Starting phenix.real_space_refine on Thu Oct 29 01:30:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11hd_75686/10_2026/11hd_75686.cif Found real_map, /net/cci-nas-00/data/ceres_data/11hd_75686/10_2026/11hd_75686.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/11hd_75686/10_2026/11hd_75686.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11hd_75686/10_2026/11hd_75686.map" model { file = "/net/cci-nas-00/data/ceres_data/11hd_75686/10_2026/11hd_75686.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11hd_75686/10_2026/11hd_75686.cif" } resolution = 3.21 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= 0.022 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 84 5.49 5 Mg 2 5.21 5 S 75 5.16 5 C 18931 2.51 5 N 4967 2.21 5 O 5743 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 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: 29803 Number of models: 1 Model: "" Number of chains: 18 Chain: "B" 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: 2358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2358 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 14, 'TRANS': 288} Chain: "G" 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: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 891 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 1, 'TRANS': 110} Chain: "L" 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: "M" 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: "N" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 883 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 1, 'TRANS': 109} 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: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 762 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain: "Q" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 1005 Classifications: {'RNA': 47} Modifications used: {'rna2p_pur': 13, 'rna2p_pyr': 11, 'rna3p_pur': 14, 'rna3p_pyr': 9} Link IDs: {'rna2p': 24, 'rna3p': 22} Chain: "A" Number of atoms: 4210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 4210 Classifications: {'peptide': 517} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 495} Chain breaks: 2 Chain: "C" Number of atoms: 2296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2296 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 14, 'TRANS': 280} Chain breaks: 1 Chain: "F" Number of atoms: 2316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2316 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 14, 'TRANS': 282} Chain breaks: 1 Chain: "H" Number of atoms: 2316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2316 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 14, 'TRANS': 282} Chain breaks: 1 Chain: "I" Number of atoms: 2054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2054 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 14, 'TRANS': 249} Chain breaks: 2 Chain: "J" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 882 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 1, 'TRANS': 109} 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 18439 SG CYS A 382 46.128 75.578 36.565 1.00495.19 S ATOM 18463 SG CYS A 385 48.396 72.904 35.105 1.00489.11 S ATOM 18509 SG CYS A 420 44.966 73.265 33.669 1.00498.27 S ATOM 18527 SG CYS A 423 45.307 71.894 37.100 1.00491.05 S Time building chain proxies: 6.14, per 1000 atoms: 0.21 Number of scatterers: 29803 At special positions: 0 Unit cell: (110.21, 127.33, 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 75 16.00 P 84 15.00 Mg 2 11.99 O 5743 8.00 N 4967 7.00 C 18931 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=2.03 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: 2.72 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 701 " pdb="ZN ZN A 701 " - pdb=" SG CYS A 420 " pdb="ZN ZN A 701 " - pdb=" SG CYS A 423 " pdb="ZN ZN A 701 " - pdb=" SG CYS A 385 " pdb="ZN ZN A 701 " - pdb=" SG CYS A 382 " Number of angles added : 6 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6574 Finding SS restraints... Secondary structure from input PDB file: 154 helices and 51 sheets defined 50.8% alpha, 15.8% beta 30 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 3.53 Creating SS restraints... Processing helix chain 'B' and resid 45 through 72 Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 104 through 112 Processing helix chain 'B' and resid 116 through 123 Processing helix chain 'B' and resid 144 through 146 No H-bonds generated for 'chain 'B' and resid 144 through 146' Processing helix chain 'B' and resid 147 through 154 Processing helix chain 'B' and resid 164 through 167 Processing helix chain 'B' and resid 179 through 186 Processing helix chain 'B' and resid 196 through 200 removed outlier: 3.551A pdb=" N VAL B 199 " --> pdb=" O VAL B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 244 Processing helix