Starting phenix.real_space_refine on Sat Dec 28 01:26:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qg9_13953/12_2024/7qg9_13953.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qg9_13953/12_2024/7qg9_13953.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qg9_13953/12_2024/7qg9_13953.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qg9_13953/12_2024/7qg9_13953.map" model { file = "/net/cci-nas-00/data/ceres_data/7qg9_13953/12_2024/7qg9_13953.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qg9_13953/12_2024/7qg9_13953.cif" } resolution = 3.45 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= 0.001 sd= 0.009 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 150 5.16 5 C 32001 2.51 5 N 8466 2.21 5 O 10212 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 50829 Number of models: 1 Model: "" Number of chains: 27 Chain: "R" Number of atoms: 1048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1048 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain: "I" Number of atoms: 2423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2423 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 14, 'TRANS': 283} Chain: "a" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1610 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 189} Chain: "Q" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1056 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "S" Number of atoms: 1048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1048 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain: "F" Number of atoms: 3546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3546 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 449} Chain: "N" Number of atoms: 1048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1048 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain: "H" Number of atoms: 2423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2423 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 14, 'TRANS': 283} Chain: "X" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1610 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 189} Chain: "Y" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1610 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 189} Chain: "M" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1056 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "O" Number of atoms: 1048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1048 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain: "E" Number of atoms: 3546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3546 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 449} Chain: "C" Number of atoms: 3546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3546 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 449} Chain: "J" Number of atoms: 1048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1048 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain: "L" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1056 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "G" Number of atoms: 2423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2423 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 14, 'TRANS': 283} Chain: "W" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1610 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 189} Chain: "U" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1056 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "K" Number of atoms: 1048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1048 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain: "D" Number of atoms: 3546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3546 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 449} Chain: "A" Number of atoms: 3546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3546 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 449} Chain: "B" Number of atoms: 3546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3546 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 449} Chain: "P" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1056 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "T" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1056 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "V" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1610 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 189} Chain: "Z" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1610 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 189} Time building chain proxies: 21.10, per 1000 atoms: 0.42 Number of scatterers: 50829 At special positions: 0 Unit cell: (170.226, 185.087, 178.332, 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 150 16.00 O 10212 8.00 N 8466 7.00 C 32001 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.97 Conformation dependent library (CDL) restraints added in 4.8 seconds 13044 Ramachandran restraints generated. 6522 Oldfield, 0 Emsley, 6522 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12264 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 100 sheets defined 10.2% alpha, 27.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.23 Creating SS restraints... Processing helix chain 'R' and resid 3 through 7 removed outlier: 3.972A pdb=" N VAL R 7 " --> pdb=" O GLU R 4 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 92 Processing helix chain 'I' and resid 73 through 75 No H-bonds generated for 'chain 'I' and resid 73 through 75' Processing helix chain 'I' and resid 76 through 83 Processing helix chain 'I' and resid 200 through 204 removed outlier: 3.597A pdb=" N ILE I 204 " --> pdb=" O ILE I 201 " (cutoff:3.500A) Processing helix chain 'a' and resid 12 through 16 Processing helix chain 'a' and resid 58 through 76 Processing helix chain 'a' and resid 83 through 87 Processing helix chain 'Q' and resid 81 through 91 Processing helix chain 'S' and resid 81 through 92 removed outlier: 3.654A pdb=" N LYS S 91 " --> pdb=" O THR S 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 7 No H-bonds generated for 'chain 'F' and resid 5 through 7' Processing helix chain 'F' and resid 91 through 100 Processing helix chain 'F' and resid 185 through 190 Processing helix chain 'F' and resid 192 through 201 Processing helix chain 'F' and resid 275 through 287 removed outlier: 3.521A pdb=" N LEU F 287 " --> pdb=" O LEU F 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 346 removed outlier: 4.255A pdb=" N GLY F 346 " --> pdb=" O LEU F 343 " (cutoff:3.500A) Processing helix chain 'F' and resid 358 through 369 Processing helix chain 'N' and resid 3 through 7 removed outlier: 3.973A pdb=" N VAL N 7 " --> pdb=" O GLU N 4 " (cutoff:3.500A) Processing helix chain 'N' and resid 81 through 92 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 76 through 83 Processing helix chain 'H' and resid 200 through 204 removed outlier: 3.595A pdb=" N ILE H 204 " --> pdb=" O ILE H 201 " (cutoff:3.500A) Processing helix chain 'X' and resid 58 through 76 Processing helix chain 'Y' and resid 12 through 16 Processing helix chain 'Y' and resid 58 through 76 Processing helix chain 'Y' and resid 83 through 87 Processing helix chain 'M' and resid 81 through 91 Processing helix chain 'O' and resid 81 through 92 removed outlier: 3.654A pdb=" N LYS O 91 " --> pdb=" O THR O 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 7 No H-bonds generated for 'chain 'E' and resid 5 through 7' Processing helix chain 'E' and resid 91 through 100 Processing helix chain 'E' and resid 185 through 190 Processing helix chain 'E' and resid 192 through 201 Processing helix chain 'E' and resid 275 through 287 removed outlier: 3.520A pdb=" N LEU E 287 " --> pdb=" O LEU E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 346 removed outlier: 4.256A pdb=" N GLY E 346 " --> pdb=" O LEU E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 369 Processing helix chain 'C' and resid 91 through 100 removed outlier: 3.685A pdb=" N TRP C 95 " --> pdb=" O ASP C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 190 removed outlier: 3.830A pdb=" N ILE C 189 " --> pdb=" O ASP C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 201 Processing helix chain 'C' and resid 275 through 286 Processing helix chain 'C' and resid 358 through 369 Processing helix chain 'J' and resid 3 through 7 removed outlier: 3.972A pdb=" N VAL J 7 " --> pdb=" O GLU J 4 " (cutoff:3.500A) Processing helix chain 'J' and resid 81 through 92 Processing helix chain 'L' and resid 81 through 91 Processing helix chain 'G' and resid 73 through 75 No H-bonds generated for 'chain 'G' and resid 73 through 75' Processing helix chain 'G' and resid 76 through 83 Processing helix chain 'G' and resid 200 through 204 removed outlier: 3.594A pdb=" N ILE G 204 " --> pdb=" O ILE G 201 " (cutoff:3.500A) Processing helix chain 'W' and resid 12 through 16 Processing helix chain 'W' and resid 58 through 76 Processing helix chain 'W' and resid 83 through 87 Processing helix chain 'U' and resid 81 through 91 Processing helix chain 'K' and resid 81 through 92 removed outlier: 3.654A pdb=" N LYS K 91 " --> pdb=" O THR K 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 7 No H-bonds generated for 'chain 'D' and resid 5 through 7' Processing helix chain 'D' and resid 91 through 100 Processing helix chain 'D' and resid 185 through 190 Processing helix chain 'D' and resid 192 through 201 Processing helix chain 'D' and resid 275 through 287 removed outlier: 3.521A pdb=" N LEU D 287 " --> pdb=" O LEU D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 346 removed outlier: 4.255A pdb=" N GLY D 346 " --> pdb=" O LEU D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 369 Processing helix chain 'A' and resid 91 through 100 removed outlier: 3.687A pdb=" N TRP A 95 " --> pdb=" O ASP A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 190 removed outlier: 3.829A pdb=" N ILE A 189 " --> pdb=" O ASP A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 201 Processing helix chain 'A' and resid 275 through 286 Processing helix chain 'A' and resid 358 through 369 Processing helix chain 'B' and resid 91 through 100 removed outlier: 3.684A pdb=" N TRP B 95 " --> pdb=" O ASP B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 190 removed outlier: 3.829A pdb=" N ILE B 189 " --> pdb=" O ASP B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 201 Processing helix chain 'B' and resid 275 through 286 Processing helix chain 'B' and resid 358 through 369 Processing helix chain 'P' and resid 81 through 91 Processing helix chain 'T' and resid 81 through 91 Processing helix chain 'V' and resid 58 through 76 Processing helix chain 'Z' and resid 58 through 76 Processing sheet with id=AA1, first strand: chain 'R' and resid 10 through 13 removed outlier: 6.339A pdb=" N LEU R 10 " --> pdb=" O TYR R 133 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N SER R 135 " --> pdb=" O LEU R 10 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL R 12 " --> pdb=" O SER R 135 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL R 111 " --> pdb=" O ILE R 127 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLU R 129 " --> pdb=" O TYR R 109 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N TYR R 109 " --> pdb=" O GLU R 129 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N LYS R 131 " --> pdb=" O GLY R 107 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLY R 107 " --> pdb=" O LYS R 131 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N TYR R 133 " --> pdb=" O LEU R 105 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LEU R 105 " --> pdb=" O TYR R 133 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N SER R 135 " --> pdb=" O GLN R 103 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLN R 103 " --> pdb=" O SER R 135 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP R 110 " --> pdb=" O SER R 49 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE R 50 " --> pdb=" O VAL R 61 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 18 through 23 removed outlier: 3.784A pdb=" N LEU R 80 " --> pdb=" O TYR R 18 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL R 75 " --> pdb=" O ASP R 70 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N SER R 77 " --> pdb=" O ILE R 68 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ILE R 68 " --> pdb=" O SER R 77 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'R' and resid 25 through 27 Processing sheet with id=AA4, first strand: chain 'I' and resid 2 through 3 removed outlier: 3.577A pdb=" N LYS H 230 " --> pdb=" O PHE I 2 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 9 through 15 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 18 through 21 current: chain 'I' and resid 62 through 68 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 62 through 68 current: chain 'I' and resid 90 through 92 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 90 through 92 current: chain 'I' and resid 115 through 131 removed outlier: 6.411A pdb=" N GLY I 141 " --> pdb=" O SER I 125 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL I 127 " --> pdb=" O ASN I 139 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ASN I 139 " --> pdb=" O VAL I 127 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N PHE I 129 " --> pdb=" O ILE I 137 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ILE I 137 " --> pdb=" O PHE I 129 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 137 through 143 current: chain 'I' and resid 177 through 178 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 177 through 178 current: chain 'I' and resid 213 through 227 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 213 through 227 current: chain 'I' and resid 255 through 269 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 275 through 282 current: chain 'G' and resid 52 through 59 Processing sheet with id=AA6, first strand: chain 'I' and resid 31 through 39 removed outlier: 4.643A pdb=" N SER I 33 " --> pdb=" O ASP I 59 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA I 57 " --> pdb=" O GLN I 35 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N PHE I 37 " --> pdb=" O ILE I 55 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ILE I 55 " --> pdb=" O PHE I 37 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N THR I 39 " --> pdb=" O SER I 53 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N SER I 53 " --> pdb=" O THR I 39 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 52 through 59 current: chain 'H' and resid 18 through 21 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 18 through 21 current: chain 'H' and resid 62 through 68 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 62 through 68 current: chain 'H' and resid 90 through 92 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 90 through 92 current: chain 'H' and resid 115 through 131 removed outlier: 6.408A pdb=" N GLY H 141 " --> pdb=" O SER H 125 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL H 127 " --> pdb=" O ASN H 139 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ASN H 139 " --> pdb=" O VAL H 127 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N PHE H 129 " --> pdb=" O ILE H 137 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ILE H 137 " --> pdb=" O PHE H 129 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 137 through 143 current: chain 'H' and resid 177 through 178 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 177 through 178 current: chain 'H' and resid 213 through 227 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 213 through 227 current: chain 'H' and resid 255 through 269 Processing sheet with id=AA7, first strand: chain 'a' and resid 79 through 81 removed outlier: 5.239A pdb=" N TRP a 48 " --> pdb=" O GLU a 202 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN a 25 " --> pdb=" O TYR a 47 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER a 19 " --> pdb=" O SER a 53 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL a 20 " --> pdb=" O LEU Z 187 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N THR Z 186 " --> pdb=" O SER Z 194 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER Z 194 " --> pdb=" O THR Z 186 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'a' and resid 29 through 32 Processing sheet with id=AA9, first strand: chain 'a' and resid 92 through 93 Processing sheet with id=AB1, first strand: chain 'a' and resid 108 through 112 removed outlier: 7.157A pdb=" N VAL a 147 " --> pdb=" O SER a 143 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N SER a 143 " --> pdb=" O VAL a 147 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ASN a 149 " --> pdb=" O PHE a 141 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N PHE a 141 " --> pdb=" O ASN a 149 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N SER a 151 " --> pdb=" O THR a 139 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'a' and resid 182 through 183 WARNING: can't find start of bonding for strands! previous: chain 'a' and resid 182 through 183 current: chain 'a' and resid 193 through 194 WARNING: can't find start of bonding for strands! previous: chain 'a' and resid 193 through 194 current: chain 'V' and resid 47 through 53 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 47 through 53 current: chain 'V' and resid 173 through 177 Processing sheet with id=AB3, first strand: chain 'Q' and resid 10 through 13 removed outlier: 6.530A pdb=" N LEU Q 10 " --> pdb=" O TYR Q 133 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N SER Q 135 " --> pdb=" O