Starting phenix.real_space_refine on Sat Sep 28 20:29:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cep_45506/09_2024/9cep_45506.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cep_45506/09_2024/9cep_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cep_45506/09_2024/9cep_45506.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cep_45506/09_2024/9cep_45506.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cep_45506/09_2024/9cep_45506.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cep_45506/09_2024/9cep_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): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 33.34, per 1000 atoms: 0.47 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: 14.78 Conformation dependent library (CDL) restraints added in 8.1 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: 4.29 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: 29.05 Time building geometry restraints manager: 17.70 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.100 Extract box with map and model: 2.250 Check model and map are aligned: 0.420 Set scattering table: 0.540 Process input model: 133.030 Find NCS groups from input model: 3.120 Set up NCS constraints: 0.930 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 153.600 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 1 poor density : 127 time to evaluate : 6.165 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: 0.6278 time to fit residues: 150.7797 Evaluate side-chains 121 residues out of total 7770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 6.066 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 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 fitting. rotamer outliers: 6 poor density : 126 time to evaluate : 6.240 Fit side-chains REVERT: E 25 GLU cc_start: 0.9017 (tp30) cc_final: 0.8501 (mm-30) REVERT: J 93 MET cc_start: 0.8170 (mtp) cc_final: 0.7963 (mtp) REVERT: T 93 MET cc_start: 0.9105 (mtp) cc_final: 0.8904 (mtp) REVERT: e 60 ASN cc_start: 0.9032 (m-40) cc_final: 0.8733 (m-40) outliers start: 6 outliers final: 2 residues processed: 132 average time/residue: 0.6446 time to fit residues: 157.8789 Evaluate side-chains 124 residues out of total 7770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 122 time to evaluate : 6.172 ------------------------------------------------------------------------------- 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 504 optimal weight: 5.9990 chunk 281 optimal weight: 10.0000 chunk 755 optimal weight: 20.0000 chunk 617 optimal weight: 10.0000 chunk 250 optimal weight: 9.9990 chunk 908 optimal weight: 5.9990 chunk 981 optimal weight: 5.9990 chunk 809 optimal weight: 9.9990 chunk 901 optimal weight: 10.0000 chunk 309 optimal weight: 8.9990 chunk 729 optimal weight: 0.1980 overall best weight: 5.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 54 ASN Q 123 GLN R 63 ASN ** S 151 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 d 195 GLN ** i 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 72039 Z= 0.265 Angle : 0.464 9.244 97532 Z= 0.268 Chirality : 0.032 0.137 12580 Planarity : 0.002 0.040 12469 Dihedral : 3.858 22.763 10101 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 0.24 % Allowed : 4.22 % Favored : 95.53 % 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: 4.32 (0.08), residues: 9953 helix: 3.77 (0.05), residues: 7289 sheet: -2.35 (0.25), residues: 370 loop : 0.59 (0.13), residues: 2294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 49 HIS 0.006 0.002 HIS K 214 PHE 0.024 0.002 PHE L 148 ARG 0.004 0.000 ARG B 32 *********************** 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 142 residues out of total 7770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 123 time to evaluate : 6.416 Fit side-chains REVERT: E 25 GLU cc_start: 0.9056 (tp30) cc_final: 0.8576 (mm-30) REVERT: J 93 MET cc_start: 0.8183 (mtp) cc_final: 0.7905 (mtp) REVERT: N 26 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8307 (mm) REVERT: Q 26 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8374 (mm) REVERT: T 62 MET cc_start: 0.9223 (mmm) cc_final: 0.8942 (mtp) REVERT: d 30 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7819 (mp-120) REVERT: e 60 ASN cc_start: 0.9054 (m-40) cc_final: 0.8789 (m-40) REVERT: g 186 MET cc_start: 0.8918 (tpt) cc_final: 0.8627 (tpp) REVERT: h 19 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8366 (tt) outliers start: 19 outliers final: 3 residues processed: 141 average time/residue: 0.6417 time to fit residues: 169.0936 Evaluate side-chains 127 residues out of total 7770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 120 time to evaluate : 6.