chain 'B' and resid 252 through 256 Processing helix chain 'B' and resid 268 through 286 Processing helix chain 'B' and resid 286 through 296 Processing helix chain 'B' and resid 297 through 303 removed outlier: 4.085A pdb=" N PHE B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N PHE B 302 " --> pdb=" O PRO B 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 43 Processing helix chain 'D' and resid 44 through 47 removed outlier: 3.569A pdb=" N ASP D 47 " --> pdb=" O LEU D 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 44 through 47' Processing helix chain 'D' and resid 50 through 61 Processing helix chain 'D' and resid 132 through 144 Processing helix chain 'D' and resid 186 through 201 Processing helix chain 'D' and resid 248 through 258 Processing helix chain 'E' and resid 45 through 73 Processing helix chain 'E' and resid 81 through 89 Processing helix chain 'E' and resid 104 through 112 Processing helix chain 'E' and resid 116 through 123 Processing helix chain 'E' and resid 147 through 154 Processing helix chain 'E' and resid 164 through 167 Processing helix chain 'E' and resid 179 through 186 Processing helix chain 'E' and resid 232 through 245 Processing helix chain 'E' and resid 268 through 296 removed outlier: 5.841A pdb=" N THR E 288 " --> pdb=" O ARG E 284 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ASP E 289 " --> pdb=" O ASP E 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 303 removed outlier: 3.778A pdb=" N PHE E 301 " --> pdb=" O PRO E 298 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 73 Processing helix chain 'G' and resid 81 through 89 Processing helix chain 'G' and resid 104 through 112 Processing helix chain 'G' and resid 116 through 123 Processing helix chain 'G' and resid 147 through 154 Processing helix chain 'G' and resid 164 through 167 Processing helix chain 'G' and resid 179 through 186 Processing helix chain 'G' and resid 232 through 246 Processing helix chain 'G' and resid 252 through 256 Processing helix chain 'G' and resid 268 through 286 Processing helix chain 'G' and resid 286 through 296 Processing helix chain 'G' and resid 297 through 303 removed outlier: 3.606A pdb=" N PHE G 301 " --> pdb=" O PRO G 298 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG G 303 " --> pdb=" O ASP G 300 " (cutoff:3.500A) Processing helix chain 'K' and resid 15 through 30 Processing helix chain 'K' and resid 37 through 43 Processing helix chain 'K' and resid 43 through 59 removed outlier: 3.677A pdb=" N ILE K 47 " --> pdb=" O LYS K 43 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 73 Processing helix chain 'K' and resid 81 through 98 removed outlier: 3.664A pdb=" N HIS K 98 " --> pdb=" O LYS K 94 " (cutoff:3.500A) Processing helix chain 'K' and resid 98 through 109 Processing helix chain 'K' and resid 109 through 124 Processing helix chain 'L' and resid 15 through 30 Processing helix chain 'L' and resid 38 through 43 removed outlier: 3.537A pdb=" N LYS L 43 " --> pdb=" O LYS L 39 " (cutoff:3.500A) Processing helix chain 'L' and resid 43 through 59 removed outlier: 3.665A pdb=" N LYS L 50 " --> pdb=" O SER L 46 " (cutoff:3.500A) Processing helix chain 'L' and resid 61 through 73 Processing helix chain 'L' and resid 81 through 98 Processing helix chain 'L' and resid 98 through 109 removed outlier: 4.026A pdb=" N LYS L 104 " --> pdb=" O GLY L 100 " (cutoff:3.500A) Processing helix chain 'L' and resid 109 through 124 removed outlier: 3.603A pdb=" N ILE L 124 " --> pdb=" O TYR L 120 " (cutoff:3.500A) Processing helix chain 'M' and resid 15 through 31 Processing helix chain 'M' and resid 37 through 43 Processing helix chain 'M' and resid 43 through 59 Processing helix chain 'M' and resid 61 through 74 Processing helix chain 'M' and resid 81 through 98 Processing helix chain 'M' and resid 98 through 109 Processing helix chain 'M' and resid 109 through 124 removed outlier: 3.597A pdb=" N ILE M 124 " --> pdb=" O TYR M 120 " (cutoff:3.500A) Processing helix chain 'N' and resid 15 through 30 removed outlier: 3.604A pdb=" N ILE N 30 " --> pdb=" O ALA N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 32 through 36 removed outlier: 3.553A pdb=" N SER N 35 " --> pdb=" O ASP N 32 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET N 36 " --> pdb=" O TRP N 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 32 through 36' Processing helix chain 'N' and resid 37 through 43 removed outlier: 3.608A pdb=" N LYS N 43 " --> pdb=" O LYS N 39 " (cutoff:3.500A) Processing helix chain 'N' and resid 43 through 59 Processing helix chain 'N' and resid 61 through 74 removed outlier: 3.617A pdb=" N VAL N 73 " --> pdb=" O LEU N 69 " (cutoff:3.500A) Processing helix chain 'N' and resid 75 through 77 No H-bonds generated for 'chain 'N' and resid 75 through 77' Processing helix chain 'N' and resid 81 through 