Starting phenix.real_space_refine on Thu May 29 20:38:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jx3_36689/05_2025/8jx3_36689.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jx3_36689/05_2025/8jx3_36689.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jx3_36689/05_2025/8jx3_36689.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jx3_36689/05_2025/8jx3_36689.map" model { file = "/net/cci-nas-00/data/ceres_data/8jx3_36689/05_2025/8jx3_36689.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jx3_36689/05_2025/8jx3_36689.cif" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.053 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 112 5.16 5 C 20577 2.51 5 N 5627 2.21 5 O 6510 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 32826 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2345 Classifications: {'peptide': 293} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 283} Chain: "B" Number of atoms: 2345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2345 Classifications: {'peptide': 293} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 283} Chain: "C" Number of atoms: 2345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2345 Classifications: {'peptide': 293} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 283} Chain: "D" Number of atoms: 2345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2345 Classifications: {'peptide': 293} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 283} Chain: "E" Number of atoms: 2345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2345 Classifications: {'peptide': 293} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 283} Chain: "F" Number of atoms: 2345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2345 Classifications: {'peptide': 293} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 283} Chain: "G" Number of atoms: 2345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2345 Classifications: {'peptide': 293} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 283} Chain: "H" Number of atoms: 2345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2345 Classifications: {'peptide': 293} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 283} Chain: "I" Number of atoms: 2345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2345 Classifications: {'peptide': 293} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 283} Chain: "J" Number of atoms: 2345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2345 Classifications: {'peptide': 293} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 283} Chain: "K" Number of atoms: 2345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2345 Classifications: {'peptide': 293} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 283} Chain: "L" Number of atoms: 2345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2345 Classifications: {'peptide': 293} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 283} Chain: "M" Number of atoms: 2345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2345 Classifications: {'peptide': 293} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 283} Chain: "N" Number of atoms: 2341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2341 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 283} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 17.67, per 1000 atoms: 0.54 Number of scatterers: 32826 At special positions: 0 Unit cell: (112.684, 111.896, 211.184, 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 112 16.00 O 6510 8.00 N 5627 7.00 C 20577 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 237 " - pdb=" SG CYS L 237 " distance=2.04 Simple disulfide: pdb=" SG CYS B 237 " - pdb=" SG CYS K 237 " distance=2.04 Simple disulfide: pdb=" SG CYS C 237 " - pdb=" SG CYS J 237 " distance=2.04 Simple disulfide: pdb=" SG CYS D 237 " - pdb=" SG CYS I 237 " distance=2.04 Simple disulfide: pdb=" SG CYS E 237 " - pdb=" SG CYS H 237 " distance=2.04 Simple disulfide: pdb=" SG CYS F 237 " - pdb=" SG CYS N 237 " distance=2.04 Simple disulfide: pdb=" SG CYS G 237 " - pdb=" SG CYS M 237 " distance=2.04 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: 7.09 Conformation dependent library (CDL) restraints added in 3.7 seconds 8148 Ramachandran restraints generated. 4074 Oldfield, 0 Emsley, 4074 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7616 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 58 sheets defined 7.4% alpha, 58.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.10 Creating SS restraints... Processing helix chain 'A' and resid 2 through 6 Processing helix chain 'A' and resid 205 through 209 Processing helix chain 'A' and resid 212 through 216 Processing helix chain 'A' and resid 217 through 222 removed outlier: 4.171A pdb=" N SER A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 6 Processing helix chain 'B' and resid 205 through 209 Processing helix chain 'B' and resid 212 through 216 Processing helix chain 'B' and resid 217 through 222 removed outlier: 4.180A pdb=" N SER B 221 " --> pdb=" O SER B 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 1 through 6 Processing helix chain 'C' and resid 205 through 209 Processing helix chain 'C' and resid 212 through 216 Processing helix chain 'C' and resid 217 through 222 removed outlier: 4.177A pdb=" N SER C 221 " --> pdb=" O SER C 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 6 Processing helix chain 'D' and resid 205 through 209 Processing helix chain 'D' and resid 212 through 216 Processing helix chain 'D' and resid 217 through 222 removed outlier: 4.152A pdb=" N SER D 221 " --> pdb=" O SER D 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 6 Processing helix chain 'E' and resid 205 through 209 Processing helix chain 'E' and resid 212 through 216 Processing helix chain 'E' and resid 217 through 222 removed outlier: 4.183A pdb=" N SER E 221 " --> pdb=" O SER E 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 6 Processing helix chain 'F' and resid 205 through 209 Processing helix chain 'F' and resid 212 through 216 Processing helix chain 'F' and resid 217 through 222 removed outlier: 4.154A pdb=" N SER F 221 " --> pdb=" O SER F 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 1 through 6 Processing helix chain 'G' and resid 205 through 209 Processing helix chain 'G' and resid 212 through 216 Processing helix chain 'G' and resid 217 through 222 removed outlier: 4.118A pdb=" N SER G 221 " --> pdb=" O SER G 217 " (cutoff:3.500A) Processing helix chain 'H' and resid 1 through 6 Processing helix chain 'H' and resid 205 through 209 Processing helix chain 'H' and resid 212 through 216 Processing helix chain 'H' and resid 217 through 222 removed outlier: 4.108A pdb=" N SER H 221 " --> pdb=" O SER H 217 " (cutoff:3.500A) Processing helix chain 'I' and resid 1 through 6 Processing helix chain 'I' and resid 205 through 209 Processing helix chain 'I' and resid 212 through 216 Processing helix chain 'I' and resid 217 through 222 removed outlier: 4.156A pdb=" N SER I 221 " --> pdb=" O SER I 217 " (cutoff:3.500A) Processing helix chain 'J' and resid 1 through 6 removed outlier: 3.503A pdb=" N ASN J 6 " --> pdb=" O SER J 3 " (cutoff:3.500A) Processing helix chain 'J' and resid 205 through 209 Processing helix chain 'J' and resid 212 through 216 Processing helix chain 'J' and resid 217 through 222 removed outlier: 4.158A pdb=" N SER J 221 " --> pdb=" O SER J 217 " (cutoff:3.500A) Processing helix chain 'K' and resid 1 through 6 removed outlier: 3.548A pdb=" N ASN K 6 " --> pdb=" O SER K 3 " (cutoff:3.500A) Processing helix chain 'K' and resid 205 through 209 Processing helix chain 'K' and resid 212 through 216 Processing helix chain 'K' and resid 217 through 222 removed outlier: 4.124A pdb=" N SER K 221 " --> pdb=" O SER K 217 " (cutoff:3.500A) Processing helix chain 'L' and resid 1 through 6 removed outlier: 3.523A pdb=" N ASN L 6 " --> pdb=" O SER L 3 " (cutoff:3.500A) Processing helix chain 'L' and resid 205 through 209 Processing helix chain 'L' and resid 212 through 216 Processing helix chain 'L' and resid 217 through 222 removed outlier: 4.154A pdb=" N SER L 221 " --> pdb=" O SER L 217 " (cutoff:3.500A) Processing helix chain 'M' and resid 1 through 6 Processing helix chain 'M' and resid 205 through 209 Processing helix chain 'M' and resid 212 through 216 Processing helix chain 'M' and resid 217 through 222 removed outlier: 4.157A pdb=" N SER M 221 " --> pdb=" O SER M 217 " (cutoff:3.500A) Processing helix chain 'N' and resid 1 through 6 Processing helix chain 'N' and resid 205 through 209 Processing helix chain 'N' and resid 212 through 216 Processing helix chain 'N' and resid 217 through 222 removed outlier: 4.153A pdb=" N SER N 221 " --> pdb=" O SER N 217 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 29 removed outlier: 6.666A pdb=" N ALA A 229 " --> pdb=" O TYR A 101 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N TYR A 101 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N VAL A 231 " --> pdb=" O SER A 99 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 66 through 71 removed outlier: 6.773A pdb=" N GLY A 77 " --> pdb=" O TYR A 68 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N GLU A 70 " --> pdb=" O LYS A 75 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N LYS A 75 " --> pdb=" O GLU A 70 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N SER A 82 " --> pdb=" O PHE A 171 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLY A 166 " --> pdb=" O GLU A 158 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 66 through 71 removed outlier: 6.773A pdb=" N GLY A 77 " --> pdb=" O TYR A 68 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N GLU A 70 " --> pdb=" O LYS A 75 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N LYS A 75 " --> pdb=" O GLU A 70 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LYS A 75 " --> pdb=" O TRP A 260 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N TRP A 260 " --> pdb=" O LYS A 75 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N GLY A 77 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N LEU A 258 " --> pdb=" O GLY A 77 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ALA A 79 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N TYR A 256 " --> pdb=" O ALA A 79 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ASP A 254 " --> pdb=" O PRO A 81 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ASP A 255 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N ASP A 272 " --> pdb=" O ASP A 255 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N GLN A 257 " --> pdb=" O THR A 270 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N THR A 270 " --> pdb=" O GLN A 257 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N HIS A 259 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N THR A 268 " --> pdb=" O HIS A 259 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 109 through 126 removed outlier: 7.476A pdb=" N THR A 109 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N VAL A 149 " --> pdb=" O THR A 109 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N THR G 109 " --> pdb=" O VAL G 149 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N VAL G 149 " --> pdb=" O THR G 109 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N THR F 109 " --> pdb=" O VAL F 149 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N VAL F 149 " --> pdb=" O THR F 109 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N THR E 109 " --> pdb=" O VAL E 149 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N VAL E 149 " --> pdb=" O THR E 109 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N THR D 109 " --> pdb=" O VAL D 149 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N VAL D 149 " --> pdb=" O THR D 109 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N THR C 109 " --> pdb=" O VAL C 149 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N VAL C 149 " --> pdb=" O THR C 109 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N THR B 109 " --> pdb=" O VAL B 149 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N VAL B 149 " --> pdb=" O THR B 109 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 174 through 176 removed outlier: 7.065A pdb=" N ASN A 176 " --> pdb=" O GLY A 180 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N GLY A 180 " --> pdb=" O ASN A 176 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 21 through 29 removed outlier: 6.663A pdb=" N ALA B 229 " --> pdb=" O TYR B 101 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N TYR B 101 " --> pdb=" O ALA B 229 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N VAL B 231 " --> pdb=" O SER B 99 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 66 through 71 removed outlier: 6.728A pdb=" N GLY B 77 " --> pdb=" O TYR B 68 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N GLU B 70 " --> pdb=" O LYS B 75 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N LYS B 75 " --> pdb=" O GLU