LEU Q 10 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL Q 12 " --> pdb=" O SER Q 135 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ARG Q 126 " --> pdb=" O ILE Q 113 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ILE Q 113 " --> pdb=" O ARG Q 126 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N MET Q 128 " --> pdb=" O VAL Q 111 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY Q 130 " --> pdb=" O TYR Q 109 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ILE Q 134 " --> pdb=" O LEU Q 105 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N LEU Q 105 " --> pdb=" O ILE Q 134 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA Q 62 " --> pdb=" O ILE Q 50 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Q' and resid 18 through 23 removed outlier: 7.474A pdb=" N VAL Q 75 " --> pdb=" O VAL Q 69 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL Q 69 " --> pdb=" O VAL Q 75 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'Q' and resid 25 through 28 removed outlier: 3.814A pdb=" N THR Q 35 " --> pdb=" O ASP Q 28 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 10 through 13 removed outlier: 6.413A pdb=" N LEU S 10 " --> pdb=" O TYR S 133 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N SER S 135 " --> pdb=" O LEU S 10 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL S 12 " --> pdb=" O SER S 135 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL S 111 " --> pdb=" O ILE S 127 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLU S 129 " --> pdb=" O TYR S 109 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N TYR S 109 " --> pdb=" O GLU S 129 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N LYS S 131 " --> pdb=" O GLY S 107 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N GLY S 107 " --> pdb=" O LYS S 131 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N TYR S 133 " --> pdb=" O LEU S 105 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU S 105 " --> pdb=" O TYR S 133 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N SER S 135 " --> pdb=" O GLN S 103 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLN S 103 " --> pdb=" O SER S 135 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASP S 110 " --> pdb=" O SER S 49 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N SER S 49 " --> pdb=" O ASP S 110 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'S' and resid 18 through 23 removed outlier: 3.750A pdb=" N TYR S 18 " --> pdb=" O LEU S 80 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'S' and resid 26 through 28 removed outlier: 3.730A pdb=" N LYS S 37 " --> pdb=" O ASP S 26 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP S 28 " --> pdb=" O THR S 35 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 9 through 14 removed outlier: 4.239A pdb=" N ILE F 11 " --> pdb=" O ILE F 28 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 25 through 28 current: chain 'F' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 68 through 75 current: chain 'F' and resid 119 through 122 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 119 through 122 current: chain 'F' and resid 143 through 159 removed outlier: 5.644A pdb=" N ILE F 152 " --> pdb=" O ASN F 172 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ASN F 172 " --> pdb=" O ILE F 152 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASN F 158 " --> pdb=" O ARG F 166 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N ARG F 166 " --> pdb=" O ASN F 158 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 166 through 173 current: chain 'F' and resid 221 through 222 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 221 through 222 current: chain 'F' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 260 through 268 current: chain 'F' and resid 309 through 319 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 309 through 319 current: chain 'F' and resid 331 through 338 Processing sheet with id=AC1, first strand: chain 'F' and resid 40 through 44 removed outlier: 3.918A pdb=" N SER F 64 " --> pdb=" O ASN F 41 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N THR F 43 " --> pdb=" O ASN F 62 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ASN F 62 " --> pdb=" O THR F 43 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 79 through 80 Processing sheet with id=AC3, first strand: chain 'F' and resid 238 through 239 Processing sheet with id=AC4, first strand: chain 'F' and resid 378 through 382 removed outlier: 3.558A pdb=" N ALA F 378 " --> pdb=" O THR F 403 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR F 380 " --> pdb=" O GLU F 401 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU F 401 " --> pdb=" O THR F 380 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 389 through 390 removed outlier: 3.917A pdb=" N LEU F 390 " --> pdb=" O THR F 459 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL F 440 " --> pdb=" O ILE F 458 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 396 through 397 Processing sheet with id=AC7, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.339A pdb=" N LEU N 10 " --> pdb=" O TYR N 133 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N SER N 135 " --> pdb=" O LEU N 10 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL N 12 " --> pdb=" O SER N 135 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL N 111 " --> pdb=" O ILE N 127 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLU N 129 " --> pdb=" O TYR N 109 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N TYR N 109 " --> pdb=" O GLU N 129 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N LYS N 131 " --> pdb=" O GLY N 107 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLY N 107 " --> pdb=" O LYS N 131 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N TYR N 133 " --> pdb=" O LEU N 105 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LEU N 105 " --> pdb=" O TYR N 133 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N SER N 135 " --> pdb=" O GLN N 103 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLN N 103 " --> pdb=" O SER N 135 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP N 110 " --> pdb=" O SER N 49 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE N 50 " --> pdb=" O VAL N 61 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'N' and resid 18 through 23 removed outlier: 3.785A pdb=" N LEU N 80 " --> pdb=" O TYR N 18 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL N 75 " --> pdb=" O ASP N 70 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N SER N 77 " --> pdb=" O ILE N 68 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ILE N 68 " --> pdb=" O SER N 77 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 25 through 27 Processing sheet with id=AD1, first strand: chain 'H' and resid 31 through 39 removed outlier: 4.643A pdb=" N SER H 33 " --> pdb=" O ASP H 59 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA H 57 " --> pdb=" O GLN H 35 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N PHE H 37 " --> pdb=" O ILE H 55 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ILE H 55 " --> pdb=" O PHE H 37 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N THR H 39 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N SER H 53 " --> pdb=" O THR H 39 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 52 through 59 current: chain 'G' and resid 18 through 21 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 18 through 21 current: chain 'G' and resid 62 through 68 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 62 through 68 current: chain 'G' and resid 90 through 92 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 90 through 92 current: chain 'G' and resid 115 through 131 removed outlier: 6.407A pdb=" N GLY G 141 " --> pdb=" O SER G 125 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VAL G 127 " --> pdb=" O ASN G 139 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ASN G 139 " --> pdb=" O VAL G 127 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N PHE G 129 " --> pdb=" O ILE G 137 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ILE G 137 " --> pdb=" O PHE G 129 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 137 through 143 current: chain 'G' and resid 177 through 178 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 177 through 178 current: chain 'G' and resid 213 through 227 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 213 through 227 current: chain 'G' and resid 255 through 269 Processing sheet with id=AD2, first strand: chain 'X' and resid 19 through 25 removed outlier: 3.530A pdb=" N ASN X 25 " --> pdb=" O TYR X 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 47 through 53 current: chain 'X' and resid 173 through 177 WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 197 through 202 current: chain 'W' and resid 193 through 194 Processing sheet with id=AD3, first strand: chain 'X' and resid 29 through 32 Processing sheet with id=AD4, first strand: chain 'X' and resid 108 through 112 removed outlier: 6.965A pdb=" N VAL X 147 " --> pdb=" O SER X 143 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N SER X 143 " --> pdb=" O VAL X 147 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ASN X 149 " --> pdb=" O PHE X 141 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N PHE X 141 " --> pdb=" O ASN X 149 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N SER X 151 " --> pdb=" O THR X 139 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS X 128 " --> pdb=" O VAL X 167 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'X' and resid 193 through 194 removed outlier: 3.506A pdb=" N SER X 194 " --> pdb=" O THR X 186 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N THR X 186 " --> pdb=" O SER X 194 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL Y 20 " --> pdb=" O LEU X 187 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N SER Y 19 " --> pdb=" O SER Y 53 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN Y 25 " --> pdb=" O TYR Y 47 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N TRP Y 48 " --> pdb=" O GLU Y 202 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Y' and resid 29 through 32 Processing sheet with id=AD7, first strand: chain 'Y' and resid 92 through 93 Processing sheet with id=AD8, first strand: chain 'Y' and resid 108 through 112 removed outlier: 7.157A pdb=" N VAL Y 147 " --> pdb=" O SER Y 143 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N SER Y 143 " --> pdb=" O VAL Y 147 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASN Y 149 " --> pdb=" O PHE Y 141 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N PHE Y 141 " --> pdb=" O ASN Y 149 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N SER Y 151 " --> pdb=" O THR Y 139 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Y' and resid 182 through 183 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 182 through 183 current: chain 'Y' and resid 193 through 194 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 193 through 194 current: chain 'Z' and resid 47 through 53 WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 47 through 53 current: chain 'Z' and resid 173 through 177 Processing sheet with id=AE1, first strand: chain 'M' and resid 10 through 13 removed outlier: 6.527A pdb=" N LEU M 10 " --> pdb=" O TYR M 133 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N SER M 135 " --> pdb=" O LEU M 10 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL M 12 " --> pdb=" O SER M 135 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ARG M 126 " --> pdb=" O ILE M 113 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ILE M 113 " --> pdb=" O ARG M 126 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N MET M 128 " --> pdb=" O VAL M 111 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY M 130 " --> pdb=" O TYR M 109 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N ILE M 134 " --> pdb=" O LEU M 105 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N LEU M 105 " --> pdb=" O ILE M 134 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA M 62 " --> pdb=" O ILE M 50 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'M' and resid 18 through 23 removed outlier: 7.474A pdb=" N VAL M 75 " --> pdb=" O VAL M 69 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL M 69 " --> pdb=" O VAL M 75 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'M' and resid 25 through 28 removed outlier: 3.813A pdb=" N THR M 35 " --> pdb=" O ASP M 28 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'O' and resid 10 through 13 removed outlier: 6.413A pdb=" N LEU O 10 " --> pdb=" O TYR O 133 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N SER O 135 " --> pdb=" O LEU O 10 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL O 12 " --> pdb=" O SER O 135 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL O 111 " --> pdb=" O ILE O 127 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N GLU O 129 " --> pdb=" O TYR O 109 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N TYR O 109 " --> pdb=" O GLU O 129 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N LYS O 131 " --> pdb=" O GLY O 107 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N GLY O 107 " --> pdb=" O LYS O 131 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N TYR O 133 " --> pdb=" O LEU O 105 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU O 105 " --> pdb=" O TYR O 133 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N SER O 135 " --> pdb=" O GLN O 103 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N GLN O 103 " --> pdb=" O SER O 135 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASP O 110 " --> pdb=" O SER O 49 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER O 49 " --> pdb=" O ASP O 110 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'O' and resid 18 through 23 removed outlier: 3.751A pdb=" N TYR O 18 " --> pdb=" O LEU O 80 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'O' and resid 26 through 28 removed outlier: 3.732A pdb=" N LYS O 37 " --> pdb=" O ASP O 26 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP O 28 " --> pdb=" O THR O 35 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 9 through 14 removed outlier: 4.239A pdb=" N ILE E 11 " --> pdb=" O ILE E 28 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 25 through 28 current: chain 'E' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 68 through 75 current: chain 'E' and resid 119 through 122 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 119 through 122 current: chain 'E' and resid 143 through 159 removed outlier: 5.644A pdb=" N ILE E 152 " --> pdb=" O ASN E 172 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASN E 172 " --> pdb=" O ILE E 152 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASN E 158 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N ARG E 166 " --> pdb=" O ASN E 158 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 166 through 173 current: chain 'E' and resid 221 through 222 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 221 through 222 current: chain 'E' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 260 through 268 current: chain 'E' and resid 309 through 319 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 309 through 319 current: chain 'E' and resid 331 through 338 Processing sheet with id=AE8, first strand: chain 'E' and resid 40 through 44 removed outlier: 3.918A pdb=" N SER E 64 " --> pdb=" O ASN E 41 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N THR E 43 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ASN E 62 " --> pdb=" O THR E 43 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 79 through 80 Processing sheet with id=AF1, first strand: chain 'E' and resid 238 through 239 Processing sheet with id=AF2, first strand: chain 'E' and resid 378 through 382 removed outlier: 3.557A pdb=" N ALA E 378 " --> pdb=" O THR E 403 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR E 380 " --> pdb=" O GLU E 401 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU E 401 " --> pdb=" O THR E 380 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 389 through 390 removed outlier: 3.915A pdb=" N LEU E 390 " --> pdb=" O THR E 459 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL E 440 " --> pdb=" O ILE E 458 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 396 through 397 Processing sheet with id=AF5, first strand: chain 'C' and resid 9 through 14 removed outlier: 3.582A pdb=" N VAL C 13 " --> pdb=" O GLN C 26 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN C 26 " --> pdb=" O VAL C 13 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 25 through 27 current: chain 'C' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 68 through 75 current: chain 'C' and resid 119 through 122 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 119 through 122 current: chain 'C' and resid 143 through 160 removed outlier: 5.715A pdb=" N ILE C 152 " --> pdb=" O ASN C 172 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ASN C 172 " --> pdb=" O ILE C 152 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ARG C 166 " --> pdb=" O ASN C 158 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 166 through 173 current: chain 'C' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 260 through 268 current: chain 'C' and resid 307 through 319 Processing sheet with id=AF6, first strand: chain 'C' and resid 40 through 46 removed outlier: 6.772A pdb=" N ASN C 41 " --> pdb=" O ASP C 63 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 79 through 80 Processing