98 Processing helix chain 'N' and resid 98 through 109 Processing helix chain 'N' and resid 109 through 123 Processing helix chain 'O' and resid 15 through 30 Processing helix chain 'O' and resid 33 through 36 Processing helix chain 'O' and resid 37 through 42 removed outlier: 3.851A pdb=" N HIS O 41 " --> pdb=" O GLY O 37 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG O 42 " --> pdb=" O GLU O 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 37 through 42' Processing helix chain 'O' and resid 43 through 59 Processing helix chain 'O' and resid 61 through 73 Processing helix chain 'O' and resid 81 through 98 removed outlier: 3.504A pdb=" N HIS O 98 " --> pdb=" O LYS O 94 " (cutoff:3.500A) Processing helix chain 'O' and resid 98 through 109 Processing helix chain 'O' and resid 109 through 124 removed outlier: 3.601A pdb=" N ILE O 124 " --> pdb=" O TYR O 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 45 removed outlier: 3.655A pdb=" N PHE A 45 " --> pdb=" O GLN A 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 41 through 45' 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 127 Processing helix chain 'A' and resid 135 through 146 removed outlier: 3.576A pdb=" N VAL A 139 " --> pdb=" O ASN A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 160 Processing helix chain 'A' and resid 167 through 172 removed outlier: 3.936A pdb=" N THR A 170 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU A 172 " --> pdb=" O GLU A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 222 removed outlier: 4.135A pdb=" N ARG A 195 " --> pdb=" O PRO A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 256 Processing helix chain 'A' and resid 308 through 310 No H-bonds generated for 'chain 'A' and resid 308 through 310' Processing helix chain 'A' and resid 335 through 351 Processing helix chain 'A' and resid 352 through 358 removed outlier: 3.748A pdb=" N THR A 358 " --> pdb=" O ASP A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 374 Processing helix chain 'A' and resid 420 through 433 Processing helix chain 'A' and resid 468 through 486 removed outlier: 3.551A pdb=" N LEU A 485 " --> pdb=" O VAL A 481 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N HIS A 486 " --> pdb=" O TYR A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 500 No H-bonds generated for 'chain 'A' and resid 498 through 500' Processing helix chain 'A' and resid 501 through 507 removed outlier: 3.827A pdb=" N TYR A 505 " --> pdb=" O ALA A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 569 Processing helix chain 'A' and resid 572 through 584 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 147 through 155 Processing helix chain 'C' and resid 165 through 167 No H-bonds generated for 'chain 'C' and resid 165 through 167' Processing helix chain 'C' and resid 179 through 186 Processing helix chain 'C' and resid 187 through 189 No H-bonds generated for 'chain 'C' and resid 187 through 189' Processing helix chain 'C' and resid 232 through 245 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: 3.659A pdb=" N PHE C 301 " --> pdb=" O PRO C 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 73 Processing helix chain 'F' and resid 81 through 89 Processing helix chain 'F' and resid 104 through 112 Processing helix chain 'F' and resid 116 through 123 Processing helix chain 'F' and resid 144 through 146 No H-bonds generated for 'chain 'F' and resid 144 through 146' Processing helix chain 'F' and resid 147 through 155 Processing helix chain 'F' and resid 164 through 167 Processing helix chain 'F' and resid 179 through 186 Processing helix chain 'F' and resid 232 through 245 Processing helix chain 'F' and resid 252 through 256 Processing helix chain 'F' and resid 268 through 286 Processing helix chain 'F' and resid 286 through 296 Processing helix chain 'F' and resid 297 through 301 Processing helix chain 'H' and resid 45 through 73 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 144 through 146 No H-bonds generated for 'chain 'H' and resid 144 through 146' Processing helix chain 'H' and resid 147 through 155 Processing helix chain 'H' and resid 164 through 167 Processing helix chain 'H' and resid 179 through 186 Processing helix chain 'H' and resid 232 through 246 removed outlier: 3.538A pdb=" N HIS H 245 " --> pdb=" O LYS H 241 " (cutoff:3.500A) Processing helix chain 'H' and resid 268 through 286 Processing helix chain 'H' and resid 286 through 295 removed outlier: 3.778A pdb=" N LYS H 295 " --> pdb=" O GLN H 291 " (cutoff:3.500A) Processing helix chain 'H' and resid 296 through 302 removed outlier: 6.191A pdb=" N ASN H 299 " --> pdb=" O LYS H 296 " (cutoff:3.500A) removed outlier: 3.549A 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 155 Processing helix chain 'I' and resid 164 through 168 removed outlier: 3.878A pdb=" N ILE I 