e' and resid 145 through 149 Processing sheet with id=AD5, first strand: chain 'f' and resid 145 through 149 Processing sheet with id=AD6, first strand: chain 'g' and resid 148 through 149 Processing sheet with id=AD7, first strand: chain 'h' and resid 145 through 149 Processing sheet with id=AD8, first strand: chain 'i' and resid 145 through 149 Processing sheet with id=AD9, first strand: chain 'j' and resid 145 through 149 Processing sheet with id=AE1, first strand: chain 'k' and resid 145 through 149 6525 hydrogen bonds defined for protein. 19290 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 27.80 Time building geometry restraints manager: 17.11 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: 23101 1.33 - 1.45: 7063 1.45 - 1.57: 41653 1.57 - 1.69: 0 1.69 - 1.81: 222 Bond restraints: 72039 Sorted by residual: bond pdb=" CA SER M 152 " pdb=" CB SER M 152 " ideal model delta sigma weight residual 1.528 1.480 0.049 1.56e-02 4.11e+03 9.82e+00 bond pdb=" N ASN M 151 " pdb=" CA ASN M 151 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.16e-02 7.43e+03 8.07e+00 bond pdb=" CB MET S 93 " pdb=" CG MET S 93 " ideal model delta sigma weight residual 1.520 1.445 0.075 3.00e-02 1.11e+03 6.30e+00 bond pdb=" CG1 ILE E 124 " pdb=" CD1 ILE E 124 " ideal model delta sigma weight residual 1.513 1.416 0.097 3.90e-02 6.57e+02 6.14e+00 bond pdb=" N ASP M 153 " pdb=" CA ASP M 153 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.30e-02 5.92e+03 5.99e+00 ... (remaining 72034 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 95288 2.06 - 4.13: 2051 4.13 - 6.19: 168 6.19 - 8.25: 21 8.25 - 10.32: 4 Bond angle restraints: 97532 Sorted by residual: angle pdb=" C SER H 155 " pdb=" N GLY H 156 " pdb=" CA GLY H 156 " ideal model delta sigma weight residual 122.33 119.42 2.91 7.30e-01 1.88e+00 1.59e+01 angle pdb=" C LEU J 232 " pdb=" N VAL J 233 " pdb=" CA VAL J 233 " ideal model delta sigma weight residual 122.77 118.64 4.13 1.05e+00 9.07e-01 1.55e+01 angle pdb=" N GLY A 156 " pdb=" CA GLY A 156 " pdb=" C GLY A 156 " ideal model delta sigma weight residual 110.71 116.71 -6.00 1.53e+00 4.27e-01 1.54e+01 angle pdb=" N GLY D 156 " pdb=" CA GLY D 156 " pdb=" C GLY D 156 " ideal model delta sigma weight residual 110.71 116.39 -5.68 1.53e+00 4.27e-01 1.38e+01 angle pdb=" C LEU N 232 " pdb=" N VAL N 233 " pdb=" CA VAL N 233 " ideal model delta sigma weight residual 122.66 119.07 3.59 9.70e-01 1.06e+00 1.37e+01 ... (remaining 97527 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 40479 17.91 - 35.81: 2772 35.81 - 53.72: 410 53.72 - 71.63: 132 71.63 - 89.53: 89 Dihedral angle restraints: 43882 sinusoidal: 15318 harmonic: 28564 Sorted by residual: dihedral pdb=" CA GLY j 156 " pdb=" C GLY j 156 " pdb=" N PHE j 157 " pdb=" CA PHE j 157 " ideal model delta harmonic sigma weight residual 180.00 159.92 20.08 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA SER k 263 " pdb=" C SER k 263 " pdb=" N SER k 264 " pdb=" CA SER k 264 " ideal model delta harmonic sigma weight residual -180.00 -160.39 -19.61 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA SER F 263 " pdb=" C SER F 263 " pdb=" N SER F 264 " pdb=" CA SER F 264 " ideal model delta harmonic sigma weight residual -180.00 -161.46 -18.54 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 43879 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 10190 0.048 - 0.097: 2206 0.097 - 0.145: 177 0.145 - 0.194: 5 0.194 - 0.242: 2 Chirality restraints: 12580 Sorted by residual: chirality pdb=" CG LEU U 26 " pdb=" CB LEU U 26 " pdb=" CD1 LEU U 26 " pdb=" CD2 LEU U 26 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA VAL M 159 " pdb=" N VAL M 159 " pdb=" C VAL M 159 " pdb=" CB VAL M 159 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CG LEU V 26 " pdb=" CB LEU V 26 " pdb=" CD1 LEU V 26 " pdb=" CD2 LEU V 26 " both_signs ideal model delta sigma weight residual False -2.59 -2.75 0.16 2.00e-01 2.50e+01 6.55e-01 ... (remaining 12577 not shown) Planarity restraints: 12469 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE L 148 " -0.022 2.00e-02 2.50e+03 2.42e-02 1.02e+01 pdb=" CG PHE L 148 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 PHE L 148 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE L 148 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE L 148 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE L 148 " -0.015 2.00e-02 2.50e+03 pdb=" CZ PHE L 148 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE I 148 " 0.021 2.00e-02 2.50e+03 2.29e-02 9.19e+00 pdb=" CG PHE I 148 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 PHE I 148 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE I 148 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE I 148 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE I 148 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE I 148 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE J 148 " 0.021 2.00e-02 2.50e+03 2.24e-02 8.74e+00 pdb=" CG PHE J 148 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE J 148 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE J 148 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE J 148 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE J 148 " 0.012 2.00e-02 2.50e+03 pdb=" CZ PHE J 148 " 0.001 2.00e-02 2.50e+03 ... (remaining 12466 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 808 2.65 - 3.21: 76059 3.21 - 3.78: 113728 3.78 - 4.34: 154342 4.34 - 4.90: 251044 Nonbonded interactions: 595981 Sorted by model distance: nonbonded pdb=" OG SER g 246 " pdb=" O ILE j 6 " model vdw 2.092 3.040 nonbonded pdb=" NZ LYS T 96 " pdb=" OD2 ASP T 116 " model vdw 2.133 3.120 nonbonded pdb=" ND2 ASN V 4 " pdb=" OD1 ASP W 236 " model vdw 2.146 3.120 nonbonded pdb=" NH1 ARG P 121 " pdb=" O ALA P 173 " model vdw 2.150 3.120 nonbonded pdb=" O ASP G 122 " pdb=" OG1 THR G 125 " model vdw 2.155 3.040 ... (remaining 595976 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' } 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: 11.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.120 Extract box with map and model: 2.150 Check model and map are aligned: 0.410 Set scattering table: 0.490 Process input model: 123.280 Find NCS groups from input model: 2.960 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: 0.030 Load rotamer database and sin/cos tables:2.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 144.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 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 : 0.007 0.097 72039 Z= 0.463 Angle : 0.752 10.318 97532 Z= 0.456 Chirality : 0.038 0.242 12580 Planarity : 0.004 0.058 12469 Dihedral : 13.526 89.532 25308 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.34 % Favored : 98.55 % Rotamer: Outliers : 0.01 % Allowed : 0.09 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.07), residues: 9953 helix: 0.67 (0.05), residues: 7400 sheet: -2.92 (0.23), residues: 370 loop : 1.21 (0.14), residues: 2183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP U 49 HIS 0.009 0.003 HIS K 214 PHE 0.053 0.003 PHE L 148 ARG 0.007 0.001 ARG V 32 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19906 Ramachandran restraints generated. 9953 Oldfield, 0 Emsley, 9953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19906 Ramachandran restraints generated. 9953 Oldfield, 0 Emsley, 9953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 7770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 127 time to evaluate : 6.015 Fit side-chains REVERT: e 60 ASN cc_start: 0.9010 (m-40) cc_final: 0.8687 (m-40) REVERT: j 60 ASN cc_start: 0.8248 (m-40) cc_final: 0.8035 (m-40) outliers start: 1 outliers final: 0 residues processed: 128 average time/residue: 0.6164 time to fit residues: 147.5531 Evaluate side-chains 121 residues out of total 7770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 6.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 999 random chunks: chunk 843 optimal weight: 6.9990 chunk 757 optimal weight: 5.9990 chunk 420 optimal weight: 8.9990 chunk 258 optimal weight: 7.9990 chunk 510 optimal weight: 2.9990 chunk 404 optimal weight: 9.9990 chunk 783 optimal weight: 9.9990 chunk 303 optimal weight: 5.9990 chunk 476 optimal weight: 8.9990 chunk 582 optimal weight: 10.0000 chunk 907 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 252 GLN F 28 GLN J 251 GLN M 106 ASN N 151 ASN O 28 GLN O 30 GLN P 18 ASN P 123 GLN R 252 GLN S 55 GLN ** S 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 23 ASN U 30 GLN U 251 GLN W 28 GLN ** W 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 18 ASN ** X 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 123 GLN Z 111 ASN ** i 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 151 ASN k 262 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.050333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.046485 restraints weight = 361295.927| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.40 r_work: 0.3188 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.0798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 72039 Z= 0.287 Angle : 0.512 7.490 97532 Z= 0.296 Chirality : 0.034 0.144 12580 Planarity : 0.003 0.049 12469 Dihedral : 4.032 23.959 10101 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 0.08 % Allowed : 2.66 % Favored : 97.26 % 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: 3.79 (0.08), residues: 9953 helix: 3.25 (0.05), residues: 7289 sheet: -2.66 (0.24), residues: 370 loop : 0.93 (0.14), residues: 2294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP g 49 HIS 0.006 0.002 HIS K 214 PHE 0.033 0.002 PHE L 148 ARG 0.005 0.001 ARG V 121 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19906 Ramachandran restraints generated. 