B 70 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N SER B 82 " --> pdb=" O PHE B 171 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLY B 166 " --> pdb=" O GLU B 158 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 66 through 71 removed outlier: 6.728A pdb=" N GLY B 77 " --> pdb=" O TYR B 68 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N GLU B 70 " --> pdb=" O LYS B 75 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N LYS B 75 " --> pdb=" O GLU B 70 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N LYS B 75 " --> pdb=" O TRP B 260 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N TRP B 260 " --> pdb=" O LYS B 75 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N GLY B 77 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N LEU B 258 " --> pdb=" O GLY B 77 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N ALA B 79 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N TYR B 256 " --> pdb=" O ALA B 79 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ASP B 254 " --> pdb=" O PRO B 81 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ASP B 255 " --> pdb=" O ASP B 272 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ASP B 272 " --> pdb=" O ASP B 255 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N GLN B 257 " --> pdb=" O THR B 270 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N THR B 270 " --> pdb=" O GLN B 257 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N HIS B 259 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N THR B 268 " --> pdb=" O HIS B 259 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 174 through 176 removed outlier: 7.080A pdb=" N ASN B 176 " --> pdb=" O GLY B 180 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N GLY B 180 " --> pdb=" O ASN B 176 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 21 through 29 removed outlier: 6.693A pdb=" N ALA C 229 " --> pdb=" O TYR C 101 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N TYR C 101 " --> pdb=" O ALA C 229 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL C 231 " --> pdb=" O SER C 99 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 66 through 71 removed outlier: 6.778A pdb=" N GLY C 77 " --> pdb=" O TYR C 68 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N GLU C 70 " --> pdb=" O LYS C 75 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N LYS C 75 " --> pdb=" O GLU C 70 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N SER C 82 " --> pdb=" O PHE C 171 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N GLY C 166 " --> pdb=" O GLU C 158 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 66 through 71 removed outlier: 6.778A pdb=" N GLY C 77 " --> pdb=" O TYR C 68 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N GLU C 70 " --> pdb=" O LYS C 75 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N LYS C 75 " --> pdb=" O GLU C 70 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL C 252 " --> pdb=" O SER C 82 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N PHE C 84 " --> pdb=" O GLU C 250 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N GLU C 250 " --> pdb=" O PHE C 84 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N VAL C 86 " --> pdb=" O ILE C 248 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE C 248 " --> pdb=" O VAL C 86 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU C 88 " --> pdb=" O ASP C 246 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ASP C 246 " --> pdb=" O LEU C 88 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ASP C 255 " --> pdb=" O ASP C 272 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ASP C 272 " --> pdb=" O ASP C 255 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N GLN C 257 " --> pdb=" O THR C 270 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N THR C 270 " --> pdb=" O GLN C 257 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N HIS C 259 " --> pdb=" O THR C 268 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N THR C 268 " --> pdb=" O HIS C 259 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 174 through 176 removed outlier: 7.078A pdb=" N ASN C 176 " --> pdb=" O GLY C 180 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N GLY C 180 " --> pdb=" O ASN C 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 21 through 29 removed outlier: 6.721A pdb=" N ALA D 229 " --> pdb=" O TYR D 101 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N TYR D 101 " --> pdb=" O ALA D 229 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL D 231 " --> pdb=" O SER D 99 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 66 through 71 removed outlier: 6.644A pdb=" N GLY D 77 " --> pdb=" O TYR D 68 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N GLU D 70 " --> pdb=" O LYS D 75 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS D 75 " --> pdb=" O GLU D 70 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N SER D 82 " --> pdb=" O PHE D 171 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLY D 166 " --> pdb=" O GLU D 158 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 66 through 71 removed outlier: 6.644A pdb=" N GLY D 77 " --> pdb=" O TYR D 68 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N GLU D 70 " --> pdb=" O LYS D 75 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS D 75 " --> pdb=" O GLU D 70 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL D 252 " --> pdb=" O SER D 82 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N PHE D 84 " --> pdb=" O GLU D 250 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLU D 250 " --> pdb=" O PHE D 84 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL D 86 " --> pdb=" O ILE D 248 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE D 248 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LEU D 88 " --> pdb=" O ASP D 246 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ASP D 246 " --> pdb=" O LEU D 88 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N ASP D 255 " --> pdb=" O ASP D 272 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ASP D 272 " --> pdb=" O ASP D 255 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N GLN D 257 " --> pdb=" O THR D 270 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N THR D 270 " --> pdb=" O GLN D 257 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N HIS D 259 " --> pdb=" O THR D 268 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N THR D 268 " --> pdb=" O HIS D 259 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 174 through 176 removed outlier: 7.124A pdb=" N ASN D 176 " --> pdb=" O GLY D 180 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N GLY D 180 " --> pdb=" O ASN D 176 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 21 through 29 removed outlier: 6.698A pdb=" N ALA E 229 " --> pdb=" O TYR E 101 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N TYR E 101 " --> pdb=" O ALA E 229 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL E 231 " --> pdb=" O SER E 99 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 66 through 71 removed outlier: 6.727A pdb=" N GLY E 77 " --> pdb=" O TYR E 68 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N GLU E 70 " --> pdb=" O LYS E 75 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N LYS E 75 " --> pdb=" O GLU E 70 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N SER E 82 " --> pdb=" O PHE E 171 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLY E 166 " --> pdb=" O GLU E 158 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 66 through 71 removed outlier: 6.727A pdb=" N GLY E 77 " --> pdb=" O TYR E 68 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N GLU E 70 " --> pdb=" O LYS E 75 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N LYS E 75 " --> pdb=" O GLU E 70 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LYS E 75 " --> pdb=" O TRP E 260 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N TRP E 260 " --> pdb=" O LYS E 75 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N GLY E 77 " --> pdb=" O LEU E 258 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N LEU E 258 " --> pdb=" O GLY E 77 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N ALA E 79 " --> pdb=" O TYR E 256 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N TYR E 256 " --> pdb=" O ALA E 79 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ASP E 254 " --> pdb=" O PRO E 81 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ASP E 255 " --> pdb=" O ASP E 272 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ASP E 272 " --> pdb=" O ASP E 255 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N GLN E 257 " --> pdb=" O THR E 270 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N THR E 270 " --> pdb=" O GLN E 257 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N HIS E 259 " --> pdb=" O THR E 268 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N THR E 268 " --> pdb=" O HIS E 259 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 174 through 176 removed outlier: 7.076A pdb=" N ASN E 176 " --> pdb=" O GLY E 180 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N GLY E 180 " --> pdb=" O ASN E 176 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 21 through 29 removed outlier: 6.746A pdb=" N ALA F 229 " --> pdb=" O TYR F 101 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N TYR F 101 " --> pdb=" O ALA F 229 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL F 231 " --> pdb=" O SER F 99 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 66 through 71 removed outlier: 6.835A pdb=" N GLY F 77 " --> pdb=" O TYR F 68 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N GLU F 70 " --> pdb=" O LYS F 75 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N LYS F 75 " --> pdb=" O GLU F 70 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N SER F 82 " --> pdb=" O PHE F 171 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLY F 166 " --> pdb=" O GLU F 158 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 66 through 71 removed outlier: 6.835A pdb=" N GLY F 77 " --> pdb=" O TYR F 68 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N GLU F 70 " --> pdb=" O LYS F 75 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N LYS F 75 " --> pdb=" O GLU F 70 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL F 252 " --> pdb=" O SER F 82 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N PHE F 84 " --> pdb=" O GLU F 250 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLU F 250 " --> pdb=" O PHE F 84 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N VAL F 86 " --> pdb=" O ILE F 248 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE F 248 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU F 88 " --> pdb=" O ASP F 246 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASP F 246 " --> pdb=" O LEU F 88 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N ASP F 255 " --> pdb=" O ASP F 272 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ASP F 272 " --> pdb=" O ASP F 255 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N GLN F 257 " --> pdb=" O THR F 270 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N THR F 270 " --> pdb=" O GLN F 257 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N HIS F 259 " --> pdb=" O THR F 268 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N THR F 268 " --> pdb=" O HIS F 259 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 174 through 176 removed outlier: 7.048A pdb=" N ASN F 176 " --> pdb=" O GLY F 180 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N GLY F 180 " --> pdb=" O ASN F 176 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 21 through 29 removed outlier: 6.768A pdb=" N ALA G 229 " --> pdb=" O TYR G 101 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N TYR G 101 " --> pdb=" O ALA G 229 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL G 231 " --> pdb=" O SER G 99 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 66 through 71 removed outlier: 6.760A pdb=" N GLY G 77 " --> pdb=" O TYR G 68 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N GLU G 70 " --> pdb=" O LYS G 75 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N LYS G 75 " --> pdb=" O GLU G 70 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N SER G 82 " --> pdb=" O PHE G 171 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLY G 166 " --> pdb=" O GLU G 158 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 66 through 71 removed outlier: 6.760A pdb=" N GLY G 77 " --> pdb=" O TYR G 68 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N GLU G 70 " --> pdb=" O LYS G 75 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N LYS G 75 " --> pdb=" O GLU G 70 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LYS G 75 " --> pdb=" O TRP G 260 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N TRP G 260 " --> pdb=" O LYS G 75 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N GLY G 77 " --> pdb=" O LEU G 258 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N