168 " --> pdb=" O THR I 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 164 through 168' Processing helix chain 'I' and resid 232 through 246 Processing helix chain 'I' and resid 268 through 286 Processing helix chain 'I' and resid 286 through 296 removed outlier: 3.771A pdb=" N LYS I 295 " --> pdb=" O GLN I 291 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS I 296 " --> pdb=" O GLU I 292 " (cutoff:3.500A) Processing helix chain 'I' and resid 297 through 301 removed outlier: 3.657A pdb=" N PHE I 301 " --> pdb=" O PRO I 298 " (cutoff:3.500A) Processing helix chain 'J' and resid 15 through 31 removed outlier: 3.915A pdb=" N ILE J 30 " --> pdb=" O ALA J 26 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE J 31 " --> pdb=" O ILE J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 33 through 37 removed outlier: 3.731A pdb=" N MET J 36 " --> pdb=" O TRP J 33 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLY J 37 " --> pdb=" O GLY J 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 33 through 37' Processing helix chain 'J' and resid 38 through 59 removed outlier: 6.660A pdb=" N TYR J 45 " --> pdb=" O HIS J 41 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N SER J 46 " --> pdb=" O ARG J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 72 Processing helix chain 'J' and resid 81 through 98 Processing helix chain 'J' and resid 98 through 109 Processing helix chain 'J' and resid 109 through 121 Processing sheet with id=AA1, first strand: chain 'B' and resid 135 through 137 removed outlier: 3.561A pdb=" N TYR B 141 " --> pdb=" O TYR B 222 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 135 through 137 Processing sheet with id=AA3, first strand: chain 'B' and resid 19 through 20 Processing sheet with id=AA4, first strand: chain 'B' and resid 28 through 32 Processing sheet with id=AA5, first strand: chain 'B' and resid 78 through 80 removed outlier: 5.757A pdb=" N ALA B 79 " --> pdb=" O GLN C 193 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 125 through 126 Processing sheet with id=AA7, first strand: chain 'B' and resid 169 through 176 Processing sheet with id=AA8, first strand: chain 'B' and resid 191 through 193 removed outlier: 3.588A pdb=" N ALA E 79 " --> pdb=" O ASN B 191 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 71 through 72 removed outlier: 4.458A pdb=" N MET D 177 " --> pdb=" O CYS D 78 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE D 109 " --> pdb=" O VAL D 96 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASN D 98 " --> pdb=" O TYR D 107 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N TYR D 107 " --> pdb=" O ASN D 98 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N ASP D 100 " --> pdb=" O ALA D 105 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ALA D 105 " --> pdb=" O ASP D 100 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 15 through 19 removed outlier: 3.787A pdb=" N SER D 18 " --> pdb=" O GLU D 22 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N GLU D 22 " --> pdb=" O SER D 18 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG D 170 " --> pdb=" O LEU D 23 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N GLN D 25 " --> pdb=" O ARG D 170 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE D 123 " --> pdb=" O LEU D 171 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 146 through 147 removed outlier: 5.643A pdb=" N ARG D 146 " --> pdb=" O ALA C 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 231 through 235 removed outlier: 3.790A pdb=" N ALA D 291 " --> pdb=" O THR D 243 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N LEU D 286 " --> pdb=" O GLY D 275 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLY D 275 " --> pdb=" O LEU D 286 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N VAL D 288 " --> pdb=" O GLY D 273 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLY D 273 " --> pdb=" O VAL D 288 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASP D 269 " --> pdb=" O LEU D 292 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU D 294 " --> pdb=" O LEU D 267 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU D 267 " --> pdb=" O LEU D 294 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 135 through 137 Processing sheet with id=AB5, first strand: chain 'E' and resid 135 through 137 Processing sheet with id=AB6, first strand: chain 'E' and resid 19 through 20 Processing sheet with id=AB7, first strand: chain 'E' and resid 28 through 29 Processing sheet with id=AB8, first strand: chain 'E' and resid 124 through 126 Processing sheet with id=AB9, first strand: chain 'E' and resid 169 through 176 Processing sheet with id=AC1, first strand: chain 'E' and resid 192 through 193 Processing sheet with id=AC2, first strand: chain 'G' and resid 135 through 137 Processing sheet with id=AC3, first