9953 Oldfield, 0 Emsley, 9953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19906 Ramachandran restraints generated. 9953 Oldfield, 0 Emsley, 9953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 7770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 126 time to evaluate : 6.426 Fit side-chains REVERT: E 25 GLU cc_start: 0.9031 (tp30) cc_final: 0.8494 (mm-30) REVERT: J 93 MET cc_start: 0.8146 (mtp) cc_final: 0.7916 (mtp) REVERT: T 93 MET cc_start: 0.9232 (mtp) cc_final: 0.9020 (mtp) REVERT: e 60 ASN cc_start: 0.8986 (m-40) cc_final: 0.8682 (m-40) outliers start: 6 outliers final: 2 residues processed: 132 average time/residue: 0.6563 time to fit residues: 160.4326 Evaluate side-chains 124 residues out of total 7770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 122 time to evaluate : 6.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 167 THR Chi-restraints excluded: chain d residue 167 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 999 random chunks: chunk 305 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 604 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 359 optimal weight: 5.9990 chunk 421 optimal weight: 0.8980 chunk 174 optimal weight: 5.9990 chunk 596 optimal weight: 5.9990 chunk 736 optimal weight: 6.9990 chunk 340 optimal weight: 10.0000 chunk 696 optimal weight: 5.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 251 GLN Q 123 GLN R 63 ASN ** S 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 123 GLN Y 7 ASN ** a 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 54 ASN ** i 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.050933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.047102 restraints weight = 359647.673| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.40 r_work: 0.3204 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 72039 Z= 0.229 Angle : 0.437 8.844 97532 Z= 0.255 Chirality : 0.031 0.135 12580 Planarity : 0.002 0.040 12469 Dihedral : 3.813 22.192 10101 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 0.21 % Allowed : 4.03 % Favored : 95.77 % 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: 4.43 (0.08), residues: 9953 helix: 3.85 (0.05), residues: 7289 sheet: -2.37 (0.25), residues: 370 loop : 0.66 (0.13), residues: 2294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP g 49 HIS 0.005 0.002 HIS K 214 PHE 0.021 0.002 PHE L 148 ARG 0.004 0.000 ARG L 121 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19906 Ramachandran restraints generated. 9953 Oldfield, 0 Emsley, 9953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19906 Ramachandran restraints generated. 9953 Oldfield, 0 Emsley, 9953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 7770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 7.647 Fit side-chains REVERT: E 25 GLU cc_start: 0.9057 (tp30) cc_final: 0.8550 (mm-30) REVERT: J 93 MET cc_start: 0.8137 (mtp) cc_final: 0.7830 (mtp) REVERT: Q 26 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8386 (mm) REVERT: T 62 MET cc_start: 0.9177 (mmm) cc_final: 0.8855 (mtp) REVERT: e 60 ASN cc_start: 0.8998 (m-40) cc_final: 0.8743 (m-40) REVERT: g 186 MET cc_start: 0.8899 (tpt) cc_final: 0.8545 (tpp) REVERT: h 19 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8385 (tt) outliers start: 16 outliers final: 3 residues processed: 139 average time/residue: 0.6150 time to fit residues: 159.9636 Evaluate side-chains 125 residues out of total 7770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 120 time to evaluate : 6.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain Q residue 26 LEU Chi-restraints excluded: chain Z residue 167 THR Chi-restraints excluded: chain d residue 167 THR Chi-restraints excluded: chain h residue 19 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 999 random chunks: chunk 735 optimal weight: 4.9990 chunk 420 optimal weight: 10.0000 chunk 559 optimal weight: 5.9990 chunk 747 optimal weight: 9.9990 chunk 369 optimal weight: 5.9990 chunk 244 optimal weight: 5.9990 chunk 860 optimal weight: 10.0000 chunk 568 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 891 optimal weight: 40.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 54 ASN ** S 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 23 ASN U 251 GLN ** X 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 123 GLN a 123 GLN b 73 GLN ** i 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.050377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.046501 restraints weight = 362969.638| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.40 r_work: 0.3185 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 72039 Z= 0.277 Angle : 0.456 7.697 97532 Z= 0.262 Chirality : 0.032 0.135 12580 Planarity : 0.002 0.037 12469 Dihedral : 3.782 22.272 10101 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 0.31 % Allowed : 4.81 % Favored : 94.