LEU G 258 " --> pdb=" O GLY G 77 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N ALA G 79 " --> pdb=" O TYR G 256 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N TYR G 256 " --> pdb=" O ALA G 79 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ASP G 254 " --> pdb=" O PRO G 81 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ASP G 255 " --> pdb=" O ASP G 272 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ASP G 272 " --> pdb=" O ASP G 255 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N GLN G 257 " --> pdb=" O THR G 270 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N THR G 270 " --> pdb=" O GLN G 257 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N HIS G 259 " --> pdb=" O THR G 268 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N THR G 268 " --> pdb=" O HIS G 259 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 174 through 176 removed outlier: 7.100A pdb=" N ASN G 176 " --> pdb=" O GLY G 180 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N GLY G 180 " --> pdb=" O ASN G 176 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 20 through 29 removed outlier: 6.662A pdb=" N ALA H 229 " --> pdb=" O TYR H 101 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N TYR H 101 " --> pdb=" O ALA H 229 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL H 231 " --> pdb=" O SER H 99 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 66 through 70 removed outlier: 6.680A pdb=" N GLY H 77 " --> pdb=" O TYR H 68 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N GLU H 70 " --> pdb=" O LYS H 75 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N LYS H 75 " --> pdb=" O GLU H 70 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N SER H 82 " --> pdb=" O PHE H 171 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLY H 166 " --> pdb=" O GLU H 158 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 66 through 70 removed outlier: 6.680A pdb=" N GLY H 77 " --> pdb=" O TYR H 68 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N GLU H 70 " --> pdb=" O LYS H 75 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N LYS H 75 " --> pdb=" O GLU H 70 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL H 252 " --> pdb=" O SER H 82 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N PHE H 84 " --> pdb=" O GLU H 250 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLU H 250 " --> pdb=" O PHE H 84 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL H 86 " --> pdb=" O ILE H 248 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE H 248 " --> pdb=" O VAL H 86 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LEU H 88 " --> pdb=" O ASP H 246 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ASP H 246 " --> pdb=" O LEU H 88 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ASP H 255 " --> pdb=" O ASP H 272 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N ASP H 272 " --> pdb=" O ASP H 255 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N GLN H 257 " --> pdb=" O THR H 270 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N THR H 270 " --> pdb=" O GLN H 257 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N HIS H 259 " --> pdb=" O THR H 268 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N THR H 268 " --> pdb=" O HIS H 259 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 109 through 127 removed outlier: 7.567A pdb=" N THR H 109 " --> pdb=" O VAL H 149 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N VAL H 149 " --> pdb=" O THR H 109 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N THR N 109 " --> pdb=" O VAL N 149 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N VAL N 149 " --> pdb=" O THR N 109 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N THR M 109 " --> pdb=" O VAL M 149 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N VAL M 149 " --> pdb=" O THR M 109 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N THR L 109 " --> pdb=" O VAL L 149 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N VAL L 149 " --> pdb=" O THR L 109 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY L 134 " --> pdb=" O GLY K 126 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N THR K 109 " --> pdb=" O VAL K 149 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N VAL K 149 " --> pdb=" O THR K 109 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY K 134 " --> pdb=" O GLY J 126 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N THR J 109 " --> pdb=" O VAL J 149 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N VAL J 149 " --> pdb=" O THR J 109 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N THR I 109 " --> pdb=" O VAL I 149 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N VAL I 149 " --> pdb=" O THR I 109 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 174 through 176 removed outlier: 7.044A pdb=" N ASN H 176 " --> pdb=" O GLY H 180 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N GLY H 180 " --> pdb=" O ASN H 176 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 21 through 29 removed outlier: 6.665A pdb=" N ALA I 229 " --> pdb=" O TYR I 101 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N TYR I 101 " --> pdb=" O ALA I 229 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N VAL I 231 " --> pdb=" O SER I 99 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 66 through 71 removed outlier: 6.632A pdb=" N GLY I 77 " --> pdb=" O TYR I 68 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N GLU I 70 " --> pdb=" O LYS I 75 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N LYS I 75 " --> pdb=" O GLU I 70 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N SER I 82 " --> pdb=" O PHE I 171 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLY I 166 " --> pdb=" O GLU I 158 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 66 through 71 removed outlier: 6.632A pdb=" N GLY I 77 " --> pdb=" O TYR I 68 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N GLU I 70 " --> pdb=" O LYS I 75 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N LYS I 75 " --> pdb=" O GLU I 70 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LYS I 75 " --> pdb=" O TRP I 260 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N TRP I 260 " --> pdb=" O LYS I 75 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N GLY I 77 " --> pdb=" O LEU I 258 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N LEU I 258 " --> pdb=" O GLY I 77 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ALA I 79 " --> pdb=" O TYR I 256 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N TYR I 256 " --> pdb=" O ALA I 79 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ASP I 254 " --> pdb=" O PRO I 81 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N THR I 243 " --> pdb=" O TYR I 282 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N TYR I 282 " --> pdb=" O THR I 243 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE I 245 " --> pdb=" O GLU I 280 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLU I 280 " --> pdb=" O ILE I 245 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL I 247 " --> pdb=" O SER I 278 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N SER I 278 " --> pdb=" O VAL I 247 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N TYR I 249 " --> pdb=" O ASP I 276 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ASP I 276 " --> pdb=" O TYR I 249 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ARG I 251 " --> pdb=" O TRP I 274 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TRP I 274 " --> pdb=" O ARG I 251 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ARG I 253 " --> pdb=" O ASP I 272 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ASP I 272 " --> pdb=" O ARG I 253 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 174 through 176 removed outlier: 7.095A pdb=" N ASN I 176 " --> pdb=" O GLY I 180 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N GLY I 180 " --> pdb=" O ASN I 176 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 20 through 29 removed outlier: 6.699A pdb=" N ALA J 229 " --> pdb=" O TYR J 101 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N TYR J 101 " --> pdb=" O ALA J 229 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL J 231 " --> pdb=" O SER J 99 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 66 through 70 removed outlier: 6.625A pdb=" N GLY J 77 " --> pdb=" O TYR J 68 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N GLU J 70 " --> pdb=" O LYS J 75 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N LYS J 75 " --> pdb=" O GLU J 70 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N SER J 82 " --> pdb=" O PHE J 171 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLY J 166 " --> pdb=" O GLU J 158 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 66 through 70 removed outlier: 6.625A pdb=" N GLY J 77 " --> pdb=" O TYR J 68 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N GLU J 70 " --> pdb=" O LYS J 75 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N LYS J 75 " --> pdb=" O GLU J 70 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL J 252 " --> pdb=" O SER J 82 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N PHE J 84 " --> pdb=" O GLU J 250 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLU J 250 " --> pdb=" O PHE J 84 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL J 86 " --> pdb=" O ILE J 248 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE J 248 " --> pdb=" O VAL J 86 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU J 88 " --> pdb=" O ASP J 246 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ASP J 246 " --> pdb=" O LEU J 88 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N ASP J 255 " --> pdb=" O ASP J 272 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N ASP J 272 " --> pdb=" O ASP J 255 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N GLN J 257 " --> pdb=" O THR J 270 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N THR J 270 " --> pdb=" O GLN J 257 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N HIS J 259 " --> pdb=" O THR J 268 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N THR J 268 " --> pdb=" O HIS J 259 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 174 through 176 removed outlier: 6.985A pdb=" N ASN J 176 " --> pdb=" O GLY J 180 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N GLY J 180 " --> pdb=" O ASN J 176 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 21 through 29 removed outlier: 6.694A pdb=" N ALA K 229 " --> pdb=" O TYR K 101 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N TYR K 101 " --> pdb=" O ALA K 229 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL K 231 " --> pdb=" O SER K 99 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 66 through 70 removed outlier: 6.561A pdb=" N GLY K 77 " --> pdb=" O TYR K 68 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N GLU K 70 " --> pdb=" O LYS K 75 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N LYS K 75 " --> pdb=" O GLU K 70 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N SER K 82 " --> pdb=" O PHE K 171 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLY K 166 " --> pdb=" O GLU K 158 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 66 through 70 removed outlier: 6.561A pdb=" N GLY K 77 " --> pdb=" O TYR K 68 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N GLU K 70 " --> pdb=" O LYS K 75 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N LYS K 75 " --> pdb=" O GLU K 70 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LYS K 75 " --> pdb=" O TRP K 260 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N TRP K 260 " --> pdb=" O LYS K 75 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N GLY K 77 " --> pdb=" O LEU K 258 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LEU K 258 " --> pdb=" O GLY K 77 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N ALA K 79 " --> pdb=" O TYR K 256 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N TYR K 256 " --> pdb=" O ALA K 79 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ASP K 254 " --> pdb=" O PRO K 81 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N THR K 243 " --> pdb=" O TYR K 282 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TYR K 282 " --> pdb=" O THR K 243 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE K 245 " --> pdb=" O GLU K 280 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N GLU K 280 " --> pdb=" O ILE K 245 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL K 247 " --> pdb=" O SER K 278 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N SER K 278 " --> pdb=" O VAL K 247 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TYR K 249 " --> pdb=" O ASP K 276 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ASP K 276 " --> pdb=" O TYR K 249 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ARG K 251 " --> pdb=" O TRP K 274 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N