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 26 LEU 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 30 GLN 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 897 optimal weight: 9.9990 chunk 683 optimal weight: 7.9990 chunk 471 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 433 optimal weight: 5.9990 chunk 610 optimal weight: 3.9990 chunk 912 optimal weight: 8.9990 chunk 965 optimal weight: 10.0000 chunk 476 optimal weight: 30.0000 chunk 864 optimal weight: 0.0570 chunk 260 optimal weight: 20.0000 overall best weight: 3.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 195 GLN ** S 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 23 ASN U 251 GLN ** W 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 123 GLN b 73 GLN e 54 ASN ** i 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 63 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 72039 Z= 0.184 Angle : 0.391 6.533 97532 Z= 0.231 Chirality : 0.030 0.130 12580 Planarity : 0.002 0.035 12469 Dihedral : 3.650 20.386 10101 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 0.31 % Allowed : 4.89 % Favored : 94.80 % 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: 4.77 (0.08), residues: 9953 helix: 4.15 (0.05), residues: 7289 sheet: -2.07 (0.26), residues: 370 loop : 0.51 (0.13), residues: 2294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP g 49 HIS 0.004 0.001 HIS K 214 PHE 0.017 0.001 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 150 residues out of total 7770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 126 time to evaluate : 6.386 Fit side-chains REVERT: D 149 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8688 (pp) REVERT: E 25 GLU cc_start: 0.9042 (tp30) cc_final: 0.8590 (mm-30) REVERT: F 62 MET cc_start: 0.9211 (mmt) cc_final: 0.8869 (mmt) REVERT: J 93 MET cc_start: 0.8045 (mtp) cc_final: 0.7738 (mtp) REVERT: Q 26 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8428 (mm) REVERT: T 62 MET cc_start: 0.9171 (mmm) cc_final: 0.8875 (mtp) REVERT: V 186 MET cc_start: 0.8916 (tpt) cc_final: 0.8584 (tpp) REVERT: e 60 ASN cc_start: 0.9019 (m-40) cc_final: 0.8801 (m-40) REVERT: g 186 MET cc_start: 0.8892 (tpt) cc_final: 0.8532 (tpp) REVERT: h 19 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8319 (tt) outliers start: 24 outliers final: 4 residues processed: 150 average time/residue: 0.6312 time to fit residues: 175.2073 Evaluate side-chains 128 residues out of total 7770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 121 time to evaluate : 6.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain Q residue 26 LEU Chi-restraints excluded: chain d residue 167 THR Chi-restraints excluded: chain f residue 3 LEU Chi-restraints excluded: chain g residue 124 ILE Chi-restraints excluded: chain h residue 19 LEU Chi-restraints excluded: chain h residue 179 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 999 random chunks: chunk 804 optimal weight: 9.9990 chunk 548 optimal weight: 9.9990 chunk 14 optimal weight: 0.4980 chunk 718 optimal weight: 7.9990 chunk 398 optimal weight: 6.9990 chunk 824 optimal weight: 7.9990 chunk 667 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 493 optimal weight: 9.9990 chunk 866 optimal weight: 9.9990 chunk 243 optimal weight: 20.0000 overall best weight: 5.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 f 262 ASN ** i 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 151 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 72039 Z= 0.280 Angle : 0.462 11.772 97532 Z= 0.262 Chirality : 0.032 0.133 12580 Planarity : 0.002 0.035 12469 Dihedral : 3.712 21.823 10101 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 0.46 % Allowed : 5.46 % Favored : 94.08 % 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: 4.02 (0.05), residues: 7289 sheet: -1.97 (0.26), residues: 370 loop : 0.33 (0.13), residues: 2294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 49 HIS 0.007 0.002 HIS K 214 PHE 0.020 0.002 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 159 residues out of total 7770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 123 time to evaluate : 6.621 Fit side-chains REVERT: D 149 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8734 (pp) REVERT: E 25 GLU cc_start: 0.9065 (tp30) cc_final: 0.8633 (mm-30) REVERT: P 25 GLU cc_start: 0.8779 (tp30) cc_final: 0.8495 (tp30) REVERT: Q 26 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8449 (mm) REVERT: T 62 MET cc_start: 0.9209 (mmm) cc_final: 0.8955 (mtp) REVERT: V 186 MET cc_start: 0.8937 (tpt) cc_final: 0.8607 (tpp) REVERT: X 149 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8820 (pp) REVERT: Z 37 LYS cc_start: 0.8969 (OUTLIER) cc_final: 0.8584 (mttp) REVERT: d 30 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7787 (mp-120) REVERT: e 60 ASN cc_start: 0.9055 (m-40) cc_final: 0.8828 (m-40) REVERT: g 186 MET cc_start: 0.8919 (tpt) cc_final: 0.8578 (tpp) REVERT: h 19 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8377 (tt) outliers start: 36 outliers final: 10 residues processed: 158 average time/residue: 0.6631 time to fit residues: 196.1818 Evaluate side-chains 138 residues out of total 7770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 122 time to evaluate : 6.663 ------------------------------------------------------------------------------- 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 G residue 149 LEU Chi-restraints excluded: chain H residue 124 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 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 324 optimal weight: 8.9990 chunk 869 optimal weight: 6.9990 chunk 190 optimal weight: 5.9990 chunk 566 optimal weight: 20.0000 chunk 238 optimal weight: 7.9990 chunk 966 optimal weight: 3.9990 chunk 802 optimal weight: 5.9990 chunk 447 optimal weight: 8.9990 chunk 80 optimal weight: 10.0000 chunk 319 optimal weight: 5.9990 chunk 507 optimal weight: 1.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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** ** 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 ** i 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 151 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 72039 Z= 0.237 Angle : 0.429 12.334 97532 Z= 0.247 Chirality : 0.031 0.146 12580 Planarity : 0.002 0.031 12469 Dihedral : 3.670 22.361 10101 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 0.42 % Allowed : 5.95 % Favored : 93.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.62 (0.08), residues: 9953 helix: 4.08 (0.05), residues: 7289 sheet: -1.90 (0.26), residues: 370 loop : 0.27 (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 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 156 residues out of total 7770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 123 time to evaluate : 6.162 Fit side-chains revert: symmetry clash REVERT: D 149 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8721 (pp) REVERT: E 25 GLU cc_start: 0.9050 (tp30) cc_final: 0.8674 (mm-30) REVERT: Q 26 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8409 (mm) REVERT: T 62 MET cc_start: 0.9204 (mmm) cc_final: 0.8925 (mtp) REVERT: U 93 MET cc_start: 0.8747 (mtt) cc_final: 0.8476 (mtt) REVERT: V 186 MET cc_start: 0.8929 (tpt) cc_final: 0.8609 (tpp) REVERT: Z 37 LYS cc_start: 0.8985 (OUTLIER) cc_final: 0.8606 (mttp) REVERT: d 30 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.7710 (mp-120) REVERT: e 60 ASN cc_start: 0.9042 (m-40) cc_final: 0.8814 (m-40) REVERT: g 186 MET cc_start: 0.8909 (tpt) cc_final: 0.8546 (tpp) REVERT: h 19 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8387 (tt) outliers start: 33 outliers final: 13 residues processed: 155 average time/residue: 0.6247 time to fit residues: 181.0580 Evaluate side-chains 140 residues out of total 7770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 122 time to evaluate : 6.351 ------------------------------------------------------------------------------- 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 G residue 149 LEU Chi-restraints excluded: chain H residue 30 GLN Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain Q residue 6 ILE 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 Chi-restraints excluded: chain h residue 31 GLN Chi-restraints excluded: chain h residue 179 THR Chi-restraints excluded: chain j residue 151 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 999 random chunks: chunk 931 optimal weight: 7.9990 chunk 108 optimal weight: 0.0370 chunk 550 optimal weight: 10.0000 chunk 705 optimal weight: 0.7980 chunk 546 optimal weight: 10.0000 chunk 813 optimal weight: 10.0000 chunk 539 optimal weight: 0.8980 chunk 962 optimal weight: 3.9990 chunk 602 optimal weight: 10.0000 chunk 587 optimal weight: 7.9990 chunk 444 optimal weight: 5.9990 overall best weight: 2.3462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 151 ASN ** U 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 130 ASN X 123 GLN g 140 ASN ** i 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 72039 Z= 0.152 Angle : 0.373 11.207 97532 Z= 0.217 Chirality : 0.029 0.142 12580 Planarity : 0.002 0.026 12469 Dihedral : 3.507 21.577 10101 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 0.42 % Allowed : 6.13 % Favored : 93.45 % 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: 4.99 (0.08), residues: 9953 helix: 4.37 (0.05), residues: 7289 sheet: -1.81 (0.26), residues: 370 loop : 0.31 (0.13), residues: 2294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 49 HIS 0.004 0.001 HIS H 214 PHE 0.011 0.001 PHE e 117 ARG 0.003 0.000 ARG U 32 *********************** 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 164 residues out of