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.46 (0.08), residues: 9953 helix: 3.91 (0.05), residues: 7289 sheet: -2.16 (0.25), residues: 370 loop : 0.47 (0.13), residues: 2294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 49 HIS 0.006 0.002 HIS K 214 PHE 0.021 0.002 PHE L 148 ARG 0.005 0.000 ARG L 121 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19906 Ramachandran restraints generated. 9953 Oldfield, 0 Emsley, 9953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19906 Ramachandran restraints generated. 9953 Oldfield, 0 Emsley, 9953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 7770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 6.128 Fit side-chains REVERT: D 149 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8841 (pp) REVERT: E 25 GLU cc_start: 0.9035 (tp30) cc_final: 0.8549 (mm-30) REVERT: J 93 MET cc_start: 0.8203 (mtp) cc_final: 0.7879 (mtp) REVERT: Q 26 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8388 (mm) REVERT: T 62 MET cc_start: 0.9194 (mmm) cc_final: 0.8888 (mtp) REVERT: Z 37 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8579 (mtpp) REVERT: d 30 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.7801 (mp-120) REVERT: e 60 ASN cc_start: 0.9005 (m-40) cc_final: 0.8751 (m-40) REVERT: g 186 MET cc_start: 0.8921 (tpt) cc_final: 0.8525 (tpp) REVERT: h 19 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8401 (tt) outliers start: 24 outliers final: 5 residues processed: 146 average time/residue: 0.6012 time to fit residues: 163.6613 Evaluate side-chains 130 residues out of total 7770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 120 time to evaluate : 6.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain Q residue 26 LEU Chi-restraints excluded: chain Z residue 37 LYS Chi-restraints excluded: chain Z residue 167 THR Chi-restraints excluded: chain d residue 30 GLN Chi-restraints excluded: chain d residue 167 THR Chi-restraints excluded: chain f residue 3 LEU Chi-restraints excluded: chain h residue 19 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 999 random chunks: chunk 339 optimal weight: 5.9990 chunk 412 optimal weight: 6.9990 chunk 389 optimal weight: 10.0000 chunk 384 optimal weight: 5.9990 chunk 982 optimal weight: 6.9990 chunk 709 optimal weight: 7.9990 chunk 771 optimal weight: 9.9990 chunk 765 optimal weight: 5.9990 chunk 482 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 chunk 755 optimal weight: 30.0000 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 123 GLN f 262 ASN ** i 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 151 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.050988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.047205 restraints weight = 359269.432| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.40 r_work: 0.3205 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 72039 Z= 0.212 Angle : 0.410 8.177 97532 Z= 0.240 Chirality : 0.031 0.130 12580 Planarity : 0.002 0.034 12469 Dihedral : 3.676 21.337 10101 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 0.37 % Allowed : 5.33 % Favored : 94.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.67 (0.08), residues: 9953 helix: 4.09 (0.05), residues: 7289 sheet: -2.00 (0.26), residues: 370 loop : 0.39 (0.13), residues: 2294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 49 HIS 0.005 0.002 HIS K 214 PHE 0.015 0.001 PHE L 148 ARG 0.004 0.000 ARG L 121 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19906 Ramachandran restraints generated. 9953 Oldfield, 0 Emsley, 9953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19906 Ramachandran restraints generated. 9953 Oldfield, 0 Emsley, 9953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 7770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 122 time to evaluate : 6.093 Fit side-chains REVERT: D 149 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8786 (pp) REVERT: E 25 GLU cc_start: 0.9028 (tp30) cc_final: 0.8564 (mm-30) REVERT: H 258 LEU cc_start: 0.6597 (OUTLIER) cc_final: 0.6185 (tp) REVERT: J 93 MET cc_start: 0.8132 (mtp) cc_final: 0.7814 (mtp) REVERT: P 25 GLU cc_start: 0.8794 (tp30) cc_final: 0.8552 (tp30) REVERT: Q 26 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8383 (mm) REVERT: T 62 MET cc_start: 0.9174 (mmm) cc_final: 0.8849 (mtp) REVERT: V 186 MET cc_start: 0.8969 (tpt) cc_final: 0.8597 (tpp) REVERT: Z 37 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8530 (mtpp) REVERT: d 30 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7688 (mp-120) REVERT: e 60 ASN cc_start: 0.8961 (m-40) cc_final: 0.8732 (m-40) REVERT: g 186 MET cc_start: 0.8917 (tpt) cc_final: 0.8490 (tpp) REVERT: h 19 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8373 (tt) outliers start: 29 outliers final: 9 residues processed: 150 average time/residue: 0.5944 time to fit residues: 166.8457 Evaluate side-chains 136 residues out of total 7770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 6.