TRP K 274 " --> pdb=" O ARG K 251 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ARG K 253 " --> pdb=" O ASP K 272 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASP K 272 " --> pdb=" O ARG K 253 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 174 through 176 removed outlier: 7.065A pdb=" N ASN K 176 " --> pdb=" O GLY K 180 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N GLY K 180 " --> pdb=" O ASN K 176 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 20 through 29 removed outlier: 6.668A pdb=" N ALA L 229 " --> pdb=" O TYR L 101 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N TYR L 101 " --> pdb=" O ALA L 229 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL L 231 " --> pdb=" O SER L 99 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 66 through 70 removed outlier: 6.538A pdb=" N GLY L 77 " --> pdb=" O TYR L 68 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLU L 70 " --> pdb=" O LYS L 75 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N LYS L 75 " --> pdb=" O GLU L 70 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N SER L 82 " --> pdb=" O PHE L 171 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLY L 166 " --> pdb=" O GLU L 158 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 66 through 70 removed outlier: 6.538A pdb=" N GLY L 77 " --> pdb=" O TYR L 68 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLU L 70 " --> pdb=" O LYS L 75 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N LYS L 75 " --> pdb=" O GLU L 70 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL L 252 " --> pdb=" O SER L 82 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N PHE L 84 " --> pdb=" O GLU L 250 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLU L 250 " --> pdb=" O PHE L 84 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL L 86 " --> pdb=" O ILE L 248 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE L 248 " --> pdb=" O VAL L 86 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU L 88 " --> pdb=" O ASP L 246 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ASP L 246 " --> pdb=" O LEU L 88 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ASP L 255 " --> pdb=" O ASP L 272 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ASP L 272 " --> pdb=" O ASP L 255 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N GLN L 257 " --> pdb=" O THR L 270 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N THR L 270 " --> pdb=" O GLN L 257 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N HIS L 259 " --> pdb=" O THR L 268 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N THR L 268 " --> pdb=" O HIS L 259 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 174 through 176 removed outlier: 7.036A pdb=" N ASN L 176 " --> pdb=" O GLY L 180 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N GLY L 180 " --> pdb=" O ASN L 176 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'M' and resid 21 through 29 removed outlier: 6.709A pdb=" N ALA M 229 " --> pdb=" O TYR M 101 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N TYR M 101 " --> pdb=" O ALA M 229 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N VAL M 231 " --> pdb=" O SER M 99 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'M' and resid 66 through 70 removed outlier: 6.538A pdb=" N GLY M 77 " --> pdb=" O TYR M 68 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N GLU M 70 " --> pdb=" O LYS M 75 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N LYS M 75 " --> pdb=" O GLU M 70 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N SER M 82 " --> pdb=" O PHE M 171 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLY M 166 " --> pdb=" O GLU M 158 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'M' and resid 66 through 70 removed outlier: 6.538A pdb=" N GLY M 77 " --> pdb=" O TYR M 68 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N GLU M 70 " --> pdb=" O LYS M 75 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N LYS M 75 " --> pdb=" O GLU M 70 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LYS M 75 " --> pdb=" O TRP M 260 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N TRP M 260 " --> pdb=" O LYS M 75 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N GLY M 77 " --> pdb=" O LEU M 258 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LEU M 258 " --> pdb=" O GLY M 77 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ALA M 79 " --> pdb=" O TYR M 256 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N TYR M 256 " --> pdb=" O ALA M 79 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ASP M 254 " --> pdb=" O PRO M 81 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N ASP M 255 " --> pdb=" O ASP M 272 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ASP M 272 " --> pdb=" O ASP M 255 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N GLN M 257 " --> pdb=" O THR M 270 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N THR M 270 " --> pdb=" O GLN M 257 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N HIS M 259 " --> pdb=" O THR M 268 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N THR M 268 " --> pdb=" O HIS M 259 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'M' and resid 174 through 176 removed outlier: 7.063A pdb=" N ASN M 176 " --> pdb=" O GLY M 180 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N GLY M 180 " --> pdb=" O ASN M 176 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'N' and resid 21 through 29 removed outlier: 6.704A pdb=" N ALA N 229 " --> pdb=" O TYR N 101 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N TYR N 101 " --> pdb=" O ALA N 229 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL N 231 " --> pdb=" O SER N 99 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'N' and resid 66 through 70 removed outlier: 6.561A pdb=" N GLY N 77 " --> pdb=" O TYR N 68 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N GLU N 70 " --> pdb=" O LYS N 75 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N LYS N 75 " --> pdb=" O GLU N 70 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N SER N 82 " --> pdb=" O PHE N 171 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLY N 166 " --> pdb=" O GLU N 158 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'N' and resid 66 through 70 removed outlier: 6.561A pdb=" N GLY N 77 " --> pdb=" O TYR N 68 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N GLU N 70 " --> pdb=" O LYS N 75 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N LYS N 75 " --> pdb=" O GLU N 70 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL N 252 " --> pdb=" O SER N 82 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N PHE N 84 " --> pdb=" O GLU N 250 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLU N 250 " --> pdb=" O PHE N 84 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N VAL N 86 " --> pdb=" O ILE N 248 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE N 248 " --> pdb=" O VAL N 86 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LEU N 88 " --> pdb=" O ASP N 246 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ASP N 246 " --> pdb=" O LEU N 88 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ASP N 255 " --> pdb=" O ASP N 272 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ASP N 272 " --> pdb=" O ASP N 255 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N GLN N 257 " --> pdb=" O THR N 270 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N THR N 270 " --> pdb=" O GLN N 257 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N HIS N 259 " --> pdb=" O THR N 268 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N THR N 268 " --> pdb=" O HIS N 259 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'N' and resid 174 through 176 removed outlier: 7.056A pdb=" N ASN N 176 " --> pdb=" O GLY N 180 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N GLY N 180 " --> pdb=" O ASN N 176 " (cutoff:3.500A) 1609 hydrogen bonds defined for protein. 4164 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: 11.49 Time building geometry restraints manager: 8.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10752 1.34 - 1.46: 8357 1.46 - 1.59: 14235 1.59 - 1.71: 0 1.71 - 1.83: 210 Bond restraints: 33554 Sorted by residual: bond pdb=" C LYS D 58 " pdb=" N GLY D 59 " ideal model delta sigma weight residual 1.334 1.314 0.020 1.12e-02 7.97e+03 3.32e+00 bond pdb=" C LYS A 58 " pdb=" N GLY A 59 " ideal model delta sigma weight residual 1.334 1.314 0.020 1.12e-02 7.97e+03 3.23e+00 bond pdb=" CB ASP A 24 " pdb=" CG ASP A 24 " ideal model delta sigma weight residual 1.516 1.473 0.043 2.50e-02 1.60e+03 2.96e+00 bond pdb=" C LYS F 58 " pdb=" N GLY F 59 " ideal model delta sigma weight residual 1.334 1.315 0.019 1.12e-02 7.97e+03 2.91e+00 bond pdb=" C ILE I 5 " pdb=" O ILE I 5 " ideal model delta sigma weight residual 1.236 1.219 0.017 1.19e-02 7.06e+03 2.08e+00 ... (remaining 33549 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 45132 2.52 - 5.04: 302 5.04 - 7.56: 4 7.56 - 10.08: 1 10.08 - 12.60: 1 Bond angle restraints: 45440 Sorted by residual: angle pdb=" CA TYR B 65 " pdb=" CB TYR B 65 " pdb=" CG TYR B 65 " ideal model delta sigma weight residual 113.90 118.91 -5.01 1.80e+00 3.09e-01 7.75e+00 angle pdb=" N THR D 263 " pdb=" CA THR D 263 " pdb=" C THR D 263 " ideal model delta sigma weight residual 114.62 111.50 3.12 1.14e+00 7.69e-01 7.51e+00 angle pdb=" CA TYR A 65 " pdb=" CB TYR A 65 " pdb=" CG TYR A 65 " ideal model delta sigma weight residual 113.90 118.82 -4.92 1.80e+00 3.09e-01 7.47e+00 angle pdb=" CA TYR G 65 " pdb=" CB TYR G 65 " pdb=" CG TYR G 65 " ideal model delta sigma weight residual 113.90 118.75 -4.85 1.80e+00 3.09e-01 7.27e+00 angle pdb=" CA TYR N 65 " pdb=" CB TYR N 65 " pdb=" CG TYR N 65 " ideal model delta sigma weight residual 113.90 118.74 -4.84 1.80e+00 3.09e-01 7.22e+00 ... (remaining 45435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 17552 17.96 - 35.91: 1813 35.91 - 53.87: 422 53.87 - 71.82: 112 71.82 - 89.78: 54 Dihedral angle restraints: 19953 sinusoidal: 8053 harmonic: 11900 Sorted by residual: dihedral pdb=" CG ARG I 147 " pdb=" CD ARG I 147 " pdb=" NE ARG I 147 " pdb=" CZ ARG I 147 " ideal model delta sinusoidal sigma weight residual 90.00 41.06 48.94 2 1.50e+01 4.44e-03 1.21e+01 dihedral pdb=" CG ARG M 147 " pdb=" CD ARG M 147 " pdb=" NE ARG M 147 " pdb=" CZ ARG M 147 " ideal model delta sinusoidal sigma weight residual 90.00 41.10 48.90 2 1.50e+01 4.44e-03 1.21e+01 dihedral pdb=" CG ARG H 147 " pdb=" CD ARG H 147 " pdb=" NE ARG H 147 " pdb=" CZ ARG H 147 " ideal model delta sinusoidal sigma weight residual 90.00 41.22 48.78 2 1.50e+01 4.44e-03 1.21e+01 ... (remaining 19950 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 3269 0.044 - 0.087: 1125 0.087 - 0.131: 449 0.131 - 0.175: 25 0.175 - 0.219: 4 Chirality restraints: 4872 Sorted by residual: chirality pdb=" CB ILE E 284 " pdb=" CA ILE E 284 " pdb=" CG1 ILE E 284 " pdb=" CG2 ILE E 284 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CB ILE C 284 " pdb=" CA ILE C 284 " pdb=" CG1 ILE C 284 " pdb=" CG2 ILE C 284 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.56e-01 chirality pdb=" CB ILE A 284 " pdb=" CA ILE A 284 " pdb=" CG1 ILE A 284 " pdb=" CG2 ILE A 284 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.31e-01 ... (remaining 4869 not shown) Planarity restraints: 5866 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU K 90 " 0.024 5.00e-02 4.00e+02 3.63e-02 2.11e+00 pdb=" N PRO K 91 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO K 91 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO K 91 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 65 " 0.014 2.00e-02 2.50e+03 1.01e-02 2.04e+00 pdb=" CG TYR A 65 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR A 65 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR A 65 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 65 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 65 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 65 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 65 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 65 " -0.014 2.00e-02 2.50e+03 1.01e-02 2.02e+00 pdb=" CG TYR B 65 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR B 65 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR B 65 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 65 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 65 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 65 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 65 " -0.003 2.00e-02 2.50e+03 ... (remaining 5863 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 7251 2.78 - 3.31: 25731 3.31 - 3.84: 56864 3.84 - 4.37: 69119 4.37 - 4.90: 121483 Nonbonded interactions: 280448 Sorted by model distance: nonbonded pdb=" OE1 GLU L 111 " pdb=" NH1 ARG L 147 " model vdw 2.256 3.120 nonbonded pdb=" O SER B 203 " pdb=" OG SER B 203 " model vdw 2.271 3.040 nonbonded pdb=" O