strand: chain 'G' and resid 135 through 137 Processing sheet with id=AC4, first strand: chain 'G' and resid 19 through 20 removed outlier: 6.902A pdb=" N THR G 24 " --> pdb=" O GLN G 213 " (cutoff:3.500A) removed outlier: 9.042A pdb=" N VAL G 215 " --> pdb=" O THR G 24 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 28 through 32 Processing sheet with id=AC6, first strand: chain 'G' and resid 79 through 80 removed outlier: 6.912A pdb=" N ALA G 79 " --> pdb=" O GLN F 193 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'G' and resid 124 through 126 Processing sheet with id=AC8, first strand: chain 'G' and resid 191 through 193 removed outlier: 5.953A pdb=" N ASN G 191 " --> pdb=" O ALA H 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'A' and resid 48 through 51 removed outlier: 6.472A pdb=" N ILE A 48 " --> pdb=" O ILE A 511 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N TYR A 513 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N GLY A 50 " --> pdb=" O TYR A 513 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 104 through 105 Processing sheet with id=AD2, first strand: chain 'A' and resid 183 through 189 Processing sheet with id=AD3, first strand: chain 'A' and resid 260 through 262 removed outlier: 6.246A pdb=" N TYR A 280 " --> pdb=" O VAL A 303 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N VAL A 305 " --> pdb=" O TYR A 280 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N GLU A 282 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ILE A 300 " --> pdb=" O ASP A 294 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ASP A 294 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY A 302 " --> pdb=" O ASP A 292 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 135 through 137 removed outlier: 3.516A pdb=" N TYR C 141 " --> pdb=" O TYR C 222 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 135 through 137 Processing sheet with id=AD6, first strand: chain 'C' and resid 18 through 20 removed outlier: 4.082A pdb=" N GLU C 18 " --> pdb=" O LEU C 25 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N THR C 24 " --> pdb=" O GLN C 213 " (cutoff:3.500A) removed outlier: 9.276A pdb=" N VAL C 215 " --> pdb=" O THR C 24 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 28 through 32 Processing sheet with id=AD8, first strand: chain 'C' and resid 125 through 126 Processing sheet with id=AD9, first strand: chain 'F' and resid 135 through 137 Processing sheet with id=AE1, first strand: chain 'F' and resid 135 through 137 Processing sheet with id=AE2, first strand: chain 'F' and resid 19 through 20 removed outlier: 6.961A pdb=" N THR F 24 " --> pdb=" O GLN F 213 " (cutoff:3.500A) removed outlier: 9.148A pdb=" N VAL F 215 " --> pdb=" O THR F 24 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 28 through 30 Processing sheet with id=AE4, first strand: chain 'F' and resid 124 through 126 Processing sheet with id=AE5, first strand: chain 'H' and resid 135 through 137 Processing sheet with id=AE6, first strand: chain 'H' and resid 135 through 137 Processing sheet with id=AE7, first strand: chain 'H' and resid 19 through 20 removed outlier: 6.695A pdb=" N THR H 24 " --> pdb=" O GLN H 213 " (cutoff:3.500A) removed outlier: 8.955A pdb=" N VAL H 215 " --> pdb=" O THR H 24 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 28 through 30 Processing sheet with id=AE9, first strand: chain 'H' and resid 124 through 126 Processing sheet with id=AF1, first strand: chain 'H' and resid 190 through 193 removed outlier: 5.880A pdb=" N ASN H 191 " --> pdb=" O ALA I 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'I' and resid 135 through 137 Processing sheet with id=AF3, first strand: chain 'I' and resid 135 through 137 Processing sheet with id=AF4, first strand: chain 'I' and resid 23 through 24 removed outlier: 6.796A pdb=" N THR I 24 " --> pdb=" O GLN I 213 " (cutoff:3.500A) removed outlier: 9.148A pdb=" N VAL I 215 " --> pdb=" O THR I 24 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 28 through 32 Processing sheet with id=AF6, first strand: chain 'I' and resid 124 through 126 1487 hydrogen bonds defined for protein. 