Starting phenix.real_space_refine on Thu Oct 29 05:46:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11fs_75667/10_2026/11fs_75667.cif Found real_map, /net/cci-nas-00/data/ceres_data/11fs_75667/10_2026/11fs_75667.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/11fs_75667/10_2026/11fs_75667.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11fs_75667/10_2026/11fs_75667.map" model { file = "/net/cci-nas-00/data/ceres_data/11fs_75667/10_2026/11fs_75667.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11fs_75667/10_2026/11fs_75667.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.000 sd= 0.021 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 104 5.49 5 Mg 2 5.21 5 S 76 5.16 5 C 19323 2.51 5 N 5102 2.21 5 O 5939 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30547 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 4478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4478 Classifications: {'peptide': 550} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 527} Chain breaks: 1 Chain: "C" Number of atoms: 2358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2358 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 14, 'TRANS': 288} Chain: "D" Number of atoms: 2438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2438 Classifications: {'peptide': 297} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 280} Chain: "E" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 200 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "F" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 972 Classifications: {'DNA': 47} Link IDs: {'rna3p': 46} Chain: "G" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 1005 Classifications: {'RNA': 47} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 11, 'rna3p_pur': 16, 'rna3p_pyr': 9} Link IDs: {'rna2p': 22, 'rna3p': 24} Chain: "H" Number of atoms: 2358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2358 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 14, 'TRANS': 288} Chain: "I" Number of atoms: 2358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2358 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 14, 'TRANS': 288} Chain: "J" Number of atoms: 2358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2358 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 14, 'TRANS': 288} Chain: "K" Number of atoms: 2358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2358 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 14, 'TRANS': 288} Chain: "L" Number of atoms: 2358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2358 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 14, 'TRANS': 288} Chain: "M" Number of atoms: 2022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2022 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 14, 'TRANS': 246} Chain breaks: 1 Chain: "N" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 891 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 1, 'TRANS': 110} Chain: "O" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 891 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 1, 'TRANS': 110} Chain: "P" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 891 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 1, 'TRANS': 110} Chain: "Q" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 891 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 1, 'TRANS': 110} Chain: "R" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 891 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 1, 'TRANS': 110} Chain: "S" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 826 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 1, 'TRANS': 102} Chain breaks: 1 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2738 SG CYS A 382 56.039 73.540 202.300 1.00278.84 S ATOM 2762 SG CYS A 385 56.177 69.705 202.542 1.00271.86 S ATOM 3035 SG CYS A 420 57.123 71.858 205.476 1.00284.41 S ATOM 3053 SG CYS A 423 59.303 72.039 202.233 1.00285.93 S Time building chain proxies: 5.85, per 1000 atoms: 0.19 Number of scatterers: 30547 At special positions: 0 Unit cell: (110.21, 125.19, 231.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 76 16.00 P 104 15.00 Mg 2 11.99 O 5939 8.00 N 5102 7.00 C 19323 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 152 " - pdb=" SG CYS A 156 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.22 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 703 " pdb="ZN ZN A 703 " - pdb=" SG CYS A 382 " pdb="ZN ZN A 703 " - pdb=" SG CYS A 420 " pdb="ZN ZN A 703 " - pdb=" SG CYS A 423 " pdb="ZN ZN A 703 " - pdb=" SG CYS A 385 " Number of angles added : 6 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6654 Finding SS restraints... Secondary structure from input PDB file: 158 helices and 51 sheets defined 50.0% alpha, 16.5% beta 39 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 3.19 Creating SS restraints... Processing helix chain 'A' and resid 39 through 44 Processing helix chain 'A' and resid 66 through 79 Processing helix chain 'A' and resid 80 through 82 No H-bonds generated for 'chain 'A' and resid 80 through 82' Processing helix chain 'A' and resid 83 through 92 Processing helix chain 'A' and resid 119 through 128 Processing helix chain 'A' and resid 135 through 143 Processing helix chain 'A' and resid 153 through 162 Processing helix chain 'A' and resid 167 through 171 removed outlier: 4.376A pdb=" N THR A 170 " --> pdb=" O ALA A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 223 removed outlier: 3.697A pdb=" N SER A 212 " --> pdb=" O LYS A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 256 Processing helix chain 'A' and resid 307 through 312 Processing helix chain 'A' and resid 335 through 351 removed outlier: 3.725A pdb=" N SER A 350 " --> pdb=" O ASP A 346 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 351 " --> pdb=" O LEU A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 356 Processing helix chain 'A' and resid 364 through 374 Processing helix chain 'A' and resid 395 through 400 Processing helix chain 'A' and resid 420 through 433 Processing helix chain 'A' and resid 468 through 486 removed outlier: 4.191A pdb=" N HIS A 486 " --> pdb=" O TYR A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 492 Processing helix chain 'A' and resid 495 through 501 removed outlier: 3.922A pdb=" N GLU A 499 " --> pdb=" O LYS A 496 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N TRP A 500 " --> pdb=" O LYS A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 507 removed outlier: 3.512A pdb=" N ASN A 507 " --> pdb=" O ALA A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 538 removed outlier: 3.772A pdb=" N GLN A 538 " --> pdb=" O PHE A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 569 Processing helix chain 'A' and resid 572 through 582 removed outlier: 3.681A pdb=" N VAL A 577 " --> pdb=" O GLY A 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 73 Processing helix chain 'C' and resid 80 through 89 Processing helix chain 'C' and resid 104 through 112 Processing helix chain 'C' and resid 116 through 123 Processing helix chain 'C' and resid 164 through 168 removed outlier: 3.580A pdb=" N ILE C 168 " --> pdb=" O LEU C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 185 Processing helix chain 'C' and resid 232 through 245 removed outlier: 3.624A pdb=" N HIS C 245 " --> pdb=" O LYS C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 286 Processing helix chain 'C' and resid 286 through 296 Processing helix chain 'C' and resid 297 through 303 removed outlier: 3.997A pdb=" N ARG C 303 " --> pdb=" O ASP C 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 43 Processing helix chain 'D' and resid 50 through 60 Processing helix chain 'D' and resid 132 through 144 Processing helix chain 'D' and resid 186 through 199 removed outlier: 3.726A pdb=" N LYS D 199 " --> pdb=" O ARG D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 209 Processing helix chain 'D' and resid 248 through 258 Processing helix chain 'H' and resid 45 through 72 Processing helix chain 'H' and resid 81 through 89 Processing helix chain 'H' and resid 104 through 112 Processing helix chain 'H' and resid 116 through 123 Processing helix chain 'H' and resid 147 through 155 removed outlier: 3.508A pdb=" N ASP H 153 " --> pdb=" O SER H 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 167 Processing helix chain 'H' and resid 179 through 185 Processing helix chain 'H' and resid 195 through 200 removed outlier: 4.255A pdb=" N VAL H 199 " --> pdb=" O LYS H 195 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS H 200 " --> pdb=" O VAL H 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 195 through 200' Processing helix chain 'H' and resid 232 through 244 Processing helix chain 'H' and resid 252 through 256 Processing helix chain 'H' and resid 268 through 286 Processing helix chain 'H' and resid 286 through 295 removed outlier: 3.618A pdb=" N LYS H 295 " --> pdb=" O GLN H 291 " (cutoff:3.500A) Processing helix chain 'H' and resid 297 through 303 removed outlier: 3.651A pdb=" N PHE H 301 " --> pdb=" O PRO H 298 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 73 Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 104 through 112 Processing helix chain 'I' and resid 116 through 123 Processing helix chain 'I' and resid 147 through 154 Processing helix chain 'I' and resid 164 through 167 Processing helix chain 'I' and resid 179 through 185 Processing helix chain 'I' and resid 196 through 201 removed outlier: 3.523A pdb=" N VAL I 199 " --> pdb=" O VAL I 196 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ALA I 201 " --> pdb=" O GLU I 198 " (cutoff:3.500A) Processing helix chain 'I' and resid 232 through 244 Processing helix chain 'I' and resid 252 through 256 Processing helix chain 'I' and resid 268 through 286 Processing helix chain 'I' and resid 286 through 296 Processing helix chain 'I' and resid 297 through 303 removed outlier: 3.753A pdb=" N PHE I 301 " --> pdb=" O PRO I 298 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 73 Processing helix chain 'J' and resid 81 through 89 Processing helix chain 'J' and resid 104 through 112 Processing helix chain 'J' and resid 116 through 123 Processing helix chain 'J' and resid 147 through 153 removed outlier: 3.599A pdb=" N ASP J 153 " --> pdb=" O SER J 149 " (cutoff:3.500A) Processing helix chain 'J' and resid 164 through 168 Processing helix chain 'J' and resid 179 through 185 Processing helix chain 'J' and resid 232 through 244 Processing helix chain 'J' and resid 252 through 256 Processing helix chain 'J' and resid 268 through 286 Processing helix chain 'J' and resid 286 through 296 removed outlier: 3.567A pdb=" N LYS J 295 " --> pdb=" O GLN J 291 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS J 296 " --> pdb=" O GLU J 292 " (cutoff:3.500A) Processing helix chain 'J' and resid 297 through 303 removed outlier: 3.542A pdb=" N ARG J 303 " --> pdb=" O ASP J 300 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 72 Processing helix chain 'K' and resid 81 through 89 Processing helix chain 'K' and resid 104 through 112 Processing helix chain 'K' and resid 116 through 123 Processing helix chain 'K' and resid 144 through 146 No H-bonds generated for 'chain 'K' and resid 144 through 146' Processing helix chain 'K' and resid 147 through 153 Processing helix chain 'K' and resid 164 through 167 Processing helix chain 'K' and resid 179 through 186 Processing helix chain 'K' and resid 196 through 200 removed outlier: 3.573A pdb=" N VAL K 199 " --> pdb=" O VAL K 196 " (cutoff:3.500A) Processing helix chain 'K' and resid 232 through 245 removed outlier: 3.629A pdb=" N HIS K 245 " --> pdb=" O LYS K 241 " (cutoff:3.500A) Processing helix chain 'K' and resid 252 through 256 Processing helix chain 'K' and resid 268 through 286 Processing helix chain 'K' and resid 286 through 295 removed outlier: 3.663A pdb=" N LYS K 295 " --> pdb=" O GLN K 291 " (cutoff:3.500A) Processing helix chain 'K' and resid 296 through 302 removed outlier: 7.077A pdb=" N ASN K 299 " --> pdb=" O LYS K 296 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 72 Processing helix chain 'L' and