ASN K 32 " pdb=" NH2 ARG K 251 " model vdw 2.280 3.120 nonbonded pdb=" O SER F 203 " pdb=" OG SER F 203 " model vdw 2.284 3.040 nonbonded pdb=" O ASN M 32 " pdb=" NH2 ARG M 251 " model vdw 2.288 3.120 ... (remaining 280443 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' and (resid 1 through 29 or (resid 30 and (name N or name CA or name C \ or name O or name CB )) or resid 31 through 293)) selection = (chain 'B' and (resid 1 through 29 or (resid 30 and (name N or name CA or name C \ or name O or name CB )) or resid 31 through 293)) selection = (chain 'C' and (resid 1 through 29 or (resid 30 and (name N or name CA or name C \ or name O or name CB )) or resid 31 through 293)) selection = (chain 'D' and (resid 1 through 29 or (resid 30 and (name N or name CA or name C \ or name O or name CB )) or resid 31 through 293)) selection = (chain 'E' and (resid 1 through 29 or (resid 30 and (name N or name CA or name C \ or name O or name CB )) or resid 31 through 293)) selection = (chain 'F' and (resid 1 through 29 or (resid 30 and (name N or name CA or name C \ or name O or name CB )) or resid 31 through 293)) selection = (chain 'G' and (resid 1 through 29 or (resid 30 and (name N or name CA or name C \ or name O or name CB )) or resid 31 through 293)) selection = (chain 'H' and (resid 1 through 29 or (resid 30 and (name N or name CA or name C \ or name O or name CB )) or resid 31 through 293)) selection = (chain 'I' and (resid 1 through 29 or (resid 30 and (name N or name CA or name C \ or name O or name CB )) or resid 31 through 293)) selection = (chain 'J' and (resid 1 through 29 or (resid 30 and (name N or name CA or name C \ or name O or name CB )) or resid 31 through 293)) selection = (chain 'K' and (resid 1 through 29 or (resid 30 and (name N or name CA or name C \ or name O or name CB )) or resid 31 through 293)) selection = (chain 'L' and (resid 1 through 29 or (resid 30 and (name N or name CA or name C \ or name O or name CB )) or resid 31 through 293)) selection = (chain 'M' and (resid 1 through 29 or (resid 30 and (name N or name CA or name C \ or name O or name CB )) or resid 31 through 293)) selection = chain 'N' } 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: 0.010 Normalize map: mean=0, sd=1: 3.750 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: 0.030 Extract box with map and model: 1.250 Check model and map are aligned: 0.210 Set scattering table: 0.300 Process input model: 65.940 Find NCS groups from input model: 1.720 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 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 : 0.006 0.044 33561 Z= 0.278 Angle : 0.595 12.596 45454 Z= 0.336 Chirality : 0.049 0.219 4872 Planarity : 0.003 0.036 5866 Dihedral : 16.331 89.776 12316 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.09 % Allowed : 17.61 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: 0.68 (0.13), residues: 4074 helix: -3.60 (0.17), residues: 84 sheet: 1.28 (0.10), residues: 2268 loop : -0.47 (0.15), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 179 HIS 0.011 0.001 HIS C 259 PHE 0.011 0.002 PHE L 84 TYR 0.024 0.002 TYR A 65 ARG 0.012 0.000 ARG M 147 Details of bonding type rmsd hydrogen bonds : bond 0.10690 ( 1567) hydrogen bonds : angle 6.75616 ( 4164) SS BOND : bond 0.00581 ( 7) SS BOND : angle 2.29610 ( 14) covalent geometry : bond 0.00644 (33554) covalent geometry : angle 0.59355 (45440) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8148 Ramachandran restraints generated. 4074 Oldfield, 0 Emsley, 4074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8148 Ramachandran restraints generated. 4074 Oldfield, 0 Emsley, 4074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 438 time to evaluate : 3.713 Fit side-chains REVERT: C 31 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7226 (pm20) REVERT: C 118 TYR cc_start: 0.8276 (p90) cc_final: 0.8038 (p90) REVERT: C 150 GLN cc_start: 0.8616 (mt0) cc_final: 0.8368 (mt0) REVERT: E 212 ASP cc_start: 0.8283 (t0) cc_final: 0.8015 (t70) REVERT: I 8 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8070 (mptt) outliers start: 76 outliers final: 71 residues processed: 505 average time/residue: 1.6231 time to fit residues: 957.4234 Evaluate side-chains 507 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 434 time to evaluate : 3.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 283 LYS Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 273 LYS Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 239 SER Chi-restraints excluded: chain F residue 263 THR Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain F residue 283 LYS Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 239 SER Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 195 LEU Chi-restraints excluded: chain I residue 8 LYS Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 99 SER Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain I residue 195 LEU Chi-restraints excluded: chain I residue 276 ASP Chi-restraints excluded: chain I residue 278 SER Chi-restraints excluded: chain J residue 69 SER Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 203 SER Chi-restraints excluded: chain J residue 263 THR Chi-restraints excluded: chain J residue 276 ASP Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain K residue 195 LEU Chi-restraints excluded: chain K residue 276 ASP Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain L residue 99 SER Chi-restraints excluded: chain L residue 106 SER Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 195 LEU Chi-restraints excluded: chain L residue 263 THR Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain M residue 122 SER Chi-restraints excluded: chain M residue 195 LEU Chi-restraints excluded: chain M residue 268 THR Chi-restraints excluded: chain N residue 69 SER Chi-restraints excluded: chain N residue 116 LEU Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain N residue 155 THR Chi-restraints excluded: chain N residue 195 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 342 optimal weight: 2.9990 chunk 307 optimal weight: 2.9990 chunk 170 optimal weight: 10.0000 chunk 105 optimal weight: 7.9990 chunk 207 optimal weight: 4.9990 chunk 164 optimal weight: 4.9990 chunk 318 optimal weight: 4.9990 chunk 123 optimal weight: 10.0000 chunk 193 optimal weight: 6.9990 chunk 236 optimal weight: 2.9990 chunk 368 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN A 89 GLN A 178 ASN A 242 GLN B 242 GLN C 242 GLN D 87 GLN D 242 GLN D 293 ASN E 89 GLN E 178 ASN E 242 GLN F 89 GLN F 178 ASN G 178 ASN G 242 GLN H 89 GLN I 89 GLN I 178 ASN I 242 GLN J 242 GLN K 178 ASN M 242 GLN N 89 GLN N 293 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.102872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.075191 restraints weight = 38051.423| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 2.14 r_work: 0.2764 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8978 moved from start: 0.0400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 33561 Z= 0.303 Angle : 0.593 11.679 45454 Z= 0.327 Chirality : 0.049 0.219 4872 Planarity : 0.004 0.036 5866 Dihedral : 6.235 57.780 4545 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.56 % Allowed : 15.47 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: 0.74 (0.13), residues: 4074 helix: -3.58 (0.18), residues: 84 sheet: 1.38 (0.10), residues: 2240 loop : -0.49 (0.14), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP G 179 HIS 0.009 0.001 HIS F 259 PHE 0.012 0.002 PHE L 84 TYR 0.024 0.002 TYR I 65 ARG 0.008 0.001 ARG H 147 Details of bonding type rmsd hydrogen bonds : bond 0.04222 ( 1567) hydrogen bonds : angle 5.73185 ( 4164) SS BOND : bond 0.00618 ( 7) SS BOND : angle 2.38837 ( 14) covalent geometry : bond 0.00708 (33554) covalent geometry : angle 0.59141 (45440) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8148 Ramachandran restraints generated. 4074 Oldfield, 0 Emsley, 4074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8148 Ramachandran restraints generated. 4074 Oldfield, 0 Emsley, 4074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 473 time to evaluate : 4.066 Fit side-chains REVERT: C 118 TYR cc_start: 0.8483 (p90) cc_final: 0.8170 (p90) REVERT: C 123 ASN cc_start: 0.8691 (p0) cc_final: 0.8412 (p0) REVERT: D 200 ARG cc_start: 0.7785 (OUTLIER) cc_final: 0.7053 (mtm-85) REVERT: D 257 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8585 (mt0) REVERT: D 273 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8669 (tttp) REVERT: E 212 ASP cc_start: 0.8483 (t70) cc_final: 0.8183 (t70) REVERT: F 147 ARG cc_start: 0.8783 (ttp80) cc_final: 0.8568 (ttp80) REVERT: I 212 ASP cc_start: 0.8774 (t70) cc_final: 0.8550 (t0) REVERT: K 58 LYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8786 (mtpt) REVERT: K 75 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8422 (ptmt) outliers start: 93 outliers final: 49 residues processed: 534 average time/residue: 1.7364 time to fit residues: 1072.1489 Evaluate side-chains 515 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 461 time to evaluate : 3.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 277 ARG Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 283 LYS Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 200 ARG Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 257 GLN Chi-restraints excluded: chain D residue 273 LYS Chi-restraints excluded: chain D residue 283 LYS Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 283 LYS Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 263 THR Chi-restraints excluded: chain G residue 131 LYS Chi-restraints excluded: chain G residue 132 ILE Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 195 LEU Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 195 LEU Chi-restraints excluded: chain I residue 279 SER Chi-restraints excluded: chain J residue 69 SER Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 125 THR Chi-restraints excluded: chain J residue 263 THR Chi-restraints excluded: chain K residue 58 LYS Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 99 SER Chi-restraints excluded: chain K residue 195 LEU Chi-restraints excluded: chain K residue 287 GLU Chi-restraints excluded: chain L residue 99 SER Chi-restraints excluded: chain L residue 195 LEU Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain M residue 195 LEU Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain N residue 155 THR Chi-restraints excluded: chain N residue 195 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 378 optimal weight: 1.9990 chunk 271 optimal weight: 7.9990 chunk 334 optimal weight: 3.9990 chunk 381 optimal weight: 3.9990 chunk 128 optimal weight: 9.9990 chunk 262 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 chunk 395 optimal weight: 0.9990 chunk 317 optimal weight: 0.9990 chunk 261 optimal weight: 6.9990 chunk 222 optimal weight: 5.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 242 GLN B 242 GLN D 87 GLN D 242 GLN E 89 GLN E 242 GLN F 89 GLN G 242 GLN H 89 GLN I 89 GLN I 242 GLN J 242 GLN J 264 ASN K 123 ASN M 242 GLN N 89 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.104515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.077071 restraints weight = 38040.506| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 2.12 r_work: 0.2797 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8964 moved from start: 0.0571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 33561 Z= 0.177 Angle : 0.516 10.648 45454 Z= 0.284 Chirality : 0.046 0.160 4872 Planarity : 0.003 0.035 5866 Dihedral : 5.457 58.871 4487 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.42 % Allowed : 15.53 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: 0.83 (0.13), residues: 4074 helix: -3.30 (0.23), residues: 84 sheet: 1.41 (0.10), residues: 2240 loop : -0.40 (0.15), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 167 HIS 0.008 0.001 HIS F 259 PHE 0.009 0.001 PHE L 84 TYR 0.020 0.002 TYR B 65 ARG 0.009 0.000 ARG H 147 Details of bonding type rmsd hydrogen bonds : bond 0.03609 ( 1567) hydrogen bonds : angle 5.40435 ( 4164) SS BOND : bond 0.00515 ( 7) SS BOND : angle 1.75230 ( 14) covalent geometry : bond 0.00403 (33554) covalent geometry : angle 0.51508 (45440) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8148 Ramachandran restraints generated. 4074 Oldfield, 0 Emsley, 4074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8148 Ramachandran restraints generated. 4074 Oldfield, 0 Emsley, 4074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 474 time to evaluate : 4.085 Fit side-chains revert: symmetry clash REVERT: A 200 ARG cc_start: 0.8466 (mtm-85) cc_final: 0.8238 (mtm-85) REVERT: D 200 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.7062 (mtm-85) REVERT: D 257 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.8593 (mt0) REVERT: D 273 LYS cc_start: 0.9046 (OUTLIER) cc_final: 0.8803 (tttp) REVERT: D 280 GLU cc_start: 0.8396 (tp30) cc_final: 0.8116 (tp30) REVERT: I 212 ASP cc_start: 0.8779 (t70) cc_final: 0.8536 (t0) REVERT: K 75 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8493 (ptmt) outliers start: 88 outliers final: 43 residues processed: 529 average time/residue: 1.7571 time to fit residues: 1073.1455 Evaluate side-chains 509 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 462 time to evaluate : 4.