sheet with id=AF8, first strand: chain 'C' and resid 237 through 239 removed outlier: 4.150A pdb=" N THR C 238 " --> pdb=" O PHE C 255 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 378 through 382 removed outlier: 3.893A pdb=" N ALA C 378 " --> pdb=" O THR C 403 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR C 380 " --> pdb=" O GLU C 401 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU C 401 " --> pdb=" O THR C 380 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 389 through 390 removed outlier: 3.913A pdb=" N LEU C 390 " --> pdb=" O THR C 459 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS C 456 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL C 442 " --> pdb=" O LYS C 456 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL C 440 " --> pdb=" O ILE C 458 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 395 through 397 Processing sheet with id=AG3, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.337A pdb=" N LEU J 10 " --> pdb=" O TYR J 133 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N SER J 135 " --> pdb=" O LEU J 10 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL J 12 " --> pdb=" O SER J 135 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL J 111 " --> pdb=" O ILE J 127 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLU J 129 " --> pdb=" O TYR J 109 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N TYR J 109 " --> pdb=" O GLU J 129 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N LYS J 131 " --> pdb=" O GLY J 107 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLY J 107 " --> pdb=" O LYS J 131 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N TYR J 133 " --> pdb=" O LEU J 105 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LEU J 105 " --> pdb=" O TYR J 133 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N SER J 135 " --> pdb=" O GLN J 103 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLN J 103 " --> pdb=" O SER J 135 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP J 110 " --> pdb=" O SER J 49 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE J 50 " --> pdb=" O VAL J 61 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'J' and resid 18 through 23 removed outlier: 3.784A pdb=" N LEU J 80 " --> pdb=" O TYR J 18 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL J 75 " --> pdb=" O ASP J 70 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N SER J 77 " --> pdb=" O ILE J 68 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ILE J 68 " --> pdb=" O SER J 77 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'J' and resid 25 through 27 Processing sheet with id=AG6, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.503A pdb=" N LEU L 10 " --> pdb=" O TYR L 133 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N SER L 135 " --> pdb=" O LEU L 10 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL L 12 " --> pdb=" O SER L 135 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N SER L 124 " --> pdb=" O ARG L 115 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N ARG L 115 " --> pdb=" O SER L 124 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ARG L 126 " --> pdb=" O ILE L 113 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE L 113 " --> pdb=" O ARG L 126 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N MET L 128 " --> pdb=" O VAL L 111 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL L 111 " --> pdb=" O MET L 128 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE L 134 " --> pdb=" O LEU L 105 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N LEU L 105 " --> pdb=" O ILE L 134 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER L 49 " --> pdb=" O ASP L 110 " (cutoff:3.500A) removed outlier: 10.080A pdb=" N PHE L 44 " --> pdb=" O ILE L 68 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE L 68 " --> pdb=" O PHE L 44 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU L 46 " --> pdb=" O THR L 66 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N THR L 66 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLY L 48 " --> pdb=" O PHE L 64 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA L 62 " --> pdb=" O ILE L 50 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N THR L 66 " --> pdb=" O SER L 79 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N SER L 79 " --> pdb=" O THR L 66 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ILE L 68 " --> pdb=" O SER L 77 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N SER L 77 " --> pdb=" O ILE L 68 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'L' and resid 25 through 26 Processing sheet with id=AG8, first strand: chain 'W' and resid 79 through 81 removed outlier: 5.237A pdb=" N TRP W 48 " --> pdb=" O GLU W 202 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN W 25 " --> pdb=" O TYR W 47 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N SER W 19 " --> pdb=" O SER W 53 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL W 20 " --> pdb=" O LEU V 187 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N THR V 186 " --> pdb=" O SER V 194 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER V 194 " --> pdb=" O THR V 186 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'W' and resid 29 through 32 Processing sheet with id=AH1, first strand: chain 'W' and resid 92 through 93 Processing sheet with id=AH2, first strand: chain 'W' and resid 108 through 112 removed outlier: 7.156A pdb=" N VAL W 147 " --> pdb=" O SER W 143 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N SER W 143 " --> pdb=" O VAL W 147 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASN W 149 " --> pdb=" O PHE W 141 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N PHE W 141 " --> pdb=" O ASN W 149 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N SER W 151 " --> pdb=" O THR W 139 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'U' and resid 10 through 13 removed outlier: 6.528A pdb=" N LEU U 10 " --> pdb=" O TYR U 133 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N SER U 135 " --> pdb=" O LEU U 10 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL U 12 " --> pdb=" O SER U 135 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ARG U 126 " --> pdb=" O ILE U 113 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ILE U 113 " --> pdb=" O ARG U 126 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N MET U 128 " --> pdb=" O VAL U 111 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY U 130 " --> pdb=" O TYR U 109 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N ILE U 134 " --> pdb=" O LEU U 105 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N LEU U 105 " --> pdb=" O ILE U 134 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA U 62 " --> pdb=" O ILE U 50 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'U' and resid 18 through 23 removed outlier: 7.474A pdb=" N VAL U 75 " --> pdb=" O VAL U 69 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL U 69 " --> pdb=" O VAL U 75 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'U' and resid 25 through 28 removed outlier: 3.814A pdb=" N THR U 35 " --> pdb=" O ASP U 28 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.415A pdb=" N LEU K 10 " --> pdb=" O TYR K 133 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N SER K 135 " --> pdb=" O LEU K 10 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL K 12 " --> pdb=" O SER K 135 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL K 111 " --> pdb=" O ILE K 127 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N GLU K 129 " --> pdb=" O TYR K 109 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N TYR K 109 " --> pdb=" O GLU K 129 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N LYS K 131 " --> pdb=" O GLY K 107 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLY K 107 " --> pdb=" O LYS K 131 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N TYR K 133 " --> pdb=" O LEU K 105 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LEU K 105 " --> pdb=" O TYR K 133 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N SER K 135 " --> pdb=" O GLN K 103 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N GLN K 103 " --> pdb=" O SER K 135 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASP K 110 " --> pdb=" O SER K 49 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N SER K 49 " --> pdb=" O ASP K 110 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'K' and resid 18 through 23 removed outlier: 3.751A pdb=" N TYR K 18 " --> pdb=" O LEU K 80 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'K' and resid 26 through 28 removed outlier: 3.731A pdb=" N LYS K 37 " --> pdb=" O ASP K 26 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP K 28 " --> pdb=" O THR K 35 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'D' and resid 9 through 14 removed outlier: 4.239A pdb=" N ILE D 11 " --> pdb=" O ILE D 28 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 25 through 28 current: chain 'D' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 68 through 75 current: chain 'D' and resid 119 through 122 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 119 through 122 current: chain 'D' and resid 143 through 159 removed outlier: 5.642A pdb=" N ILE D 152 " --> pdb=" O ASN D 172 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ASN D 172 " --> pdb=" O ILE D 152 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASN D 158 " --> pdb=" O ARG D 166 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ARG D 166 " --> pdb=" O ASN D 158 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 166 through 173 current: chain 'D' and resid 221 through 222 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 221 through 222 current: chain 'D' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 260 through 268 current: chain 'D' and resid 309 through 319 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 309 through 319 current: chain 'D' and resid 331 through 338 Processing sheet with id=AI1, first strand: chain 'D' and resid 40 through 44 removed outlier: 3.918A pdb=" N SER D 64 " --> pdb=" O ASN D 41 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N THR D 43 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N ASN D 62 " --> pdb=" O THR D 43 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'D' and resid 79 through 80 Processing sheet with id=AI3, first strand: chain 'D' and resid 238 through 239 Processing sheet with id=AI4, first strand: chain 'D' and resid 378 through 382 removed outlier: 3.557A pdb=" N ALA D 378 " --> pdb=" O THR D 403 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR D 380 " --> pdb=" O GLU D 401 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU D 401 " --> pdb=" O THR D 380 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'D' and resid 389 through 390 removed outlier: 3.916A pdb=" N LEU D 390 " --> pdb=" O THR D 459 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL D 440 " --> pdb=" O ILE D 458 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'D' and resid 396 through 397 Processing sheet with id=AI7, first strand: chain 'A' and resid 9 through 14 removed outlier: 3.582A pdb=" N VAL A 13 " --> pdb=" O GLN A 26 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN A 26 " --> pdb=" O VAL A 13 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 25 through 27 current: chain 'A' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 68 through 75 current: chain 'A' and resid 119 through 122 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 119 through 122 current: chain 'A' and resid 143 through 160 removed outlier: 5.714A pdb=" N ILE A 152 " --> pdb=" O ASN A 172 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ASN A 172 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ARG A 166 " --> pdb=" O ASN A 158 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 166 through 173 current: chain 'A' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 260 through 268 current: chain 'A' and resid 307 through 319 Processing sheet with id=AI8, first strand: chain 'A' and resid 40 through 46 removed outlier: 6.773A pdb=" N ASN A 41 " --> pdb=" O ASP A 63 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'A' and resid 79 through 80 Processing sheet with id=AJ1, first strand: chain 'A' and resid 237 through 239 removed outlier: 4.149A pdb=" N THR A 238 " --> pdb=" O PHE A 255 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'A' and resid 378 through 382 removed outlier: 3.892A pdb=" N ALA A 378 " --> pdb=" O THR A 403 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR A 380 " --> pdb=" O GLU A 401 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU A 401 " --> pdb=" O THR A 380 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'A' and resid 389 through 390 removed outlier: 3.912A pdb=" N LEU A 390 " --> pdb=" O THR A 459 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS A 456 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL A 442 " --> pdb=" O LYS A 456 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL A 440 " --> pdb=" O ILE A 458 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'A' and resid 395 through 397 Processing sheet with id=AJ5, first strand: chain 'B' and resid 9 through 14 removed outlier: 3.583A pdb=" N VAL B 13 " --> pdb=" O GLN B 26 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN B 26 " --> pdb=" O VAL B 13 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 25 through 27 current: chain 'B' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 68 through 75 current: chain 'B' and resid 119 through 122 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 119 through 122 current: chain 'B' and resid 143 through 160 removed outlier: 5.716A pdb=" N ILE B 152 " --> pdb=" O ASN B 172 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ASN B 172 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ARG B 166 " --> pdb=" O ASN B 158 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 166 through 173 current: chain 'B' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 260 through 268 current: chain 'B' and resid 307 through 319 Processing sheet with id=AJ6, first strand: chain 'B' and resid 40 through 46 removed outlier: 6.773A pdb=" N ASN B 41 " --> pdb=" O ASP B 63 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'B' and resid 79 through 80 Processing sheet with id=AJ8, first strand: chain 'B' and resid 237 through 239 removed outlier: 4.149A pdb=" N THR B 238 " --> pdb=" O PHE B 255 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'B' and resid 378 through 382 removed outlier: 3.893A pdb=" N ALA B 378 " --> pdb=" O THR B 403 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR B 380 " --> pdb=" O GLU B 401 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU B 401 " --> pdb=" O THR B 380 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'B' and resid 389 through 390 removed outlier: 3.914A pdb=" N LEU B 390 " --> pdb=" O THR B 459 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS B 456 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL B 442 " --> pdb=" O LYS B 456 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL B 440 " --> pdb=" O ILE B 458 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'B' and resid 395 through 397 Processing sheet with id=AK3, first strand: chain 'P' and resid 10 through 13 removed outlier: 6.544A pdb=" N SER P 124 " --> pdb=" O ARG P 115 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N ARG P 115 " --> pdb=" O SER P 124 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N ARG P 126 " --> pdb=" O ILE P 113 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE P 113 " --> pdb=" O ARG P 126 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N MET P 128 " --> pdb=" O VAL P 111 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL P 111 " --> pdb=" O MET P 128 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE P 134 " --> pdb=" O LEU P 105 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N LEU P 105 " --> pdb=" O ILE P 134 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER P 49 " --> pdb=" O ASP P 110 " (cutoff:3.500A) removed outlier: 10.081A pdb=" N PHE P 44 " --> pdb=" O ILE P 68 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE P 68 " --> pdb=" O PHE P 44 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU P 46 " --> pdb=" O THR P 66 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N THR P 66 " --> pdb=" O LEU P 46 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N GLY P 48 " --> pdb=" O PHE P 64 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA P 62 " --> pdb=" O ILE P 50 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N THR P 66 " --> pdb=" O SER P 79 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N SER P 79 " --> pdb=" O THR P 66 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ILE P 68 " --> pdb=" O SER P 77 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N SER P 77 " --> pdb=" O ILE P 68 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'P' and resid 25 through 26 Processing sheet with id=AK5, first strand: chain 'T' and resid 10 through 13 removed outlier: 6.505A pdb=" N LEU T 10 " --> pdb=" O TYR T 133 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N SER T 135 " --> pdb=" O LEU T 10 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL T 12 " --> pdb=" O SER T 135 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N SER T 124 " --> pdb=" O ARG T 115 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N ARG T 115 " --> pdb=" O SER T 124 