4245 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 78 hydrogen bonds 156 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 6.11 Time building geometry restraints manager: 3.60 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: 7064 1.33 - 1.45: 5723 1.45 - 1.57: 17398 1.57 - 1.69: 166 1.69 - 1.81: 143 Bond restraints: 30494 Sorted by residual: bond pdb=" C3' DC P 30 " pdb=" C2' DC P 30 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.79e+00 bond pdb=" C3' DG P 19 " pdb=" C2' DG P 19 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.30e+00 bond pdb=" O4' DG P 19 " pdb=" C1' DG P 19 " ideal model delta sigma weight residual 1.420 1.391 0.029 1.10e-02 8.26e+03 7.02e+00 bond pdb=" C2' DT P 7 " pdb=" C1' DT P 7 " ideal model delta sigma weight residual 1.518 1.544 -0.026 1.00e-02 1.00e+04 6.66e+00 bond pdb=" C2' DG P 37 " pdb=" C1' DG P 37 " ideal model delta sigma weight residual 1.518 1.543 -0.025 1.00e-02 1.00e+04 6.45e+00 ... (remaining 30489 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 40211 1.23 - 2.45: 967 2.45 - 3.68: 269 3.68 - 4.90: 36 4.90 - 6.13: 11 Bond angle restraints: 41494 Sorted by residual: angle pdb=" O4' DG P 19 " pdb=" C1' DG P 19 " pdb=" N9 DG P 19 " ideal model delta sigma weight residual 108.00 112.68 -4.68 7.00e-01 2.04e+00 4.47e+01 angle pdb=" C4' DG P 19 " pdb=" O4' DG P 19 " pdb=" C1' DG P 19 " ideal model delta sigma weight residual 110.10 103.97 6.13 1.00e+00 1.00e+00 3.76e+01 angle pdb=" O4' DG P 37 " pdb=" C4' DG P 37 " pdb=" C3' DG P 37 " ideal model delta sigma weight residual 106.00 102.58 3.42 6.00e-01 2.78e+00 3.25e+01 angle pdb=" O4' DG P 13 " pdb=" C4' DG P 13 " pdb=" C3' DG P 13 " ideal model delta sigma weight residual 106.00 102.61 3.39 6.00e-01 2.78e+00 3.19e+01 angle pdb=" O4' DT P 7 " pdb=" C4' DT P 7 " pdb=" C3' DT P 7 " ideal model delta sigma weight residual 106.00 102.74 3.26 6.00e-01 2.78e+00 2.96e+01 ... (remaining 41489 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.14: 18085 35.14 - 70.27: 446 70.27 - 105.41: 42 105.41 - 140.54: 3 140.54 - 175.68: 7 Dihedral angle restraints: 18583 sinusoidal: 8339 harmonic: 10244 Sorted by residual: dihedral pdb=" O4' U Q 2 " pdb=" C1' U Q 2 " pdb=" N1 U Q 2 " pdb=" C2 U Q 2 " ideal model delta sinusoidal sigma weight residual 200.00 64.42 135.58 1 1.50e+01 4.44e-03 7.31e+01 dihedral pdb=" O4' U Q 20 " pdb=" C1' U Q 20 " pdb=" N1 U Q 20 " pdb=" C2 U Q 20 " ideal model delta sinusoidal sigma weight residual -128.00 41.75 -169.75 1 1.70e+01 3.46e-03 6.59e+01 dihedral pdb=" O4' G Q 4 " pdb=" C1' G Q 4 " pdb=" N9 G Q 4 " pdb=" C4 G Q 4 " ideal model delta sinusoidal sigma weight residual 254.00 173.96 80.04 1 1.70e+01 3.46e-03 2.75e+01 ... (remaining 18580 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 3500 0.039 - 0.078: 891 0.078 - 0.116: 356 0.116 - 0.155: 77 0.155 - 0.194: 4 Chirality restraints: 4828 Sorted by residual: chirality pdb=" C3' DT P 18 " pdb=" C4' DT P 18 " pdb=" O3' DT P 18 " pdb=" C2' DT P 18 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 9.41e-01 chirality pdb=" C3' A Q 6 " pdb=" C4' A Q 6 " pdb=" O3' A Q 6 " pdb=" C2' A Q 6 " both_signs ideal model delta sigma weight residual False -2.48 -2.31 -0.16 2.00e-01 2.50e+01 6.61e-01 chirality pdb=" C3' DC P 30 " pdb=" C4' DC P 30 " pdb=" O3' DC P 30 " pdb=" C2' DC P 30 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.50e-01 ... (remaining 4825 not shown) Planarity restraints: 4868 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG P 19 " -0.035 2.00e-02 2.50e+03 1.58e-02 7.45e+00 pdb=" N9 DG P 19 " 0.039 2.00e-02 2.50e+03 pdb=" C8 DG P 19 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DG P 19 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DG P 19 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG P 19 " 0.006 2.00e-02 2.50e+03 pdb=" O6 DG P 19 " -0.014 2.00e-02 2.50e+03 pdb=" N1 DG P 19 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DG P 19 " 0.001 2.00e-02 2.50e+03 pdb=" N2 DG P 19 " -0.000 2.00e-02 2.50e+03 pdb=" N3 DG P 19 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DG P 19 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U Q 18 " -0.027 2.00e-02 2.50e+03 1.50e-02 5.03e+00 pdb=" N1 U Q 18 " 0.035 2.00e-02 2.50e+03 pdb=" C2 U Q 18 " -0.002 2.00e-02 2.50e+03 pdb=" O2 U Q 18 " 0.003 2.00e-02 2.50e+03 pdb=" N3 U Q 18 " -0.003 2.00e-02 2.50e+03 pdb=" C4 U Q 18 " -0.006 2.00e-02 2.50e+03 pdb=" O4 U Q 18 " -0.004 2.00e-02 2.50e+03 pdb=" C5 U Q 18 " -0.001 2.00e-02 2.50e+03 pdb=" C6 U Q 18 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG P 37 " 0.029 2.00e-02 2.50e+03 1.24e-02 4.61e+00 pdb=" N9 DG P 37 " -0.030 2.00e-02 2.50e+03 pdb=" C8 DG P 37 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DG P 37 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DG P 37 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DG P 37 " 0.003 2.00e-02 2.50e+03 pdb=" O6 DG P 37 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DG P 37 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DG P 37 " -0.001 2.00e-02 2.50e+03 pdb=" N2 DG P 37 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DG P 37 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DG P 37 " -0.004 2.00e-02 2.50e+03 ... (remaining 4865 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.31: 9 2.31 - 2.96: 13536 2.96 - 3.61: 44094 3.61 - 4.25: 69851 4.25 - 4.90: 118146 Nonbonded interactions: 245636 Sorted by model distance: nonbonded pdb=" NE2 HIS A 146 " pdb=" CD2 HIS A 147 " model vdw 1.668 3.340 nonbonded