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 277 ARG Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 283 LYS Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 200 ARG Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 257 GLN Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 273 LYS Chi-restraints excluded: chain D residue 283 LYS Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 263 THR Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 195 LEU Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 195 LEU Chi-restraints excluded: chain J residue 125 THR Chi-restraints excluded: chain J residue 263 THR Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain K residue 99 SER Chi-restraints excluded: chain K residue 195 LEU Chi-restraints excluded: chain K residue 197 MET Chi-restraints excluded: chain K residue 287 GLU Chi-restraints excluded: chain L residue 195 LEU Chi-restraints excluded: chain L residue 263 THR Chi-restraints excluded: chain M residue 195 LEU Chi-restraints excluded: chain M residue 291 MET Chi-restraints excluded: chain N residue 116 LEU Chi-restraints excluded: chain N residue 155 THR Chi-restraints excluded: chain N residue 195 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 83 optimal weight: 9.9990 chunk 160 optimal weight: 4.9990 chunk 288 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 165 optimal weight: 10.0000 chunk 235 optimal weight: 5.9990 chunk 117 optimal weight: 10.0000 chunk 96 optimal weight: 2.9990 chunk 327 optimal weight: 4.9990 chunk 192 optimal weight: 10.0000 chunk 85 optimal weight: 0.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 242 GLN B 242 GLN C 242 GLN D 87 GLN D 242 GLN E 89 GLN E 242 GLN F 89 GLN G 242 GLN H 89 GLN I 89 GLN I 242 GLN J 242 GLN M 242 GLN N 89 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.102762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.075122 restraints weight = 38073.719| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 2.13 r_work: 0.2762 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2628 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8980 moved from start: 0.0517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 33561 Z= 0.316 Angle : 0.595 11.310 45454 Z= 0.327 Chirality : 0.050 0.211 4872 Planarity : 0.004 0.041 5866 Dihedral : 5.432 58.118 4472 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.75 % Allowed : 15.28 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: 0.80 (0.13), residues: 4074 helix: -3.47 (0.20), residues: 84 sheet: 1.43 (0.10), residues: 2240 loop : -0.48 (0.14), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP G 179 HIS 0.011 0.001 HIS C 259 PHE 0.012 0.002 PHE L 84 TYR 0.024 0.002 TYR I 65 ARG 0.009 0.001 ARG H 147 Details of bonding type rmsd hydrogen bonds : bond 0.04099 ( 1567) hydrogen bonds : angle 5.58942 ( 4164) SS BOND : bond 0.00738 ( 7) SS BOND : angle 2.23247 ( 14) covalent geometry : bond 0.00739 (33554) covalent geometry : angle 0.59359 (45440) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8148 Ramachandran restraints generated. 4074 Oldfield, 0 Emsley, 4074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8148 Ramachandran restraints generated. 4074 Oldfield, 0 Emsley, 4074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 472 time to evaluate : 3.691 Fit side-chains REVERT: A 78 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.8933 (tt) REVERT: A 131 LYS cc_start: 0.7756 (OUTLIER) cc_final: 0.7544 (ttmt) REVERT: C 118 TYR cc_start: 0.8545 (p90) cc_final: 0.8242 (p90) REVERT: D 158 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8192 (mt-10) REVERT: D 200 ARG cc_start: 0.7784 (OUTLIER) cc_final: 0.7058 (mtm-85) REVERT: D 257 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.8597 (mt0) REVERT: D 280 GLU cc_start: 0.8415 (tp30) cc_final: 0.8049 (tp30) REVERT: F 287 GLU cc_start: 0.8365 (pt0) cc_final: 0.7969 (mt-10) REVERT: I 8 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8136 (mptt) REVERT: J 8 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8226 (mttt) REVERT: J 31 GLU cc_start: 0.8403 (pm20) cc_final: 0.8202 (pm20) REVERT: J 37 LYS cc_start: 0.9203 (OUTLIER) cc_final: 0.8890 (tttt) REVERT: K 75 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8519 (ptmt) outliers start: 100 outliers final: 47 residues processed: 533 average time/residue: 1.7663 time to fit residues: 1088.6819 Evaluate side-chains 524 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 468 time to evaluate : 3.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 277 ARG Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 283 LYS Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 158 GLU Chi-restraints excluded: chain D residue 200 ARG Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 257 GLN Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 283 LYS Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 263 THR Chi-restraints excluded: chain G residue 132 ILE Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 195 LEU Chi-restraints excluded: chain I residue 8 LYS Chi-restraints excluded: chain I residue 99 SER Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 195 LEU Chi-restraints excluded: chain I residue 279 SER Chi-restraints excluded: chain J residue 8 LYS Chi-restraints excluded: chain J residue 37 LYS Chi-restraints excluded: chain J residue 125 THR Chi-restraints excluded: chain J residue 263 THR Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain K residue 99 SER Chi-restraints excluded: chain K residue 195 LEU Chi-restraints excluded: chain K residue 287 GLU Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain L residue 195 LEU Chi-restraints excluded: chain L residue 263 THR Chi-restraints excluded: chain M residue 195 LEU Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain N residue 142 ILE Chi-restraints excluded: chain N residue 155 THR Chi-restraints excluded: chain N residue 195 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 160 optimal weight: 0.9980 chunk 106 optimal weight: 7.9990 chunk 225 optimal weight: 2.9990 chunk 327 optimal weight: 1.9990 chunk 154 optimal weight: 3.9990 chunk 221 optimal weight: 3.9990 chunk 335 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 240 optimal weight: 2.9990 chunk 238 optimal weight: 0.9990 chunk 260 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN A 89 GLN A 242 GLN C 242 GLN D 87 GLN D 242 GLN E 89 GLN E 242 GLN F 89 GLN G 242 GLN H 89 GLN I 89 GLN I 242 GLN J 242 GLN M 242 GLN N 89 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.104444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.077046 restraints weight = 37757.814| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 2.12 r_work: 0.2797 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8964 moved from start: 0.0657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 33561 Z= 0.177 Angle : 0.515 10.519 45454 Z= 0.283 Chirality : 0.046 0.164 4872 Planarity : 0.003 0.035 5866 Dihedral : 5.005 48.531 4465 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.42 % Allowed : 15.99 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: 0.89 (0.13), residues: 4074 helix: -3.14 (0.26), residues: 84 sheet: 1.45 (0.10), residues: 2240 loop : -0.37 (0.15), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 167 HIS 0.009 0.001 HIS F 259 PHE 0.009 0.001 PHE L 84 TYR 0.020 0.002 TYR B 65 ARG 0.010 0.000 ARG H 147 Details of bonding type rmsd hydrogen bonds : bond 0.03536 ( 1567) hydrogen bonds : angle 5.31746 ( 4164) SS BOND : bond 0.00558 ( 7) SS BOND : angle 1.62896 ( 14) covalent geometry : bond 0.00403 (33554) covalent geometry : angle 0.51461 (45440) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8148 Ramachandran restraints generated. 4074 Oldfield, 0 Emsley, 4074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8148 Ramachandran restraints generated. 4074 Oldfield, 0 Emsley, 4074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 478 time to evaluate : 3.954 Fit side-chains REVERT: A 78 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.8912 (tt) REVERT: A 200 ARG cc_start: 0.8489 (mtm-85) cc_final: 0.8231 (mtm-85) REVERT: D 147 ARG cc_start: 0.8667 (ttp80) cc_final: 0.8215 (ttp-110) REVERT: D 158 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8169 (mt-10) REVERT: D 200 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.7053 (mtm-85) REVERT: D 257 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.8575 (mt0) REVERT: I 8 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8135 (mptt) REVERT: J 8 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8223 (mttt) REVERT: J 37 LYS cc_start: 0.9158 (OUTLIER) cc_final: 0.8857 (tttt) REVERT: J 277 ARG cc_start: 0.8904 (OUTLIER) cc_final: 0.8632 (ttt90) REVERT: K 75 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8469 (ptmt) REVERT: L 111 GLU cc_start: 0.9075 (tt0) cc_final: 0.8838 (tt0) outliers start: 88 outliers final: 43 residues processed: 531 average time/residue: 1.8304 time to fit residues: 1120.1486 Evaluate side-chains 529 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 477 time to evaluate : 3.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 277 ARG Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 283 LYS Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 158 GLU Chi-restraints excluded: chain D residue 200 ARG Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 257 GLN Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 283 LYS Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 263 THR Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 195 LEU Chi-restraints excluded: chain I residue 8 LYS Chi-restraints excluded: chain I residue 99 SER Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 195 LEU Chi-restraints excluded: chain J residue 8 LYS Chi-restraints excluded: chain J residue 37 LYS Chi-restraints excluded: chain J residue 125 THR Chi-restraints excluded: chain J residue 277 ARG Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain K residue 99 SER Chi-restraints excluded: chain K residue 195 LEU Chi-restraints excluded: chain K residue 287 GLU Chi-restraints excluded: chain L residue 195 LEU Chi-restraints excluded: chain L residue 263 THR Chi-restraints excluded: chain M residue 195 LEU Chi-restraints excluded: chain N residue 116 LEU Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain N residue 155 THR Chi-restraints excluded: chain N residue 195 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 131 optimal weight: 0.9990 chunk 202 optimal weight: 0.9990 chunk 383 optimal weight: 5.9990 chunk 325 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 192 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 157 optimal weight: 8.9990 chunk 399 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 288 optimal weight: 5.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN C 242 GLN D 87 GLN D 242 GLN E 89 GLN E 242 GLN F 89 GLN G 242 GLN H 89 GLN I 89 GLN I 123 ASN I 242 GLN J 242 GLN M 242 GLN N 89 GLN N 123 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.105575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.078259 restraints weight = 37793.196| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.12 r_work: 0.2817 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8950 moved from start: 0.0790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 33561 Z= 0.135 Angle : 0.489 9.749 45454 Z= 0.268 Chirality : 0.045 0.153 4872 Planarity : 0.003 0.042 5866 Dihedral : 4.765 47.914 4464 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.20 % Allowed : 16.43 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: 0.96 (0.13), residues: 4074 helix: -2.94 (0.30), residues: 84 sheet: 1.47 (0.10), residues: 2240 loop : -0.28 (0.15), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 167 HIS 0.011 0.001 HIS C 259 PHE 0.008 0.001 PHE L 84 TYR 0.018 0.001 TYR I 65 ARG 0.010 0.000 ARG H 147 Details of bonding type rmsd hydrogen bonds : bond 0.03234 ( 1567) hydrogen bonds : angle 5.15194 ( 4164) SS BOND : bond 0.00425 ( 7) SS BOND : angle 1.41356 ( 14) covalent geometry : bond 0.00303 (33554) covalent geometry : angle 0.48815 (45440) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8148 Ramachandran restraints generated. 4074 Oldfield, 0 Emsley, 4074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8148 Ramachandran restraints generated. 