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ARG T 126 " --> pdb=" O ILE T 113 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE T 113 " --> pdb=" O ARG T 126 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N MET T 128 " --> pdb=" O VAL T 111 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL T 111 " --> pdb=" O MET T 128 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE T 134 " --> pdb=" O LEU T 105 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N LEU T 105 " --> pdb=" O ILE T 134 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER T 49 " --> pdb=" O ASP T 110 " (cutoff:3.500A) removed outlier: 10.079A pdb=" N PHE T 44 " --> pdb=" O ILE T 68 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE T 68 " --> pdb=" O PHE T 44 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU T 46 " --> pdb=" O THR T 66 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N THR T 66 " --> pdb=" O LEU T 46 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLY T 48 " --> pdb=" O PHE T 64 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA T 62 " --> pdb=" O ILE T 50 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N THR T 66 " --> pdb=" O SER T 79 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N SER T 79 " --> pdb=" O THR T 66 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ILE T 68 " --> pdb=" O SER T 77 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N SER T 77 " --> pdb=" O ILE T 68 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'T' and resid 25 through 26 Processing sheet with id=AK7, first strand: chain 'V' and resid 29 through 32 Processing sheet with id=AK8, first strand: chain 'V' and resid 108 through 112 removed outlier: 6.966A pdb=" N VAL V 147 " --> pdb=" O SER V 143 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N SER V 143 " --> pdb=" O VAL V 147 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ASN V 149 " --> pdb=" O PHE V 141 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N PHE V 141 " --> pdb=" O ASN V 149 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N SER V 151 " --> pdb=" O THR V 139 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS V 128 " --> pdb=" O VAL V 167 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'Z' and resid 29 through 32 Processing sheet with id=AL1, first strand: chain 'Z' and resid 108 through 112 removed outlier: 6.966A pdb=" N VAL Z 147 " --> pdb=" O SER Z 143 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N SER Z 143 " --> pdb=" O VAL Z 147 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ASN Z 149 " --> pdb=" O PHE Z 141 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N PHE Z 141 " --> pdb=" O ASN Z 149 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N SER Z 151 " --> pdb=" O THR Z 139 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS Z 128 " --> pdb=" O VAL Z 167 " (cutoff:3.500A) 971 hydrogen bonds defined for protein. 2583 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: 16.08 Time building geometry restraints manager: 10.68 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: 16757 1.34 - 1.46: 11046 1.46 - 1.58: 23671 1.58 - 1.70: 0 1.70 - 1.81: 285 Bond restraints: 51759 Sorted by residual: bond pdb=" N VAL V 41 " pdb=" CA VAL V 41 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.20e-02 6.94e+03 8.07e+00 bond pdb=" N VAL Z 41 " pdb=" CA VAL Z 41 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.20e-02 6.94e+03 8.06e+00 bond pdb=" N THR L 66 " pdb=" CA THR L 66 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.21e-02 6.83e+03 7.90e+00 bond pdb=" N VAL X 41 " pdb=" CA VAL X 41 " ideal model delta sigma weight residual 1.459 1.492 -0.034 1.20e-02 6.94e+03 7.84e+00 bond pdb=" N VAL V 38 " pdb=" CA VAL V 38 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.24e-02 6.50e+03 7.79e+00 ... (remaining 51754 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 68823 1.53 - 3.06: 1323 3.06 - 4.59: 201 4.59 - 6.13: 12 6.13 - 7.66: 9 Bond angle restraints: 70368 Sorted by residual: angle pdb=" CA PRO L 33 " pdb=" N PRO L 33 " pdb=" CD PRO L 33 " ideal model delta sigma weight residual 112.00 105.06 6.94 1.40e+00 5.10e-01 2.46e+01 angle pdb=" CA PRO T 33 " pdb=" N PRO T 33 " pdb=" CD PRO T 33 " ideal model delta sigma weight residual 112.00 105.07 6.93 1.40e+00 5.10e-01 2.45e+01 angle pdb=" CA PRO P 33 " pdb=" N PRO P 33 " pdb=" CD PRO P 33 " ideal model delta sigma weight residual 112.00 105.07 6.93 1.40e+00 5.10e-01 2.45e+01 angle pdb=" CA GLY C 253 " pdb=" C GLY C 253 " pdb=" O GLY C 253 " ideal model delta sigma weight residual 122.74 118.34 4.40 1.30e+00 5.92e-01 1.15e+01 angle pdb=" CA GLY B 253 " pdb=" C GLY B 253 " pdb=" O GLY B 253 " ideal model delta sigma weight residual 122.74 118.40 4.34 1.30e+00 5.92e-01 1.11e+01 ... (remaining 70363 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 28535 17.80 - 35.61: 2170 35.61 - 53.41: 342 53.41 - 71.22: 45 71.22 - 89.02: 48 Dihedral angle restraints: 31140 sinusoidal: 12045 harmonic: 19095 Sorted by residual: dihedral pdb=" CA TYR F 357 " pdb=" C TYR F 357 " pdb=" N THR F 358 " pdb=" CA THR F 358 " ideal model delta harmonic sigma weight residual 180.00 158.09 21.91 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA TYR E 357 " pdb=" C TYR E 357 " pdb=" N THR E 358 " pdb=" CA THR E 358 " ideal model delta harmonic sigma weight residual 180.00 158.10 21.90 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA TYR D 357 " pdb=" C TYR D 357 " pdb=" N THR D 358 " pdb=" CA THR D 358 " ideal model delta harmonic sigma weight residual 180.00 158.31 21.69 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 31137 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 5690 0.038 - 0.077: 1569 0.077 - 0.115: 790 0.115 - 0.154: 131 0.154 - 0.192: 16 Chirality restraints: 8196 Sorted by residual: chirality pdb=" CA ILE L 78 " pdb=" N ILE L 78 " pdb=" C ILE L 78 " pdb=" CB ILE L 78 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.22e-01 chirality pdb=" CA ILE T 78 " pdb=" N ILE T 78 " pdb=" C ILE T 78 " pdb=" CB ILE T 78 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.99e-01 chirality pdb=" CA ILE P 78 " pdb=" N ILE P 78 " pdb=" C ILE P 78 " pdb=" CB ILE P 78 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.87e-01 ... (remaining 8193 not shown) Planarity restraints: 9093 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR L 32 " 0.076 5.00e-02 4.00e+02 1.11e-01 1.98e+01 pdb=" N PRO L 33 " -0.192 5.00e-02 4.00e+02 pdb=" CA PRO L 33 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO L 33 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR P 32 " -0.076 5.00e-02 4.00e+02 1.11e-01 1.96e+01 pdb=" N PRO P 33 " 0.191 5.00e-02 4.00e+02 pdb=" CA PRO P 33 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO P 33 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR T 32 " -0.076 5.00e-02 4.00e+02 1.11e-01 1.96e+01 pdb=" N PRO T 33 " 0.191 5.00e-02 4.00e+02 pdb=" CA PRO T 33 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO T 33 " -0.060 5.00e-02 4.00e+02 ... (remaining 9090 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 1642 2.70 - 3.25: 50750 3.25 - 3.80: 78580 3.80 - 4.35: 104511 4.35 - 4.90: 177900 Nonbonded interactions: 413383 Sorted by model distance: nonbonded pdb=" OD1 ASP F 163 " pdb=" N ILE F 164 " model vdw 2.156 3.120 nonbonded pdb=" OD1 ASP D 163 " pdb=" N ILE D 164 " model vdw 2.157 3.120 nonbonded pdb=" OD1 ASP E 163 " pdb=" N ILE E 164 " model vdw 2.158 3.120 nonbonded pdb=" O ASN B 172 " pdb=" OH TYR B 239 " model vdw 2.230 3.040 nonbonded pdb=" O ASN A 172 " pdb=" OH TYR A 239 " model vdw 2.231 3.040 ... (remaining 413378 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = (chain 'L' and resid 2 through 140) selection = (chain 'M' and resid 2 through 140) selection = chain 'N' selection = chain 'O' selection = (chain 'P' and resid 2 through 140) selection = (chain 'Q' and resid 2 through 140) selection = chain 'R' selection = chain 'S' selection = (chain 'T' and resid 2 through 140) selection = (chain 'U' and resid 2 through 140) } ncs_group { reference = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 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: 0.040 Extract box with map and model: 1.560 Check model and map are aligned: 0.340 Set scattering table: 0.380 Process input model: 81.500 Find NCS groups from input model: 1.350 Set up NCS constraints: 0.250 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:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 51759 Z= 0.201 Angle : 0.542 7.657 70368 Z= 0.307 Chirality : 0.045 0.192 8196 Planarity : 0.004 0.111 9093 Dihedral : 13.209 89.024 18876 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.73 (0.10), residues: 6522 helix: 0.52 (0.23), residues: 525 sheet: -1.01 (0.10), residues: 2649 loop : -1.49 (0.10), residues: 3348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 70 HIS 0.006 0.001 HIS A 129 PHE 0.014 0.001 PHE H 92 TYR 0.023 0.001 TYR B 239 ARG 0.009 0.001 ARG F 102 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13044 Ramachandran restraints generated. 6522 Oldfield, 0 Emsley, 6522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13044 Ramachandran restraints generated. 6522 Oldfield, 0 Emsley, 6522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 939 residues out of total 5691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 939 time to evaluate : 4.369 Fit side-chains revert: symmetry clash REVERT: R 22 MET cc_start: 0.7271 (mtp) cc_final: 0.6607 (mtp) REVERT: R 100 ASN cc_start: 0.7485 (t0) cc_final: 0.6977 (t0) REVERT: I 38 LYS cc_start: 0.9080 (ttpt) cc_final: 0.8864 (tttt) REVERT: I 87 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7715 (mt-10) REVERT: I 233 VAL cc_start: 0.9185 (t) cc_final: 0.8974 (t) REVERT: a 40 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7460 (mt-10) REVERT: Q 94 LYS cc_start: 0.8962 (mmmt) cc_final: 0.8562 (mmmm) REVERT: Q 109 TYR cc_start: 0.8725 (p90) cc_final: 0.8507 (p90) REVERT: Q 128 MET cc_start: 0.8405 (mtp) cc_final: 0.7920 (mtp) REVERT: S 40 ASP cc_start: 0.7943 (t70) cc_final: 0.7073 (m-30) REVERT: S 94 LYS cc_start: 0.8282 (mmpt) cc_final: 0.7553 (mmtp) REVERT: S 103 GLN cc_start: 0.8655 (mt0) cc_final: 0.8111 (mt0) REVERT: S 104 ARG cc_start: 0.8586 (mtm180) cc_final: 0.8315 (mtm110) REVERT: F 49 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7383 (mt-10) REVERT: F 83 ASN cc_start: 0.6922 (m-40) cc_final: 0.6653 (m-40) REVERT: F 362 ILE cc_start: 0.8993 (pt) cc_final: 0.8496 (mt) REVERT: H 55 ILE cc_start: 0.8868 (mm) cc_final: 0.8663 (mm) REVERT: H 176 SER cc_start: 0.8997 (p) cc_final: 0.8595 (p) REVERT: X 31 ASP cc_start: 0.7455 (t70) cc_final: 0.7072 (t0) REVERT: O 104 ARG cc_start: 0.8691 (mtm180) cc_final: 0.8457 (mtm110) REVERT: C 5 LEU cc_start: 0.4250 (mm) cc_final: 0.3568 (tp) REVERT: C 53 ARG cc_start: 0.6244 (mmt-90) cc_final: 0.5147 (mtp85) REVERT: C 160 ASP cc_start: 0.5318 (t0) cc_final: 0.4605 (t0) REVERT: C 161 ILE cc_start: 0.6449 (pt) cc_final: 0.5950 (pt) REVERT: C 255 PHE cc_start: 0.7338 (m-80) cc_final: 0.6542 (p90) REVERT: J 13 ASP cc_start: 0.7909 (m-30) cc_final: 0.7698 (m-30) REVERT: L 128 MET cc_start: 0.8268 (mtm) cc_final: 0.7977 (mtp) REVERT: G 1 MET cc_start: 0.7018 (pmm) cc_final: 0.6530 (mtt) REVERT: G 80 ASP cc_start: 0.7841 (t0) cc_final: 0.7604 (t0) REVERT: G 168 SER cc_start: 0.9019 (t) cc_final: 0.8812 (t) REVERT: G 267 ARG cc_start: 0.7923 (ttm110) cc_final: 0.7718 (ttm110) REVERT: W 46 GLN cc_start: 0.8738 (tm-30) cc_final: 0.7969 (tm-30) REVERT: W 68 ARG cc_start: 0.7599 (mmt90) cc_final: 0.7335 (mmm160) REVERT: W 122 LYS cc_start: 0.9061 (ttmt) cc_final: 0.8765 (ttpt) REVERT: U 94 LYS cc_start: 0.8799 (mmmt) cc_final: 0.8445 (mmmm) REVERT: U 97 ASP cc_start: 0.7910 (t70) cc_final: 0.7556 (t0) REVERT: U 98 ARG cc_start: 0.7834 (mtm110) cc_final: 0.7208 (ptp90) REVERT: U 136 ASP cc_start: 0.7917 (m-30) cc_final: 0.7685 (m-30) REVERT: K 22 MET cc_start: 0.7902 (mtm) cc_final: 0.7609 (mtm) REVERT: K 40 ASP cc_start: 0.7733 (t70) cc_final: 0.7491 (t0) REVERT: K 94 LYS cc_start: 0.7946 (mmpt) cc_final: 0.7459 (mmtp) REVERT: K 100 ASN cc_start: 0.8469 (t0) cc_final: 0.8097 (t0) REVERT: K 103 GLN cc_start: 0.8867 (mt0) cc_final: 0.8620 (mt0) REVERT: D 49 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7662 (mt-10) REVERT: D 288 LYS cc_start: 0.8885 (mtmm) cc_final: 0.8495 (mtpp) REVERT: D 305 ASP cc_start: 0.7735 (p0) cc_final: 0.7432 (p0) REVERT: D 408 ARG cc_start: 0.7483 (ttp80) cc_final: 0.7099 (mtp-110) REVERT: D 447 LYS cc_start: 0.7788 (mttt) cc_final: 0.7555 (mttm) REVERT: A 95 TRP cc_start: 0.7836 (m100) cc_final: 0.7255 (m-90) REVERT: A 156 GLU cc_start: 0.7427 (tm-30) cc_final: 0.6831 (tm-30) REVERT: A 161 ILE cc_start: 0.5501 (pt) cc_final: 0.5202 (pt) REVERT: A 170 SER cc_start: 0.8151 (m) cc_final: 0.7942 (p) REVERT: A 255 PHE cc_start: 0.7550 (m-80) cc_final: 0.6687 (p90) REVERT: A 298 VAL cc_start: 0.7731 (t) cc_final: 0.7498 (p) REVERT: B 1 MET cc_start: 0.4061 (mmp) cc_final: 0.3396 (ptm) REVERT: B 142 LYS cc_start: 0.5137 (tmtt) cc_final: 0.4916 (tppt) REVERT: B 161 ILE cc_start: 0.6797 (pt) cc_final: 0.6261 (pt) REVERT: B 255 PHE cc_start: 0.7339 (m-80) cc_final: 0.6496 (p90) REVERT: B 281 LYS cc_start: 0.7032 (pttt) cc_final: 0.6829 (ttpt) REVERT: B 298 VAL cc_start: 0.7858 (t) cc_final: 0.7532 (p) REVERT: B 398 MET cc_start: 0.1501 (mmm) cc_final: 0.0943 (mpp) REVERT: B 431 ARG cc_start: 0.5856 (ttm170) cc_final: 0.5089 (ttp80) REVERT: T 9 ASP cc_start: 0.7661 (m-30) cc_final: 0.7412 (m-30) REVERT: T 26 ASP cc_start: 0.7791 (t0) cc_final: 0.7246 (m-30) REVERT: T 54 LEU cc_start: 0.8429 (mt) cc_final: 0.8149 (mt) REVERT: T 96 ARG cc_start: 0.7876 (mmt90) cc_final: 0.7320 (mmt90) REVERT: T 128 MET cc_start: 0.7877 (mtm) cc_final: 0.7595 (mtp) REVERT: V 87 GLU cc_start: 0.7700 (tp30) cc_final: 0.7469 (tp30) REVERT: Z 26 ASP cc_start: 0.8506 (p0) cc_final: 0.8157 (p0) REVERT: Z 105 LYS cc_start: 0.8493 (ptpp) cc_final: 0.8253 (ptpt) REVERT: Z 122 LYS cc_start: 0.7691 (ptpt) cc_final: 0.7344 (mmtt) REVERT: Z 128 LYS cc_start: 0.9213 (tttt) cc_final: 0.8753 (tttp) REVERT: Z 164 GLU cc_start: 0.7883 (mp0) cc_final: 0.7597 (mp0) REVERT: Z 178 MET cc_start: 0.8490 (mmm) cc_final: 0.8228 (mmp) outliers start: 0 outliers final: 0 residues processed: 939 average time/residue: 0.5044 time to fit residues: 781.4510 Evaluate side-chains 655 residues out of total 5691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 655 time to evaluate : 4.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 645 random chunks: chunk 544 optimal weight: 7.9990 chunk 488 optimal weight: 10.0000 chunk 271 optimal weight: 9.9990 chunk 167 optimal weight: 6.9990 chunk 329 optimal weight: 30.0000 chunk 261 optimal weight: 5.9990 chunk 505 optimal weight: 5.9990 chunk 195 optimal weight: 8.9990 chunk 307 optimal weight: 10.0000 chunk 376 optimal weight: 5.9990 chunk 585 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 113 ASN I 210 ASN S 103 GLN F 31 GLN F 151 GLN H 161 GLN Y 108 GLN O 103 GLN E 31 GLN L 15 ASN ** L 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 292 ASN U 100 ASN ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 GLN D 151 GLN ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 GLN T 103 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.075 51759 Z= 0.665 Angle : 0.764 9.977 70368 Z= 0.403 Chirality : 0.053 0.195 8196 Planarity : 0.006 0.067 9093 Dihedral : 5.319 55.348 7119 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.55 % Allowed : 10.58 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.98 (0.10), residues: 6522 helix: 0.08 (0.22), residues: 534 sheet: -1.24 (0.10), residues: 2691 loop : -1.55 (0.10), residues: 3297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 144 HIS 0.012 0.003 HIS H 21 PHE 0.037 0.003 PHE A 231 TYR 0.031 0.003 TYR Y 136 ARG 0.009 0.001 ARG V 201 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13044 Ramachandran restraints generated. 6522 Oldfield, 0 Emsley, 6522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13044 Ramachandran restraints generated. 