pdb=" NE2 HIS A 146 " pdb=" NE2 HIS A 147 " model vdw 2.113 3.200 nonbonded pdb=" OD1 ASP A 94 " pdb="MG MG A 702 " model vdw 2.122 2.170 nonbonded pdb=" NE2 HIS A 115 " pdb="MG MG A 702 " model vdw 2.158 2.250 nonbonded pdb=" CD2 HIS A 146 " pdb=" CD2 HIS A 147 " model vdw 2.188 3.480 ... (remaining 245631 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 'B' and (resid 1 through 92 or resid 103 through 174 or resid 209 through \ 303)) selection = (chain 'C' and (resid 1 through 92 or resid 103 through 174 or resid 209 through \ 303)) selection = (chain 'E' and (resid 1 through 92 or resid 103 through 174 or resid 209 through \ 303)) selection = (chain 'F' and (resid 1 through 92 or resid 103 through 174 or resid 209 through \ 303)) selection = (chain 'G' and (resid 1 through 92 or resid 103 through 174 or resid 209 through \ 303)) selection = (chain 'H' and (resid 1 through 92 or resid 103 through 174 or resid 209 through \ 303)) selection = (chain 'I' and (resid 1 through 92 or resid 103 through 303)) } ncs_group { reference = (chain 'J' and resid 13 through 121) selection = (chain 'K' and resid 13 through 121) selection = (chain 'L' and resid 13 through 121) selection = (chain 'M' and resid 13 through 121) selection = (chain 'N' and resid 13 through 121) selection = (chain 'O' and resid 13 through 121) } 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: 5.600 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: 0.530 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 33.930 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.080 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 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 0.034 30499 Z= 0.208 Angle : 0.504 6.129 41502 Z= 0.341 Chirality : 0.042 0.194 4828 Planarity : 0.003 0.060 4868 Dihedral : 15.387 175.675 12006 Min Nonbonded Distance : 1.668 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.28 (0.15), residues: 3500 helix: 2.42 (0.13), residues: 1626 sheet: -0.48 (0.22), residues: 564 loop : -0.54 (0.17), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 51 TYR 0.023 0.001 TYR K 117 PHE 0.009 0.001 PHE C 158 TRP 0.022 0.001 TRP D 244 HIS 0.003 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.21 (30494) covalent geometry : angle 0.50349 / 0.34 (41494) SS BOND : bond 0.00207 / 0.11 ( 1) SS BOND : angle 0.17767 / 0.09 ( 2) hydrogen bonds : bond 0.13197 / 9.05 ( 1551) hydrogen bonds : angle 6.12397 / 4.34 ( 4401) metal coordination : bond 0.00808 / 0.40 ( 4) metal coordination : angle 2.34656 / 1.06 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 3117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 689 time to evaluate : 1.226 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 122 MET cc_start: 0.9341 (mmm) cc_final: 0.9085 (mmm) REVERT: B 233 GLU cc_start: 0.8913 (mt-10) cc_final: 0.8687 (tt0) REVERT: B 248 LYS cc_start: 0.9264 (mttt) cc_final: 0.8868 (mptt) REVERT: B 261 LYS cc_start: 0.8722 (tttm) cc_final: 0.8396 (tppt) REVERT: D 111 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8047 (tp30) REVERT: D 123 ILE cc_start: 0.7717 (mm) cc_final: 0.7382 (mm) REVERT: D 177 MET cc_start: 0.8049 (mtp) cc_final: 0.7039 (ttm) REVERT: D 226 ILE cc_start: 0.8872 (tt) cc_final: 0.7998 (mt) REVERT: D 240 PHE cc_start: 0.7597 (m-80) cc_final: 0.7226 (m-80) REVERT: D 254 GLU cc_start: 0.8894 (mt-10) cc_final: 0.8594 (pt0) REVERT: D 274 TYR cc_start: 0.7731 (m-80) cc_final: 0.7464 (m-10) REVERT: E 35 ASP cc_start: 0.9147 (m-30) cc_final: 0.8913 (p0) REVERT: E 56 LYS cc_start: 0.9116 (mmtt) cc_final: 0.8902 (tppp) REVERT: E 104 ASN cc_start: 0.8511 (t0) cc_final: 0.8280 (t0) REVERT: E 211 TYR cc_start: 0.9292 (m-80) cc_final: 0.8948 (m-10) REVERT: E 299 ASN cc_start: 0.9161 (m-40) cc_final: 0.8931 (m-40) REVERT: G 1 MET cc_start: 0.8657 (ttm) cc_final: 0.8416 (ttp) REVERT: G 11 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8430 (mt-10) REVERT: G 57 MET cc_start: 0.8990 (ttm) cc_final: 0.8699 (mtp) REVERT: G 73 LYS cc_start: 0.9303 (mttt) cc_final: 0.9049 (mmmt) REVERT: G 78 GLU cc_start: 0.8807 (mt-10) cc_final: 0.8436 (mp0) REVERT: G 145 LYS cc_start: 0.9232 (mttt) cc_final: 0.8977 (mmtm) REVERT: G 248 LYS cc_start: 0.8970 (mttt) cc_final: 0.8735 (mttp) REVERT: G 261 LYS cc_start: 0.8611 (tttt) cc_final: 0.8280 (tppt) REVERT: K 47 ILE cc_start: 0.9202 (mt) cc_final: 0.8887 (mm) REVERT: K 77 SER cc_start: 0.8536 (m) cc_final: 0.8249 (p) REVERT: L 17 GLU cc_start: 0.8730 (tt0) cc_final: 0.8375 (tm-30) REVERT: L 18 ASP cc_start: 0.9170 (m-30) cc_final: 0.8568 (m-30) REVERT: L 32 ASP cc_start: 0.7362 (t0) cc_final: 0.6216 (t0) REVERT: M 72 GLN cc_start: 0.8423 (tt0) cc_final: 0.8220 (tt0) REVERT: M 79 PHE cc_start: 0.7171 (t80) cc_final: 0.6853 (t80) REVERT: N 17 GLU cc_start: 0.8349 (mp0) cc_final: 0.7763 (tm-30) REVERT: N 32 ASP cc_start: 