total 7770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 131 time to evaluate : 6.234 Fit side-chains revert: symmetry clash REVERT: D 149 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8679 (pp) REVERT: E 25 GLU cc_start: 0.9031 (tp30) cc_final: 0.8633 (mm-30) REVERT: F 62 MET cc_start: 0.9158 (mmt) cc_final: 0.8842 (mmt) REVERT: P 25 GLU cc_start: 0.8774 (tp30) cc_final: 0.8494 (tp30) REVERT: Q 26 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8430 (mm) REVERT: V 186 MET cc_start: 0.8815 (tpt) cc_final: 0.8550 (tpp) REVERT: d 30 GLN cc_start: 0.7991 (OUTLIER) cc_final: 0.7577 (mp-120) REVERT: h 19 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8307 (tt) outliers start: 33 outliers final: 11 residues processed: 164 average time/residue: 0.6040 time to fit residues: 184.5677 Evaluate side-chains 139 residues out of total 7770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 124 time to evaluate : 6.102 ------------------------------------------------------------------------------- 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 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 Q residue 6 ILE Chi-restraints excluded: chain Q residue 26 LEU Chi-restraints excluded: chain Z residue 167 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 999 random chunks: chunk 595 optimal weight: 9.9990 chunk 384 optimal weight: 8.9990 chunk 575 optimal weight: 5.9990 chunk 290 optimal weight: 10.0000 chunk 189 optimal weight: 30.0000 chunk 186 optimal weight: 6.9990 chunk 612 optimal weight: 7.9990 chunk 656 optimal weight: 6.9990 chunk 476 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 chunk 756 optimal weight: 0.6980 overall best weight: 5.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN D 54 ASN ** T 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 151 ASN ** U 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 251 GLN ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 72039 Z= 0.278 Angle : 0.453 11.926 97532 Z= 0.257 Chirality : 0.032 0.141 12580 Planarity : 0.002 0.031 12469 Dihedral : 3.617 20.656 10101 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 0.39 % Allowed : 6.42 % Favored : 93.19 % 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: 4.14 (0.05), residues: 7289 sheet: -1.76 (0.26), residues: 370 loop : 0.19 (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 0.016 0.002 PHE Q 217 ARG 0.004 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 150 residues out of total 7770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 120 time to evaluate : 6.207 Fit side-chains REVERT: I 179 THR cc_start: 0.8866 (OUTLIER) cc_final: 0.8653 (p) REVERT: P 25 GLU cc_start: 0.8768 (tp30) cc_final: 0.8503 (tp30) REVERT: Q 26 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8458 (mm) REVERT: V 186 MET cc_start: 0.8900 (tpt) cc_final: 0.8601 (tpp) REVERT: a 225 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8561 (mp) REVERT: d 30 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.7745 (mp-120) REVERT: h 19 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8412 (tt) outliers start: 30 outliers final: 12 residues processed: 150 average time/residue: 0.5949 time to fit residues: 167.5452 Evaluate side-chains 137 residues out of total 7770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 120 time to evaluate : 6.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain G residue 130 ASN Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain I residue 179 THR Chi-restraints excluded: chain M residue 124 ILE 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 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 179 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 999 random chunks: chunk 875 optimal weight: 4.9990 chunk 922 optimal weight: 7.9990 chunk 841 optimal weight: 7.9990 chunk 897 optimal weight: 10.0000 chunk 540 optimal weight: 50.0000 chunk 390 optimal weight: 10.0000 chunk 704 optimal weight: 5.9990 chunk 275 optimal weight: 6.9990 chunk 810 optimal weight: 0.8980 chunk 848 optimal weight: 9.9990 chunk 894 optimal weight: 5.