6522 Oldfield, 0 Emsley, 6522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 731 residues out of total 5691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 643 time to evaluate : 4.453 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 22 MET cc_start: 0.6838 (mtp) cc_final: 0.6210 (mtp) REVERT: R 100 ASN cc_start: 0.7647 (t0) cc_final: 0.7194 (t0) REVERT: a 40 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7243 (mt-10) REVERT: Q 94 LYS cc_start: 0.8940 (mmmt) cc_final: 0.8495 (mmmm) REVERT: Q 128 MET cc_start: 0.8374 (mtp) cc_final: 0.8110 (mtp) REVERT: S 94 LYS cc_start: 0.8323 (mmpt) cc_final: 0.7606 (mmtp) REVERT: S 103 GLN cc_start: 0.8755 (mt0) cc_final: 0.8378 (mt0) REVERT: S 104 ARG cc_start: 0.8587 (mtm180) cc_final: 0.8116 (mtm110) REVERT: F 49 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7898 (mt-10) REVERT: F 362 ILE cc_start: 0.9149 (pt) cc_final: 0.8502 (mt) REVERT: H 55 ILE cc_start: 0.8939 (mm) cc_final: 0.8733 (mm) REVERT: X 31 ASP cc_start: 0.7678 (t70) cc_final: 0.7337 (t0) REVERT: X 40 GLU cc_start: 0.7539 (pt0) cc_final: 0.7257 (pt0) REVERT: O 104 ARG cc_start: 0.8748 (mtm180) cc_final: 0.8372 (mtm110) REVERT: C 53 ARG cc_start: 0.6532 (mmt-90) cc_final: 0.5465 (mtp85) REVERT: C 152 ILE cc_start: 0.8011 (mm) cc_final: 0.7749 (mm) REVERT: C 162 GLU cc_start: 0.7162 (tm-30) cc_final: 0.6899 (tm-30) REVERT: C 216 MET cc_start: 0.7397 (OUTLIER) cc_final: 0.7155 (ptp) REVERT: L 22 MET cc_start: 0.7925 (mtt) cc_final: 0.7584 (mtp) REVERT: L 128 MET cc_start: 0.8481 (mtm) cc_final: 0.8154 (mtp) REVERT: G 1 MET cc_start: 0.7484 (pmm) cc_final: 0.6997 (mtt) REVERT: G 80 ASP cc_start: 0.7862 (t0) cc_final: 0.7567 (t0) REVERT: G 267 ARG cc_start: 0.8169 (ttm110) cc_final: 0.7646 (ttp-110) REVERT: W 37 LYS cc_start: 0.8841 (ttmm) cc_final: 0.8380 (ttpp) REVERT: W 46 GLN cc_start: 0.9028 (tm-30) cc_final: 0.8783 (tm-30) REVERT: W 122 LYS cc_start: 0.9014 (ttmt) cc_final: 0.8618 (ttmm) REVERT: U 94 LYS cc_start: 0.8844 (mmmt) cc_final: 0.8451 (mmmm) REVERT: U 97 ASP cc_start: 0.8174 (t70) cc_final: 0.7816 (t0) REVERT: K 22 MET cc_start: 0.8109 (mtm) cc_final: 0.7842 (mtm) REVERT: K 94 LYS cc_start: 0.8044 (mmpt) cc_final: 0.7556 (mmtp) REVERT: K 100 ASN cc_start: 0.8548 (t0) cc_final: 0.8207 (t0) REVERT: K 103 GLN cc_start: 0.8857 (mt0) cc_final: 0.8580 (mt0) REVERT: D 408 ARG cc_start: 0.7291 (ttp80) cc_final: 0.7063 (mtp-110) REVERT: D 447 LYS cc_start: 0.7910 (mttt) cc_final: 0.7701 (mttm) REVERT: A 1 MET cc_start: 0.4342 (mtt) cc_final: 0.3386 (mmt) REVERT: A 82 LYS cc_start: 0.6848 (ptmt) cc_final: 0.6470 (mppt) REVERT: A 156 GLU cc_start: 0.6867 (tm-30) cc_final: 0.6183 (tm-30) REVERT: B 142 LYS cc_start: 0.5193 (tmtt) cc_final: 0.4980 (tppt) REVERT: P 100 ASN cc_start: 0.8280 (t0) cc_final: 0.7976 (t0) REVERT: T 128 MET cc_start: 0.8106 (mtm) cc_final: 0.7833 (mtp) REVERT: V 87 GLU cc_start: 0.7904 (tp30) cc_final: 0.7635 (tp30) REVERT: V 107 SER cc_start: 0.8607 (p) cc_final: 0.8376 (t) REVERT: Z 18 GLU cc_start: 0.7635 (tt0) cc_final: 0.7318 (tt0) REVERT: Z 31 ASP cc_start: 0.7429 (t70) cc_final: 0.7183 (t70) REVERT: Z 61 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8341 (mt-10) REVERT: Z 164 GLU cc_start: 0.7621 (mp0) cc_final: 0.7371 (mp0) outliers start: 88 outliers final: 82 residues processed: 697 average time/residue: 0.5226 time to fit residues: 598.2207 Evaluate side-chains 670 residues out of total 5691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 587 time to evaluate : 4.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 8 ILE Chi-restraints excluded: chain I residue 6 MET Chi-restraints excluded: chain I residue 35 GLN Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain I residue 172 VAL Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain a residue 38 VAL Chi-restraints excluded: chain a residue 91 VAL Chi-restraints excluded: chain Q residue 37 LYS Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain Q residue 43 ASP Chi-restraints excluded: chain Q residue 68 ILE Chi-restraints excluded: chain S residue 8 ILE Chi-restraints excluded: chain S residue 27 VAL Chi-restraints excluded: chain S residue 78 ILE Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 357 TYR Chi-restraints excluded: chain N residue 13 ASP Chi-restraints excluded: chain N residue 112 ILE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 207 ILE Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain Y residue 18 GLU Chi-restraints excluded: chain Y residue 38 VAL Chi-restraints excluded: chain Y residue 204 LEU Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 43 ASP Chi-restraints excluded: chain M residue 60 THR Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 78 ILE Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 357 TYR Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain J residue 134 ILE Chi-restraints excluded: chain L residue 97 ASP Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain W residue 204 LEU Chi-restraints excluded: chain U residue 7 VAL Chi-restraints excluded: chain U residue 39 VAL Chi-restraints excluded: chain U residue 43 ASP Chi-restraints excluded: chain U residue 60 THR Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 68 ILE Chi-restraints excluded: chain K residue 8 ILE Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 357 TYR Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain P residue 128 MET Chi-restraints excluded: chain T residue 82 VAL Chi-restraints excluded: chain T residue 97 ASP Chi-restraints excluded: chain V residue 167 VAL Chi-restraints excluded: chain Z residue 60 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 645 random chunks: chunk 325 optimal weight: 10.0000 chunk 181 optimal weight: 1.9990 chunk 487 optimal weight: 4.9990 chunk 398 optimal weight: 0.9980 chunk 161 optimal weight: 4.9990 chunk 586 optimal weight: 3.9990 chunk 633 optimal weight: 0.6980 chunk 522 optimal weight: 20.0000 chunk 581 optimal weight: 6.9990 chunk 200 optimal weight: 4.9990 chunk 470 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 103 GLN E 151 GLN K 103 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 51759 Z= 0.240 Angle : 0.553 8.879 70368 Z= 0.293 Chirality : 0.046 0.180 8196 Planarity : 0.004 0.053 9093 Dihedral : 4.841 57.192 7119 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.62 % Allowed : 13.27 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.80 (0.10), residues: 6522 helix: 0.50 (0.22), residues: 537 sheet: -1.10 (0.10), residues: 2697 loop : -1.51 (0.10), residues: 3288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 36 HIS 0.005 0.001 HIS A 20 PHE 0.027 0.002 PHE A 231 TYR 0.021 0.001 TYR B 239 ARG 0.007 0.001 ARG D 102 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13044 Ramachandran restraints generated. 6522 Oldfield, 0 Emsley, 6522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13044 Ramachandran restraints generated. 6522 Oldfield, 0 Emsley, 6522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 781 residues out of total 5691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 689 time to evaluate : 4.432 Fit side-chains revert: symmetry clash REVERT: R 22 MET cc_start: 0.6774 (mtp) cc_final: 0.6130 (mtp) REVERT: R 100 ASN cc_start: 0.7730 (t0) cc_final: 0.7330 (t0) REVERT: a 40 GLU cc_start: 0.7521 (mt-10) cc_final: 0.7161 (mt-10) REVERT: Q 109 TYR cc_start: 0.8858 (p90) cc_final: 0.8566 (p90) REVERT: S 40 ASP cc_start: 0.7781 (t70) cc_final: 0.6819 (m-30) REVERT: S 94 LYS cc_start: 0.8377 (mmpt) cc_final: 0.7694 (mmtp) REVERT: S 103 GLN cc_start: 0.8673 (mt0) cc_final: 0.8215 (mt0) REVERT: S 104 ARG cc_start: 0.8620 (mtm180) cc_final: 0.8171 (mtm110) REVERT: F 49 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7431 (mt-10) REVERT: F 362 ILE cc_start: 0.9093 (pt) cc_final: 0.8529 (mt) REVERT: N 128 MET cc_start: 0.8523 (mtp) cc_final: 0.8002 (mtp) REVERT: N 134 ILE cc_start: 0.8959 (tp) cc_final: 0.8662 (tt) REVERT: X 31 ASP cc_start: 0.7542 (t70) cc_final: 0.7260 (t0) REVERT: X 40 GLU cc_start: 0.7552 (pt0) cc_final: 0.7321 (pt0) REVERT: Y 1 MET cc_start: 0.7061 (OUTLIER) cc_final: 0.6240 (ttt) REVERT: C 53 ARG cc_start: 0.6685 (mmt-90) cc_final: 0.5708 (mtp85) REVERT: C 162 GLU cc_start: 0.7071 (tm-30) cc_final: 0.6783 (tm-30) REVERT: C 216 MET cc_start: 0.7317 (mpp) cc_final: 0.7072 (ptp) REVERT: C 431 ARG cc_start: 0.5860 (mmt180) cc_final: 0.4501 (ttp80) REVERT: L 22 MET cc_start: 0.7911 (mtt) cc_final: 0.7591 (mtp) REVERT: G 168 SER cc_start: 0.9085 (t) cc_final: 0.8880 (t) REVERT: G 267 ARG cc_start: 0.8109 (ttm110) cc_final: 0.7869 (ttm110) REVERT: W 46 GLN cc_start: 0.8942 (tm-30) cc_final: 0.8736 (tm-30) REVERT: W 78 TYR cc_start: 0.7821 (m-80) cc_final: 0.7566 (m-10) REVERT: W 122 LYS cc_start: 0.9061 (ttmt) cc_final: 0.8713 (ttmm) REVERT: U 14 GLU cc_start: 0.7171 (tt0) cc_final: 0.6925 (tt0) REVERT: U 25 MET cc_start: 0.8390 (ptm) cc_final: 0.8172 (ptm) REVERT: U 94 LYS cc_start: 0.8821 (mmmt) cc_final: 0.8466 (mmmm) REVERT: U 97 ASP cc_start: 0.8039 (t70) cc_final: 0.7654 (t0) REVERT: U 98 ARG cc_start: 0.7969 (mtm110) cc_final: 0.7407 (ptp90) REVERT: U 136 ASP cc_start: 0.7614 (m-30) cc_final: 0.7170 (m-30) REVERT: K 94 LYS cc_start: 0.8053 (mmpt) cc_final: 0.7724 (mmmt) REVERT: D 7 ARG cc_start: 0.8020 (mtp85) cc_final: 0.7771 (ttm-80) REVERT: D 102 ARG cc_start: 0.8425 (mtp85) cc_final: 0.8176 (mtp85) REVERT: D 408 ARG cc_start: 0.7263 (ttp80) cc_final: 0.7017 (mtp-110) REVERT: D 447 LYS cc_start: 0.7874 (mttt) cc_final: 0.7667 (mttm) REVERT: A 36 TRP cc_start: 0.7760 (p90) cc_final: 0.7297 (p90) REVERT: A 82 LYS cc_start: 0.6876 (ptmt) cc_final: 0.6571 (mppt) REVERT: A 95 TRP cc_start: 0.7584 (m100) cc_final: 0.7328 (m-90) REVERT: A 156 GLU cc_start: 0.6709 (tm-30) cc_final: 0.6455 (tm-30) REVERT: A 216 MET cc_start: 0.7644 (mpp) cc_final: 0.6925 (mpp) REVERT: B 142 LYS cc_start: 0.5156 (tmtt) cc_final: 0.4924 (tppt) REVERT: B 150 CYS cc_start: 0.7326 (m) cc_final: 0.7052 (m) REVERT: B 170 SER cc_start: 0.7875 (t) cc_final: 0.7184 (p) REVERT: B 216 MET cc_start: 0.7570 (mpp) cc_final: 0.7260 (ptp) REVERT: P 100 ASN cc_start: 0.8086 (t0) cc_final: 0.7804 (t0) REVERT: T 54 LEU cc_start: 0.8586 (mt) cc_final: 0.8171 (mt) REVERT: T 100 ASN cc_start: 0.8359 (t0) cc_final: 0.7804 (p0) REVERT: T 128 MET cc_start: 0.7809 (mtm) cc_final: 0.7590 (mtp) REVERT: V 26 ASP cc_start: 0.8571 (p0) cc_final: 0.8232 (p0) REVERT: V 87 GLU cc_start: 0.7870 (tp30) cc_final: 0.7542 (tp30) REVERT: V 107 SER cc_start: 0.8590 (p) cc_final: 0.8358 (t) REVERT: Z 61 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8278 (mt-10) REVERT: Z 122 LYS cc_start: 0.7988 (ptpt) cc_final: 0.7623 (mmtt) REVERT: Z 164 GLU cc_start: 0.7661 (mp0) cc_final: 0.7409 (mp0) outliers start: 92 outliers final: 64 residues processed: 746 average time/residue: 0.5143 time to fit residues: 631.0444 Evaluate side-chains 687 residues out of total 5691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 622 time to evaluate : 4.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 6 MET Chi-restraints excluded: chain a residue 91 VAL Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 43 ASP Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 120 MET Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 357 TYR Chi-restraints excluded: chain N residue 13 ASP Chi-restraints excluded: chain N residue 66 THR Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain Y residue 18 GLU Chi-restraints excluded: chain Y residue 204 LEU Chi-restraints excluded: chain M residue 3 THR Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 43 ASP Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 60 THR Chi-restraints excluded: chain M residue 75 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 342 ASP Chi-restraints excluded: chain E residue 357 TYR Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain J residue 134 ILE Chi-restraints excluded: chain L residue 97 ASP Chi-restraints excluded: chain L residue 134 ILE Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain W residue 38 VAL Chi-restraints excluded: chain W residue 91 VAL Chi-restraints excluded: chain W residue 204 LEU Chi-restraints excluded: chain U residue 7 VAL Chi-restraints excluded: chain U residue 22 MET Chi-restraints excluded: chain U residue 43 ASP Chi-restraints excluded: chain U residue 60 THR Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain T residue 22 MET Chi-restraints excluded: chain T residue 59 GLU Chi-restraints excluded: chain T residue 82 VAL Chi-restraints excluded: chain T residue 97 ASP Chi-restraints excluded: chain V residue 167 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 645 random chunks: chunk 579 optimal weight: 5.9990 chunk 441 optimal weight: 0.7980 chunk 304 optimal weight: 20.0000 chunk 64 optimal weight: 7.9990 chunk 280 optimal weight: 1.9990 chunk 394 optimal weight: 0.0020 chunk 588 optimal weight: 1.9990 chunk 623 optimal weight: 0.9990 chunk 307 optimal weight: 7.9990 chunk 558 optimal weight: 10.0000 chunk 168 optimal weight: 1.9990 overall best weight: 1.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 113 ASN I 161 GLN I 216 ASN H 161 GLN Y 51 ASN O 103 GLN B 151 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 51759 Z= 0.174 Angle : 0.502 8.437 70368 Z= 0.266 Chirality : 0.045 0.210 8196 Planarity : 0.004 0.046 9093 Dihedral : 4.480 59.819 7119 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.16 % Allowed : 14.25 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.62 (0.10), residues: 6522 helix: 0.78 (0.22), residues: 546 sheet: -0.97 (0.10), residues: 2658 loop : -1.44 (0.10), residues: 3318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 144 HIS 0.005 0.001 HIS E 113 PHE 0.026 0.001 PHE K 64 TYR 0.019 0.001 TYR B 239 ARG 0.006 0.000 ARG D 102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13044 Ramachandran restraints generated. 6522 Oldfield, 0 Emsley, 6522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13044 Ramachandran restraints generated. 6522 Oldfield, 0 Emsley, 6522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 837 residues out of total 5691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 714 time to evaluate : 4.326 Fit side-chains revert: symmetry clash REVERT: R 22 MET cc_start: 0.6776 (mtp) cc_final: 0.6283 (mtp) REVERT: R 100 ASN cc_start: 0.7691 (t0) cc_final: 0.7292 (t0) REVERT: a 40 GLU cc_start: 0.7457 (mt-10) cc_final: 0.7186 (mt-10) REVERT: a 78 TYR cc_start: 0.7913 (m-80) cc_final: 0.7635 (m-10) REVERT: S 94 LYS cc_start: 0.8338 (mmpt) cc_final: 0.7658 (mmtp) REVERT: S 103 GLN cc_start: 0.8657 (mt0) cc_final: 0.8206 (mt0) REVERT: S 104 ARG cc_start: 0.8568 (mtm180) cc_final: 0.8092 (mtm110) REVERT: F 49 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7714 (mt-10) REVERT: F 362 ILE cc_start: 0.9057 (pt) cc_final: 0.8534 (mt) REVERT: N 128 MET cc_start: 0.8416 (mtp) cc_final: 0.7882 (mtp) REVERT: X 31 ASP cc_start: 0.7523 (t70) cc_final: 0.7155 (t0) REVERT: Y 1 MET cc_start: 0.7086 (OUTLIER) cc_final: 0.6308 (ttt) REVERT: O 22 MET cc_start: 0.7984 (mtm) cc_final: 0.7769 (mtm) REVERT: O 29 ASP cc_start: 0.6744 (t0) cc_final: 0.6511 (t70) REVERT: E 362 ILE cc_start: 0.8884 (OUTLIER) cc_final: 0.8629 (mt) REVERT: E 398 MET cc_start: 0.6507 (OUTLIER) cc_final: 0.6207 (mtp) REVERT: C 53 ARG cc_start: 0.6590 (mmt-90) cc_final: 0.5724 (mtp85) REVERT: C 152 ILE cc_start: 0.8025 (mm) cc_final: 0.7807 (mm) REVERT: C 280 TYR cc_start: 0.7098 (t80) cc_final: 0.6897 (t80) REVERT: C 363 ASN cc_start: 0.7574 (t0) cc_final: 0.7342 (t0) REVERT: C 431 ARG cc_start: 0.5950 (mmt180) cc_final: 0.4593 (ttp80) REVERT: L 100 ASN cc_start: 0.8293 (t0) cc_final: 0.7996 (t0) REVERT: G 168 SER cc_start: 0.9113 (t) cc_final: 0.8817 (t) REVERT: G 267 ARG cc_start: 0.8027 (ttm110) cc_final: 0.7643 (ttp-110) REVERT: W 46 GLN cc_start: 0.8977 (tm-30) cc_final: 0.8774 (tm-30) REVERT: W 122 LYS cc_start: 0.9022 (ttmt) cc_final: 0.8722 (ttmm) REVERT: U 3 THR cc_start: 0.8739 (OUTLIER) cc_final: 0.8239 (m) REVERT: U 7 VAL cc_start: 0.8865 (OUTLIER) cc_final: 0.8639 (m) REVERT: U 14 GLU cc_start: 0.6988 (tt0) cc_final: 0.6726 (tt0) REVERT: U 22 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.8165 (ptm) REVERT: U 94 LYS cc_start: 0.8801 (mmmt) cc_final: 0.8440 (mmmm) REVERT: U 97 ASP cc_start: 0.7882 (t70) cc_final: 0.7524 (t0) REVERT: U 98 ARG cc_start: 0.7780 (mtm110) cc_final: 0.7190 (ptp90) REVERT: K 94 LYS cc_start: 0.7975 (mmpt) cc_final: 0.7619 (mmmt) REVERT: K 100 ASN cc_start: 0.8476 (t0) cc_final: 0.8120 (t0) REVERT: D 26 GLN cc_start: 0.7815 (OUTLIER) cc_final: 0.7573 (pm20) REVERT: D 303 TYR cc_start: 0.8309 (m-80) cc_final: 0.7962 (m-80) REVERT: D 362 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8614 (mt) REVERT: D 408 ARG cc_start: 0.7200 (ttp80) cc_final: 0.6969 (mtp-110) REVERT: D 447 LYS cc_start: 0.7882 (mttt) cc_final: 0.7679 (mttm) REVERT: A 1 MET cc_start: 0.4031 (mpp) cc_final: 0.2683 (tpt) REVERT: A 36 TRP cc_start: 0.7710 (p90) cc_final: 0.7391 (p90) REVERT: A 82 LYS cc_start: 0.6894 (ptmt) cc_final: 0.6593 (mppt) REVERT: A 92 TYR cc_start: 0.5885 (p90) cc_final: 0.5663 (p90) REVERT: A 139 LEU cc_start: 0.6178 (mt) cc_final: 0.4436 (tp) REVERT: A 150 CYS cc_start: 0.7643 (m) cc_final: 0.7396 (m) REVERT: B 1 MET cc_start: 0.3745 (mmp) cc_final: 0.3291 (ptm) REVERT: B 82 LYS cc_start: 0.6876 (ptmt) cc_final: 0.6541 (mmtm) REVERT: B 139 LEU cc_start: 0.6078 (mt) cc_final: 0.5660 (mt) REVERT: B 170 SER cc_start: 0.7829 (t) cc_final: 0.7167 (p) REVERT: P 91 LYS cc_start: 0.7538 (mmmt) cc_final: 0.7198 (mmmm) REVERT: T 128 MET cc_start: 0.7782 (mtm) cc_final: 0.7569 (mtp) REVERT: V 26 ASP cc_start: 0.8594 (p0) cc_final: 0.8294 (p0) REVERT: V 87 GLU cc_start: 0.7794 (tp30) cc_final: 0.7488 (tp30) REVERT: V 107 SER cc_start: 0.8543 (p) cc_final: 0.8296 (t) REVERT: Z 31 ASP cc_start: 0.7356 (t70) cc_final: 0.7114 (t70) REVERT: Z 90 ARG cc_start: 0.8955 (ttm-80) cc_final: 0.8404 (ttp-170) REVERT: Z 164 GLU cc_start: 0.7807 (mp0) cc_final: 0.7539 (mp0) outliers start: 123 outliers final: 78 residues processed: 796 average time/residue: 0.5125 time to fit residues: 670.3107 Evaluate side-chains 725 residues out of total 5691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 639 time to evaluate : 4.