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain G residue 130 ASN Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain H residue 258 LEU Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain Q residue 26 LEU Chi-restraints excluded: chain Z residue 37 LYS Chi-restraints excluded: chain Z residue 167 THR Chi-restraints excluded: chain d residue 30 GLN Chi-restraints excluded: chain d residue 167 THR Chi-restraints excluded: chain g residue 124 ILE Chi-restraints excluded: chain h residue 19 LEU Chi-restraints excluded: chain h residue 179 THR Chi-restraints excluded: chain j residue 151 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 999 random chunks: chunk 573 optimal weight: 20.0000 chunk 590 optimal weight: 1.9990 chunk 272 optimal weight: 9.9990 chunk 931 optimal weight: 8.9990 chunk 388 optimal weight: 9.9990 chunk 108 optimal weight: 10.0000 chunk 361 optimal weight: 10.0000 chunk 731 optimal weight: 6.9990 chunk 785 optimal weight: 5.9990 chunk 72 optimal weight: 9.9990 chunk 978 optimal weight: 2.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN L 4 ASN ** S 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 123 GLN Y 123 GLN e 30 GLN ** i 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 151 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.050489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.046603 restraints weight = 362560.924| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.40 r_work: 0.3187 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 72039 Z= 0.260 Angle : 0.444 12.254 97532 Z= 0.254 Chirality : 0.032 0.134 12580 Planarity : 0.002 0.032 12469 Dihedral : 3.691 21.181 10101 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 0.45 % Allowed : 5.80 % Favored : 93.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.56 (0.08), residues: 9953 helix: 4.03 (0.05), residues: 7289 sheet: -1.94 (0.26), residues: 370 loop : 0.28 (0.13), residues: 2294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 49 HIS 0.006 0.002 HIS K 214 PHE 0.017 0.002 PHE L 148 ARG 0.004 0.000 ARG L 121 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19906 Ramachandran restraints generated. 9953 Oldfield, 0 Emsley, 9953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19906 Ramachandran restraints generated. 9953 Oldfield, 0 Emsley, 9953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 7770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 123 time to evaluate : 6.213 Fit side-chains REVERT: D 149 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8780 (pp) REVERT: E 25 GLU cc_start: 0.9040 (tp30) cc_final: 0.8638 (mm-30) REVERT: J 93 MET cc_start: 0.8183 (mtp) cc_final: 0.7843 (mtp) REVERT: Q 26 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8407 (mm) REVERT: T 62 MET cc_start: 0.9198 (mmm) cc_final: 0.8893 (mtp) REVERT: X 149 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8706 (pp) REVERT: Z 37 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8543 (mtpp) REVERT: d 30 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.7822 (mp-120) REVERT: e 60 ASN cc_start: 0.8975 (m-40) cc_final: 0.8755 (m-40) REVERT: g 186 MET cc_start: 0.8912 (tpt) cc_final: 0.8498 (tpp) REVERT: h 19 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8414 (tt) outliers start: 35 outliers final: 10 residues processed: 157 average time/residue: 0.6044 time to fit residues: 176.5687 Evaluate side-chains 136 residues out of total 7770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 5.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain G residue 101 SER Chi-restraints excluded: chain G residue 130 ASN Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain Q residue 6 ILE Chi-restraints excluded: chain Q residue 26 LEU Chi-restraints excluded: chain X residue 149 LEU Chi-restraints excluded: chain Z residue 37 LYS Chi-restraints excluded: chain Z residue 167 THR Chi-restraints excluded: chain d residue 30 GLN Chi-restraints excluded: chain d residue 167 THR Chi-restraints excluded: chain f residue 3 LEU Chi-restraints excluded: chain h residue 19 LEU Chi-restraints excluded: chain h residue 179 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 999 random chunks: chunk 328 optimal weight: 20.0000 chunk 125 optimal weight: 30.0000 chunk 95 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 854 optimal weight: 8.9990 chunk 466 optimal weight: 9.9990 chunk 313 optimal weight: 9.9990 chunk 198 optimal weight: 0.9980 chunk 469 optimal weight: 10.0000 chunk 471 optimal weight: 0.7980 chunk 716 optimal weight: 10.0000 overall best weight: 4.