4074 Oldfield, 0 Emsley, 4074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 475 time to evaluate : 3.732 Fit side-chains REVERT: A 8 LYS cc_start: 0.8429 (mttp) cc_final: 0.8202 (mmtt) REVERT: A 78 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.8920 (tt) REVERT: A 200 ARG cc_start: 0.8520 (mtm-85) cc_final: 0.8271 (mtm-85) REVERT: C 283 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8573 (ttmt) REVERT: D 147 ARG cc_start: 0.8675 (ttp80) cc_final: 0.8258 (ttp-110) REVERT: D 158 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8183 (mt-10) REVERT: D 200 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.7072 (mtm-85) REVERT: D 280 GLU cc_start: 0.8474 (tp30) cc_final: 0.8070 (tp30) REVERT: F 287 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7915 (mt-10) REVERT: I 31 GLU cc_start: 0.8182 (mp0) cc_final: 0.7928 (pm20) REVERT: J 8 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8213 (mttt) REVERT: J 37 LYS cc_start: 0.9131 (OUTLIER) cc_final: 0.8845 (tttt) REVERT: J 101 TYR cc_start: 0.9447 (OUTLIER) cc_final: 0.9125 (p90) REVERT: J 277 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.8644 (ttt90) REVERT: K 75 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8430 (ptmt) REVERT: M 147 ARG cc_start: 0.9134 (ttp80) cc_final: 0.8890 (ttm110) REVERT: M 287 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8276 (mm-30) REVERT: N 287 GLU cc_start: 0.8588 (pt0) cc_final: 0.8268 (mt-10) outliers start: 80 outliers final: 42 residues processed: 529 average time/residue: 1.8015 time to fit residues: 1101.8142 Evaluate side-chains 516 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 464 time to evaluate : 3.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 277 ARG Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 283 LYS Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 158 GLU Chi-restraints excluded: chain D residue 200 ARG Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 263 THR Chi-restraints excluded: chain F residue 287 GLU Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 195 LEU Chi-restraints excluded: chain I residue 99 SER Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 195 LEU Chi-restraints excluded: chain I residue 279 SER Chi-restraints excluded: chain J residue 8 LYS Chi-restraints excluded: chain J residue 37 LYS Chi-restraints excluded: chain J residue 101 TYR Chi-restraints excluded: chain J residue 125 THR Chi-restraints excluded: chain J residue 277 ARG Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain K residue 99 SER Chi-restraints excluded: chain K residue 195 LEU Chi-restraints excluded: chain K residue 287 GLU Chi-restraints excluded: chain L residue 195 LEU Chi-restraints excluded: chain L residue 263 THR Chi-restraints excluded: chain M residue 195 LEU Chi-restraints excluded: chain N residue 116 LEU Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain N residue 155 THR Chi-restraints excluded: chain N residue 195 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 398 optimal weight: 3.9990 chunk 196 optimal weight: 5.9990 chunk 131 optimal weight: 0.8980 chunk 84 optimal weight: 8.9990 chunk 190 optimal weight: 0.8980 chunk 109 optimal weight: 5.9990 chunk 386 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 343 optimal weight: 3.9990 chunk 367 optimal weight: 7.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN C 242 GLN D 87 GLN D 242 GLN E 89 GLN E 242 GLN F 89 GLN G 242 GLN H 89 GLN I 89 GLN ** I 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 242 GLN J 242 GLN M 242 GLN N 89 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.104838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.077416 restraints weight = 37806.893| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.12 r_work: 0.2804 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8960 moved from start: 0.0764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 33561 Z= 0.173 Angle : 0.514 9.223 45454 Z= 0.282 Chirality : 0.046 0.155 4872 Planarity : 0.003 0.064 5866 Dihedral : 4.831 47.852 4459 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.34 % Allowed : 16.46 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: 0.98 (0.13), residues: 4074 helix: -2.95 (0.30), residues: 84 sheet: 1.50 (0.10), residues: 2240 loop : -0.30 (0.15), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 167 HIS 0.010 0.001 HIS F 259 PHE 0.009 0.001 PHE L 84 TYR 0.020 0.002 TYR B 65 ARG 0.010 0.000 ARG H 147 Details of bonding type rmsd hydrogen bonds : bond 0.03400 ( 1567) hydrogen bonds : angle 5.22381 ( 4164) SS BOND : bond 0.00587 ( 7) SS BOND : angle 1.54316 ( 14) covalent geometry : bond 0.00395 (33554) covalent geometry : angle 0.51306 (45440) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8148 Ramachandran restraints generated. 4074 Oldfield, 0 Emsley, 4074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8148 Ramachandran restraints generated. 4074 Oldfield, 0 Emsley, 4074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 463 time to evaluate : 4.220 Fit side-chains REVERT: A 8 LYS cc_start: 0.8436 (mttp) cc_final: 0.8194 (mttt) REVERT: A 78 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.8909 (tt) REVERT: A 131 LYS cc_start: 0.7810 (OUTLIER) cc_final: 0.7602 (ttmt) REVERT: A 200 ARG cc_start: 0.8548 (mtm-85) cc_final: 0.8294 (mtm-85) REVERT: B 89 GLN cc_start: 0.8396 (pt0) cc_final: 0.8155 (tt0) REVERT: B 93 ASN cc_start: 0.8379 (OUTLIER) cc_final: 0.8094 (p0) REVERT: D 147 ARG cc_start: 0.8670 (ttp80) cc_final: 0.8220 (ttp-110) REVERT: D 158 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8175 (mt-10) REVERT: D 200 ARG cc_start: 0.7812 (OUTLIER) cc_final: 0.7104 (mtm-85) REVERT: F 287 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7961 (mt-10) REVERT: J 8 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8206 (mttt) REVERT: J 37 LYS cc_start: 0.9170 (OUTLIER) cc_final: 0.8866 (tttt) REVERT: J 101 TYR cc_start: 0.9459 (OUTLIER) cc_final: 0.9131 (p90) REVERT: J 277 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.8669 (ttt90) REVERT: K 75 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8463 (ptmt) REVERT: M 204 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.8309 (pmm) REVERT: M 287 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8291 (mm-30) REVERT: N 287 GLU cc_start: 0.8589 (pt0) cc_final: 0.8316 (mt-10) outliers start: 85 outliers final: 48 residues processed: 516 average time/residue: 1.7292 time to fit residues: 1040.2271 Evaluate side-chains 530 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 470 time to evaluate : 3.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 277 ARG Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 283 LYS Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 158 GLU Chi-restraints excluded: chain D residue 200 ARG Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 263 THR Chi-restraints excluded: chain F residue 287 GLU Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 195 LEU Chi-restraints excluded: chain I residue 99 SER Chi-restraints excluded: chain I residue 123 ASN Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 195 LEU Chi-restraints excluded: chain I residue 279 SER Chi-restraints excluded: chain J residue 8 LYS Chi-restraints excluded: chain J residue 37 LYS Chi-restraints excluded: chain J residue 101 TYR Chi-restraints excluded: chain J residue 125 THR Chi-restraints excluded: chain J residue 277 ARG Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain K residue 99 SER Chi-restraints excluded: chain K residue 195 LEU Chi-restraints excluded: chain K residue 287 GLU Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain L residue 195 LEU Chi-restraints excluded: chain L residue 263 THR Chi-restraints excluded: chain L residue 287 GLU Chi-restraints excluded: chain M residue 195 LEU Chi-restraints excluded: chain M residue 204 MET Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain N residue 155 THR Chi-restraints excluded: chain N residue 195 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 225 optimal weight: 6.9990 chunk 117 optimal weight: 9.9990 chunk 180 optimal weight: 10.0000 chunk 212 optimal weight: 0.0470 chunk 159 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 272 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 161 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 240 optimal weight: 4.9990 overall best weight: 2.3284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN A 242 GLN C 242 GLN D 87 GLN D 242 GLN E 89 GLN E 242 GLN F 89 GLN G 242 GLN H 89 GLN I 89 GLN ** I 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 242 GLN J 242 GLN M 242 GLN N 89 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.104333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.076892 restraints weight = 37891.110| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.11 r_work: 0.2796 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8967 moved from start: 0.0702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 33561 Z= 0.198 Angle : 0.531 9.792 45454 Z= 0.291 Chirality : 0.047 0.152 4872 Planarity : 0.003 0.064 5866 Dihedral : 4.919 48.007 4459 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.20 % Allowed : 16.74 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: 0.96 (0.13), residues: 4074 helix: -3.01 (0.29), residues: 84 sheet: 1.49 (0.10), residues: 2240 loop : -0.31 (0.15), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 167 HIS 0.011 0.001 HIS C 259 PHE 0.009 0.001 PHE L 84 TYR 0.021 0.002 TYR I 65 ARG 0.012 0.001 ARG M 147 Details of bonding type rmsd hydrogen bonds : bond 0.03526 ( 1567) hydrogen bonds : angle 5.28942 ( 4164) SS BOND : bond 0.00577 ( 7) SS BOND : angle 1.62649 ( 14) covalent geometry : bond 0.00457 (33554) covalent geometry : angle 0.53032 (45440) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8148 Ramachandran restraints generated. 4074 Oldfield, 0 Emsley, 4074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8148 Ramachandran restraints generated. 4074 Oldfield, 0 Emsley, 4074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 462 time to evaluate : 3.714 Fit side-chains REVERT: A 8 LYS cc_start: 0.8445 (mttp) cc_final: 0.8196 (mttt) REVERT: A 78 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.8914 (tt) REVERT: A 131 LYS cc_start: 0.7781 (OUTLIER) cc_final: 0.7574 (ttmt) REVERT: A 200 ARG cc_start: 0.8541 (mtm-85) cc_final: 0.8282 (mtm-85) REVERT: B 89 GLN cc_start: 0.8395 (pt0) cc_final: 0.8171 (tt0) REVERT: D 147 ARG cc_start: 0.8673 (ttp80) cc_final: 0.8216 (ttp-110) REVERT: D 158 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8163 (mt-10) REVERT: D 200 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7082 (mtm-85) REVERT: D 280 GLU cc_start: 0.8434 (tp30) cc_final: 0.8074 (tp30) REVERT: F 287 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7955 (mt-10) REVERT: I 31 GLU cc_start: 0.8207 (mp0) cc_final: 0.7973 (pm20) REVERT: J 8 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8226 (mttt) REVERT: J 37 LYS cc_start: 0.9178 (OUTLIER) cc_final: 0.8866 (tttt) REVERT: J 101 TYR cc_start: 0.9466 (OUTLIER) cc_final: 0.9136 (p90) REVERT: J 277 ARG cc_start: 0.8925 (OUTLIER) cc_final: 0.8659 (ttt90) REVERT: K 75 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8477 (ptmt) REVERT: M 31 GLU cc_start: 0.8194 (mp0) cc_final: 0.7968 (pm20) REVERT: M 204 MET cc_start: 0.8870 (OUTLIER) cc_final: 0.8351 (pmm) REVERT: N 287 GLU cc_start: 0.8596 (pt0) cc_final: 0.8320 (mt-10) outliers start: 80 outliers final: 48 residues processed: 513 average time/residue: 1.6750 time to fit residues: 995.9161 Evaluate side-chains 522 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 463 time to evaluate : 3.