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 60 THR Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 6 MET Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 172 VAL Chi-restraints excluded: chain a residue 38 VAL Chi-restraints excluded: chain a residue 91 VAL Chi-restraints excluded: chain a residue 98 VAL Chi-restraints excluded: chain a residue 200 LEU Chi-restraints excluded: chain a residue 204 LEU Chi-restraints excluded: chain Q residue 3 THR Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 43 ASP Chi-restraints excluded: chain S residue 75 VAL Chi-restraints excluded: chain S residue 105 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 120 MET Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 316 GLN Chi-restraints excluded: chain F residue 357 TYR Chi-restraints excluded: chain N residue 13 ASP Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 29 ASP Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain X residue 152 LEU Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain Y residue 18 GLU Chi-restraints excluded: chain Y residue 38 VAL Chi-restraints excluded: chain M residue 3 THR Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 60 THR Chi-restraints excluded: chain M residue 75 VAL Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 245 MET Chi-restraints excluded: chain E residue 342 ASP Chi-restraints excluded: chain E residue 357 TYR Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 398 MET Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain J residue 134 ILE Chi-restraints excluded: chain L residue 97 ASP Chi-restraints excluded: chain L residue 134 ILE Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain W residue 38 VAL Chi-restraints excluded: chain W residue 98 VAL Chi-restraints excluded: chain W residue 204 LEU Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 7 VAL Chi-restraints excluded: chain U residue 22 MET Chi-restraints excluded: chain U residue 60 THR Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 22 MET Chi-restraints excluded: chain K residue 28 ASP Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 357 TYR Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain P residue 128 MET Chi-restraints excluded: chain T residue 12 VAL Chi-restraints excluded: chain T residue 22 MET Chi-restraints excluded: chain T residue 59 GLU Chi-restraints excluded: chain T residue 82 VAL Chi-restraints excluded: chain T residue 97 ASP Chi-restraints excluded: chain V residue 152 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 645 random chunks: chunk 519 optimal weight: 9.9990 chunk 353 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 464 optimal weight: 6.9990 chunk 257 optimal weight: 4.9990 chunk 532 optimal weight: 8.9990 chunk 430 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 318 optimal weight: 10.0000 chunk 559 optimal weight: 8.9990 chunk 157 optimal weight: 2.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 113 ASN H 161 GLN Y 51 ASN O 103 GLN L 100 ASN ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 100 ASN A 316 GLN B 154 GLN B 182 GLN T 5 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 51759 Z= 0.503 Angle : 0.660 9.076 70368 Z= 0.347 Chirality : 0.049 0.184 8196 Planarity : 0.005 0.053 9093 Dihedral : 5.079 60.212 7119 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.22 % Allowed : 16.01 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.82 (0.10), residues: 6522 helix: 0.45 (0.22), residues: 537 sheet: -1.10 (0.10), residues: 2616 loop : -1.52 (0.10), residues: 3369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 36 HIS 0.009 0.002 HIS H 21 PHE 0.024 0.002 PHE H 22 TYR 0.022 0.002 TYR B 239 ARG 0.007 0.001 ARG V 201 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13044 Ramachandran restraints generated. 6522 Oldfield, 0 Emsley, 6522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13044 Ramachandran restraints generated. 6522 Oldfield, 0 Emsley, 6522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 801 residues out of total 5691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 618 time to evaluate : 4.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 8 ILE cc_start: 0.8336 (OUTLIER) cc_final: 0.8047 (tp) REVERT: R 22 MET cc_start: 0.6646 (mtp) cc_final: 0.6350 (mtp) REVERT: R 100 ASN cc_start: 0.7739 (t0) cc_final: 0.7183 (t0) REVERT: a 40 GLU cc_start: 0.7513 (mt-10) cc_final: 0.7293 (mt-10) REVERT: S 94 LYS cc_start: 0.8359 (mmpt) cc_final: 0.7669 (mmtp) REVERT: S 103 GLN cc_start: 0.8771 (mt0) cc_final: 0.8345 (mt0) REVERT: S 104 ARG cc_start: 0.8603 (mtm180) cc_final: 0.8115 (mtm110) REVERT: F 49 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7745 (mt-10) REVERT: F 224 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8525 (mt) REVERT: F 264 SER cc_start: 0.8991 (m) cc_final: 0.8548 (p) REVERT: N 128 MET cc_start: 0.8472 (mtp) cc_final: 0.8189 (mtp) REVERT: X 31 ASP cc_start: 0.7524 (t70) cc_final: 0.7198 (t0) REVERT: Y 1 MET cc_start: 0.7223 (OUTLIER) cc_final: 0.6228 (ttt) REVERT: E 102 ARG cc_start: 0.8353 (mtp85) cc_final: 0.7858 (mtp85) REVERT: E 120 MET cc_start: 0.7999 (OUTLIER) cc_final: 0.7582 (ptt) REVERT: E 398 MET cc_start: 0.6465 (mtp) cc_final: 0.6176 (mtp) REVERT: C 53 ARG cc_start: 0.6696 (mmt-90) cc_final: 0.5730 (mtp85) REVERT: C 281 LYS cc_start: 0.6839 (ptmt) cc_final: 0.6543 (ttpt) REVERT: C 398 MET cc_start: 0.1334 (mmm) cc_final: 0.1021 (mmm) REVERT: L 52 SER cc_start: 0.8984 (p) cc_final: 0.8601 (m) REVERT: L 95 GLU cc_start: 0.7358 (tp30) cc_final: 0.7101 (tp30) REVERT: G 82 MET cc_start: 0.9005 (ttp) cc_final: 0.8759 (ttp) REVERT: G 267 ARG cc_start: 0.8113 (ttm110) cc_final: 0.7593 (ttp-110) REVERT: W 46 GLN cc_start: 0.8982 (tm-30) cc_final: 0.8714 (tm-30) REVERT: U 3 THR cc_start: 0.8749 (OUTLIER) cc_final: 0.8288 (m) REVERT: U 14 GLU cc_start: 0.7271 (tt0) cc_final: 0.6819 (tt0) REVERT: U 94 LYS cc_start: 0.8810 (mmmt) cc_final: 0.8376 (mmmm) REVERT: U 97 ASP cc_start: 0.8136 (t70) cc_final: 0.7787 (t0) REVERT: K 94 LYS cc_start: 0.8026 (mmpt) cc_final: 0.7534 (mmtp) REVERT: D 26 GLN cc_start: 0.7860 (OUTLIER) cc_final: 0.7573 (pm20) REVERT: D 224 ILE cc_start: 0.9035 (OUTLIER) cc_final: 0.8829 (mm) REVERT: D 447 LYS cc_start: 0.7747 (mttt) cc_final: 0.7480 (mttm) REVERT: A 36 TRP cc_start: 0.8006 (p90) cc_final: 0.7479 (p90) REVERT: A 82 LYS cc_start: 0.6961 (ptmt) cc_final: 0.6461 (mppt) REVERT: A 211 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7789 (tp) REVERT: B 36 TRP cc_start: 0.8028 (p90) cc_final: 0.7594 (p90) REVERT: B 170 SER cc_start: 0.7802 (OUTLIER) cc_final: 0.7296 (p) REVERT: T 128 MET cc_start: 0.8061 (mtm) cc_final: 0.7824 (mtp) REVERT: V 87 GLU cc_start: 0.7990 (tp30) cc_final: 0.7690 (tp30) REVERT: Z 18 GLU cc_start: 0.7580 (tt0) cc_final: 0.7259 (tt0) REVERT: Z 31 ASP cc_start: 0.7487 (t70) cc_final: 0.7192 (t70) REVERT: Z 164 GLU cc_start: 0.7638 (mp0) cc_final: 0.7406 (mp0) outliers start: 183 outliers final: 143 residues processed: 755 average time/residue: 0.5068 time to fit residues: 637.8166 Evaluate side-chains 742 residues out of total 5691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 590 time to evaluate : 4.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 8 ILE Chi-restraints excluded: chain R residue 60 THR Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 6 MET Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain I residue 172 VAL Chi-restraints excluded: chain I residue 249 ILE Chi-restraints excluded: chain a residue 38 VAL Chi-restraints excluded: chain a residue 91 VAL Chi-restraints excluded: chain a residue 98 VAL Chi-restraints excluded: chain a residue 200 LEU Chi-restraints excluded: chain a residue 204 LEU Chi-restraints excluded: chain Q residue 3 THR Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 43 ASP Chi-restraints excluded: chain Q residue 68 ILE Chi-restraints excluded: chain S residue 8 ILE Chi-restraints excluded: chain S residue 27 VAL Chi-restraints excluded: chain S residue 75 VAL Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 120 MET Chi-restraints excluded: chain F residue 129 HIS Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain F residue 316 GLN Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 357 TYR Chi-restraints excluded: chain N residue 13 ASP Chi-restraints excluded: chain N residue 66 THR Chi-restraints excluded: chain N residue 112 ILE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 29 ASP Chi-restraints excluded: chain H residue 55 ILE Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 137 ILE Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 207 ILE Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain H residue 249 ILE Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain Y residue 18 GLU Chi-restraints excluded: chain Y residue 38 VAL Chi-restraints excluded: chain Y residue 72 TYR Chi-restraints excluded: chain Y residue 98 VAL Chi-restraints excluded: chain Y residue 204 LEU Chi-restraints excluded: chain M residue 3 THR Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 43 ASP Chi-restraints excluded: chain M residue 60 THR Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 75 VAL Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 129 HIS Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 245 MET Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 357 TYR Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain J residue 8 ILE Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain J residue 134 ILE Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain L residue 97 ASP Chi-restraints excluded: chain L residue 134 ILE Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 55 ILE Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 246 THR Chi-restraints excluded: chain G residue 249 ILE Chi-restraints excluded: chain W residue 38 VAL Chi-restraints excluded: chain W residue 91 VAL Chi-restraints excluded: chain W residue 98 VAL Chi-restraints excluded: chain W residue 113 THR Chi-restraints excluded: chain W residue 204 LEU Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 7 VAL Chi-restraints excluded: chain U residue 22 MET Chi-restraints excluded: chain U residue 43 ASP Chi-restraints excluded: chain U residue 60 THR Chi-restraints excluded: chain U residue 68 ILE Chi-restraints excluded: chain K residue 8 ILE Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 22 MET Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 129 HIS Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 270 ASN Chi-restraints excluded: chain D residue 357 TYR Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain P residue 79 SER Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 128 MET Chi-restraints excluded: chain P residue 134 ILE Chi-restraints excluded: chain T residue 12 VAL Chi-restraints excluded: chain T residue 59 GLU Chi-restraints excluded: chain T residue 82 VAL Chi-restraints excluded: chain T residue 97 ASP Chi-restraints excluded: chain V residue 167 VAL Chi-restraints excluded: chain Z residue 99 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 645 random chunks: chunk 209 optimal weight: 2.9990 chunk 561 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 366 optimal weight: 2.9990 chunk 153 optimal weight: 0.9990 chunk 624 optimal weight: 0.9990 chunk 518 optimal weight: 20.0000 chunk 288 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 206 optimal weight: 0.8980 chunk 327 optimal weight: 20.0000 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 113 ASN H 161 GLN Y 51 ASN O 103 GLN L 100 ASN G 49 ASN U 100 ASN A 316 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 51759 Z= 0.187 Angle : 0.515 8.440 70368 Z= 0.272 Chirality : 0.045 0.205 8196 Planarity : 0.004 0.049 9093 Dihedral : 4.589 61.580 7119 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.62 % Allowed : 17.17 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.62 (0.10), residues: 6522 helix: 0.81 (0.22), residues: 546 sheet: -0.96 (0.10), residues: 2655 loop : -1.45 (0.10), residues: 3321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 144 HIS 0.004 0.001 HIS A 20 PHE 0.025 0.001 PHE O 64 TYR 0.016 0.001 TYR C 239 ARG 0.006 0.000 ARG a 74 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13044 Ramachandran restraints generated. 6522 Oldfield, 0 Emsley, 6522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13044 Ramachandran restraints generated. 6522 Oldfield, 0 Emsley, 6522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 835 residues out of total 5691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 686 time to evaluate : 4.422 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 100 ASN cc_start: 0.7664 (t0) cc_final: 0.7107 (t0) REVERT: a 40 GLU cc_start: 0.7481 (mt-10) cc_final: 0.7273 (mt-10) REVERT: S 94 LYS cc_start: 0.8285 (mmpt) cc_final: 0.7598 (mmtp) REVERT: S 103 GLN cc_start: 0.8657 (mt0) cc_final: 0.8193 (mt0) REVERT: S 104 ARG cc_start: 0.8629 (mtm180) cc_final: 0.7985 (mtm110) REVERT: F 264 SER cc_start: 0.8959 (m) cc_final: 0.8494 (p) REVERT: N 115 ARG cc_start: 0.6272 (ttt90) cc_final: 0.6068 (ttt90) REVERT: N 128 MET cc_start: 0.8581 (mtp) cc_final: 0.8198 (mtp) REVERT: X 31 ASP cc_start: 0.7483 (t70) cc_final: 0.7086 (t70) REVERT: X 87 GLU cc_start: 0.7953 (tp30) cc_final: 0.7544 (tp30) REVERT: Y 1 MET cc_start: 0.7025 (OUTLIER) cc_final: 0.6226 (ttt) REVERT: Y 188 ASN cc_start: 0.8177 (OUTLIER) cc_final: 0.7732 (m-40) REVERT: E 102 ARG cc_start: 0.8299 (mtp85) cc_final: 0.7837 (mtp85) REVERT: E 120 MET cc_start: 0.8003 (OUTLIER) cc_final: 0.7581 (ptt) REVERT: E 398 MET cc_start: 0.6387 (mtp) cc_final: 0.6070 (mtp) REVERT: C 53 ARG cc_start: 0.6605 (mmt-90) cc_final: 0.5728 (mtp85) REVERT: C 281 LYS cc_start: 0.7129 (ptmt) cc_final: 0.6776 (ttpt) REVERT: C 398 MET cc_start: 0.1132 (mmm) cc_final: 0.0767 (mmm) REVERT: C 431 ARG cc_start: 0.6464 (mmt180) cc_final: 0.4783 (ttp80) REVERT: L 52 SER cc_start: 0.8939 (p) cc_final: 0.8561 (m) REVERT: L 91 LYS cc_start: 0.7889 (mmmm) cc_final: 0.7656 (mmmm) REVERT: L 100 ASN cc_start: 0.8510 (t0) cc_final: 0.8165 (t0) REVERT: G 168 SER cc_start: 0.9091 (t) cc_final: 0.8772 (t) REVERT: G 267 ARG cc_start: 0.8051 (ttm110) cc_final: 0.7660 (ttp-110) REVERT: W 46 GLN cc_start: 0.9017 (tm-30) cc_final: 0.8757 (tm-30) REVERT: U 3 THR cc_start: 0.8714 (OUTLIER) cc_final: 0.8188 (m) REVERT: U 7 VAL cc_start: 0.8854 (OUTLIER) cc_final: 0.8650 (m) REVERT: U 14 GLU cc_start: 0.7037 (tt0) cc_final: 0.6590 (tt0) REVERT: U 94 LYS cc_start: 0.8849 (mmmt) cc_final: 0.8416 (mmmm) REVERT: U 97 ASP cc_start: 0.7857 (t70) cc_final: 0.7544 (t0) REVERT: U 98 ARG cc_start: 0.7942 (mtm110) cc_final: 0.7381 (ptp90) REVERT: K 94 LYS cc_start: 0.8215 (mmpt) cc_final: 0.7619 (mmmt) REVERT: D 26 GLN cc_start: 0.7878 (OUTLIER) cc_final: 0.7538 (pm20) REVERT: D 156 GLU cc_start: 0.7757 (tt0) cc_final: 0.7414 (tt0) REVERT: D 447 LYS cc_start: 0.7749 (mttt) cc_final: 0.7477 (mttm) REVERT: A 36 TRP cc_start: 0.7724 (p90) cc_final: 0.7289 (p90) REVERT: A 82 LYS cc_start: 0.6872 (ptmt) cc_final: 0.6430 (mppt) REVERT: B 82 LYS cc_start: 0.6770 (ptmt) cc_final: 0.6441 (mmtm) REVERT: B 170 SER cc_start: 0.7834 (t) cc_final: 0.7166 (p) REVERT: T 54 LEU cc_start: 0.8616 (mt) cc_final: 0.8148 (mt) REVERT: V 26 ASP cc_start: 0.8644 (p0) cc_final: 0.8355 (p0) REVERT: V 87 GLU cc_start: 0.7735 (tp30) cc_final: 0.7415 (tp30) REVERT: Z 31 ASP cc_start: 0.7175 (t70) cc_final: 0.6943 (t70) REVERT: Z 164 GLU cc_start: 0.7660 (mp0) cc_final: 0.7420 (mp0) outliers start: 149 outliers final: 115 residues processed: 794 average time/residue: 0.4973 time to fit residues: 651.4852 Evaluate side-chains 756 residues out of total 5691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 635 time to evaluate : 4.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 20 LEU Chi-restraints excluded: chain R residue 44 PHE Chi-restraints excluded: chain R residue 60 THR Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 6 MET Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 172 VAL Chi-restraints excluded: chain I residue 246 THR Chi-restraints excluded: chain a residue 38 VAL Chi-restraints excluded: chain a residue 53 SER Chi-restraints excluded: chain a residue 98 VAL Chi-restraints excluded: chain a residue 200 LEU Chi-restraints excluded: chain a residue 204 LEU Chi-restraints excluded: chain Q residue 3 THR Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 43 ASP Chi-restraints excluded: chain S residue 75 VAL Chi-restraints excluded: chain S residue 78 ILE Chi-restraints excluded: chain S residue 105 LEU Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 120 MET Chi-restraints excluded: chain F residue 129 HIS Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 316 GLN Chi-restraints excluded: chain F residue 357 TYR Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain F residue 398 MET Chi-restraints excluded: chain N residue 13 ASP Chi-restraints excluded: chain N residue 66 THR Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain X residue 152 LEU Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain Y residue 18 GLU Chi-restraints excluded: chain Y residue 38 VAL Chi-restraints excluded: chain Y residue 98 VAL Chi-restraints excluded: chain Y residue 188 ASN Chi-restraints excluded: chain Y residue 204 LEU Chi-restraints excluded: chain M residue 3 THR Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 60 THR Chi-restraints excluded: chain M residue 75 VAL Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 129 HIS Chi-restraints excluded: chain E residue 154 GLN Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 245 MET Chi-restraints excluded: chain E residue 342 ASP Chi-restraints excluded: chain E residue 357 TYR Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain J residue 134 ILE Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 97 ASP Chi-restraints excluded: chain L residue 134 ILE Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 246 THR Chi-restraints excluded: chain W residue 38 VAL Chi-restraints excluded: chain W residue 98 VAL Chi-restraints excluded: chain W residue 113 THR Chi-restraints excluded: chain W residue 179 ASN Chi-restraints excluded: chain W residue 204 LEU Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 7 VAL Chi-restraints excluded: chain U residue 22 MET Chi-restraints excluded: chain U residue 60 THR Chi-restraints excluded: chain U residue 68 ILE Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 22 MET Chi-restraints excluded: chain K residue 28 ASP Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 129 HIS Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 357 TYR Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 79 SER Chi-restraints excluded: chain T residue 12 VAL Chi-restraints excluded: chain T residue 22 MET Chi-restraints excluded: chain T residue 59 GLU Chi-restraints excluded: chain T residue 82 VAL Chi-restraints excluded: chain T residue 97 ASP Chi-restraints excluded: chain V residue 152 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 645 random chunks: chunk 601 optimal weight: 8.9990 chunk 70 optimal weight: 5.9990 chunk 355 optimal weight: 10.0000 chunk 455 optimal weight: 7.9990 chunk 353 optimal weight: 10.0000 chunk 525 optimal weight: 1.9990 chunk 348 optimal weight: 6.9990 chunk 621 optimal weight: 7.9990 chunk 389 optimal weight: 7.9990 chunk 379 optimal weight: 6.9990 chunk 287 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 113 ASN H 161 GLN Y 51 ASN ** O 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 100 ASN A 182 GLN A 316 GLN B 291 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.065 51759 Z= 0.604 Angle : 0.711 8.791 70368 Z= 0.373 Chirality : 0.051 0.213 8196 Planarity : 0.005 0.061 9093 Dihedral : 5.284 60.484 7119 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.65 % Allowed : 17.40 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.93 (0.10), residues: 6522 helix: 0.35 (0.22), residues: 537 sheet: -1.23 (0.10), residues: 2673 loop : -1.54 (0.10), residues: 3312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 144 HIS 0.009 0.002 HIS A 20 PHE 0.027 0.003 PHE H 22 TYR 0.023 0.003 TYR F 146 ARG 0.007 0.001 ARG D 7 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13044 Ramachandran restraints generated. 