resid 81 through 89 Processing helix chain 'L' and resid 104 through 112 Processing helix chain 'L' and resid 116 through 123 Processing helix chain 'L' and resid 147 through 153 removed outlier: 3.582A pdb=" N ASP L 153 " --> pdb=" O SER L 149 " (cutoff:3.500A) Processing helix chain 'L' and resid 164 through 167 Processing helix chain 'L' and resid 179 through 185 Processing helix chain 'L' and resid 232 through 244 Processing helix chain 'L' and resid 268 through 286 Processing helix chain 'L' and resid 286 through 296 removed outlier: 3.578A pdb=" N LYS L 295 " --> pdb=" O GLN L 291 " (cutoff:3.500A) Processing helix chain 'L' and resid 299 through 303 Processing helix chain 'M' and resid 45 through 73 Processing helix chain 'M' and resid 81 through 89 Processing helix chain 'M' and resid 104 through 112 Processing helix chain 'M' and resid 116 through 123 Processing helix chain 'M' and resid 147 through 153 removed outlier: 3.926A pdb=" N ASP M 153 " --> pdb=" O SER M 149 " (cutoff:3.500A) Processing helix chain 'M' and resid 164 through 168 Processing helix chain 'M' and resid 232 through 245 removed outlier: 3.557A pdb=" N HIS M 245 " --> pdb=" O LYS M 241 " (cutoff:3.500A) Processing helix chain 'M' and resid 268 through 286 Processing helix chain 'M' and resid 286 through 295 removed outlier: 3.696A pdb=" N LYS M 295 " --> pdb=" O GLN M 291 " (cutoff:3.500A) Processing helix chain 'M' and resid 296 through 301 removed outlier: 6.908A pdb=" N ASN M 299 " --> pdb=" O LYS M 296 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N PHE M 301 " --> pdb=" O PRO M 298 " (cutoff:3.500A) Processing helix chain 'N' and resid 15 through 30 removed outlier: 3.631A pdb=" N ILE N 30 " --> pdb=" O ALA N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 43 Processing helix chain 'N' and resid 43 through 58 Processing helix chain 'N' and resid 61 through 74 Processing helix chain 'N' and resid 81 through 97 Processing helix chain 'N' and resid 98 through 109 Processing helix chain 'N' and resid 109 through 124 removed outlier: 3.585A pdb=" N ILE N 124 " --> pdb=" O TYR N 120 " (cutoff:3.500A) Processing helix chain 'O' and resid 15 through 30 removed outlier: 3.686A pdb=" N ILE O 30 " --> pdb=" O ALA O 26 " (cutoff:3.500A) Processing helix chain 'O' and resid 31 through 36 removed outlier: 5.822A pdb=" N GLY O 34 " --> pdb=" O ILE O 31 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N SER O 35 " --> pdb=" O ASP O 32 " (cutoff:3.500A) Processing helix chain 'O' and resid 37 through 43 removed outlier: 3.818A pdb=" N HIS O 41 " --> pdb=" O GLY O 37 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS O 43 " --> pdb=" O LYS O 39 " (cutoff:3.500A) Processing helix chain 'O' and resid 43 through 58 Processing helix chain 'O' and resid 61 through 74 Processing helix chain 'O' and resid 81 through 98 Processing helix chain 'O' and resid 98 through 109 Processing helix chain 'O' and resid 109 through 124 Processing helix chain 'P' and resid 15 through 30 removed outlier: 3.850A pdb=" N ILE P 30 " --> pdb=" O ALA P 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 33 through 36 Processing helix chain 'P' and resid 37 through 43 Processing helix chain 'P' and resid 43 through 58 Processing helix chain 'P' and resid 61 through 74 Processing helix chain 'P' and resid 81 through 97 Processing helix chain 'P' and resid 98 through 109 Processing helix chain 'P' and resid 109 through 124 Processing helix chain 'Q' and resid 15 through 30 removed outlier: 3.848A pdb=" N ILE Q 30 " --> pdb=" O ALA Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 33 through 37 removed outlier: 4.023A pdb=" N GLY Q 37 " --> pdb=" O GLY Q 34 " (cutoff:3.500A) Processing helix chain 'Q' and resid 38 through 43 Processing helix chain 'Q' and resid 43 through 59 removed outlier: 3.666A pdb=" N ILE Q 47 " --> pdb=" O LYS Q 43 " (cutoff:3.500A) Processing helix chain 'Q' and resid 61 through 74 removed outlier: 3.555A pdb=" N ALA Q 74 " --> pdb=" O LEU Q 70 " (cutoff:3.500A) Processing helix chain 'Q' and resid 81 through 97 Processing helix chain 'Q' and resid 98 through 109 Processing helix chain 'Q' and resid 109 through 123 Processing helix chain 'R' and resid 15 through 30 removed outlier: 3.625A pdb=" N ILE R 30 " --> pdb=" O ALA R 26 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 42 No H-bonds generated for 'chain 'R' and resid 40 through 42' Processing helix chain 'R' and resid 43 through 58 Processing helix chain 'R' and resid 61 through 74 Processing helix chain 'R' and resid 81 through 98 removed outlier: 3.764A pdb=" N HIS R 98 " --> pdb=" O LYS R 94 " (cutoff:3.500A) Processing helix chain 'R' and resid 98 through 109 Processing helix chain 'R' and resid 111 through 124 removed outlier: 3.610A pdb=" N ILE R 124 " --> pdb=" O TYR R 120 " (cutoff:3.500A) Processing helix chain 'S' and resid 16 through 30 removed outlier: 3.776A pdb=" N ILE S 30 " --> pdb=" O ALA S 26 " (cutoff:3.500A) Processing helix chain 'S' and resid 33 through 36 Processing helix chain 'S' and resid 37 through 43 removed outlier: 4.182A pdb=" N LYS S 43 " --> pdb=" O LYS S 39 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 59 Processing helix chain 'S' and resid 61 through 75 removed outlier: 3.775A pdb=" N VAL S 73 " --> pdb=" O LEU S 69 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY S 75 " --> pdb=" O SER S 71 " (cutoff:3.500A) Processing helix chain 'S' and resid 83 through 97 removed outlier: 3.547A pdb=" N ASN S 87 " --> pdb=" O GLU S 83 " (cutoff:3.500A) Processing helix chain 'S' and resid 98 through 107 Processing helix chain 'S' and resid 109 through 124 Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 51 removed outlier: 6.544A pdb=" N ILE A 48 " --> pdb=" O ILE A 511 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N TYR A 513 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N GLY A 50 " --> pdb=" O TYR A 513 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N ASP A 518 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU A 448 " --> pdb=" O ASP A 518 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N THR A 520 " --> pdb=" O ALA A 446 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ALA A 446 " --> pdb=" O THR A 520 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLN A 522 " --> pdb=" O GLU A 444 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 51 removed outlier: 6.544A pdb=" N ILE A 48 " --> pdb=" O ILE A 511 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N TYR A 513 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N GLY A 50 " --> pdb=" O TYR A 513 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 183 through 184 Processing sheet with id=AA4, first strand: chain 'A' and resid 183 through 184 Processing sheet with id=AA5, first strand: chain 'A' and resid 265 through 268 removed outlier: 7.221A pdb=" N ARG A 226 " --> pdb=" O MET A 266 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ILE A 268 " --> pdb=" O ARG A 226 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ARG A 228 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N SER A 272 " --> pdb=" O GLU A 230 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ARG A 232 " --> pdb=" O SER A 272 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 265 through 268 removed outlier: 7.221A pdb=" N ARG A 226 " --> pdb=" O MET A 266 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ILE A 268 " --> pdb=" O ARG A 226 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ARG A 228 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ASP A 292 " --> pdb=" O ARG A 301 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N VAL A 303 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL A 290 " --> pdb=" O VAL A 303 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 493 through 494 Processing sheet with id=AA8, first strand: chain 'C' and resid 135 through 137 removed outlier: 3.794A pdb=" N TYR C 141 " --> pdb=" O TYR C 222 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 135 through 137 Processing sheet with id=AB1, first strand: chain 'C' and resid 19 through 20 removed outlier: 6.766A pdb=" N THR C 24 " --> pdb=" O GLN C 213 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 28 through 32 Processing sheet with id=AB3, first strand: chain 'C' and resid 78 through 79 removed outlier: 3.778A pdb=" N ALA C 79 " --> pdb=" O ARG D 146 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 124 through 126 Processing sheet with id=AB5, first strand: chain 'C' and resid 190 through 193 removed outlier: 3.542A pdb=" N ALA H 79 " --> pdb=" O ASN C 191 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 71 through 72 removed outlier: 4.562A pdb=" N MET D 177 " --> pdb=" O CYS D 78 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N LYS D 94 " --> pdb=" O SER D 110 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N SER D 110 " --> pdb=" O LYS D 94 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N VAL D 96 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS D 108 " --> pdb=" O VAL D 96 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ALA D 105 " --> pdb=" O LYS D 222 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 15 through 19 removed outlier: 6.068A pdb=" N GLU D 22 " --> pdb=" O SER D 18 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU D 23 " --> pdb=" O SER D 168 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG D 170 " --> pdb=" O LEU D 23 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLN D 25 " --> pdb=" O ARG D 170 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ILE D 123 " --> pdb=" O LEU D 171 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 230 through 235 removed outlier: 4.547A pdb=" N ARG D 239 " --> pdb=" O VAL D 295 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA D 291 " --> pdb=" O THR D 243 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LYS D 271 " --> pdb=" O LYS D 289 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ALA D 291 " --> pdb=" O ASP D 269 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASP D 269 " --> pdb=" O ALA D 291 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N PHE D 293 " --> pdb=" O LEU D 267 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N LEU D 267 " --> pdb=" O PHE D 293 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N VAL D 295 " --> pdb=" O LEU D 265 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LEU D 265 " --> pdb=" O VAL D 295 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 135 through 137 Processing sheet with id=AC1, first strand: chain 'H' and resid 135 through 137 Processing sheet with id=AC2, first strand: chain 'H' and resid 19 through 20 Processing sheet with id=AC3, first strand: chain 'H' and resid 28 through 32 Processing sheet with id=AC4, first strand: chain 'H' and resid 124 through 125 Processing sheet with id=AC5, first strand: chain 'H' and resid 169 through 176 Processing sheet with id=AC6, first strand: chain 'H' and resid 191 through 193 Processing sheet with id=AC7, first strand: chain 'I' and resid 135 through 137 Processing sheet with id=AC8, first strand: chain 'I' and resid 135 through 137 Processing sheet with id=AC9, first strand: chain 'I' and resid 19 through 20 removed outlier: 7.091A pdb=" N THR I 24 " --> pdb=" O GLN I 213 " (cutoff:3.500A) removed outlier: 9.251A pdb=" N VAL I 215 " --> pdb=" O THR I 24 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 28 through 32 Processing sheet with id=AD2, first strand: chain 'I' and resid 124 through 125 Processing sheet with id=AD3, first strand: chain 'I' and resid 192 through 193 Processing sheet with id=AD4, first strand: chain 'J' and resid 135 through 137 Processing sheet with id=AD5, first strand: chain 'J' and resid 135 through 137 Processing sheet with id=AD6, first strand: chain 'J' and resid 18 through 20 removed outlier: 4.054A pdb=" N GLU J 18 " --> pdb=" O LEU J 25 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N THR J 24 " --> pdb=" O GLN J 213 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 28 through 32 Processing sheet with id=AD8, first strand: chain 'J' and