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 151 ASN T 151 ASN ** U 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 130 ASN X 123 GLN ** i 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.050917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.047142 restraints weight = 358923.432| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.40 r_work: 0.3202 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 72039 Z= 0.214 Angle : 0.411 9.031 97532 Z= 0.238 Chirality : 0.031 0.149 12580 Planarity : 0.002 0.029 12469 Dihedral : 3.629 20.775 10101 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 0.48 % Allowed : 6.18 % Favored : 93.35 % 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: 4.70 (0.08), residues: 9953 helix: 4.15 (0.05), residues: 7289 sheet: -1.86 (0.26), residues: 370 loop : 0.26 (0.13), residues: 2294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 49 HIS 0.005 0.002 HIS K 214 PHE 0.013 0.001 PHE L 148 ARG 0.003 0.000 ARG L 121 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19906 Ramachandran restraints generated. 9953 Oldfield, 0 Emsley, 9953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19906 Ramachandran restraints generated. 9953 Oldfield, 0 Emsley, 9953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 7770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 122 time to evaluate : 6.131 Fit side-chains revert: symmetry clash REVERT: D 149 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8714 (pp) REVERT: E 25 GLU cc_start: 0.9034 (tp30) cc_final: 0.8656 (mm-30) REVERT: J 93 MET cc_start: 0.8147 (mtp) cc_final: 0.7835 (mtp) REVERT: Q 26 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8404 (mm) REVERT: T 62 MET cc_start: 0.9181 (mmm) cc_final: 0.8860 (mtp) REVERT: X 149 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8710 (pp) REVERT: Z 37 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8548 (mtpp) REVERT: d 30 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7749 (mp-120) REVERT: e 60 ASN cc_start: 0.8955 (m-40) cc_final: 0.8735 (m-40) REVERT: h 19 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8407 (tt) outliers start: 37 outliers final: 12 residues processed: 159 average time/residue: 0.6041 time to fit residues: 179.5596 Evaluate side-chains 139 residues out of total 7770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 6.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain G residue 101 SER Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain Q residue 26 LEU Chi-restraints excluded: chain X residue 149 LEU Chi-restraints excluded: chain Z residue 37 LYS Chi-restraints excluded: chain Z residue 167 THR Chi-restraints excluded: chain d residue 30 GLN Chi-restraints excluded: chain d residue 167 THR Chi-restraints excluded: chain h residue 19 LEU Chi-restraints excluded: chain h residue 31 GLN Chi-restraints excluded: chain h residue 179 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 999 random chunks: chunk 211 optimal weight: 10.0000 chunk 307 optimal weight: 10.0000 chunk 332 optimal weight: 10.0000 chunk 915 optimal weight: 5.9990 chunk 782 optimal weight: 5.9990 chunk 137 optimal weight: 5.9990 chunk 957 optimal weight: 10.0000 chunk 604 optimal weight: 9.9990 chunk 430 optimal weight: 0.7980 chunk 228 optimal weight: 8.9990 chunk 222 optimal weight: 9.9990 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 123 GLN a 251 GLN ** i 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.050367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.046496 restraints weight = 362059.865| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.40 r_work: 0.3183 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 72039 Z= 0.265 Angle : 0.448 11.416 97532 Z= 0.256 Chirality : 0.032 0.149 12580 Planarity : 0.002 0.033 12469 Dihedral : 3.675 21.255 10101 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.45 % Allowed : 6.40 % Favored : 93.15 % 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: 4.55 (0.08), residues: 9953 helix: 4.04 (0.05), residues: 7289 sheet: -1.83 (0.26), residues: 370 loop : 0.16 (0.13), residues: 2294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 49 HIS 0.006 0.002 HIS K 214 PHE 0.017 0.002 PHE L 148 ARG 0.003 0.000 ARG V 121 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19906 Ramachandran restraints generated. 9953 Oldfield, 0 Emsley, 9953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19906 Ramachandran restraints generated. 