6522 Oldfield, 0 Emsley, 6522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13044 Ramachandran restraints generated. 6522 Oldfield, 0 Emsley, 6522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 816 residues out of total 5691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 208 poor density : 608 time to evaluate : 4.533 Fit side-chains revert: symmetry clash REVERT: R 100 ASN cc_start: 0.7679 (t0) cc_final: 0.7053 (t0) REVERT: a 1 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.7350 (ttt) REVERT: a 40 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7397 (mt-10) REVERT: S 94 LYS cc_start: 0.8371 (mmpt) cc_final: 0.7550 (mmtp) REVERT: S 103 GLN cc_start: 0.8777 (mt0) cc_final: 0.8344 (mt0) REVERT: S 104 ARG cc_start: 0.8611 (mtm180) cc_final: 0.8099 (mtm110) REVERT: F 224 ILE cc_start: 0.8817 (OUTLIER) cc_final: 0.8560 (mt) REVERT: F 264 SER cc_start: 0.9063 (m) cc_final: 0.8619 (p) REVERT: N 128 MET cc_start: 0.8617 (mtp) cc_final: 0.8366 (mtp) REVERT: X 31 ASP cc_start: 0.7542 (t70) cc_final: 0.7150 (t70) REVERT: Y 1 MET cc_start: 0.7425 (OUTLIER) cc_final: 0.6486 (ttt) REVERT: Y 188 ASN cc_start: 0.8270 (OUTLIER) cc_final: 0.7819 (m-40) REVERT: E 102 ARG cc_start: 0.8376 (mtp85) cc_final: 0.7904 (mtp85) REVERT: E 120 MET cc_start: 0.8016 (OUTLIER) cc_final: 0.7618 (ptt) REVERT: E 398 MET cc_start: 0.6419 (mtp) cc_final: 0.6113 (mtp) REVERT: C 53 ARG cc_start: 0.6719 (mmt-90) cc_final: 0.5721 (mtp85) REVERT: C 281 LYS cc_start: 0.6911 (ptmt) cc_final: 0.6571 (ttpt) REVERT: L 52 SER cc_start: 0.9015 (p) cc_final: 0.8628 (m) REVERT: L 91 LYS cc_start: 0.8011 (mmmm) cc_final: 0.7788 (mmmm) REVERT: G 80 ASP cc_start: 0.7752 (t0) cc_final: 0.7541 (t0) REVERT: G 267 ARG cc_start: 0.8190 (ttm110) cc_final: 0.7618 (ttp-110) REVERT: W 46 GLN cc_start: 0.9078 (tm-30) cc_final: 0.8767 (tm-30) REVERT: U 3 THR cc_start: 0.8759 (OUTLIER) cc_final: 0.8256 (m) REVERT: U 14 GLU cc_start: 0.7213 (tt0) cc_final: 0.6872 (tt0) REVERT: U 94 LYS cc_start: 0.8706 (mmmt) cc_final: 0.8358 (mmmm) REVERT: K 94 LYS cc_start: 0.8098 (mmpt) cc_final: 0.7452 (mmtp) REVERT: D 26 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.7507 (pm20) REVERT: D 447 LYS cc_start: 0.7804 (mttt) cc_final: 0.7537 (mttm) REVERT: A 82 LYS cc_start: 0.6851 (ptmt) cc_final: 0.6436 (mmtm) REVERT: A 91 ASP cc_start: 0.7943 (OUTLIER) cc_final: 0.7541 (m-30) REVERT: A 211 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7717 (tp) REVERT: A 398 MET cc_start: 0.0575 (mmm) cc_final: 0.0338 (mmm) REVERT: B 431 ARG cc_start: 0.7001 (mmt180) cc_final: 0.5615 (ttp80) REVERT: P 25 MET cc_start: 0.7444 (mtp) cc_final: 0.7116 (mtp) REVERT: T 95 GLU cc_start: 0.7915 (tp30) cc_final: 0.7697 (tp30) REVERT: Z 18 GLU cc_start: 0.7626 (tt0) cc_final: 0.7304 (tt0) REVERT: Z 31 ASP cc_start: 0.7287 (t70) cc_final: 0.7044 (t70) REVERT: Z 61 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8437 (mt-10) REVERT: Z 164 GLU cc_start: 0.7638 (mp0) cc_final: 0.7407 (mp0) outliers start: 208 outliers final: 167 residues processed: 769 average time/residue: 0.4991 time to fit residues: 640.4717 Evaluate side-chains 754 residues out of total 5691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 578 time to evaluate : 4.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 20 LEU Chi-restraints excluded: chain R residue 60 THR Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain I residue 6 MET Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 172 VAL Chi-restraints excluded: chain I residue 246 THR Chi-restraints excluded: chain I residue 249 ILE Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain a residue 38 VAL Chi-restraints excluded: chain a residue 53 SER Chi-restraints excluded: chain a residue 91 VAL Chi-restraints excluded: chain a residue 98 VAL Chi-restraints excluded: chain a residue 200 LEU Chi-restraints excluded: chain a residue 204 LEU Chi-restraints excluded: chain Q residue 3 THR Chi-restraints excluded: chain Q residue 4 GLU Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 43 ASP Chi-restraints excluded: chain Q residue 68 ILE Chi-restraints excluded: chain S residue 8 ILE Chi-restraints excluded: chain S residue 27 VAL Chi-restraints excluded: chain S residue 65 THR Chi-restraints excluded: chain S residue 75 VAL Chi-restraints excluded: chain S residue 78 ILE Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 120 MET Chi-restraints excluded: chain F residue 129 HIS Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 316 GLN Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 357 TYR Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain F residue 427 THR Chi-restraints excluded: chain F residue 458 ILE Chi-restraints excluded: chain N residue 13 ASP Chi-restraints excluded: chain N residue 16 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 66 THR Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 29 ASP Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 132 ASP Chi-restraints excluded: chain H residue 137 ILE Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 207 ILE Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain H residue 249 ILE Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain Y residue 18 GLU Chi-restraints excluded: chain Y residue 38 VAL Chi-restraints excluded: chain Y residue 72 TYR Chi-restraints excluded: chain Y residue 98 VAL Chi-restraints excluded: chain Y residue 188 ASN Chi-restraints excluded: chain Y residue 204 LEU Chi-restraints excluded: chain M residue 3 THR Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 43 ASP Chi-restraints excluded: chain M residue 60 THR Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 75 VAL Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain O residue 95 GLU Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 129 HIS Chi-restraints excluded: chain E residue 154 GLN Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 245 MET Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 357 TYR Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain J residue 8 ILE Chi-restraints excluded: chain J residue 16 VAL Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain J residue 66 THR Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain J residue 134 ILE Chi-restraints excluded: chain L residue 8 ILE Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 97 ASP Chi-restraints excluded: chain L residue 134 ILE Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 55 ILE Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 246 THR Chi-restraints excluded: chain G residue 249 ILE Chi-restraints excluded: chain W residue 38 VAL Chi-restraints excluded: chain W residue 91 VAL Chi-restraints excluded: chain W residue 98 VAL Chi-restraints excluded: chain W residue 179 ASN Chi-restraints excluded: chain W residue 204 LEU Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 7 VAL Chi-restraints excluded: chain U residue 43 ASP Chi-restraints excluded: chain U residue 60 THR Chi-restraints excluded: chain U residue 68 ILE Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 129 GLU Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 129 HIS Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 270 ASN Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 357 TYR Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 79 SER Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 128 MET Chi-restraints excluded: chain P residue 134 ILE Chi-restraints excluded: chain T residue 12 VAL Chi-restraints excluded: chain T residue 59 GLU Chi-restraints excluded: chain T residue 82 VAL Chi-restraints excluded: chain T residue 97 ASP Chi-restraints excluded: chain V residue 99 THR Chi-restraints excluded: chain V residue 167 VAL Chi-restraints excluded: chain Z residue 99 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 645 random chunks: chunk 384 optimal weight: 2.9990 chunk 248 optimal weight: 3.9990 chunk 371 optimal weight: 1.9990 chunk 187 optimal weight: 0.0970 chunk 122 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 chunk 395 optimal weight: 0.1980 chunk 423 optimal weight: 5.9990 chunk 307 optimal weight: 9.9990 chunk 57 optimal weight: 0.9980 chunk 488 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 161 GLN Y 51 ASN ** Y 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 GLN U 100 ASN A 316 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 51759 Z= 0.174 Angle : 0.529 10.242 70368 Z= 0.278 Chirality : 0.045 0.207 8196 Planarity : 0.004 0.059 9093 Dihedral : 4.640 62.021 7119 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.53 % Allowed : 18.82 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.63 (0.10), residues: 6522 helix: 0.83 (0.22), residues: 546 sheet: -0.98 (0.10), residues: 2646 loop : -1.45 (0.10), residues: 3330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 144 HIS 0.003 0.001 HIS A 20 PHE 0.036 0.001 PHE A 231 TYR 0.018 0.001 TYR P 109 ARG 0.007 0.000 ARG I 267 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13044 Ramachandran restraints generated. 6522 Oldfield, 0 Emsley, 6522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13044 Ramachandran restraints generated. 6522 Oldfield, 0 Emsley, 6522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 816 residues out of total 5691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 672 time to evaluate : 4.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 100 ASN cc_start: 0.7667 (t0) cc_final: 0.7119 (t0) REVERT: a 40 GLU cc_start: 0.7510 (mt-10) cc_final: 0.7262 (mt-10) REVERT: S 94 LYS cc_start: 0.8302 (mmpt) cc_final: 0.7622 (mmtp) REVERT: S 103 GLN cc_start: 0.8652 (mt0) cc_final: 0.8194 (mt0) REVERT: S 104 ARG cc_start: 0.8629 (mtm180) cc_final: 0.8001 (mtm110) REVERT: F 224 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8426 (mt) REVERT: F 264 SER cc_start: 0.9052 (m) cc_final: 0.8602 (p) REVERT: F 348 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7365 (mt-10) REVERT: H 142 ILE cc_start: 0.8832 (pt) cc_final: 0.8243 (pt) REVERT: X 31 ASP cc_start: 0.7516 (t70) cc_final: 0.7081 (t70) REVERT: Y 1 MET cc_start: 0.7039 (OUTLIER) cc_final: 0.6195 (ttt) REVERT: E 102 ARG cc_start: 0.8301 (mtp85) cc_final: 0.7857 (mtp85) REVERT: E 120 MET cc_start: 0.7974 (OUTLIER) cc_final: 0.7543 (ptt) REVERT: E 398 MET cc_start: 0.6327 (mtp) cc_final: 0.6047 (mtp) REVERT: C 53 ARG cc_start: 0.6693 (mmt-90) cc_final: 0.5808 (mtp85) REVERT: C 281 LYS cc_start: 0.6928 (ptmt) cc_final: 0.6693 (ttpt) REVERT: L 21 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7903 (pp) REVERT: L 52 SER cc_start: 0.8900 (p) cc_final: 0.8524 (m) REVERT: G 142 ILE cc_start: 0.8780 (pt) cc_final: 0.8380 (pt) REVERT: G 168 SER cc_start: 0.9051 (t) cc_final: 0.8757 (t) REVERT: G 236 LYS cc_start: 0.8456 (mttp) cc_final: 0.8225 (mtpp) REVERT: G 267 ARG cc_start: 0.7999 (ttm110) cc_final: 0.7591 (ttp-110) REVERT: W 46 GLN cc_start: 0.9092 (tm-30) cc_final: 0.8776 (tm-30) REVERT: U 3 THR cc_start: 0.8693 (OUTLIER) cc_final: 0.8115 (m) REVERT: U 7 VAL cc_start: 0.8870 (OUTLIER) cc_final: 0.8651 (m) REVERT: U 14 GLU cc_start: 0.7037 (tt0) cc_final: 0.6646 (tt0) REVERT: U 94 LYS cc_start: 0.8708 (mmmt) cc_final: 0.8374 (mmmm) REVERT: U 98 ARG cc_start: 0.7953 (mtm110) cc_final: 0.7471 (ptp90) REVERT: K 94 LYS cc_start: 0.8050 (mmpt) cc_final: 0.7332 (mmmt) REVERT: D 26 GLN cc_start: 0.7988 (OUTLIER) cc_final: 0.7565 (pm20) REVERT: D 268 TYR cc_start: 0.8392 (m-80) cc_final: 0.8160 (m-10) REVERT: D 447 LYS cc_start: 0.7822 (mttt) cc_final: 0.7572 (mttm) REVERT: A 36 TRP cc_start: 0.7798 (p90) cc_final: 0.7378 (p90) REVERT: A 82 LYS cc_start: 0.6887 (ptmt) cc_final: 0.6521 (mmtm) REVERT: B 82 LYS cc_start: 0.6647 (ptmt) cc_final: 0.6402 (mmtm) REVERT: B 170 SER cc_start: 0.7854 (m) cc_final: 0.7210 (p) REVERT: T 54 LEU cc_start: 0.8603 (mt) cc_final: 0.8145 (mt) REVERT: T 94 LYS cc_start: 0.7515 (mmtp) cc_final: 0.7266 (mmmt) REVERT: T 95 GLU cc_start: 0.7957 (tp30) cc_final: 0.7694 (tp30) REVERT: V 26 ASP cc_start: 0.8561 (p0) cc_final: 0.8124 (p0) REVERT: Z 31 ASP cc_start: 0.7304 (t70) cc_final: 0.7063 (t70) REVERT: Z 164 GLU cc_start: 0.7657 (mp0) cc_final: 0.7420 (mp0) REVERT: Z 178 MET cc_start: 0.8510 (mmt) cc_final: 0.8247 (mmm) outliers start: 144 outliers final: 111 residues processed: 771 average time/residue: 0.5471 time to fit residues: 698.0699 Evaluate side-chains 756 residues out of total 5691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 638 time to evaluate : 4.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 20 LEU Chi-restraints excluded: chain R residue 44 PHE Chi-restraints excluded: chain R residue 60 THR Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 6 MET Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain I residue 172 VAL Chi-restraints excluded: chain I residue 246 THR Chi-restraints excluded: chain I residue 249 ILE Chi-restraints excluded: chain a residue 38 VAL Chi-restraints excluded: chain a residue 53 SER Chi-restraints excluded: chain a residue 98 VAL Chi-restraints excluded: chain a residue 200 LEU Chi-restraints excluded: chain Q residue 3 THR Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 43 ASP Chi-restraints excluded: chain S residue 75 VAL Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 120 MET Chi-restraints excluded: chain F residue 129 HIS Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 316 GLN Chi-restraints excluded: chain F residue 357 TYR Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain F residue 398 MET Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain X residue 152 LEU Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain Y residue 98 VAL Chi-restraints excluded: chain Y residue 204 LEU Chi-restraints excluded: chain M residue 3 THR Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 60 THR Chi-restraints excluded: chain M residue 75 VAL Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 129 HIS Chi-restraints excluded: chain E residue 154 GLN Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 245 MET Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 357 TYR Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain J residue 8 ILE Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain J residue 134 ILE Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 97 ASP Chi-restraints excluded: chain L residue 113 ILE Chi-restraints excluded: chain L residue 134 ILE Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 246 THR Chi-restraints excluded: chain W residue 38 VAL Chi-restraints excluded: chain W residue 98 VAL Chi-restraints excluded: chain W residue 200 LEU Chi-restraints excluded: chain W residue 204 LEU Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 7 VAL Chi-restraints excluded: chain U residue 10 LEU Chi-restraints excluded: chain U residue 60 THR Chi-restraints excluded: chain U residue 68 ILE Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 28 ASP Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 129 HIS Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 357 TYR Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 79 SER Chi-restraints excluded: chain P residue 128 MET Chi-restraints excluded: chain T residue 12 VAL Chi-restraints excluded: chain T residue 22 MET Chi-restraints excluded: chain T residue 97 ASP Chi-restraints excluded: chain V residue 99 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 645 random chunks: chunk 565 optimal weight: 8.9990 chunk 595 optimal weight: 5.9990 chunk 543 optimal weight: 3.9990 chunk 579 optimal weight: 5.9990 chunk 348 optimal weight: 7.9990 chunk 252 optimal weight: 1.9990 chunk 454 optimal weight: 8.9990 chunk 177 optimal weight: 1.9990 chunk 523 optimal weight: 20.0000 chunk 547 optimal weight: 2.9990 chunk 577 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 113 ASN H 161 GLN Y 51 ASN ** Y 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 103 GLN G 35 GLN U 100 ASN ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 51759 Z= 0.299 Angle : 0.570 11.727 70368 Z= 0.297 Chirality : 0.046 0.172 8196 Planarity : 0.004 0.057 9093 Dihedral : 4.747 62.782 7119 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.65 % Allowed : 19.01 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.61 (0.10), residues: 6522 helix: 0.83 (0.23), residues: 543 sheet: -1.00 (0.10), residues: 2664 loop : -1.40 (0.10), residues: 3315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 70 HIS 0.005 0.001 HIS A 20 PHE 0.026 0.002 PHE A 255 TYR 0.019 0.002 TYR P 109 ARG 0.007 0.000 ARG I 267 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13044 Ramachandran restraints generated. 