resid 192 through 193 Processing sheet with id=AD9, first strand: chain 'K' and resid 135 through 137 removed outlier: 3.946A pdb=" N TYR K 141 " --> pdb=" O TYR K 222 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 135 through 137 Processing sheet with id=AE2, first strand: chain 'K' and resid 19 through 20 removed outlier: 6.922A pdb=" N THR K 24 " --> pdb=" O GLN K 213 " (cutoff:3.500A) removed outlier: 9.025A pdb=" N VAL K 215 " --> pdb=" O THR K 24 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 28 through 32 Processing sheet with id=AE4, first strand: chain 'K' and resid 124 through 125 Processing sheet with id=AE5, first strand: chain 'K' and resid 191 through 193 Processing sheet with id=AE6, first strand: chain 'L' and resid 135 through 137 Processing sheet with id=AE7, first strand: chain 'L' and resid 135 through 137 Processing sheet with id=AE8, first strand: chain 'L' and resid 19 through 20 removed outlier: 7.064A pdb=" N THR L 24 " --> pdb=" O GLN L 213 " (cutoff:3.500A) removed outlier: 9.212A pdb=" N VAL L 215 " --> pdb=" O THR L 24 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'L' and resid 28 through 32 Processing sheet with id=AF1, first strand: chain 'L' and resid 124 through 125 Processing sheet with id=AF2, first strand: chain 'L' and resid 191 through 193 removed outlier: 6.369A pdb=" N ASN L 191 " --> pdb=" O ALA M 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'M' and resid 135 through 137 Processing sheet with id=AF4, first strand: chain 'M' and resid 135 through 137 Processing sheet with id=AF5, first strand: chain 'M' and resid 16 through 20 removed outlier: 5.489A pdb=" N GLU M 18 " --> pdb=" O LEU M 25 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU M 25 " --> pdb=" O GLU M 18 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'M' and resid 28 through 32 1457 hydrogen bonds defined for protein. 4104 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 102 hydrogen bonds 204 hydrogen bond angles 0 basepair planarities 39 basepair parallelities 45 stacking parallelities Total time for adding SS restraints: 6.23 Time building geometry restraints manager: 3.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8395 1.33 - 1.46: 5774 1.46 - 1.58: 16776 1.58 - 1.70: 205 1.70 - 1.82: 145 Bond restraints: 31295 Sorted by residual: bond pdb=" C3' DG F 6 " pdb=" C2' DG F 6 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.10e+01 bond pdb=" C3' DA F 42 " pdb=" C2' DA F 42 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.52e+00 bond pdb=" C1' DC F 30 " pdb=" N1 DC F 30 " ideal model delta sigma weight residual 1.468 1.508 -0.040 1.40e-02 5.10e+03 8.15e+00 bond pdb=" N HIS A 115 " pdb=" CA HIS A 115 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.22e-02 6.72e+03 7.64e+00 bond pdb=" C3' DA F 26 " pdb=" C2' DA F 26 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.34e+00 ... (remaining 31290 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 41557 1.45 - 2.90: 943 2.90 - 4.35: 136 4.35 - 5.79: 30 5.79 - 7.24: 2 Bond angle restraints: 42668 Sorted by residual: angle pdb=" O4' DG F 19 " pdb=" C4' DG F 19 " pdb=" C3' DG F 19 " ideal model delta sigma weight residual 106.00 102.08 3.92 6.00e-01 2.78e+00 4.26e+01 angle pdb=" O4' DG F 13 " pdb=" C4' DG F 13 " pdb=" C3' DG F 13 " ideal model delta sigma weight residual 106.00 102.58 3.42 6.00e-01 2.78e+00 3.26e+01 angle pdb=" O4' DG F 25 " pdb=" C4' DG F 25 " pdb=" C3' DG F 25 " ideal model delta sigma weight residual 106.00 102.65 3.35 6.00e-01 2.78e+00 3.12e+01 angle pdb=" O4' DA F 31 " pdb=" C4' DA F 31 " pdb=" C3' DA F 31 " ideal model delta sigma weight residual 106.00 102.80 3.20 6.00e-01 2.78e+00 2.85e+01 angle pdb=" C3' C G 9 " pdb=" O3' C G 9 " pdb=" P U G 10 " ideal model delta sigma weight residual 119.70 125.94 -6.24 1.20e+00 6.94e-01 2.70e+01 ... (remaining 42663 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 18461 35.84 - 71.68: 503 71.68 - 107.53: 26 107.53 - 143.37: 1 143.37 - 179.21: 10 Dihedral angle restraints: 19001 sinusoidal: 8629 harmonic: 10372 Sorted by residual: dihedral pdb=" O4' U G 2 " pdb=" C1' U G 2 " pdb=" N1 U G 2 " pdb=" C2 U G 2 " ideal model delta sinusoidal sigma weight residual 200.00 53.14 146.86 1 1.50e+01 4.44e-03 7.84e+01 dihedral pdb=" O4' U G 20 " pdb=" C1' U G 20 " pdb=" N1 U G 20 " pdb=" C2 U G 20 " ideal model delta sinusoidal sigma weight residual -128.00 46.66 -174.66 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" CB CYS A 152 " pdb=" SG CYS A 152 " pdb=" SG CYS A 156 " pdb=" CB CYS A 156 " ideal model delta sinusoidal sigma weight residual 93.00 26.84 66.16 1 1.00e+01 1.00e-02 5.72e+01 ... (remaining 18998 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 3930 0.050 - 0.100: 781 0.100 - 0.150: 233 0.150 - 0.200: 13 0.200 - 0.250: 1 Chirality restraints: 4958 Sorted by residual: chirality pdb=" C3' C G 9 " pdb=" C4' C G 9 " pdb=" O3' C G 9 " pdb=" C2' C G 9 " both_signs ideal model delta sigma weight residual False -2.74 -2.49 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" C3' DC F 30 " pdb=" C4' DC F 30 " pdb=" O3' DC F 30 " pdb=" C2' DC F 30 " both_signs ideal model delta sigma weight residual False -2.73 -2.53 -0.20 2.00e-01 2.50e+01 9.61e-01 chirality pdb=" C3' DT F 17 " pdb=" C4' DT F 17 " pdb=" O3' DT F 17 " pdb=" C2' DT F 17 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.54e-01 ... (remaining 4955 not shown) Planarity restraints: 4955 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN D 19 " 0.044 5.00e-02 4.00e+02 6.59e-02 6.95e+00 pdb=" N PRO D 20 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO D 20 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 20 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G G 30 " -0.034 2.00e-02 2.50e+03 1.45e-02 6.35e+00 pdb=" N9 G G 30 " 0.034 2.00e-02 2.50e+03 pdb=" C8 G G 30 " 0.005 2.00e-02 2.50e+03 pdb=" N7 G G 30 " -0.000 2.00e-02 2.50e+03 pdb=" C5 G G 30 " -0.002 2.00e-02 2.50e+03 pdb=" C6 G G 30 " -0.003 2.00e-02 2.50e+03 pdb=" O6 G G 30 " -0.009 2.00e-02 2.50e+03 pdb=" N1 G G 30 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G G 30 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G G 30 " 0.003 2.00e-02 2.50e+03 pdb=" N3 G G 30 " 0.004 2.00e-02 2.50e+03 pdb=" C4 G G 30 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A G 12 " 0.032 2.00e-02 2.50e+03 1.50e-02 6.21e+00 pdb=" N9 A G 12 " -0.036 2.00e-02 2.50e+03 pdb=" C8 A G 12 " -0.002 2.00e-02 2.50e+03 pdb=" N7 A G 12 " 0.002 2.00e-02 2.50e+03 pdb=" C5 A G 12 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A G 12 " 0.003 2.00e-02 2.50e+03 pdb=" N6 A G 12 " 0.008 2.00e-02 2.50e+03 pdb=" N1 A G 12 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A G 12 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A G 12 " -0.006 2.00e-02 2.50e+03 pdb=" C4 A G 12 " -0.003 2.00e-02 2.50e+03 ... (remaining 4952 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 21 2.59 - 3.17: 24906 3.17 - 3.74: 48567 3.74 - 4.32: 66855 4.32 - 4.90: 110513 Nonbonded interactions: 250862 Sorted by model distance: nonbonded pdb=" NE2 HIS A 70 " pdb="MG MG A 701 " model vdw 2.010 2.250 nonbonded pdb=" OD1 ASP A 94 " pdb="MG MG A 702 " model vdw 2.018 2.170 nonbonded pdb=" OD2 ASP A 94 " pdb="MG MG A 701 " model vdw 2.078 2.170 nonbonded pdb=" NE2 HIS A 93 " pdb="MG MG A 701 " model vdw 2.092 2.250 nonbonded pdb=" OE2 GLU A 159 " pdb="MG MG A 701 " model vdw 2.153 2.170 ... (remaining 250857 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 'C' and (resid 1 through 170 or resid 213 through 303)) selection = (chain 'H' and (resid 1 through 170 or resid 213 through 303)) selection = (chain 'I' and (resid 1 through 170 or resid 213 through 303)) selection = (chain 'J' and (resid 1 through 170 or resid 213 through 303)) selection = (chain 'K' and (resid 1 through 170 or resid 213 through 303)) selection = (chain 'L' and (resid 1 through 170 or resid 213 through 303)) selection = chain 'M' } ncs_group { reference = (chain 'N' and (resid 15 through 75 or resid 82 through 124)) selection = (chain 'O' and (resid 15 through 75 or resid 82 through 124)) selection = (chain 'P' and (resid 15 through 75 or resid 82 through 124)) selection = (chain 'Q' and (resid 15 through 75 or resid 82 through 124)) selection = (chain 'R' and (resid 15 through 75 or resid 82 through 124)) selection = chain 'S' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.480 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 31.110 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 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 0.040 31300 Z= 0.201 Angle : 0.530 8.235 42676 Z= 0.363 Chirality : 0.044 0.250 4958 Planarity : 0.003 0.066 4955 Dihedral : 16.414 179.212 12344 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.14), residues: 3554 helix: 2.10 (0.14), residues: 1593 sheet: -0.44 (0.22), residues: 567 loop : -1.14 (0.16), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 50 TYR 0.014 0.001 TYR A 116 PHE 0.009 0.001 PHE A 588 TRP 0.019 0.001 TRP D 244 HIS 0.006 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.20 (31295) covalent geometry : angle 0.52720 / 0.36 (42668) SS BOND : bond 0.00405 / 0.21 ( 1) SS BOND : angle 1.18929 / 0.69 ( 2) hydrogen bonds : bond 0.12589 / 8.03 ( 1539) hydrogen bonds : angle 5.77342 / 4.14 ( 4308) metal coordination : bond 0.00487 / 0.25 ( 4) metal coordination : angle 4.56097 / 2.24 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 3154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 616 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.4384 (t60) cc_final: 0.4068 (t60) REVERT: A 148 LYS cc_start: 0.5640 (mttt) cc_final: 0.4486 (ttpp) REVERT: A 281 PHE cc_start: 0.8299 (m-80) cc_final: 0.7945 (m-10) REVERT: A 309 MET cc_start: 0.8643 (mtt) cc_final: 0.8340 (mtp) REVERT: A 445 GLU cc_start: 0.8445 (pt0) cc_final: 0.8194 (pp20) REVERT: A 557 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8469 (mp0) REVERT: C 17 TYR cc_start: 0.7938 (t80) cc_final: 0.7588 (t80) REVERT: C 19 SER cc_start: 0.9051 (m) cc_final: 0.8812 (p) REVERT: C 32 ILE cc_start: 0.9208 (mm) cc_final: 0.8855 (mt) REVERT: C 74 GLN cc_start: 0.8337 (mt0) cc_final: 0.8008 (mt0) REVERT: C 296 LYS cc_start: 0.7944 (mttt) cc_final: 0.7687 (tttt) REVERT: D 19 ASN cc_start: 0.8199 (t0) cc_final: 0.7991 (t0) REVERT: D 24 SER cc_start: 0.8094 (m) cc_final: 0.7495 (t) REVERT: D 46 ASN cc_start: 0.8848 (m-40) cc_final: 0.8608 (p0) REVERT: D 124 PHE cc_start: 0.7855 (t80) cc_final: 0.7235 (t80) REVERT: D 175 ASN cc_start: 0.9242 (m110) cc_final: 0.8878 (m-40) REVERT: D 255 MET cc_start: 0.8458 (mtp) cc_final: 0.7864 (tpp) REVERT: D 296 GLN cc_start: 0.7874 (tt0) cc_final: 0.7417 (tt0) REVERT: H 18 GLU cc_start: 0.8540 (pt0) cc_final: 0.8048 (pm20) REVERT: H 23 GLU cc_start: 0.8283 (tt0) cc_final: 0.8029 (tm-30) REVERT: H 27 TYR cc_start: 0.9136 (t80) cc_final: 0.8813 (t80) REVERT: H 187 LYS cc_start: 0.9029 (tttt) cc_final: 0.8812 (tptt) REVERT: J 20 ILE cc_start: 0.9120 (mt) cc_final: 0.8819 (mm) REVERT: J 28 SER cc_start: 0.9523 (m) cc_final: 0.8995 (p) REVERT: J 40 GLU cc_start: 0.8876 (mm-30) cc_final: 0.8206 (mm-30) REVERT: J 63 GLU cc_start: 0.9038 (mt-10) cc_final: 0.8600 (tm-30) REVERT: J 104 ASN cc_start: 0.8517 (t0) cc_final: 0.8239 (t0) REVERT: K 109 MET cc_start: 0.9000 (mmm) cc_final: 0.8345 (mmm) REVERT: K 122 MET cc_start: 0.9411 (mmm) cc_final: 0.8426 (mmm) REVERT: K 180 MET cc_start: 0.8415 (tpt) cc_final: 0.7902 (tpp) REVERT: L 19 SER cc_start: 0.8548 (m) cc_final: 0.8326 (p) REVERT: L 175 THR cc_start: 0.7874 (m) cc_final: 0.7137 (p) REVERT: L 211 TYR cc_start: 0.8411 (m-80) cc_final: 0.8149 (m-80) REVERT: L 248 LYS cc_start: 0.8843 (mttt) cc_final: 0.8627 (mttp) REVERT: M 35 ASP cc_start: 0.8767 (m-30) cc_final: 0.8496 (p0) REVERT: M 64 ASP cc_start: 0.8574 (m-30) cc_final: 0.8214 (m-30) REVERT: M 109 MET cc_start: 0.8573 (mmm) cc_final: 0.7676 (mmm) REVERT: M 114 TYR cc_start: 0.7471 (m-10) cc_final: 0.5851 (m-10) REVERT: M 129 ILE cc_start: 0.8614 (mt) cc_final: 0.8196 (tp) REVERT: M 159 ASP cc_start: 0.6945 (t0) cc_final: 0.6461 (t0) REVERT: M 214 VAL cc_start: 0.7703 (m) cc_final: 0.7488 (m) REVERT: M 221 PHE cc_start: 0.7782 (m-80) cc_final: 0.7006 (m-10) REVERT: M 248 LYS cc_start: 0.5281 (mttt) cc_final: 0.4965 (ptpp) REVERT: M 281 ASN cc_start: 0.8785 (m-40) cc_final: 0.8150 (m110) REVERT: N 72 GLN cc_start: 0.8040 (mt0) cc_final: 0.7733 (mp10) REVERT: N 87 ASN cc_start: 0.9345 (t0) cc_final: 0.8961 (m110) REVERT: O 18 ASP cc_start: 0.9151 (m-30) cc_final: 0.8760 (m-30) REVERT: P 63 ASP cc_start: 0.8802 (m-30) cc_final: 0.8384 (m-30) REVERT: Q 32 ASP cc_start: 0.8235 (t0) cc_final: 0.7908 (m-30) REVERT: Q 69 LEU cc_start: 0.8947 (tp) cc_final: 0.8680 (tp) REVERT: Q 117 TYR cc_start: 0.8837 (t80) cc_final: 0.8621 (t80) REVERT: R 30 ILE cc_start: 0.9083 (pt) cc_final: 0.8866 (mm) REVERT: R 33 TRP cc_start: 0.7674 (m100) cc_final: 0.7257 (m100) REVERT: R 61 SER cc_start: 0.6864 (p) cc_final: 0.6566 (t) REVERT: R 81 SER cc_start: 0.6973 (p) cc_final: 0.5355 (m) REVERT: R 83 GLU cc_start: 0.8961 (tm-30) cc_final: 0.8387 (pm20) REVERT: S 19 LEU cc_start: 0.6836 (mt) cc_final: 0.6634 (mt) REVERT: S 43 LYS cc_start: 0.5277 (mttt) cc_final: 0.5053 (mmtp) REVERT: S 57 LYS cc_start: 0.7605 (mttt) cc_final: 0.7388 (tptp) REVERT: S 90 GLU cc_start: 0.7814 (tm-30) cc_final: 0.7589 (tm-30) outliers start: 0 outliers final: 0 residues processed: 616 average time/residue: 0.2180 time to fit residues: 205.5667 Evaluate side-chains 327 residues out of total 3154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 327 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 298] chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 105 ASN H 100 GLN H 208 GLN K 74 GLN K 213 GLN K 291 GLN L 274 ASN L 291 GLN M 47 ASN M 274 ASN M 281 ASN Q 41 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.114985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.073766 restraints weight = 72530.664| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.98 r_work: 0.2949 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.094 31300 Z= 0.329 Angle : 0.697 9.435 42676 Z= 0.361 Chirality : 0.049 0.521 4958 Planarity : 0.004 0.062 4955 Dihedral : 15.941 178.967 5158 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.30 % Allowed : 10.59 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.14), residues: 3554 helix: 1.95 (0.13), residues: 1597 sheet: -0.46 (0.21), residues: 577 loop : -1.28 (0.16), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG Q 42 TYR 0.024 0.002 TYR I 112 PHE 0.022 0.002 PHE Q 88 TRP 0.024 0.002 TRP A 474 HIS 0.007 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00756 / 0.33 (31295) covalent geometry : angle 0.69550 / 0.36 (42668) SS BOND : bond 0.00218 / 0.11 ( 1) SS BOND : angle 1.43209 / 0.84 ( 2) hydrogen bonds : bond 0.04917 / 3.26 ( 1539) hydrogen bonds : angle 5.00881 / 3.56 ( 4308) metal coordination : bond 0.02071 / 1.05 ( 4) metal coordination : angle 4.18794 / 2.20 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 3154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 310 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 LYS cc_start: 0.5557 (mttt) cc_final: 0.4415 (ttpp) REVERT: A 281 PHE cc_start: 0.8418 (m-80) cc_final: 0.8103 (m-10) REVERT: A 309 MET cc_start: 0.8635 (mtt) cc_final: 0.8261 (mtp) REVERT: A 445 GLU cc_start: 0.8435 (pt0) cc_final: 0.7899 (pp20) REVERT: A 474 TRP cc_start: 0.8576 (t-100) cc_final: 0.8307 (m100) REVERT: A 554 MET cc_start: 0.7271 (mtm) cc_final: 0.6531 (mtt) REVERT: C 17 TYR cc_start: 0.8163 (t80) cc_final: 0.7872 (t80) REVERT: C 32 ILE cc_start: 0.9355 (mm) cc_final: 0.9102 (mt) REVERT: C 296 LYS cc_start: 0.8078 (mttt) cc_final: 0.7802 (tptt) REVERT: D 19 ASN cc_start: 0.8717 (t0) cc_final: 0.8197 (m-40) REVERT: D 23 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8640 (pp) REVERT: D 124 PHE cc_start: 0.7977 (t80) cc_final: 0.7340 (t80) REVERT: D 175 ASN cc_start: 0.9271 (m110) cc_final: 0.8936 (m-40) REVERT: D 177 MET cc_start: 0.8669 (mmm) cc_final: 0.8151 (tpp) REVERT: D 217 GLN cc_start: 0.8703 (mm-40) cc_final: 0.8153 (mm-40) REVERT: D 255 MET cc_start: 0.8391 (mtp) cc_final: 0.7787 (tpp) REVERT: H 1 MET cc_start: 0.8764 (tpp) cc_final: 0.8523 (ttm) REVERT: H 27 TYR cc_start: 0.9218 (t80) cc_final: 0.8764 (t80) REVERT: I 122 MET cc_start: 0.9239 (mmm) cc_final: 0.8925 (mtp) REVERT: J 20 ILE cc_start: 0.9274 (mt) cc_final: 0.8984 (mm) REVERT: J 28 SER cc_start: 0.9488 (m) cc_final: 0.8801 (p) REVERT: J 40 GLU cc_start: 0.8664 (mm-30) cc_final: 0.8022 (mm-30) REVERT: J 63 GLU cc_start: 0.9028 (mt-10) cc_final: 0.8814 (tm-30) REVERT: J 74 GLN cc_start: 0.7915 (mp10) cc_final: 0.7684 (mp10) REVERT: K 180 MET cc_start: 0.8694 (tpt) cc_final: 0.8387 (tpp) REVERT: L 122 MET cc_start: 0.9379 (mmm) cc_final: 0.8425 (mtm) REVERT: L 150 LEU cc_start: 0.9176 (tp) cc_final: 0.8850 (tp) REVERT: L 175 THR cc_start: 0.8105 (m) cc_final: 0.7262 (p) REVERT: L 177 LYS cc_start: 0.8792 (tttm) cc_final: 0.8450 (tmtt) REVERT: L 213 GLN cc_start: 0.9152 (mt0) cc_final: 0.8524 (mt0) REVERT: M 35 ASP cc_start: 0.8701 (m-30) cc_final: 0.8473 (p0) REVERT: M 47 ASN cc_start: 0.8197 (OUTLIER) cc_final: 0.7820 (t0) REVERT: M 109 MET cc_start: 0.8831 (mmm) cc_final: 0.7975 (mmm) REVERT: M 129 ILE cc_start: 0.8765 (mt) cc_final: 0.8364 (tp) REVERT: M 159 ASP cc_start: 0.6862 (t0) cc_final: 0.6370 (t0) REVERT: M 281 ASN cc_start: 0.8677 (m110) cc_final: 0.8120 (m110) REVERT: N 72 GLN cc_start: 0.8348 (mt0) cc_final: 0.7936 (mp10) REVERT: N 87 ASN cc_start: 0.9299 (t0) cc_final: 0.8951 (m110) REVERT: P 77 SER cc_start: 0.8350 (m) cc_final: 0.7601 (p) REVERT: P 120 TYR cc_start: 0.8317 (t80) cc_final: 0.8102 (t80) REVERT: Q 32 ASP cc_start: 0.8259 (t0) cc_final: 0.7946 (m-30) REVERT: R 45 TYR cc_start: 0.8131 (m-80) cc_final: 0.7637 (m-80) REVERT: S 57 LYS cc_start: 0.8020 (mttt) cc_final: 0.7643 (tptp) outliers start: 41 outliers final: 27 residues processed: 336 average time/residue: 0.1880 time to fit residues: 100.9345 Evaluate side-chains 311 residues out of total 3154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 282 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 487 ARG Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 108 ILE Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 210 LEU Chi-restraints excluded: chain H residue 249 ILE Chi-restraints excluded: chain J residue 19 SER Chi-restraints excluded: chain K residue 190 LEU Chi-restraints excluded: chain K residue 289 ASP Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain M residue 47 ASN Chi-restraints excluded: chain M residue 289 ASP Chi-restraints excluded: chain P residue 71 SER Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 80 ILE Chi-restraints excluded: chain R residue 52 ILE Chi-restraints excluded: chain R residue 59 SER Chi-restraints excluded: chain R residue 80 ILE Chi-restraints excluded: chain S residue 24 LEU Chi-restraints excluded: chain S residue 114 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: [70, 174, 296, 245, 100, 314, 230, 310, 94, 43, 64] chunk 70 optimal weight: 0.6980 chunk 174 optimal weight: 1.9990 chunk 296 optimal weight: 9.9990 chunk 245 optimal weight: 0.9980 chunk 100 optimal weight: 0.0980 chunk 314 optimal weight: 0.9990 chunk 230 optimal weight: 1.9990 chunk 310 optimal weight: 0.7980 chunk 94 optimal weight: 7.9990 chunk 43 optimal weight: 8.9990 chunk 64 optimal weight: 10.0000 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 74 GLN K 213 GLN K 291 GLN L 291 GLN M 47 ASN M 274 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.117473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.076742 restraints weight = 72029.693| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 3.00 r_work: 0.3010 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31300 Z= 0.132 Angle : 0.546 8.458 42676 Z= 0.293 Chirality : 0.045 0.465 4958 Planarity : 0.004 0.067 4955 Dihedral : 15.940 177.103 5158 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.01 % Allowed : 11.98 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.14), residues: 3554 helix: 1.90 (0.13), residues: 1608 sheet: -0.40 (0.21), residues: 564 loop : -1.20 (0.16), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 252 TYR 0.017 0.001 TYR S 120 PHE 0.016 0.001 PHE Q 88 TRP 0.028 0.002 TRP D 282 HIS 0.008 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (31295) covalent geometry : angle 0.54455 / 0.29 (42668) SS BOND : bond 0.02205 / 1.16 ( 1) SS BOND : angle 1.60733 / 0.91 ( 2) hydrogen bonds : bond 0.04155 / 2.75 ( 1539) hydrogen bonds : angle 4.70016 / 3.35 ( 4308) metal coordination : bond 0.01001 / 0.51 ( 4) metal coordination : angle 3.70317 / 1.97 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 3154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 325 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.5505 (t60) cc_final: 0.5037 (t60) REVERT: A 111 TRP cc_start: 0.7606 (m100) cc_final: 0.7080 (m100) REVERT: A 148 LYS cc_start: 0.5561 (mttt) cc_final: 0.4404 (ttpp) REVERT: A 152 CYS cc_start: 0.2948 (OUTLIER) cc_final: 0.2289 (p) REVERT: A 281 PHE cc_start: 0.8392 (m-80) cc_final: 0.8045 (m-10) REVERT: A 309 MET cc_start: 0.8635 (mtt) cc_final: 0.8331 (mtp) REVERT: A 445 GLU cc_start: 0.8417 (pt0) cc_final: 0.7759 (pp20) REVERT: A 467 ARG cc_start: 0.7307 (ttp-170) cc_final: 0.6789 (ttp80) REVERT: A 474 TRP cc_start: 0.8640 (t-100) cc_final: 0.8398 (m100) REVERT: A 519 MET cc_start: 0.7504 (tmm) cc_final: 0.7279 (tmm) REVERT: C 17 TYR cc_start: 0.7986 (t80) cc_final: 0.7615 (t80) REVERT: C 32 ILE cc_start: 0.9341 (mm) cc_final: 0.9085 (mt) REVERT: C 296 LYS cc_start: 0.8020 (mttt) cc_final: 0.7758 (tptt) REVERT: D 91 MET cc_start: 0.8369 (mmt) cc_final: 0.8155 (mmt) REVERT: D 124 PHE cc_start: 0.7898 (t80) cc_final: 0.7177 (t80) REVERT: D 175 ASN cc_start: 0.9204 (m110) cc_final: 0.8910 (m-40) REVERT: D 177 MET cc_start: 0.8686 (mmm) cc_final: 0.8167 (tpp) REVERT: D 217 GLN cc_start: 0.8734 (mm-40) cc_final: 0.8437 (mm-40) REVERT: D 255 MET cc_start: 0.8395 (mtp) cc_final: 0.7785 (tpp) REVERT: H 27 TYR cc_start: 0.9175 (t80) cc_final: 0.8810 (t80) REVERT: I 11 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8201 (mt-10) REVERT: I 122 MET cc_start: 0.9106 (mmm) cc_final: 0.8712 (mtp) REVERT: I 224 TYR cc_start: 0.8996 (p90) cc_final: 0.8745 (p90) REVERT: I 291 GLN cc_start: 0.9162 (tt0) cc_final: 0.8631 (mt0) REVERT: J 20 ILE cc_start: 0.9199 (mt) cc_final: 0.8970 (mm) REVERT: J 28 SER cc_start: 0.9518 (m) cc_final: 0.8771 (p) REVERT: J 40 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8053 (mm-30) REVERT: J 74 GLN cc_start: 0.7990 (mp10) cc_final: 0.7747 (mp10) REVERT: J 208 GLN cc_start: 0.8016 (mt0) cc_final: 0.7812 (mt0) REVERT: K 180 MET cc_start: 0.8606 (tpt) cc_final: 0.8317 (tpp) REVERT: L 122 MET cc_start: 0.9289 (mmm) cc_final: 0.8444 (mmm) REVERT: L 175 THR cc_start: 0.7992 (m) cc_final: 0.7341 (p) REVERT: L 177 LYS cc_start: 0.8677 (tttm) cc_final: 0.8376 (tmtt) REVERT: L 180 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.8036 (ppp) REVERT: M 35 ASP cc_start: 0.8684 (m-30) cc_final: 0.8463 (p0) REVERT: M 40 GLU cc_start: 0.8628 (mp0) cc_final: 0.8299 (mm-30) REVERT: M 47 ASN cc_start: 0.8006 (m-40) cc_final: 0.7788 (t0) REVERT: M 104 ASN cc_start: 0.8850 (t0) cc_final: 0.8615 (t0) REVERT: M 109 MET cc_start: 0.8842 (mmm) cc_final: 0.7908 (mmm) REVERT: M 129 ILE cc_start: 0.8796 (mt) cc_final: 0.8353 (tp) REVERT: M 159 ASP cc_start: 0.6886 (t0) cc_final: 0.6390 (t0) REVERT: M 281 ASN cc_start: 0.8804 (m110) cc_final: 0.8306 (m110) REVERT: N 72 GLN cc_start: 0.8324 (mt0) cc_final: 0.7944 (mp10) REVERT: N 87 ASN cc_start: 0.9276 (t0) cc_final: 0.8924 (m110) REVERT: P 77 SER cc_start: 0.8314 (m) cc_final: 0.7597 (p) REVERT: P 120 TYR cc_start: 0.8288 (t80) cc_final: 0.8044 (t80) REVERT: Q 32 ASP cc_start: 0.8178 (t0) cc_final: 0.7905 (m-30) REVERT: S 57 LYS cc_start: 0.7910 (mttt) cc_final: 0.7461 (tptp) outliers start: 32 outliers final: 16 residues processed: 346 average time/residue: 0.1828 time to fit residues: 102.0054 Evaluate side-chains 302 residues out of total 3154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 284 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain H residue 210 LEU Chi-restraints excluded: chain L residue 154 LEU Chi-restraints excluded: chain L residue 180 MET Chi-restraints excluded: chain L residue 228 ILE Chi-restraints excluded: chain M residue 289 ASP Chi-restraints excluded: chain P residue 71 SER Chi-restraints excluded: chain R residue 52 ILE Chi-restraints excluded: chain R residue 59 SER Chi-restraints excluded: chain R residue 80 ILE Chi-restraints excluded: chain S residue 114 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: [268, 120, 68, 319, 113, 315, 164, 161, 29, 28, 141] chunk 268 optimal weight: 9.9990 chunk 120 optimal weight: 8.9990 chunk 68 optimal weight: 5.9990 chunk 319 optimal weight: 1.9990 chunk 113 optimal weight: 7.9990 chunk 315 optimal weight: 4.9990 chunk 164 optimal weight: 0.6980 chunk 161 optimal weight: 0.9990 chunk 29 optimal weight: 8.9990 chunk 28 optimal weight: 20.0000 chunk 141 optimal weight: 0.5980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 74 GLN K 213 GLN K 291 GLN M 274 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.115937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.074932 restraints weight = 71661.990| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.98 r_work: 0.2975 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 31300 Z= 0.195 Angle : 0.570 8.865 42676 Z= 0.301 Chirality : 0.045 0.494 4958 Planarity : 0.004 0.056 4955 Dihedral : 15.911 177.104 5158 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.49 % Allowed : 12.56 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.14), residues: 3554 helix: 1.91 (0.13), residues: 1599 sheet: -0.40 (0.21), residues: 557 loop : -1.23 (0.15), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 271 TYR 0.019 0.001 TYR S 120 PHE 0.021 0.001 PHE R 65 TRP 0.047 0.002 TRP D 282 HIS 0.006 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.19 (31295) covalent geometry : angle 0.56886 / 0.30 (42668) SS BOND : bond 0.00427 / 0.22 ( 1) SS BOND : angle 2.67176 / 1.51 ( 2) hydrogen bonds : bond 0.04139 / 2.76 ( 1539) hydrogen bonds : angle 4.62784 / 3.30 ( 4308) metal coordination : bond 0.01042 / 0.53 ( 4) metal coordination : angle 3.28331 / 1.76 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 291 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.5400 (t60) cc_final: 0.5010 (t60) REVERT: A 111 TRP cc_start: 0.7390 (m100) cc_final: 0.6958 (m100) REVERT: A 148 LYS cc_start: 0.5436 (mttt) cc_final: 0.4324 (ttpp) REVERT: A 281 PHE cc_start: 0.8384 (m-80) cc_final: 0.8036 (m-10) REVERT: A 309 MET cc_start: 0.8548 (mtt) cc_final: 0.8262 (mtp) REVERT: A 411 LEU cc_start: 0.5484 (OUTLIER) cc_final: 0.5169 (pp) REVERT: A 445 GLU cc_start: 0.8488 (pt0) cc_final: 0.7813 (pp20) REVERT: A 467 ARG cc_start: 0.7338 (ttp-170) cc_final: 0.6755 (ttp80) REVERT: A 474 TRP cc_start: 0.8673 (t-100) cc_final: 0.8455 (m100) REVERT: C 17 TYR cc_start: 0.8085 (t80) cc_final: 0.7725 (t80) REVERT: C 32 ILE cc_start: 0.9346 (mm) cc_final: 0.9133 (mt) REVERT: C 296 LYS cc_start: 0.8010 (mttt) cc_final: 0.7665 (tptt) REVERT: D 23 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8524 (pp) REVERT: D 91 MET cc_start: 0.8412 (mmt) cc_final: 0.7574 (mmt) REVERT: D 124 PHE cc_start: 0.8028 (t80) cc_final: 0.7262 (t80) REVERT: D 177 MET cc_start: 0.8690 (mmm) cc_final: 0.7986 (tpp) REVERT: D 217 GLN cc_start: 0.8729 (mm-40) cc_final: 0.7939 (tp-100) REVERT: D 255 MET cc_start: 0.8399 (mtp) cc_final: 0.7790 (tpp) REVERT: H 17 TYR cc_start: 0.9164 (t80) cc_final: 0.8870 (t80) REVERT: H 27 TYR cc_start: 0.9205 (t80) cc_final: 0.8722 (t80) REVERT: H 63 GLU cc_start: 0.8793 (tm-30) cc_final: 0.8510 (tm-30) REVERT: I 11 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8263 (mt-10) REVERT: I 122 MET cc_start: 0.9136 (mmm) cc_final: 0.8801 (mtp) REVERT: I 224 TYR cc_start: 0.9025 (p90) cc_final: 0.8727 (p90) REVERT: I 291 GLN cc_start: 0.9165 (tt0) cc_final: 0.8638 (mt0) REVERT: J 20 ILE cc_start: 0.9221 (mt) cc_final: 0.8994 (mm) REVERT: J 28 SER cc_start: 0.9530 (m) cc_final: 0.8796 (p) REVERT: J 40 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8105 (mm-30) REVERT: J 74 GLN cc_start: 0.7979 (mp10) cc_final: 0.7712 (mp10) REVERT: J 208 GLN cc_start: 0.8130 (mt0) cc_final: 0.7927 (mt0) REVERT: J 284 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.8456 (mtm110) REVERT: K 109 MET cc_start: 0.9066 (mmm) cc_final: 0.8492 (mmm) REVERT: K 180 MET cc_start: 0.8594 (tpt) cc_final: 0.8291 (tpp) REVERT: L 122 MET cc_start: 0.9313 (mmm) cc_final: 0.8447 (mmm) REVERT: L 175 THR cc_start: 0.8005 (m) cc_final: 0.7084 (p) REVERT: L 177 LYS cc_start: 0.8641 (tttm) cc_final: 0.8318 (tmtt) REVERT: L 180 MET cc_start: 0.8391 (OUTLIER) cc_final: 0.8037 (ppp) REVERT: M 35 ASP cc_start: 0.8714 (m-30) cc_final: 0.8477 (p0) REVERT: M 40 GLU cc_start: 0.8662 (mp0) cc_final: 0.8301 (mm-30) REVERT: M 47 ASN cc_start: 0.8182 (m-40) cc_final: 0.7935 (t0) REVERT: M 104 ASN cc_start: 0.8902 (t0) cc_final: 0.8633 (t0) REVERT: M 109 MET cc_start: 0.8795 (mmm) cc_final: 0.7897 (mmm) REVERT: M 129 ILE cc_start: 0.8757 (mt) cc_final: 0.8303 (tp) REVERT: M 159 ASP cc_start: 0.6884 (t0) cc_final: 0.6396 (t0) REVERT: M 281 ASN cc_start: 0.8777 (m110) cc_final: 0.8301 (m110) REVERT: N 72 GLN cc_start: 0.8277 (mt0) cc_final: 0.7906 (mp10) REVERT: N 87 ASN cc_start: 0.9329 (t0) cc_final: 0.8962 (m110) REVERT: P 77 SER cc_start: 0.8289 (m) cc_final: 0.7573 (p) REVERT: P 120 TYR cc_start: 0.8303 (t80) cc_final: 0.8045 (t80) REVERT: Q 32 ASP cc_start: 0.8155 (t0) cc_final: 0.7866 (m-30) REVERT: R 45 TYR cc_start: 0.8063 (m-80) cc_final: 0.6787 (m-80) REVERT: R 92 TYR cc_start: 0.7292 (t80) cc_final: 0.7013 (t80) REVERT: S 57 LYS cc_start: 0.7957 (mttt) cc_final: 0.7563 (tptp) outliers start: 47 outliers final: 30 residues processed: 323 average time/residue: 0.1849 time to fit residues: 96.4951 Evaluate side-chains 310 residues out of total 3154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 276 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 210 LEU Chi-restraints excluded: chain H residue 249 ILE Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain J residue 284 ARG Chi-restraints excluded: chain K residue 190 LEU Chi-restraints excluded: chain L residue 154 LEU Chi-restraints excluded: chain L residue 180 MET Chi-restraints excluded: chain L residue 228 ILE Chi-restraints excluded: chain M residue 149 SER Chi-restraints excluded: chain M residue 289 ASP Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain P residue 17 GLU Chi-restraints excluded: chain P residue 71 SER Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain R residue 52 ILE Chi-restraints excluded: chain R residue 59 SER Chi-restraints excluded: chain R residue 80 ILE Chi-restraints excluded: chain S residue 114 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: [88, 213, 297, 176, 253, 360, 2, 35, 149, 200, 20] chunk 88 optimal weight: 0.8980 chunk 213 optimal weight: 5.9990 chunk 297 optimal weight: 6.9990 chunk 176 optimal weight: 0.9980 chunk 253 optimal weight: 0.9990 chunk 360 optimal weight: 30.0000 chunk 2 optimal weight: 20.0000 chunk 35 optimal weight: 0.4980 chunk 149 optimal weight: 1.9990 chunk 200 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 208 GLN ** I 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 74 GLN K 291 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.117095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.076320 restraints weight = 71652.655| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.97 r_work: 0.3004 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 31300 Z= 0.141 Angle : 0.534 8.898 42676 Z= 0.286 Chirality : 0.044 0.480 4958 Planarity : 0.004 0.053 4955 Dihedral : 15.917 176.718 5158 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.43 % Allowed : 13.28 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.14), residues: 3554 helix: 1.89 (0.13), residues: 1607 sheet: -0.37 (0.21), residues: 557 loop : -1.22 (0.16), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 252 TYR 0.019 0.001 TYR S 120 PHE 0.021 0.001 PHE R 65 TRP 0.033 0.001 TRP D 282 HIS 0.006 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (31295) covalent geometry : angle 0.53253 / 0.29 (42668) SS BOND : bond 0.00311 / 0.16 ( 1) SS BOND : angle 2.25949 / 1.27 ( 2) hydrogen bonds : bond 0.03881 / 2.58 ( 1539) hydrogen bonds : angle 4.53798 / 3.23 ( 4308) metal coordination : bond 0.01220 / 0.62 ( 4) metal coordination : angle 3.31662 / 1.74 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 294 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.5414 (t60) cc_final: 0.5167 (t60) REVERT: A 148 LYS cc_start: 0.5536 (mttt) cc_final: 0.4413 (ttpp) REVERT: A 152 CYS cc_start: 0.2964 (OUTLIER) cc_final: 0.2381 (p) REVERT: A 281 PHE cc_start: 0.8382 (m-80) cc_final: 0.8035 (m-10) REVERT: A 309 MET cc_start: 0.8542 (mtt) cc_final: 0.8241 (mtp) REVERT: A 411 LEU cc_start: 0.5438 (OUTLIER) cc_final: 0.5042 (pp) REVERT: A 445 GLU cc_start: 0.8470 (pt0) cc_final: 0.7736 (pp20) REVERT: A 467 ARG cc_start: 0.7389 (ttp-170) cc_final: 0.6818 (ttp80) REVERT: A 474 TRP cc_start: 0.8683 (t-100) cc_final: 0.8465 (m100) REVERT: C 17 TYR cc_start: 0.7982 (t80) cc_final: 0.7670 (t80) REVERT: C 296 LYS cc_start: 0.7973 (mttt) cc_final: 0.7626 (tptt) REVERT: D 1 MET cc_start: 0.8083 (tpp) cc_final: 0.7839 (tpt) REVERT: D 113 GLN cc_start: 0.8375 (pm20) cc_final: 0.7831 (tt0) REVERT: D 124 PHE cc_start: 0.8040 (t80) cc_final: 0.7310 (t80) REVERT: D 177 MET cc_start: 0.8359 (mmm) cc_final: 0.7912 (ttm) REVERT: D 217 GLN cc_start: 0.8712 (mm-40) cc_final: 0.7913 (tp-100) REVERT: D 255 MET cc_start: 0.8367 (mtp) cc_final: 0.7775 (tpp) REVERT: H 27 TYR cc_start: 0.9188 (t80) cc_final: 0.8835 (t80) REVERT: H 63 GLU cc_start: 0.8791 (tm-30) cc_final: 0.8490 (tm-30) REVERT: I 11 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8234 (mt-10) REVERT: I 122 MET cc_start: 0.9100 (mmm) cc_final: 0.8743 (mtp) REVERT: I 224 TYR cc_start: 0.9002 (p90) cc_final: 0.8758 (p90) REVERT: I 291 GLN cc_start: 0.9154 (tt0) cc_final: 0.8619 (mt0) REVERT: J 20 ILE cc_start: 0.9214 (mt) cc_final: 0.8986 (mm) REVERT: J 28 SER cc_start: 0.9519 (m) cc_final: 0.8777 (p) REVERT: J 40 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8051 (mm-30) REVERT: J 74 GLN cc_start: 0.8032 (mp10) cc_final: 0.7751 (mp10) REVERT: J 208 GLN cc_start: 0.8116 (mt0) cc_final: 0.7897 (mt0) REVERT: K 109 MET cc_start: 0.9047 (mmm) cc_final: 0.8461 (mmm) REVERT: K 176 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7330 (ttm-80) REVERT: K 180 MET cc_start: 0.8587 (tpt) cc_final: 0.8291 (tpp) REVERT: L 122 MET cc_start: 0.9272 (mmm) cc_final: 0.8399 (mmm) REVERT: L 175 THR cc_start: 0.7998 (m) cc_final: 0.7158 (p) REVERT: L 180 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.8009 (ppp) REVERT: M 35 ASP cc_start: 0.8683 (m-30) cc_final: 0.8464 (p0) REVERT: M 47 ASN cc_start: 0.8158 (OUTLIER) cc_final: 0.7854 (t0) REVERT: M 104 ASN cc_start: 0.8932 (t0) cc_final: 0.8625 (t0) REVERT: M 109 MET cc_start: 0.8811 (mmm) cc_final: 0.7918 (mmm) REVERT: M 129 ILE cc_start: 0.8805 (mt) cc_final: 0.8350 (tp) REVERT: M 148 LYS cc_start: 0.8740 (ptmt) cc_final: 0.8516 (tttt) REVERT: M 159 ASP cc_start: 0.6900 (t0) cc_final: 0.6411 (t0) REVERT: M 221 PHE cc_start: 0.8026 (m-10) cc_final: 0.7817 (m-10) REVERT: M 281 ASN cc_start: 0.8765 (m110) cc_final: 0.8278 (m110) REVERT: N 72 GLN cc_start: 0.8276 (mt0) cc_final: 0.7921 (mp10) REVERT: N 87 ASN cc_start: 0.9298 (t0) cc_final: 0.8927 (m110) REVERT: P 17 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8441 (pm20) REVERT: P 77 SER cc_start: 0.8295 (m) cc_final: 0.7572 (p) REVERT: P 120 TYR cc_start: 0.8298 (t80) cc_final: 0.8043 (t80) REVERT: Q 32 ASP cc_start: 0.8103 (t0) cc_final: 0.7883 (m-30) REVERT: Q 64 GLU cc_start: 0.8759 (tt0) cc_final: 0.8231 (pt0) REVERT: R 45 TYR cc_start: 0.8122 (m-80) cc_final: 0.7672 (m-80) REVERT: R 92 TYR cc_start: 0.7374 (t80) cc_final: 0.7131 (t80) REVERT: S 57 LYS cc_start: 0.7968 (mttt) cc_final: 0.7614 (tptp) outliers start: 45 outliers final: 31 residues processed: 325 average time/residue: 0.1872 time to fit