9953 Oldfield, 0 Emsley, 9953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 7770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 120 time to evaluate : 6.242 Fit side-chains revert: symmetry clash REVERT: D 149 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8772 (pp) REVERT: Q 26 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8414 (mm) REVERT: T 62 MET cc_start: 0.9203 (mmm) cc_final: 0.8899 (mtp) REVERT: X 149 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8689 (pp) REVERT: Z 37 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8471 (mtpp) REVERT: a 225 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8450 (mp) REVERT: d 30 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.7772 (mp-120) REVERT: e 60 ASN cc_start: 0.8984 (m-40) cc_final: 0.8755 (m-40) REVERT: h 19 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8437 (tt) outliers start: 35 outliers final: 16 residues processed: 155 average time/residue: 0.6111 time to fit residues: 178.1967 Evaluate side-chains 143 residues out of total 7770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 6.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain G residue 101 SER Chi-restraints excluded: chain G residue 130 ASN Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain Q residue 6 ILE Chi-restraints excluded: chain Q residue 26 LEU Chi-restraints excluded: chain S residue 6 ILE Chi-restraints excluded: chain X residue 149 LEU Chi-restraints excluded: chain Z residue 37 LYS Chi-restraints excluded: chain Z residue 167 THR Chi-restraints excluded: chain a residue 225 LEU Chi-restraints excluded: chain d residue 30 GLN Chi-restraints excluded: chain d residue 167 THR Chi-restraints excluded: chain h residue 19 LEU Chi-restraints excluded: chain h residue 31 GLN Chi-restraints excluded: chain h residue 179 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 999 random chunks: chunk 676 optimal weight: 7.9990 chunk 776 optimal weight: 5.9990 chunk 843 optimal weight: 1.9990 chunk 490 optimal weight: 1.9990 chunk 663 optimal weight: 0.1980 chunk 587 optimal weight: 5.9990 chunk 897 optimal weight: 9.9990 chunk 904 optimal weight: 0.0010 chunk 455 optimal weight: 3.9990 chunk 541 optimal weight: 5.9990 chunk 407 optimal weight: 7.9990 overall best weight: 1.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 73 GLN ** U 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 123 GLN g 140 ASN ** i 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 63 ASN k 252 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.052530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.048769 restraints weight = 356206.507| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.40 r_work: 0.3254 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 72039 Z= 0.143 Angle : 0.368 10.053 97532 Z= 0.215 Chirality : 0.029 0.149 12580 Planarity : 0.002 0.028 12469 Dihedral : 3.497 18.679 10101 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 0.35 % Allowed : 6.56 % Favored : 93.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.69 (0.08), residues: 9953 helix: 4.11 (0.05), residues: 7585 sheet: -1.71 (0.26), residues: 370 loop : -0.30 (0.14), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 49 HIS 0.004 0.001 HIS H 214 PHE 0.012 0.001 PHE Q 117 ARG 0.002 0.000 ARG L 121 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19906 Ramachandran restraints generated. 9953 Oldfield, 0 Emsley, 9953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19906 Ramachandran restraints generated. 9953 Oldfield, 0 Emsley, 9953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 7770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 6.188 Fit side-chains revert: symmetry clash REVERT: C 62 MET cc_start: 0.9138 (mmt) cc_final: 0.8829 (mmt) REVERT: D 62 MET cc_start: 0.9091 (mmm) cc_final: 0.8637 (mmt) REVERT: D 149 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8723 (pp) REVERT: E 25 GLU cc_start: 0.9006 (tp30) cc_final: 0.8607 (mm-30) REVERT: F 62 MET cc_start: 0.9089 (mmt) cc_final: 0.8784 (mmt) REVERT: H 30 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.7825 (pm20) REVERT: J 93 MET cc_start: 0.7973 (mtp) cc_final: 0.7669 (mtp) REVERT: Q 26 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8409 (mm) REVERT: V 186 MET cc_start: 0.8891 (tpt) cc_final: 0.8578 (tpp) REVERT: d 30 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7590 (mp-120) REVERT: h 19 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8326 (tt) outliers start: 27 outliers final: 13 residues processed: 158 average time/residue: 0.5952 time to fit residues: 175.4198 Evaluate side-chains 141 residues out of total 7770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 5.