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1625 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= 0.242 Angle : 0.432 11.309 97532 Z= 0.247 Chirality : 0.031 0.145 12580 Planarity : 0.002 0.032 12469 Dihedral : 3.610 20.650 10101 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 0.41 % Allowed : 6.53 % Favored : 93.06 % 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: 4.14 (0.05), residues: 7289 sheet: -1.71 (0.26), residues: 370 loop : 0.15 (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 L 148 ARG 0.003 0.000 ARG V 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 153 residues out of total 7770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 121 time to evaluate : 6.192 Fit side-chains revert: symmetry clash REVERT: E 25 GLU cc_start: 0.9056 (tp30) cc_final: 0.8705 (mm-30) REVERT: F 93 MET cc_start: 0.9173 (mtp) cc_final: 0.8941 (mtp) REVERT: I 179 THR cc_start: 0.8855 (OUTLIER) cc_final: 0.8641 (p) REVERT: P 25 GLU cc_start: 0.8770 (tp30) cc_final: 0.8528 (tp30) REVERT: Q 26 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8412 (mm) REVERT: a 225 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8560 (mp) REVERT: d 30 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7722 (mp-120) REVERT: h 19 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8409 (tt) outliers start: 32 outliers final: 18 residues processed: 153 average time/residue: 0.6103 time to fit residues: 175.4447 Evaluate side-chains 144 residues out of total 7770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 121 time to evaluate : 6.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 124 ILE 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 I residue 179 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 V residue 169 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 999 random chunks: chunk 589 optimal weight: 5.9990 chunk 948 optimal weight: 9.9990 chunk 579 optimal weight: 5.9990 chunk 450 optimal weight: 5.9990 chunk 659 optimal weight: 6.9990 chunk 995 optimal weight: 7.9990 chunk 916 optimal weight: 0.9990 chunk 792 optimal weight: 7.9990 chunk 82 optimal weight: 3.9990 chunk 612 optimal weight: 0.9980 chunk 485 optimal weight: 8.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 72039 Z= 0.194 Angle : 0.399 11.052 97532 Z= 0.230 Chirality : 0.030 0.144 12580 Planarity : 0.002 0.027 12469 Dihedral : 3.533 19.179 10101 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 0.40 % Allowed : 6.51 % 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: 4.82 (0.08), residues: 9953 helix: 4.20 (0.05), residues: 7363 sheet: -1.65 (0.26), residues: 370 loop : 0.25 (0.14), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 49 HIS 0.005 0.001 HIS K 214 PHE 0.013 0.001 PHE c 117 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 152 residues out of total 7770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 121 time to evaluate : 6.287 Fit side-chains revert: symmetry clash REVERT: E 25 GLU cc_start: 0.9039 (tp30) cc_final: 0.8694 (mm-30) REVERT: I 179 THR cc_start: 0.8797 (OUTLIER) cc_final: 0.8590 (p) REVERT: Q 26 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8438 (mm) REVERT: a 225 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8696 (mm) REVERT: d 30 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7666 (mp-120) REVERT: h 19 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8368 (tt) outliers start: 31 outliers final: 18 residues processed: 152 average time/residue: 0.6001 time to fit residues: 171.6209 Evaluate side-chains 144 residues out of total 7770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 121 time to evaluate : 6.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 124 ILE 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 124 ILE Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain I residue 179 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 V residue 169 LEU 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 f residue 3 LEU 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 629 optimal weight: 9.9990 chunk 844 optimal weight: 2.9990 chunk 242 optimal weight: 9.9990 chunk 730 optimal weight: 6.9990 chunk 117 optimal weight: 20.0000 chunk 220 optimal weight: 9.9990 chunk 793 optimal weight: 6.9990 chunk 332 optimal weight: 10.0000 chunk 815 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 146 optimal weight: 4.9990 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 c 54 ASN d 195 GLN ** i 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.050475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.046652 restraints weight = 362060.062| |-----------------------------------------------------------------------------| 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: 0.8663 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 72039 Z= 0.261 Angle : 0.445 11.785 97532 Z= 0.253 Chirality : 0.032 0.143 12580 Planarity : 0.002 0.030 12469 Dihedral : 3.615 20.191 10101 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 0.39 % Allowed : 6.64 % Favored : 92.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.62 (0.08), residues: 9953 helix: 4.11 (0.05), residues: 7289 sheet: -1.66 (0.26), residues: 370 loop : 0.10 (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 0.016 0.002 PHE Q 217 ARG 0.003 0.000 ARG W 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7974.83 seconds wall clock time: 147 minutes 33.59 seconds (8853.59 seconds total)