residues: 98.1059 Evaluate side-chains 315 residues out of total 3154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 278 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 210 LEU Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 210 LEU Chi-restraints excluded: chain K residue 59 LEU Chi-restraints excluded: chain K residue 176 ARG Chi-restraints excluded: chain K residue 190 LEU Chi-restraints excluded: chain L residue 180 MET Chi-restraints excluded: chain L residue 228 ILE Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 47 ASN Chi-restraints excluded: chain M residue 149 SER Chi-restraints excluded: chain N residue 41 HIS Chi-restraints excluded: chain P residue 17 GLU Chi-restraints excluded: chain P residue 71 SER Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain R residue 52 ILE Chi-restraints excluded: chain R residue 59 SER Chi-restraints excluded: chain R residue 80 ILE Chi-restraints excluded: chain S residue 114 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: [159, 73, 103, 100, 55, 301, 278, 147, 109, 200, 90] chunk 159 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 100 optimal weight: 7.9990 chunk 55 optimal weight: 4.9990 chunk 301 optimal weight: 7.9990 chunk 278 optimal weight: 10.0000 chunk 147 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 200 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 47 ASN ** I 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 74 GLN K 291 GLN M 274 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.115418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.074243 restraints weight = 72001.927| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.98 r_work: 0.2956 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 31300 Z= 0.243 Angle : 0.596 9.213 42676 Z= 0.312 Chirality : 0.046 0.514 4958 Planarity : 0.004 0.057 4955 Dihedral : 15.924 176.664 5158 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.90 % Allowed : 13.82 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.14), residues: 3554 helix: 1.91 (0.13), residues: 1598 sheet: -0.41 (0.21), residues: 569 loop : -1.29 (0.15), residues: 1387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J 284 TYR 0.020 0.001 TYR M 114 PHE 0.022 0.001 PHE R 65 TRP 0.031 0.002 TRP D 282 HIS 0.005 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00553 / 0.24 (31295) covalent geometry : angle 0.59509 / 0.31 (42668) SS BOND : bond 0.00704 / 0.37 ( 1) SS BOND : angle 2.58750 / 1.46 ( 2) hydrogen bonds : bond 0.04170 / 2.79 ( 1539) hydrogen bonds : angle 4.60336 / 3.28 ( 4308) metal coordination : bond 0.01223 / 0.62 ( 4) metal coordination : angle 3.02994 / 1.60 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 3154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 275 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.5312 (t60) cc_final: 0.5062 (t60) REVERT: A 148 LYS cc_start: 0.5391 (mttt) cc_final: 0.4270 (ttpp) REVERT: A 152 CYS cc_start: 0.2929 (OUTLIER) cc_final: 0.2304 (p) REVERT: A 281 PHE cc_start: 0.8393 (m-80) cc_final: 0.8055 (m-10) REVERT: A 309 MET cc_start: 0.8560 (mtt) cc_final: 0.8195 (mtp) REVERT: A 411 LEU cc_start: 0.5451 (OUTLIER) cc_final: 0.5010 (pp) REVERT: A 445 GLU cc_start: 0.8507 (pt0) cc_final: 0.7783 (pp20) REVERT: A 467 ARG cc_start: 0.7358 (ttp-170) cc_final: 0.6794 (ttp80) REVERT: A 474 TRP cc_start: 0.8705 (t-100) cc_final: 0.8487 (m100) REVERT: A 480 GLU cc_start: 0.9402 (mm-30) cc_final: 0.9182 (mm-30) REVERT: A 558 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7307 (tm-30) REVERT: C 17 TYR cc_start: 0.8109 (t80) cc_final: 0.7688 (t80) REVERT: C 296 LYS cc_start: 0.8036 (mttt) cc_final: 0.7680 (tptt) REVERT: D 1 MET cc_start: 0.8068 (tpp) cc_final: 0.7807 (tpt) REVERT: D 23 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8544 (pp) REVERT: D 113 GLN cc_start: 0.8448 (pm20) cc_final: 0.7838 (tt0) REVERT: D 124 PHE cc_start: 0.8025 (t80) cc_final: 0.7176 (t80) REVERT: D 177 MET cc_start: 0.8359 (mmm) cc_final: 0.7927 (tpp) REVERT: D 217 GLN cc_start: 0.8712 (mm-40) cc_final: 0.7879 (tp40) REVERT: D 255 MET cc_start: 0.8383 (mtp) cc_final: 0.7791 (tpp) REVERT: H 27 TYR cc_start: 0.9263 (t80) cc_final: 0.8741 (t80) REVERT: H 63 GLU cc_start: 0.8898 (tm-30) cc_final: 0.8609 (tm-30) REVERT: I 112 TYR cc_start: 0.8071 (OUTLIER) cc_final: 0.6287 (m-80) REVERT: I 122 MET cc_start: 0.9163 (mmm) cc_final: 0.8913 (mtp) REVERT: J 20 ILE cc_start: 0.9275 (mt) cc_final: 0.9047 (mm) REVERT: J 28 SER cc_start: 0.9530 (m) cc_final: 0.8783 (p) REVERT: J 40 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8076 (mm-30) REVERT: J 74 GLN cc_start: 0.7986 (mp10) cc_final: 0.7695 (mp10) REVERT: J 208 GLN cc_start: 0.8220 (mt0) cc_final: 0.7941 (mt0) REVERT: K 109 MET cc_start: 0.9079 (mmm) cc_final: 0.8537 (mmm) REVERT: K 122 MET cc_start: 0.9203 (mmm) cc_final: 0.8431 (mtt) REVERT: K 180 MET cc_start: 0.8604 (tpt) cc_final: 0.8297 (tpp) REVERT: K 289 ASP cc_start: 0.9339 (t0) cc_final: 0.9085 (t0) REVERT: L 122 MET cc_start: 0.9303 (mmm) cc_final: 0.8419 (mmm) REVERT: L 150 LEU cc_start: 0.9210 (tp) cc_final: 0.8916 (tp) REVERT: L 167 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8279 (mt-10) REVERT: L 175 THR cc_start: 0.8127 (OUTLIER) cc_final: 0.7233 (p) REVERT: L 180 MET cc_start: 0.8401 (OUTLIER) cc_final: 0.8025 (ppp) REVERT: L 208 GLN cc_start: 0.8436 (mm-40) cc_final: 0.8136 (mm-40) REVERT: M 35 ASP cc_start: 0.8709 (m-30) cc_final: 0.8478 (p0) REVERT: M 40 GLU cc_start: 0.8609 (mp0) cc_final: 0.8321 (mm-30) REVERT: M 47 ASN cc_start: 0.8148 (OUTLIER) cc_final: 0.7812 (t0) REVERT: M 104 ASN cc_start: 0.8953 (t0) cc_final: 0.8643 (t0) REVERT: M 109 MET cc_start: 0.8750 (mmm) cc_final: 0.7883 (mmm) REVERT: M 129 ILE cc_start: 0.8780 (mt) cc_final: 0.8333 (tp) REVERT: M 159 ASP cc_start: 0.6886 (t0) cc_final: 0.6413 (t0) REVERT: M 281 ASN cc_start: 0.8806 (m110) cc_final: 0.8335 (m110) REVERT: N 72 GLN cc_start: 0.8287 (mt0) cc_final: 0.7921 (mp10) REVERT: N 87 ASN cc_start: 0.9321 (t0) cc_final: 0.8948 (m110) REVERT: P 77 SER cc_start: 0.8277 (m) cc_final: 0.7555 (p) REVERT: P 120 TYR cc_start: 0.8300 (t80) cc_final: 0.8079 (t80) REVERT: Q 32 ASP cc_start: 0.8184 (t0) cc_final: 0.7942 (m-30) REVERT: R 45 TYR cc_start: 0.8111 (m-80) cc_final: 0.7726 (m-80) REVERT: S 57 LYS cc_start: 0.7902 (mttt) cc_final: 0.7544 (tptp) outliers start: 60 outliers final: 38 residues processed: 319 average time/residue: 0.1825 time to fit residues: 94.9424 Evaluate side-chains 316 residues out of total 3154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 270 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 210 LEU Chi-restraints excluded: chain H residue 249 ILE Chi-restraints excluded: chain I residue 112 TYR Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 210 LEU Chi-restraints excluded: chain K residue 59 LEU Chi-restraints excluded: chain K residue 113 VAL Chi-restraints excluded: chain K residue 189 LEU Chi-restraints excluded: chain K residue 190 LEU Chi-restraints excluded: chain L residue 154 LEU Chi-restraints excluded: chain L residue 175 THR Chi-restraints excluded: chain L residue 180 MET Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 47 ASN Chi-restraints excluded: chain M residue 149 SER Chi-restraints excluded: chain M residue 289 ASP Chi-restraints excluded: chain N residue 41 HIS Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain P residue 17 GLU Chi-restraints excluded: chain P residue 71 SER Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain R residue 52 ILE Chi-restraints excluded: chain R residue 59 SER Chi-restraints excluded: chain R residue 80 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: [348, 100, 141, 183, 2, 170, 118, 238, 363, 153, 114] chunk 348 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 141 optimal weight: 0.7980 chunk 183 optimal weight: 1.9990 chunk 2 optimal weight: 20.0000 chunk 170 optimal weight: 0.6980 chunk 118 optimal weight: 9.9990 chunk 238 optimal weight: 0.9980 chunk 363 optimal weight: 0.9980 chunk 153 optimal weight: 0.5980 chunk 114 optimal weight: 30.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 47 ASN ** I 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 74 GLN K 291 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.117462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.076799 restraints weight = 71491.996| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.97 r_work: 0.3013 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 31300 Z= 0.124 Angle : 0.527 9.385 42676 Z= 0.281 Chirality : 0.044 0.473 4958 Planarity : 0.004 0.061 4955 Dihedral : 15.938 175.934 5158 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.43 % Allowed : 14.62 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.14), residues: 3554 helix: 1.92 (0.13), residues: 1602 sheet: -0.32 (0.21), residues: 571 loop : -1.22 (0.16), residues: 1381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J 284 TYR 0.020 0.001 TYR S 120 PHE 0.013 0.001 PHE M 158 TRP 0.038 0.001 TRP D 282 HIS 0.006 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (31295) covalent geometry : angle 0.52519 / 0.28 (42668) SS BOND : bond 0.00350 / 0.18 ( 1) SS BOND : angle 2.48862 / 1.40 ( 2) hydrogen bonds : bond 0.03742 / 2.50 ( 1539) hydrogen bonds : angle 4.47839 / 3.19 ( 4308) metal coordination : bond 0.00879 / 0.45 ( 4) metal coordination : angle 3.11036 / 1.63 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 293 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.5349 (t60) cc_final: 0.5127 (t60) REVERT: A 148 LYS cc_start: 0.5500 (mttt) cc_final: 0.4409 (ttpp) REVERT: A 152 CYS cc_start: 0.3004 (OUTLIER) cc_final: 0.2425 (p) REVERT: A 281 PHE cc_start: 0.8376 (m-80) cc_final: 0.8032 (m-10) REVERT: A 309 MET cc_start: 0.8562 (mtt) cc_final: 0.8205 (mtp) REVERT: A 411 LEU cc_start: 0.5392 (OUTLIER) cc_final: 0.4970 (pp) REVERT: A 445 GLU cc_start: 0.8473 (pt0) cc_final: 0.7699 (pp20) REVERT: A 467 ARG cc_start: 0.7354 (ttp-170) cc_final: 0.6805 (ttp80) REVERT: A 474 TRP cc_start: 0.8690 (t-100) cc_final: 0.8484 (m100) REVERT: A 480 GLU cc_start: 0.9388 (mm-30) cc_final: 0.9159 (mm-30) REVERT: A 544 ARG cc_start: 0.7603 (ttp80) cc_final: 0.5900 (mmm160) REVERT: C 17 TYR cc_start: 0.7943 (t80) cc_final: 0.7636 (t80) REVERT: C 296 LYS cc_start: 0.8000 (mttt) cc_final: 0.7661 (tptt) REVERT: D 1 MET cc_start: 0.8034 (tpp) cc_final: 0.7801 (tpt) REVERT: D 23 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8580 (pp) REVERT: D 91 MET cc_start: 0.7996 (mmt) cc_final: 0.7694 (mmt) REVERT: D 113 GLN cc_start: 0.8389 (pm20) cc_final: 0.7824 (tt0) REVERT: D 124 PHE cc_start: 0.8053 (t80) cc_final: 0.7348 (t80) REVERT: D 177 MET cc_start: 0.8353 (mmm) cc_final: 0.7949 (tpp) REVERT: D 217 GLN cc_start: 0.8668 (mm-40) cc_final: 0.7858 (tp-100) REVERT: D 255 MET cc_start: 0.8285 (mtp) cc_final: 0.7721 (tpp) REVERT: H 27 TYR cc_start: 0.9214 (t80) cc_final: 0.8808 (t80) REVERT: H 63 GLU cc_start: 0.8879 (tm-30) cc_final: 0.8551 (tm-30) REVERT: I 11 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8214 (mt-10) REVERT: I 112 TYR cc_start: 0.8024 (OUTLIER) cc_final: 0.6384 (m-80) REVERT: I 122 MET cc_start: 0.9085 (mmm) cc_final: 0.8747 (mtp) REVERT: I 224 TYR cc_start: 0.8976 (p90) cc_final: 0.8763 (p90) REVERT: I 291 GLN cc_start: 0.9147 (tt0) cc_final: 0.8622 (mt0) REVERT: J 20 ILE cc_start: 0.9211 (mt) cc_final: 0.8984 (mm) REVERT: J 28 SER cc_start: 0.9509 (m) cc_final: 0.8792 (p) REVERT: J 40 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8030 (mm-30) REVERT: J 74 GLN cc_start: 0.8023 (mp10) cc_final: 0.7735 (mp10) REVERT: J 208 GLN cc_start: 0.8165 (mt0) cc_final: 0.7873 (mt0) REVERT: J 284 ARG cc_start: 0.8361 (mtm110) cc_final: 0.8147 (mtm-85) REVERT: K 109 MET cc_start: 0.9042 (mmm) cc_final: 0.8481 (mmm) REVERT: K 122 MET cc_start: 0.9096 (mmm) cc_final: 0.8351 (mtt) REVERT: K 180 MET cc_start: 0.8558 (tpt) cc_final: 0.8266 (tpp) REVERT: L 122 MET cc_start: 0.9261 (mmm) cc_final: 0.8437 (mmm) REVERT: L 175 THR cc_start: 0.8060 (OUTLIER) cc_final: 0.7232 (p) REVERT: L 180 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.8010 (ppp) REVERT: L 207 GLN cc_start: 0.8638 (mm-40) cc_final: 0.8016 (tp40) REVERT: L 208 GLN cc_start: 0.8421 (mm-40) cc_final: 0.8197 (mm-40) REVERT: M 35 ASP cc_start: 0.8701 (m-30) cc_final: 0.8488 (p0) REVERT: M 40 GLU cc_start: 0.8682 (mp0) cc_final: 0.8329 (mm-30) REVERT: M 47 ASN cc_start: 0.8101 (OUTLIER) cc_final: 0.7663 (t0) REVERT: M 104 ASN cc_start: 0.8959 (t0) cc_final: 0.8632 (t0) REVERT: M 109 MET cc_start: 0.8687 (mmm) cc_final: 0.7790 (mmm) REVERT: M 129 ILE cc_start: 0.8854 (mt) cc_final: 0.8402 (tp) REVERT: M 159 ASP cc_start: 0.6789 (t0) cc_final: 0.6278 (t70) REVERT: M 281 ASN cc_start: 0.8780 (m110) cc_final: 0.8291 (m110) REVERT: N 72 GLN cc_start: 0.8275 (mt0) cc_final: 0.7945 (mp10) REVERT: N 87 ASN cc_start: 0.9280 (t0) cc_final: 0.8906 (m110) REVERT: P 17 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8408 (pm20) REVERT: P 77 SER cc_start: 0.8300 (m) cc_final: 0.7564 (p) REVERT: Q 32 ASP cc_start: 0.8162 (t0) cc_final: 0.7900 (m-30) REVERT: R 45 TYR cc_start: 0.8170 (m-80) cc_final: 0.7097 (m-80) REVERT: S 57 LYS cc_start: 0.7910 (mttt) cc_final: 0.7607 (tmtt) outliers start: 45 outliers final: 24 residues processed: 325 average time/residue: 0.1786 time to fit residues: 93.7281 Evaluate side-chains 308 residues out of total 3154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 276 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain H residue 210 LEU Chi-restraints excluded: chain I residue 112 TYR Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain J residue 210 LEU Chi-restraints excluded: chain L residue 154 LEU Chi-restraints excluded: chain L residue 175 THR Chi-restraints excluded: chain L residue 180 MET Chi-restraints excluded: chain M residue 47 ASN Chi-restraints excluded: chain N residue 41 HIS Chi-restraints excluded: chain P residue 17 GLU Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain R residue 52 ILE Chi-restraints excluded: chain R residue 80 ILE Chi-restraints excluded: chain S residue 109 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: [345, 205, 264, 344, 164, 14, 252, 150, 47, 142, 207] chunk 345 optimal weight: 0.0170 chunk 205 optimal weight: 3.9990 chunk 264 optimal weight: 0.5980 chunk 344 optimal weight: 2.9990 chunk 164 optimal weight: 0.6980 chunk 14 optimal weight: 6.9990 chunk 252 optimal weight: 5.9990 chunk 150 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 142 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 overall best weight: 1.4622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 47 ASN I 47 ASN K 74 GLN K 291 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.116627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.075530 restraints weight = 71911.650| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 3.01 r_work: 0.2988 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 31300 Z= 0.165 Angle : 0.554 9.481 42676 Z= 0.293 Chirality : 0.044 0.494 4958 Planarity : 0.004 0.050 4955 Dihedral : 15.921 176.408 5158 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.74 % Allowed : 15.00 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.14), residues: 3554 helix: 1.89 (0.13), residues: 1607 sheet: -0.28 (0.21), residues: 569 loop : -1.21 (0.16), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J 284 TYR 0.027 0.001 TYR O 120 PHE 0.013 0.001 PHE L 88 TRP 0.035 0.002 TRP R 33 HIS 0.005 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (31295) covalent geometry : angle 0.55285 / 0.29 (42668) SS BOND : bond 0.00230 / 0.12 ( 1) SS BOND : angle 2.23504 / 1.26 ( 2) hydrogen bonds : bond 0.03837 / 2.56 ( 1539) hydrogen bonds : angle 4.48525 / 3.21 ( 4308) metal coordination : bond 0.00943 / 0.48 ( 4) metal coordination : angle 2.88567 / 1.53 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 282 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.5281 (t60) cc_final: 0.5054 (t60) REVERT: A 148 LYS cc_start: 0.5480 (mttt) cc_final: 0.4438 (ttpp) REVERT: A 152 CYS cc_start: 0.2965 (OUTLIER) cc_final: 0.2380 (p) REVERT: A 281 PHE cc_start: 0.8382 (m-80) cc_final: 0.8035 (m-10) REVERT: A 309 MET cc_start: 0.8581 (mtt) cc_final: 0.8258 (mtp) REVERT: A 411 LEU cc_start: 0.5270 (OUTLIER) cc_final: 0.4819 (pp) REVERT: A 445 GLU cc_start: 0.8501 (pt0) cc_final: 0.7748 (pp20) REVERT: A 467 ARG cc_start: 0.7331 (ttp-170) cc_final: 0.6789 (ttp80) REVERT: A 474 TRP cc_start: 0.8705 (t-100) cc_final: 0.8501 (m100) REVERT: A 480 GLU cc_start: 0.9386 (mm-30) cc_final: 0.9155 (mm-30) REVERT: A 558 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7614 (pt0) REVERT: C 17 TYR cc_start: 0.7978 (t80) cc_final: 0.7678 (t80) REVERT: C 296 LYS cc_start: 0.7941 (mttt) cc_final: 0.7574 (tptt) REVERT: D 1 MET cc_start: 0.8079 (tpp) cc_final: 0.7858 (tpt) REVERT: D 23 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8500 (pp) REVERT: D 91 MET cc_start: 0.7978 (mmt) cc_final: 0.7669 (mmt) REVERT: D 113 GLN cc_start: 0.8365 (pm20) cc_final: 0.7790 (tt0) REVERT: D 124 PHE cc_start: 0.8031 (t80) cc_final: 0.7326 (t80) REVERT: D 177 MET cc_start: 0.8309 (mmm) cc_final: 0.7910 (tpp) REVERT: D 217 GLN cc_start: 0.8667 (mm-40) cc_final: 0.8442 (mm-40) REVERT: D 255 MET cc_start: 0.8389 (mtp) cc_final: 0.7788 (tpp) REVERT: H 27 TYR cc_start: 0.9268 (t80) cc_final: 0.8805 (t80) REVERT: H 63 GLU cc_start: 0.8894 (tm-30) cc_final: 0.8588 (tm-30) REVERT: I 11 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8282 (mt-10) REVERT: I 112 TYR cc_start: 0.8097 (OUTLIER) cc_final: 0.6396 (m-80) REVERT: I 122 MET cc_start: 0.9153 (mmm) cc_final: 0.8829 (mtp) REVERT: I 224 TYR cc_start: 0.9023 (p90) cc_final: 0.8800 (p90) REVERT: I 291 GLN cc_start: 0.9153 (tt0) cc_final: 0.8624 (mt0) REVERT: J 20 ILE cc_start: 0.9216 (mt) cc_final: 0.8991 (mm) REVERT: J 28 SER cc_start: 0.9522 (m) cc_final: 0.8750 (p) REVERT: J 40 GLU cc_start: 0.8641 (mm-30) cc_final: 0.8055 (mm-30) REVERT: J 74 GLN cc_start: 0.7994 (mp10) cc_final: 0.7695 (mp10) REVERT: J 208 GLN cc_start: 0.8197 (mt0) cc_final: 0.7905 (mt0) REVERT: J 284 ARG cc_start: 0.8419 (mtm110) cc_final: 0.8166 (mtm-85) REVERT: K 109 MET cc_start: 0.9067 (mmm) cc_final: 0.8516 (mmm) REVERT: K 180 MET cc_start: 0.8544 (tpt) cc_final: 0.8237 (tpp) REVERT: K 208 GLN cc_start: 0.7395 (mt0) cc_final: 0.6992 (mt0) REVERT: L 122 MET cc_start: 0.9303 (mmm) cc_final: 0.8443 (mmm) REVERT: L 167 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8246 (mt-10) REVERT: L 175 THR cc_start: 0.7986 (OUTLIER) cc_final: 0.7088 (p) REVERT: L 180 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.8009 (ppp) REVERT: L 208 GLN cc_start: 0.8407 (mm-40) cc_final: 0.8108 (mm-40) REVERT: M 35 ASP cc_start: 0.8718 (m-30) cc_final: 0.8482 (p0) REVERT: M 40 GLU cc_start: 0.8648 (mp0) cc_final: 0.8296 (mm-30) REVERT: M 104 ASN cc_start: 0.8943 (t0) cc_final: 0.8616 (t0) REVERT: M 109 MET cc_start: 0.8652 (mmm) cc_final: 0.7787 (mmm) REVERT: M 114 TYR cc_start: 0.6753 (m-10) cc_final: 0.6553 (m-10) REVERT: M 129 ILE cc_start: 0.8791 (mt) cc_final: 0.8342 (tp) REVERT: M 159 ASP cc_start: 0.6819 (t0) cc_final: 0.6314 (t70) REVERT: M 281 ASN cc_start: 0.8779 (m110) cc_final: 0.8314 (m110) REVERT: N 72 GLN cc_start: 0.8240 (mt0) cc_final: 0.7911 (mp10) REVERT: N 87 ASN cc_start: 0.9336 (t0) cc_final: 0.8951 (m110) REVERT: P 17 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8404 (pm20) REVERT: P 77 SER cc_start: 0.8218 (m) cc_final: 0.7491 (p) REVERT: Q 32 ASP cc_start: 0.8181 (t0) cc_final: 0.7887 (m-30) REVERT: R 45 TYR cc_start: 0.8068 (m-80) cc_final: 0.7672 (m-80) REVERT: S 57 LYS cc_start: 0.7903 (mttt) cc_final: 0.7549 (tptp) outliers start: 55 outliers final: 35 residues processed: 318 average time/residue: 0.1789 time to fit residues: 93.4416 Evaluate side-chains 313 residues out of total 3154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 270 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 210 LEU Chi-restraints excluded: chain I residue 112 TYR Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain J residue 210 LEU Chi-restraints excluded: chain K residue 113 VAL Chi-restraints excluded: chain K residue 190 LEU Chi-restraints excluded: chain L residue 154 LEU Chi-restraints excluded: chain L residue 175 THR Chi-restraints excluded: chain L residue 180 MET Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain N residue 41 HIS Chi-restraints excluded: chain P residue 17 GLU Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain R residue 52 ILE Chi-restraints excluded: chain R residue 59 SER Chi-restraints excluded: chain R residue 80 ILE Chi-restraints excluded: chain S residue 109 TYR Chi-restraints excluded: chain S residue 114 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: [293, 191, 254, 34, 349, 242, 317, 2, 179, 172, 13] chunk 293 optimal weight: 9.9990 chunk 191 optimal weight: 0.6980 chunk 254 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 349 optimal weight: 9.9990 chunk 242 optimal weight: 1.9990 chunk 317 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 179 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 47 ASN K 291 GLN P 72 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.116618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.075521 restraints weight = 72082.762| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.98 r_work: 0.2985 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 31300 Z= 0.180 Angle : 0.563 9.559 42676 Z= 0.296 Chirality : 0.045 0.497 4958 Planarity : 0.004 0.048 4955 Dihedral : 15.942 175.734 5158 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.74 % Allowed : 15.03 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.14), residues: 3554 helix: 1.93 (0.13), residues: 1602 sheet: -0.28 (0.21), residues: 569 loop : -1.25 (0.16), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 284 TYR 0.027 0.001 TYR O 120 PHE 0.013 0.001 PHE L 301 TRP 0.039 0.002 TRP R 33 HIS 0.005 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 (31295) covalent geometry : angle 0.56183 / 0.30 (42668) SS BOND : bond 0.00250 / 0.13 ( 1) SS BOND : angle 2.19188 / 1.23 ( 2) hydrogen bonds : bond 0.03879 / 2.59 ( 1539) hydrogen bonds : angle 4.49075 / 3.21 ( 4308) metal coordination : bond 0.00987 / 0.50 ( 4) metal coordination : angle 2.88244 / 1.54 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 274 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.5138 (t60) cc_final: 0.4889 (t60) REVERT: A 148 LYS cc_start: 0.5528 (mttt) cc_final: 0.4488 (ttpp) REVERT: A 152 CYS cc_start: 0.2915 (OUTLIER) cc_final: 0.2366 (p) REVERT: A 281 PHE cc_start: 0.8387 (m-80) cc_final: 0.8050 (m-10) REVERT: A 309 MET cc_start: 0.8598 (mtt) cc_final: 0.8273 (mtp) REVERT: A 340 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7211 (mp) REVERT: A 377 LYS cc_start: 0.7117 (OUTLIER) cc_final: 0.6833 (pptt) REVERT: A 411 LEU cc_start: 0.5391 (OUTLIER) cc_final: 0.4867 (pp) REVERT: A 445 GLU cc_start: 0.8479 (pt0) cc_final: 0.7712 (pp20) REVERT: A 467 ARG cc_start: 0.7365 (ttp-170) cc_final: 0.6792 (ttp80) REVERT: A 474 TRP cc_start: 0.8701 (t-100) cc_final: 0.8500 (m100) REVERT: A 480 GLU cc_start: 0.9402 (mm-30) cc_final: 0.9147 (mm-30) REVERT: C 17 TYR cc_start: 0.8031 (t80) cc_final: 0.7695 (t80) REVERT: C 296 LYS cc_start: 0.7998 (mttt) cc_final: 0.7632 (tptt) REVERT: D 1 MET cc_start: 0.8106 (tpp) cc_final: 0.7890 (tpt) REVERT: D 23 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8545 (pp) REVERT: D 91 MET cc_start: 0.8039 (mmt) cc_final: 0.7741 (mmt) REVERT: D 113 GLN cc_start: 0.8382 (pm20) cc_final: 0.7803 (tt0) REVERT: D 124 PHE cc_start: 0.8041 (t80) cc_final: 0.7329 (t80) REVERT: D 177 MET cc_start: 0.8384 (mmm) cc_final: 0.7970 (tpp) REVERT: D 217 GLN cc_start: 0.8667 (mm-40) cc_final: 0.8444 (mm-40) REVERT: D 255 MET cc_start: 0.8297 (mtp) cc_final: 0.7843 (tpp) REVERT: H 17 TYR cc_start: 0.8937 (t80) cc_final: 0.8367 (t80) REVERT: H 23 GLU cc_start: 0.7964 (tp30) cc_final: 0.7291 (tm-30) REVERT: H 27 TYR cc_start: 0.9255 (t80) cc_final: 0.8705 (t80) REVERT: H 63 GLU cc_start: 0.8919 (tm-30) cc_final: 0.8611 (tm-30) REVERT: I 11 GLU cc_start: 0.8495 (mt-10) cc_final: 0.8267 (mt-10) REVERT: I 112 TYR cc_start: 0.8180 (OUTLIER) cc_final: 0.6432 (m-80) REVERT: I 122 MET cc_start: 0.9141 (mmm) cc_final: 0.8853 (mtp) REVERT: I 224 TYR cc_start: 0.9019 (p90) cc_final: 0.8800 (p90) REVERT: I 291 GLN cc_start: 0.9146 (tt0) cc_final: 0.8607 (mt0) REVERT: J 20 ILE cc_start: 0.9235 (mt) cc_final: 0.9016 (mm) REVERT: J 28 SER cc_start: 0.9517 (m) cc_final: 0.8746 (p) REVERT: J 40 GLU cc_start: 0.8647 (mm-30) cc_final: 0.8072 (mm-30) REVERT: J 74 GLN cc_start: 0.8013 (mp10) cc_final: 0.7740 (mp10) REVERT: J 208 GLN cc_start: 0.8253 (mt0) cc_final: 0.7952 (mt0) REVERT: K 109 MET cc_start: 0.9051 (mmm) cc_final: 0.8523 (mmm) REVERT: K 122 MET cc_start: 0.9090 (mmm) cc_final: 0.8428 (mtt) REVERT: K 180 MET cc_start: 0.8577 (tpt) cc_final: 0.8278 (tpp) REVERT: K 208 GLN cc_start: 0.7389 (mt0) cc_final: 0.7185 (mt0) REVERT: K 289 ASP cc_start: 0.9305 (t0) cc_final: 0.9057 (t0) REVERT: L 109 MET cc_start: 0.8896 (mmm) cc_final: 0.8610 (mmm) REVERT: L 122 MET cc_start: 0.9291 (mmm) cc_final: 0.8487 (mmm) REVERT: L 167 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8252 (mt-10) REVERT: L 175 THR cc_start: 0.8076 (OUTLIER) cc_final: 0.7444 (p) REVERT: L 180 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.7999 (ppp) REVERT: L 207 GLN cc_start: 0.8700 (mm-40) cc_final: 0.8103 (tp40) REVERT: L 208 GLN cc_start: 0.8421 (mm-40) cc_final: 0.8161 (mm-40) REVERT: M 35 ASP cc_start: 0.8698 (m-30) cc_final: 0.8476 (p0) REVERT: M 40 GLU cc_start: 0.8646 (mp0) cc_final: 0.8314 (mm-30) REVERT: M 47 ASN cc_start: 0.6809 (t0) cc_final: 0.6536 (t0) REVERT: M 104 ASN cc_start: 0.8951 (t0) cc_final: 0.8613 (t0) REVERT: M 109 MET cc_start: 0.8698 (mmm) cc_final: 0.7812 (mmm) REVERT: M 114 TYR cc_start: 0.6840 (m-10) cc_final: 0.6632 (m-10) REVERT: M 129 ILE cc_start: 0.8817 (mt) cc_final: 0.8372 (tp) REVERT: M 159 ASP cc_start: 0.6758 (t0) cc_final: 0.6247 (t70) REVERT: M 281 ASN cc_start: 0.8797 (m110) cc_final: 0.8332 (m110) REVERT: N 72 GLN cc_start: 0.8256 (mt0) cc_final: 0.7927 (mp10) REVERT: N 87 ASN cc_start: 0.9318 (t0) cc_final: 0.8946 (m110) REVERT: P 17 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8410 (pm20) REVERT: Q 32 ASP cc_start: 0.8188 (t0) cc_final: 0.7909 (m-30) REVERT: R 45 TYR cc_start: 0.8162 (m-80) cc_final: 0.7741 (m-80) REVERT: S 57 LYS cc_start: 0.7899 (mttt) cc_final: 0.7620 (tptp) outliers start: 55 outliers final: 35 residues processed: 312 average time/residue: 0.1800 time to fit residues: 91.5257 Evaluate side-chains 313 residues out of total 3154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 269 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 210 LEU Chi-restraints excluded: chain H residue 249 ILE Chi-restraints excluded: chain I residue 112 TYR Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 210 LEU Chi-restraints excluded: chain K residue 59 LEU Chi-restraints excluded: chain K residue 113 VAL Chi-restraints excluded: chain K residue 190 LEU Chi-restraints excluded: chain L residue 154 LEU Chi-restraints excluded: chain L residue 175 THR Chi-restraints excluded: chain L residue 180 MET Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain N residue 41 HIS Chi-restraints excluded: chain P residue 17 GLU Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain R residue 52 ILE Chi-restraints excluded: chain R residue 59 SER Chi-restraints excluded: chain R residue 80 ILE Chi-restraints excluded: chain S residue 109 TYR Chi-restraints excluded: chain S residue 114 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: [335, 88, 188, 198, 264, 26, 237, 96, 324, 358, 184] chunk 335 optimal weight: 0.7980 chunk 88 optimal weight: 0.6980 chunk 188 optimal weight: 0.6980 chunk 198 optimal weight: 0.9980 chunk 264 optimal weight: 0.7980 chunk 26 optimal weight: 10.0000 chunk 237 optimal weight: 0.6980 chunk 96 optimal weight: 10.0000 chunk 324 optimal weight: 1.9990 chunk 358 optimal weight: 10.0000 chunk 184 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 264 ASN C 191 ASN H 47 ASN K 291 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.118036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.077364 restraints weight = 71725.870| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.98 r_work: 0.3026 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 31300 Z= 0.123 Angle : 0.532 10.139 42676 Z= 0.283 Chirality : 0.044 0.475 4958 Planarity : 0.004 0.060 4955 Dihedral : 15.940 175.605 5158 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.33 % Allowed : 15.69 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.14), residues: 3554 helix: 1.92 (0.13), residues: 1609 sheet: -0.23 (0.21), residues: 571 loop : -1.19 (0.16), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG J 284 TYR 0.028 0.001 TYR O 120 PHE 0.012 0.001 PHE L 301 TRP 0.037 0.002 TRP D 282 HIS 0.005 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (31295) covalent geometry : angle 0.53102 / 0.28 (42668) SS BOND : bond 0.01501 / 0.79 ( 1) SS BOND : angle 2.55158 / 1.44 ( 2) hydrogen bonds : bond 0.03634 / 2.42 ( 1539) hydrogen bonds : angle 4.42757 / 3.17 ( 4308) metal coordination : bond 0.00831 / 0.42 ( 4) metal coordination : angle 2.88251 / 1.55 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 3154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 292 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.5136 (t60) cc_final: 0.4886 (t60) REVERT: A 148 LYS cc_start: 0.5452 (mttt) cc_final: 0.4429 (ttpp) REVERT: A 152 CYS cc_start: 0.3060 (OUTLIER) cc_final: 0.2523 (p) REVERT: A 224 ILE cc_start: 0.7554 (OUTLIER) cc_final: 0.7212 (tp) REVERT: A 281 PHE cc_start: 0.8374 (m-80) cc_final: 0.8031 (m-10) REVERT: A 309 MET cc_start: 0.8625 (mtt) cc_final: 0.8301 (mtp) REVERT: A 377 LYS cc_start: 0.7149 (OUTLIER) cc_final: 0.6838 (pptt) REVERT: A 411 LEU cc_start: 0.5214 (OUTLIER) cc_final: 0.4737 (pp) REVERT: A 445 GLU cc_start: 0.8445 (pt0) cc_final: 0.7692 (pp20) REVERT: A 467 ARG cc_start: 0.7484 (ttp-170) cc_final: 0.6995 (ttp80) REVERT: A 480 GLU cc_start: 0.9412 (mm-30) cc_final: 0.9156 (mm-30) REVERT: C 17 TYR cc_start: 0.7923 (t80) cc_final: 0.7608 (t80) REVERT: C 296 LYS cc_start: 0.7919 (mttt) cc_final: 0.7532 (tptt) REVERT: D 23 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8563 (pp) REVERT: D 91 MET cc_start: 0.8042 (mmt) cc_final: 0.7780 (mmt) REVERT: D 113 GLN cc_start: 0.8351 (pm20) cc_final: 0.7834 (tt0) REVERT: D 124 PHE cc_start: 0.8032 (t80) cc_final: 0.7286 (t80) REVERT: D 177 MET cc_start: 0.8337 (mmm) cc_final: 0.7903 (tpp) REVERT: D 217 GLN cc_start: 0.8657 (mm-40) cc_final: 0.8391 (mm-40) REVERT: D 255 MET cc_start: 0.8253 (mtp) cc_final: 0.7820 (tpp) REVERT: H 23 GLU cc_start: 0.7874 (tp30) cc_final: 0.7255 (tm-30) REVERT: H 27 TYR cc_start: 0.9239 (t80) cc_final: 0.8719 (t80) REVERT: H 63 GLU cc_start: 0.8900 (tm-30) cc_final: 0.8578 (tm-30) REVERT: I 11 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8229 (mt-10) REVERT: I 112 TYR cc_start: 0.8085 (OUTLIER) cc_final: 0.6425 (m-80) REVERT: I 122 MET cc_start: 0.9101 (mmm) cc_final: 0.8799 (mtp) REVERT: I 224 TYR cc_start: 0.8974 (p90) cc_final: 0.8772 (p90) REVERT: I 291 GLN cc_start: 0.9141 (tt0) cc_final: 0.8613 (mt0) REVERT: J 20 ILE cc_start: 0.9216 (mt) cc_final: 0.8983 (mm) REVERT: J 28 SER cc_start: 0.9498 (m) cc_final: 0.8727 (p) REVERT: J 40 GLU cc_start: 0.8648 (mm-30) cc_final: 0.8061 (mm-30) REVERT: J 74 GLN cc_start: 0.8013 (mp10) cc_final: 0.7782 (mp10) REVERT: J 208 GLN cc_start: 0.8227 (mt0) cc_final: 0.7912 (mt0) REVERT: J 284 ARG cc_start: 0.8356 (mtm110) cc_final: 0.8145 (mtm-85) REVERT: K 109 MET cc_start: 0.9035 (mmm) cc_final: 0.8494 (mmm) REVERT: K 122 MET cc_start: 0.9037 (mmm) cc_final: 0.8391 (mtt) REVERT: K 180 MET cc_start: 0.8533 (tpt) cc_final: 0.8237 (tpp) REVERT: L 109 MET cc_start: 0.8831 (mmm) cc_final: 0.8604 (mmm) REVERT: L 122 MET cc_start: 0.9259 (mmm) cc_final: 0.8445 (mmm) REVERT: L 167 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8239 (mt-10) REVERT: L 175 THR cc_start: 0.8039 (OUTLIER) cc_final: 0.7413 (p) REVERT: L 180 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.7985 (ppp) REVERT: L 207 GLN cc_start: 0.8680 (mm-40) cc_final: 0.8047 (tp40) REVERT: L 208 GLN cc_start: 0.8412 (mm-40) cc_final: 0.8187 (mm-40) REVERT: M 35 ASP cc_start: 0.8685 (m-30) cc_final: 0.8464 (p0) REVERT: M 40 GLU cc_start: 0.8667 (mp0) cc_final: 0.8331 (mm-30) REVERT: M 47 ASN cc_start: 0.6710 (t0) cc_final: 0.6470 (t0) REVERT: M 104 ASN cc_start: 0.8963 (t0) cc_final: 0.8626 (t0) REVERT: M 109 MET cc_start: 0.8661 (mmm) cc_final: 0.7764 (mmm) REVERT: M 129 ILE cc_start: 0.8850 (mt) cc_final: 0.8396 (tp) REVERT: M 159 ASP cc_start: 0.6891 (t0) cc_final: 0.6391 (t70) REVERT: M 281 ASN cc_start: 0.8804 (m110) cc_final: 0.8338 (m110) REVERT: N 72 GLN cc_start: 0.8216 (mt0) cc_final: 0.7926 (mp10) REVERT: N 87 ASN cc_start: 0.9302 (t0) cc_final: 0.8915 (m110) REVERT: P 17 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8426 (pm20) REVERT: P 77 SER cc_start: 0.8333 (m) cc_final: 0.7598 (p) REVERT: Q 32 ASP cc_start: 0.8199 (t0) cc_final: 0.7881 (m-30) REVERT: Q 63 ASP cc_start: 0.8201 (m-30) cc_final: 0.7700 (m-30) REVERT: Q 111 TYR cc_start: 0.7766 (m-10) cc_final: 0.7448 (m-10) REVERT: R 45 TYR cc_start: 0.8179 (m-80) cc_final: 0.7807 (m-80) REVERT: S 57 LYS cc_start: 0.7859 (mttt) cc_final: 0.7514 (tptp) outliers start: 42 outliers final: 29 residues processed: 316 average time/residue: 0.1833 time to fit residues: 94.4540 Evaluate side-chains 314 residues out of total 3154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 276 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain H residue 210 LEU Chi-restraints excluded: chain H residue 249 ILE Chi-restraints excluded: chain I residue 112 TYR Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 210 LEU Chi-restraints excluded: chain L residue 154 LEU Chi-restraints excluded: chain L residue 175 THR Chi-restraints excluded: chain L residue 180 MET Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 231 MET Chi-restraints excluded: chain N residue 41 HIS Chi-restraints excluded: chain P residue 17 GLU Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain R residue 52 ILE Chi-restraints excluded: chain R residue 59 SER Chi-restraints excluded: chain R residue 80 ILE Chi-restraints excluded: chain S residue 109 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: [146, 11, 361, 2, 193, 273, 362, 303, 203, 306, 240] chunk 146 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 361 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 193 optimal weight: 4.9990 chunk 273 optimal weight: 0.9990 chunk 362 optimal weight: 6.9990 chunk 303 optimal weight: 10.0000 chunk 203 optimal weight: 3.9990 chunk 306 optimal weight: 4.9990 chunk 240 optimal weight: 4.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 47 ASN K 291 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.116567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.075429 restraints weight = 72480.887| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 3.02 r_work: 0.2982 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 31300 Z= 0.197 Angle : 0.575 10.123 42676 Z= 0.302 Chirality : 0.045 0.503 4958 Planarity : 0.004 0.065 4955 Dihedral : 15.933 176.345 5158 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.46 % Allowed : 15.92 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.14), residues: 3554 helix: 1.95 (0.13), residues: 1601 sheet: -0.23 (0.21), residues: 572 loop : -1.23 (0.16), residues: 1381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG J 284 TYR 0.033 0.001 TYR Q 92 PHE 0.014 0.001 PHE L 88 TRP 0.031 0.002 TRP D 282 HIS 0.005 0.001 HIS D 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.20 (31295) covalent geometry : angle 0.57416 / 0.30 (42668) SS BOND : bond 0.00268 / 0.14 ( 1) SS BOND : angle 2.88425 / 1.63 ( 2) hydrogen bonds : bond 0.03901 / 2.61 ( 1539) hydrogen bonds : angle 4.48737 / 3.20 ( 4308) metal coordination : bond 0.00992 / 0.50 ( 4) metal coordination : angle 2.82230 / 1.52 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7755.46 seconds wall clock time: 133 minutes 29.68 seconds (8009.68 seconds total)