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain G residue 130 ASN Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 30 GLN Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 237 LEU Chi-restraints excluded: chain Q residue 6 ILE Chi-restraints excluded: chain Q residue 26 LEU Chi-restraints excluded: chain S residue 6 ILE Chi-restraints excluded: chain d residue 30 GLN Chi-restraints excluded: chain h residue 19 LEU Chi-restraints excluded: chain h residue 31 GLN Chi-restraints excluded: chain h residue 179 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 999 random chunks: chunk 989 optimal weight: 0.0060 chunk 78 optimal weight: 2.9990 chunk 417 optimal weight: 20.0000 chunk 899 optimal weight: 8.9990 chunk 134 optimal weight: 6.9990 chunk 833 optimal weight: 2.9990 chunk 278 optimal weight: 10.0000 chunk 737 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 165 optimal weight: 9.9990 chunk 861 optimal weight: 7.9990 overall best weight: 4.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 55 GLN ** T 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 123 GLN ** i 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.051306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.047434 restraints weight = 359278.864| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.40 r_work: 0.3212 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 72039 Z= 0.215 Angle : 0.414 11.103 97532 Z= 0.236 Chirality : 0.031 0.149 12580 Planarity : 0.002 0.028 12469 Dihedral : 3.520 19.802 10101 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 0.31 % Allowed : 6.76 % Favored : 92.93 % 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: 4.86 (0.08), residues: 9953 helix: 4.28 (0.05), residues: 7289 sheet: -1.68 (0.26), residues: 370 loop : 0.23 (0.13), residues: 2294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 49 HIS 0.005 0.002 HIS K 214 PHE 0.014 0.001 PHE Q 217 ARG 0.003 0.000 ARG L 121 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19906 Ramachandran restraints generated. 9953 Oldfield, 0 Emsley, 9953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19906 Ramachandran restraints generated. 9953 Oldfield, 0 Emsley, 9953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 7770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 6.243 Fit side-chains revert: symmetry clash REVERT: Q 26 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8441 (mm) REVERT: V 186 MET cc_start: 0.8921 (tpt) cc_final: 0.8594 (tpp) REVERT: d 30 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7716 (mp-120) REVERT: h 19 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8401 (tt) outliers start: 24 outliers final: 13 residues processed: 143 average time/residue: 0.6153 time to fit residues: 164.6044 Evaluate side-chains 136 residues out of total 7770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 6.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain G residue 130 ASN Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 237 LEU Chi-restraints excluded: chain Q residue 6 ILE Chi-restraints excluded: chain Q residue 26 LEU Chi-restraints excluded: chain S residue 6 ILE Chi-restraints excluded: chain d residue 30 GLN Chi-restraints excluded: chain h residue 19 LEU Chi-restraints excluded: chain h residue 31 GLN Chi-restraints excluded: chain h residue 179 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 999 random chunks: chunk 365 optimal weight: 3.9990 chunk 694 optimal weight: 5.9990 chunk 988 optimal weight: 7.9990 chunk 428 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 chunk 979 optimal weight: 8.9990 chunk 731 optimal weight: 4.9990 chunk 534 optimal weight: 5.9990 chunk 520 optimal weight: 9.9990 chunk 349 optimal weight: 20.0000 chunk 200 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 123 GLN ** i 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.050503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.046683 restraints weight = 361490.821| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.39 r_work: 0.3189 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 72039 Z= 0.258 Angle : 0.441 11.560 97532 Z= 0.251 Chirality : 0.032 0.149 12580 Planarity : 0.002 0.031 12469 Dihedral : 3.609 20.938 10101 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 0.33 % Allowed : 6.71 % Favored : 92.96 % 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: 4.68 (0.08), residues: 9953 helix: 4.15 (0.05), residues: 7289 sheet: -1.67 (0.26), residues: 370 loop : 0.14 (0.13), residues: 2294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 49 HIS 0.006 0.002 HIS K 214 PHE 0.015 0.002 PHE c 117 ARG 0.003 0.000 ARG V 121 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15513.37 seconds wall clock time: 275 minutes 10.80 seconds (16510.80 seconds total)