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 277 ARG Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 283 LYS Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 158 GLU Chi-restraints excluded: chain D residue 200 ARG Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 263 THR Chi-restraints excluded: chain F residue 287 GLU Chi-restraints excluded: chain G residue 205 LYS Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 195 LEU Chi-restraints excluded: chain I residue 11 THR Chi-restraints excluded: chain I residue 99 SER Chi-restraints excluded: chain I residue 123 ASN Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 195 LEU Chi-restraints excluded: chain I residue 279 SER Chi-restraints excluded: chain J residue 8 LYS Chi-restraints excluded: chain J residue 37 LYS Chi-restraints excluded: chain J residue 101 TYR Chi-restraints excluded: chain J residue 125 THR Chi-restraints excluded: chain J residue 277 ARG Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain K residue 99 SER Chi-restraints excluded: chain K residue 195 LEU Chi-restraints excluded: chain K residue 287 GLU Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain L residue 195 LEU Chi-restraints excluded: chain L residue 263 THR Chi-restraints excluded: chain M residue 195 LEU Chi-restraints excluded: chain M residue 204 MET Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain N residue 155 THR Chi-restraints excluded: chain N residue 195 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 335 optimal weight: 0.2980 chunk 58 optimal weight: 10.0000 chunk 275 optimal weight: 0.5980 chunk 153 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 167 optimal weight: 1.9990 chunk 400 optimal weight: 4.9990 chunk 239 optimal weight: 10.0000 chunk 307 optimal weight: 4.9990 chunk 380 optimal weight: 5.9990 chunk 127 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN A 242 GLN C 242 GLN D 87 GLN D 242 GLN E 89 GLN E 242 GLN F 89 GLN G 242 GLN H 89 GLN I 89 GLN ** I 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 242 GLN J 242 GLN M 242 GLN N 89 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.104865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.077492 restraints weight = 37728.669| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.11 r_work: 0.2805 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8959 moved from start: 0.0768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 33561 Z= 0.174 Angle : 0.516 9.398 45454 Z= 0.283 Chirality : 0.046 0.150 4872 Planarity : 0.003 0.070 5866 Dihedral : 4.853 48.018 4459 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.12 % Allowed : 16.87 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: 0.99 (0.13), residues: 4074 helix: -2.94 (0.30), residues: 84 sheet: 1.49 (0.10), residues: 2240 loop : -0.27 (0.15), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 167 HIS 0.010 0.001 HIS F 259 PHE 0.009 0.001 PHE L 84 TYR 0.020 0.002 TYR B 65 ARG 0.015 0.001 ARG M 147 Details of bonding type rmsd hydrogen bonds : bond 0.03405 ( 1567) hydrogen bonds : angle 5.23083 ( 4164) SS BOND : bond 0.00544 ( 7) SS BOND : angle 1.51648 ( 14) covalent geometry : bond 0.00399 (33554) covalent geometry : angle 0.51560 (45440) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8148 Ramachandran restraints generated. 4074 Oldfield, 0 Emsley, 4074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8148 Ramachandran restraints generated. 4074 Oldfield, 0 Emsley, 4074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 460 time to evaluate : 3.937 Fit side-chains REVERT: A 8 LYS cc_start: 0.8442 (mttp) cc_final: 0.8193 (mttt) REVERT: A 78 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.8909 (tt) REVERT: A 131 LYS cc_start: 0.7783 (OUTLIER) cc_final: 0.7577 (ttmt) REVERT: A 200 ARG cc_start: 0.8537 (mtm-85) cc_final: 0.8275 (mtm-85) REVERT: B 89 GLN cc_start: 0.8393 (pt0) cc_final: 0.8158 (tt0) REVERT: D 147 ARG cc_start: 0.8661 (ttp80) cc_final: 0.8208 (ttp-110) REVERT: D 158 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8181 (mt-10) REVERT: D 200 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.7063 (mtm-85) REVERT: F 242 GLN cc_start: 0.8770 (mp-120) cc_final: 0.8564 (mp10) REVERT: F 287 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7936 (mt-10) REVERT: I 31 GLU cc_start: 0.8195 (mp0) cc_final: 0.7950 (pm20) REVERT: J 8 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8220 (mttt) REVERT: J 37 LYS cc_start: 0.9158 (OUTLIER) cc_final: 0.8854 (tttt) REVERT: J 101 TYR cc_start: 0.9461 (OUTLIER) cc_final: 0.9137 (p90) REVERT: J 277 ARG cc_start: 0.8932 (OUTLIER) cc_final: 0.8673 (ttt90) REVERT: K 31 GLU cc_start: 0.8198 (mp0) cc_final: 0.7913 (pm20) REVERT: K 75 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8480 (ptmt) REVERT: L 277 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.8584 (ttt90) REVERT: M 204 MET cc_start: 0.8885 (OUTLIER) cc_final: 0.8353 (pmm) REVERT: N 287 GLU cc_start: 0.8600 (pt0) cc_final: 0.8329 (mt-10) outliers start: 77 outliers final: 54 residues processed: 510 average time/residue: 1.7000 time to fit residues: 1008.5693 Evaluate side-chains 522 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 456 time to evaluate : 3.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 277 ARG Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 283 LYS Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 158 GLU Chi-restraints excluded: chain D residue 200 ARG Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 263 THR Chi-restraints excluded: chain F residue 287 GLU Chi-restraints excluded: chain G residue 205 LYS Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain H residue 9 THR Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 195 LEU Chi-restraints excluded: chain I residue 11 THR Chi-restraints excluded: chain I residue 99 SER Chi-restraints excluded: chain I residue 123 ASN Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 195 LEU Chi-restraints excluded: chain I residue 279 SER Chi-restraints excluded: chain J residue 8 LYS Chi-restraints excluded: chain J residue 37 LYS Chi-restraints excluded: chain J residue 101 TYR Chi-restraints excluded: chain J residue 125 THR Chi-restraints excluded: chain J residue 277 ARG Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain K residue 99 SER Chi-restraints excluded: chain K residue 195 LEU Chi-restraints excluded: chain K residue 287 GLU Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain L residue 195 LEU Chi-restraints excluded: chain L residue 263 THR Chi-restraints excluded: chain L residue 277 ARG Chi-restraints excluded: chain L residue 287 GLU Chi-restraints excluded: chain M residue 195 LEU Chi-restraints excluded: chain M residue 204 MET Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain N residue 142 ILE Chi-restraints excluded: chain N residue 155 THR Chi-restraints excluded: chain N residue 195 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 391 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 chunk 173 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 3 optimal weight: 7.9990 chunk 269 optimal weight: 0.8980 chunk 9 optimal weight: 0.0570 chunk 168 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 214 optimal weight: 1.9990 overall best weight: 1.5302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN C 242 GLN D 87 GLN D 242 GLN E 89 GLN E 242 GLN F 89 GLN G 242 GLN H 89 GLN I 89 GLN ** I 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 242 GLN J 242 GLN M 242 GLN N 89 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.105562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.078265 restraints weight = 37842.380| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.11 r_work: 0.2819 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8950 moved from start: 0.0851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 33561 Z= 0.145 Angle : 0.499 9.002 45454 Z= 0.273 Chirality : 0.045 0.147 4872 Planarity : 0.003 0.080 5866 Dihedral : 4.743 48.057 4459 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.84 % Allowed : 17.23 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: 1.02 (0.13), residues: 4074 helix: -2.86 (0.31), residues: 84 sheet: 1.50 (0.10), residues: 2240 loop : -0.23 (0.15), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 167 HIS 0.012 0.001 HIS C 259 PHE 0.008 0.001 PHE L 84 TYR 0.018 0.002 TYR B 65 ARG 0.013 0.001 ARG J 147 Details of bonding type rmsd hydrogen bonds : bond 0.03234 ( 1567) hydrogen bonds : angle 5.14262 ( 4164) SS BOND : bond 0.00466 ( 7) SS BOND : angle 1.37654 ( 14) covalent geometry : bond 0.00327 (33554) covalent geometry : angle 0.49844 (45440) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8148 Ramachandran restraints generated. 4074 Oldfield, 0 Emsley, 4074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8148 Ramachandran restraints generated. 4074 Oldfield, 0 Emsley, 4074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 466 time to evaluate : 3.922 Fit side-chains REVERT: A 78 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.8927 (tt) REVERT: A 200 ARG cc_start: 0.8546 (mtm-85) cc_final: 0.8296 (mtm-85) REVERT: B 89 GLN cc_start: 0.8385 (pt0) cc_final: 0.8129 (tt0) REVERT: D 147 ARG cc_start: 0.8665 (ttp80) cc_final: 0.8200 (ttp-110) REVERT: D 158 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8183 (mt-10) REVERT: D 200 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.7096 (mtm-85) REVERT: D 280 GLU cc_start: 0.8357 (tp30) cc_final: 0.8015 (tp30) REVERT: F 287 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7945 (mt-10) REVERT: I 31 GLU cc_start: 0.8212 (mp0) cc_final: 0.7970 (pm20) REVERT: J 8 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8201 (mttt) REVERT: J 37 LYS cc_start: 0.9134 (OUTLIER) cc_final: 0.8824 (tttt) REVERT: J 101 TYR cc_start: 0.9452 (OUTLIER) cc_final: 0.9124 (p90) REVERT: J 277 ARG cc_start: 0.8916 (OUTLIER) cc_final: 0.8653 (ttt90) REVERT: J 283 LYS cc_start: 0.8864 (mtpm) cc_final: 0.8314 (tmmm) REVERT: K 31 GLU cc_start: 0.8211 (mp0) cc_final: 0.7931 (pm20) REVERT: K 75 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8458 (ptmt) REVERT: K 147 ARG cc_start: 0.8980 (ttp80) cc_final: 0.8720 (ttp-110) REVERT: K 277 ARG cc_start: 0.8971 (OUTLIER) cc_final: 0.8682 (ttt90) REVERT: L 31 GLU cc_start: 0.8101 (mp0) cc_final: 0.7838 (pm20) REVERT: L 277 ARG cc_start: 0.8897 (OUTLIER) cc_final: 0.8575 (ttt90) REVERT: M 147 ARG cc_start: 0.9119 (ttp80) cc_final: 0.8882 (ttp80) REVERT: M 204 MET cc_start: 0.8916 (OUTLIER) cc_final: 0.8324 (pmm) REVERT: M 287 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8286 (mm-30) REVERT: N 287 GLU cc_start: 0.8586 (pt0) cc_final: 0.8298 (mt-10) outliers start: 67 outliers final: 48 residues processed: 508 average time/residue: 1.7281 time to fit residues: 1014.2369 Evaluate side-chains 521 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 461 time to evaluate : 3.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 277 ARG Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 158 GLU Chi-restraints excluded: chain D residue 200 ARG Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 263 THR Chi-restraints excluded: chain F residue 287 GLU Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 195 LEU Chi-restraints excluded: chain I residue 11 THR Chi-restraints excluded: chain I residue 99 SER Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 195 LEU Chi-restraints excluded: chain I residue 279 SER Chi-restraints excluded: chain J residue 8 LYS Chi-restraints excluded: chain J residue 37 LYS Chi-restraints excluded: chain J residue 101 TYR Chi-restraints excluded: chain J residue 125 THR Chi-restraints excluded: chain J residue 277 ARG Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain K residue 99 SER Chi-restraints excluded: chain K residue 195 LEU Chi-restraints excluded: chain K residue 277 ARG Chi-restraints excluded: chain K residue 287 GLU Chi-restraints excluded: chain L residue 195 LEU Chi-restraints excluded: chain L residue 263 THR Chi-restraints excluded: chain L residue 277 ARG Chi-restraints excluded: chain M residue 195 LEU Chi-restraints excluded: chain M residue 204 MET Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain N residue 142 ILE Chi-restraints excluded: chain N residue 155 THR Chi-restraints excluded: chain N residue 195 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 68 optimal weight: 3.9990 chunk 136 optimal weight: 9.9990 chunk 144 optimal weight: 5.9990 chunk 222 optimal weight: 6.9990 chunk 307 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 184 optimal weight: 0.7980 chunk 164 optimal weight: 10.0000 chunk 173 optimal weight: 0.9990 chunk 113 optimal weight: 7.9990 chunk 71 optimal weight: 10.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN C 242 GLN D 87 GLN D 242 GLN E 89 GLN E 242 GLN F 89 GLN G 242 GLN H 89 GLN I 89 GLN ** I 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 242 GLN J 242 GLN M 242 GLN N 89 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.103789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.076161 restraints weight = 37987.026| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 2.13 r_work: 0.2781 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8967 moved from start: 0.0685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 33561 Z= 0.258 Angle : 0.568 9.909 45454 Z= 0.311 Chirality : 0.048 0.156 4872 Planarity : 0.004 0.092 5866 Dihedral : 4.975 48.306 4455 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.95 % Allowed : 16.90 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: 0.94 (0.13), residues: 4074 helix: -3.16 (0.26), residues: 84 sheet: 1.50 (0.10), residues: 2240 loop : -0.34 (0.15), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 179 HIS 0.011 0.001 HIS C 259 PHE 0.010 0.002 PHE L 84 TYR 0.023 0.002 TYR I 65 ARG 0.015 0.001 ARG J 147 Details of bonding type rmsd hydrogen bonds : bond 0.03746 ( 1567) hydrogen bonds : angle 5.37710 ( 4164) SS BOND : bond 0.00672 ( 7) SS BOND : angle 1.80224 ( 14) covalent geometry : bond 0.00599 (33554) covalent geometry : angle 0.56765 (45440) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 28699.05 seconds wall clock time: 495 minutes 37.44 seconds (29737.44 seconds total)