6522 Oldfield, 0 Emsley, 6522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13044 Ramachandran restraints generated. 6522 Oldfield, 0 Emsley, 6522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 776 residues out of total 5691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 625 time to evaluate : 4.442 Fit side-chains revert: symmetry clash REVERT: R 100 ASN cc_start: 0.7725 (t0) cc_final: 0.7186 (t0) REVERT: a 40 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7368 (mt-10) REVERT: a 164 GLU cc_start: 0.7947 (mp0) cc_final: 0.7440 (mp0) REVERT: S 94 LYS cc_start: 0.8331 (mmpt) cc_final: 0.7638 (mmtp) REVERT: S 103 GLN cc_start: 0.8684 (mt0) cc_final: 0.8239 (mt0) REVERT: S 104 ARG cc_start: 0.8614 (mtm180) cc_final: 0.7969 (mtm110) REVERT: F 224 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8487 (mt) REVERT: F 264 SER cc_start: 0.9079 (m) cc_final: 0.8623 (p) REVERT: F 348 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7407 (mt-10) REVERT: N 128 MET cc_start: 0.8491 (mmm) cc_final: 0.7973 (mtp) REVERT: N 134 ILE cc_start: 0.8951 (tp) cc_final: 0.8609 (tt) REVERT: X 31 ASP cc_start: 0.7554 (t70) cc_final: 0.7119 (t70) REVERT: Y 1 MET cc_start: 0.7128 (OUTLIER) cc_final: 0.6269 (ttt) REVERT: Y 188 ASN cc_start: 0.8214 (OUTLIER) cc_final: 0.7766 (m-40) REVERT: E 102 ARG cc_start: 0.8334 (mtp85) cc_final: 0.7858 (mtp85) REVERT: E 120 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.7532 (ptp) REVERT: E 398 MET cc_start: 0.6520 (mtp) cc_final: 0.6216 (mtp) REVERT: C 53 ARG cc_start: 0.6715 (mmt-90) cc_final: 0.5818 (mtp85) REVERT: C 281 LYS cc_start: 0.6937 (ptmt) cc_final: 0.6717 (ttpt) REVERT: C 398 MET cc_start: 0.0945 (mmm) cc_final: 0.0638 (mmm) REVERT: G 168 SER cc_start: 0.9054 (t) cc_final: 0.8809 (t) REVERT: W 46 GLN cc_start: 0.9105 (tm-30) cc_final: 0.8765 (tm-30) REVERT: W 78 TYR cc_start: 0.7986 (m-80) cc_final: 0.7700 (m-10) REVERT: U 3 THR cc_start: 0.8709 (OUTLIER) cc_final: 0.8239 (m) REVERT: U 14 GLU cc_start: 0.7070 (tt0) cc_final: 0.6687 (tt0) REVERT: U 94 LYS cc_start: 0.8734 (mmmt) cc_final: 0.8388 (mmmm) REVERT: U 97 ASP cc_start: 0.7962 (t70) cc_final: 0.7650 (t0) REVERT: U 98 ARG cc_start: 0.7949 (mtm110) cc_final: 0.7401 (ptp90) REVERT: K 94 LYS cc_start: 0.8066 (mmpt) cc_final: 0.7350 (mmmt) REVERT: D 26 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7598 (pm20) REVERT: D 447 LYS cc_start: 0.7789 (mttt) cc_final: 0.7571 (mttm) REVERT: A 26 GLN cc_start: 0.6285 (pm20) cc_final: 0.5965 (pm20) REVERT: A 36 TRP cc_start: 0.7776 (p90) cc_final: 0.7319 (p90) REVERT: A 82 LYS cc_start: 0.6916 (ptmt) cc_final: 0.6555 (mmtm) REVERT: B 36 TRP cc_start: 0.7838 (p90) cc_final: 0.7574 (p90) REVERT: B 82 LYS cc_start: 0.6620 (ptmt) cc_final: 0.6333 (mmtm) REVERT: B 170 SER cc_start: 0.7885 (m) cc_final: 0.7217 (p) REVERT: B 431 ARG cc_start: 0.6868 (mmt180) cc_final: 0.6436 (mmm160) REVERT: T 94 LYS cc_start: 0.7609 (mmtp) cc_final: 0.7342 (mmmt) REVERT: T 95 GLU cc_start: 0.7994 (tp30) cc_final: 0.7744 (tp30) REVERT: Z 31 ASP cc_start: 0.7312 (t70) cc_final: 0.7066 (t70) REVERT: Z 164 GLU cc_start: 0.7621 (mp0) cc_final: 0.7406 (mp0) outliers start: 151 outliers final: 134 residues processed: 742 average time/residue: 0.4994 time to fit residues: 613.7924 Evaluate side-chains 741 residues out of total 5691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 601 time to evaluate : 4.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 20 LEU Chi-restraints excluded: chain R residue 44 PHE Chi-restraints excluded: chain R residue 60 THR Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 6 MET Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain I residue 172 VAL Chi-restraints excluded: chain I residue 246 THR Chi-restraints excluded: chain I residue 249 ILE Chi-restraints excluded: chain a residue 38 VAL Chi-restraints excluded: chain a residue 53 SER Chi-restraints excluded: chain a residue 91 VAL Chi-restraints excluded: chain a residue 98 VAL Chi-restraints excluded: chain a residue 200 LEU Chi-restraints excluded: chain Q residue 3 THR Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 43 ASP Chi-restraints excluded: chain S residue 75 VAL Chi-restraints excluded: chain S residue 105 LEU Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 120 MET Chi-restraints excluded: chain F residue 129 HIS Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 316 GLN Chi-restraints excluded: chain F residue 357 TYR Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain F residue 458 ILE Chi-restraints excluded: chain N residue 13 ASP Chi-restraints excluded: chain N residue 44 PHE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 207 ILE Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain H residue 249 ILE Chi-restraints excluded: chain X residue 152 LEU Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain Y residue 38 VAL Chi-restraints excluded: chain Y residue 98 VAL Chi-restraints excluded: chain Y residue 188 ASN Chi-restraints excluded: chain Y residue 204 LEU Chi-restraints excluded: chain M residue 3 THR Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 60 THR Chi-restraints excluded: chain M residue 75 VAL Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 129 HIS Chi-restraints excluded: chain E residue 154 GLN Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 245 MET Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 357 TYR Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain J residue 8 ILE Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain J residue 134 ILE Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 97 ASP Chi-restraints excluded: chain L residue 113 ILE Chi-restraints excluded: chain L residue 134 ILE Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 246 THR Chi-restraints excluded: chain W residue 38 VAL Chi-restraints excluded: chain W residue 98 VAL Chi-restraints excluded: chain W residue 179 ASN Chi-restraints excluded: chain W residue 204 LEU Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 7 VAL Chi-restraints excluded: chain U residue 10 LEU Chi-restraints excluded: chain U residue 60 THR Chi-restraints excluded: chain U residue 68 ILE Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 129 HIS Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 270 ASN Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 357 TYR Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 79 SER Chi-restraints excluded: chain P residue 128 MET Chi-restraints excluded: chain T residue 12 VAL Chi-restraints excluded: chain T residue 59 GLU Chi-restraints excluded: chain T residue 82 VAL Chi-restraints excluded: chain T residue 97 ASP Chi-restraints excluded: chain V residue 99 THR Chi-restraints excluded: chain V residue 167 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 645 random chunks: chunk 380 optimal weight: 0.7980 chunk 612 optimal weight: 3.9990 chunk 373 optimal weight: 2.9990 chunk 290 optimal weight: 20.0000 chunk 425 optimal weight: 1.9990 chunk 642 optimal weight: 5.9990 chunk 591 optimal weight: 0.0370 chunk 511 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 chunk 395 optimal weight: 0.9980 chunk 313 optimal weight: 8.9990 overall best weight: 1.3662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 113 ASN H 161 GLN H 216 ASN Y 51 ASN O 103 GLN G 35 GLN ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 GLN T 100 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 51759 Z= 0.194 Angle : 0.533 11.809 70368 Z= 0.277 Chirality : 0.045 0.234 8196 Planarity : 0.004 0.056 9093 Dihedral : 4.545 64.205 7119 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.39 % Allowed : 19.43 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.51 (0.10), residues: 6522 helix: 0.96 (0.23), residues: 546 sheet: -0.92 (0.10), residues: 2667 loop : -1.36 (0.10), residues: 3309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 70 HIS 0.003 0.001 HIS A 20 PHE 0.022 0.001 PHE A 255 TYR 0.020 0.001 TYR P 109 ARG 0.008 0.000 ARG I 267 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13044 Ramachandran restraints generated. 6522 Oldfield, 0 Emsley, 6522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13044 Ramachandran restraints generated. 6522 Oldfield, 0 Emsley, 6522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 5691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 658 time to evaluate : 4.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 100 ASN cc_start: 0.7685 (t0) cc_final: 0.7146 (t0) REVERT: a 40 GLU cc_start: 0.7491 (mt-10) cc_final: 0.7280 (mt-10) REVERT: S 94 LYS cc_start: 0.8295 (mmpt) cc_final: 0.7609 (mmtp) REVERT: S 103 GLN cc_start: 0.8675 (mt0) cc_final: 0.8176 (mt0) REVERT: S 104 ARG cc_start: 0.8617 (mtm180) cc_final: 0.8001 (mtm110) REVERT: F 224 ILE cc_start: 0.8776 (OUTLIER) cc_final: 0.8358 (mt) REVERT: F 264 SER cc_start: 0.9058 (m) cc_final: 0.8572 (p) REVERT: F 348 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7412 (mt-10) REVERT: X 31 ASP cc_start: 0.7467 (t70) cc_final: 0.7048 (t70) REVERT: Y 1 MET cc_start: 0.7048 (OUTLIER) cc_final: 0.6242 (ttt) REVERT: Y 188 ASN cc_start: 0.8193 (OUTLIER) cc_final: 0.7744 (m-40) REVERT: E 102 ARG cc_start: 0.8311 (mtp85) cc_final: 0.7845 (mtp85) REVERT: E 120 MET cc_start: 0.7977 (OUTLIER) cc_final: 0.7566 (ptp) REVERT: E 398 MET cc_start: 0.6422 (mtp) cc_final: 0.6152 (mtp) REVERT: C 53 ARG cc_start: 0.6704 (mmt-90) cc_final: 0.5827 (mtp85) REVERT: C 431 ARG cc_start: 0.6776 (mmt180) cc_final: 0.6413 (mmt180) REVERT: G 142 ILE cc_start: 0.8786 (pt) cc_final: 0.8421 (pt) REVERT: G 168 SER cc_start: 0.9023 (t) cc_final: 0.8757 (t) REVERT: G 236 LYS cc_start: 0.8441 (mttp) cc_final: 0.8239 (mtpp) REVERT: G 267 ARG cc_start: 0.7764 (ttm110) cc_final: 0.7510 (ttp-110) REVERT: W 46 GLN cc_start: 0.9111 (tm-30) cc_final: 0.8797 (tm-30) REVERT: W 78 TYR cc_start: 0.7926 (m-80) cc_final: 0.7642 (m-10) REVERT: U 3 THR cc_start: 0.8680 (OUTLIER) cc_final: 0.8119 (m) REVERT: U 7 VAL cc_start: 0.8874 (OUTLIER) cc_final: 0.8672 (m) REVERT: U 14 GLU cc_start: 0.6974 (tt0) cc_final: 0.6592 (tt0) REVERT: U 94 LYS cc_start: 0.8715 (mmmt) cc_final: 0.8506 (mmmm) REVERT: U 97 ASP cc_start: 0.7903 (t70) cc_final: 0.7558 (t0) REVERT: U 98 ARG cc_start: 0.7945 (mtm110) cc_final: 0.7397 (ptp90) REVERT: K 94 LYS cc_start: 0.8259 (mmpt) cc_final: 0.7604 (mmmt) REVERT: D 26 GLN cc_start: 0.7941 (OUTLIER) cc_final: 0.7597 (pm20) REVERT: D 156 GLU cc_start: 0.7793 (tt0) cc_final: 0.7495 (tt0) REVERT: D 447 LYS cc_start: 0.7754 (mttt) cc_final: 0.7537 (mttm) REVERT: A 36 TRP cc_start: 0.7799 (p90) cc_final: 0.7373 (p90) REVERT: A 82 LYS cc_start: 0.6902 (ptmt) cc_final: 0.6551 (mmtm) REVERT: A 162 GLU cc_start: 0.7197 (tm-30) cc_final: 0.6941 (tm-30) REVERT: A 231 PHE cc_start: 0.7671 (p90) cc_final: 0.7105 (p90) REVERT: B 82 LYS cc_start: 0.6707 (ptmt) cc_final: 0.6497 (mmtm) REVERT: B 170 SER cc_start: 0.7900 (m) cc_final: 0.7214 (p) REVERT: B 231 PHE cc_start: 0.7601 (p90) cc_final: 0.7377 (p90) REVERT: T 54 LEU cc_start: 0.8591 (mt) cc_final: 0.8089 (mt) REVERT: T 94 LYS cc_start: 0.7504 (mmtp) cc_final: 0.7265 (mmmt) REVERT: T 95 GLU cc_start: 0.8007 (tp30) cc_final: 0.7763 (tp30) REVERT: V 26 ASP cc_start: 0.8603 (p0) cc_final: 0.8273 (p0) REVERT: Z 31 ASP cc_start: 0.7277 (t70) cc_final: 0.7018 (t70) REVERT: Z 164 GLU cc_start: 0.7674 (mp0) cc_final: 0.7438 (mp0) REVERT: Z 178 MET cc_start: 0.8487 (mmt) cc_final: 0.8156 (mmm) outliers start: 136 outliers final: 123 residues processed: 766 average time/residue: 0.5307 time to fit residues: 675.5879 Evaluate side-chains 761 residues out of total 5691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 631 time to evaluate : 4.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 44 PHE Chi-restraints excluded: chain R residue 60 THR Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain I residue 6 MET Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain I residue 172 VAL Chi-restraints excluded: chain I residue 246 THR Chi-restraints excluded: chain I residue 249 ILE Chi-restraints excluded: chain a residue 38 VAL Chi-restraints excluded: chain a residue 53 SER Chi-restraints excluded: chain a residue 98 VAL Chi-restraints excluded: chain a residue 200 LEU Chi-restraints excluded: chain Q residue 3 THR Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 43 ASP Chi-restraints excluded: chain S residue 75 VAL Chi-restraints excluded: chain S residue 105 LEU Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 120 MET Chi-restraints excluded: chain F residue 129 HIS Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 316 GLN Chi-restraints excluded: chain F residue 357 TYR Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain F residue 458 ILE Chi-restraints excluded: chain N residue 13 ASP Chi-restraints excluded: chain N residue 44 PHE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain H residue 249 ILE Chi-restraints excluded: chain X residue 152 LEU Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain Y residue 98 VAL Chi-restraints excluded: chain Y residue 188 ASN Chi-restraints excluded: chain Y residue 204 LEU Chi-restraints excluded: chain M residue 3 THR Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 60 THR Chi-restraints excluded: chain M residue 75 VAL Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 129 HIS Chi-restraints excluded: chain E residue 154 GLN Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 245 MET Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 357 TYR Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain J residue 8 ILE Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain J residue 134 ILE Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 97 ASP Chi-restraints excluded: chain L residue 113 ILE Chi-restraints excluded: chain L residue 134 ILE Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 246 THR Chi-restraints excluded: chain W residue 38 VAL Chi-restraints excluded: chain W residue 98 VAL Chi-restraints excluded: chain W residue 179 ASN Chi-restraints excluded: chain W residue 200 LEU Chi-restraints excluded: chain W residue 204 LEU Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 7 VAL Chi-restraints excluded: chain U residue 10 LEU Chi-restraints excluded: chain U residue 60 THR Chi-restraints excluded: chain U residue 68 ILE Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 129 HIS Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 357 TYR Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 79 SER Chi-restraints excluded: chain P residue 128 MET Chi-restraints excluded: chain T residue 12 VAL Chi-restraints excluded: chain T residue 59 GLU Chi-restraints excluded: chain T residue 82 VAL Chi-restraints excluded: chain T residue 97 ASP Chi-restraints excluded: chain V residue 99 THR Chi-restraints excluded: chain V residue 167 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 645 random chunks: chunk 406 optimal weight: 0.8980 chunk 545 optimal weight: 8.9990 chunk 156 optimal weight: 5.9990 chunk 471 optimal weight: 10.0000 chunk 75 optimal weight: 0.8980 chunk 142 optimal weight: 3.9990 chunk 512 optimal weight: 6.9990 chunk 214 optimal weight: 2.9990 chunk 526 optimal weight: 40.0000 chunk 64 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 113 ASN Y 51 ASN ** Y 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 103 GLN C 4 GLN G 35 GLN ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 GLN T 100 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.131018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.100512 restraints weight = 77743.077| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.63 r_work: 0.2945 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 51759 Z= 0.277 Angle : 0.562 9.253 70368 Z= 0.292 Chirality : 0.046 0.235 8196 Planarity : 0.004 0.056 9093 Dihedral : 4.667 64.665 7119 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.62 % Allowed : 19.61 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.54 (0.10), residues: 6522 helix: 0.89 (0.23), residues: 543 sheet: -0.93 (0.10), residues: 2661 loop : -1.37 (0.10), residues: 3318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C 70 HIS 0.004 0.001 HIS A 20 PHE 0.020 0.002 PHE A 255 TYR 0.022 0.002 TYR P 109 ARG 0.012 0.000 ARG I 267 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10613.89 seconds wall clock time: 187 minutes 45.50 seconds (11265.50 seconds total)