0.8668 (t0) cc_final: 0.8115 (t0) REVERT: N 35 SER cc_start: 0.8873 (p) cc_final: 0.8371 (p) REVERT: N 64 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8474 (tt0) REVERT: N 79 PHE cc_start: 0.8142 (t80) cc_final: 0.7932 (t80) REVERT: N 86 GLU cc_start: 0.9440 (mt-10) cc_final: 0.9199 (mm-30) REVERT: N 99 GLU cc_start: 0.7770 (tt0) cc_final: 0.7525 (tm-30) REVERT: O 28 ASP cc_start: 0.8038 (t70) cc_final: 0.7803 (t0) REVERT: O 45 TYR cc_start: 0.8057 (m-80) cc_final: 0.7631 (m-80) REVERT: O 106 LEU cc_start: 0.9049 (mt) cc_final: 0.8830 (mt) REVERT: A 41 GLN cc_start: 0.7874 (mt0) cc_final: 0.7461 (pm20) REVERT: A 205 MET cc_start: 0.0742 (tpp) cc_final: 0.0120 (mmm) REVERT: A 263 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7579 (tm-30) REVERT: A 299 MET cc_start: 0.7496 (ptm) cc_final: 0.7162 (ppp) REVERT: A 315 TYR cc_start: 0.6154 (m-80) cc_final: 0.5770 (m-10) REVERT: A 537 LEU cc_start: 0.1223 (mt) cc_final: 0.0919 (tt) REVERT: C 34 GLU cc_start: 0.8533 (pt0) cc_final: 0.8119 (pp20) REVERT: C 60 GLN cc_start: 0.8574 (tp40) cc_final: 0.8353 (tp40) REVERT: C 109 MET cc_start: 0.8356 (mmm) cc_final: 0.7847 (mmm) REVERT: C 184 MET cc_start: 0.9523 (mmt) cc_final: 0.9282 (mmm) REVERT: F 122 MET cc_start: 0.9449 (mmm) cc_final: 0.8251 (mmm) REVERT: F 174 ILE cc_start: 0.9346 (mt) cc_final: 0.9120 (mt) REVERT: F 187 LYS cc_start: 0.9127 (tttt) cc_final: 0.8856 (tppt) REVERT: F 248 LYS cc_start: 0.9059 (mttt) cc_final: 0.8113 (pttt) REVERT: H 57 MET cc_start: 0.9190 (ttm) cc_final: 0.8879 (mtp) REVERT: H 104 ASN cc_start: 0.8646 (t0) cc_final: 0.8433 (t0) REVERT: H 174 ILE cc_start: 0.8874 (mt) cc_final: 0.8615 (mm) REVERT: H 207 GLN cc_start: 0.8281 (tp40) cc_final: 0.7621 (tp-100) REVERT: H 226 GLU cc_start: 0.8623 (pt0) cc_final: 0.8261 (pt0) REVERT: H 231 MET cc_start: 0.9183 (mtp) cc_final: 0.8919 (mtm) REVERT: H 279 TYR cc_start: 0.9142 (t80) cc_final: 0.8885 (t80) REVERT: H 286 ASN cc_start: 0.8956 (m-40) cc_final: 0.8705 (m-40) REVERT: H 291 GLN cc_start: 0.9096 (tt0) cc_final: 0.8882 (tp-100) REVERT: I 17 TYR cc_start: 0.8478 (t80) cc_final: 0.8058 (t80) REVERT: I 40 GLU cc_start: 0.7651 (mm-30) cc_final: 0.7336 (mm-30) REVERT: I 159 ASP cc_start: 0.8497 (t0) cc_final: 0.8150 (t70) REVERT: I 291 GLN cc_start: 0.9570 (tt0) cc_final: 0.9265 (mt0) REVERT: J 52 ILE cc_start: 0.8083 (mt) cc_final: 0.7824 (mt) REVERT: J 57 LYS cc_start: 0.8890 (mttt) cc_final: 0.8565 (tppt) REVERT: J 62 LEU cc_start: 0.9069 (tt) cc_final: 0.8476 (tp) REVERT: J 64 GLU cc_start: 0.9124 (mt-10) cc_final: 0.8917 (mt-10) REVERT: J 99 GLU cc_start: 0.8711 (tt0) cc_final: 0.8433 (mt-10) REVERT: J 114 THR cc_start: 0.6981 (m) cc_final: 0.6471 (p) outliers start: 0 outliers final: 0 residues processed: 689 average time/residue: 0.2319 time to fit residues: 240.0163 Evaluate side-chains 357 residues out of total 3117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 357 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 298] chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 30.0000 chunk 20 optimal weight: 0.0170 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 30.0000 chunk 298 optimal weight: 3.9990 overall best weight: 2.5624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 181 ASN G 213 GLN L 41 HIS A 135 ASN A 147 HIS ** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 ASN H 191 ASN ** I 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 74 GLN I 286 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.105020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.064964 restraints weight = 74012.252| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 3.36 r_work: 0.2848 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 30499 Z= 0.244 Angle : 0.638 9.238 41502 Z= 0.333 Chirality : 0.046 0.246 4828 Planarity : 0.004 0.037 4868 Dihedral : 15.273 178.591 4910 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.73 % Allowed : 9.69 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.11 (0.14), residues: 3500 helix: 2.27 (0.13), residues: 1617 sheet: -0.40 (0.23), residues: 533 loop : -0.69 (0.16), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 226 TYR 0.023 0.002 TYR D 172 PHE 0.022 0.002 PHE A 218 TRP 0.021 0.002 TRP M 33 HIS 0.010 0.001 HIS A 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00556 / 0.24 (30494) covalent geometry : angle 0.63771 / 0.33 (41494) SS BOND : bond 0.00140 / 0.07 ( 1) SS BOND : angle 0.19460 / 0.10 ( 2) hydrogen bonds : bond 0.04822 / 3.31 ( 1551) hydrogen bonds : angle 5.12526 / 3.62 ( 4401) metal coordination : bond 0.00589 / 0.29 ( 4) metal coordination : angle 2.68736 / 1.24 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 3117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 363 time to evaluate : 1.117 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: B 1 MET cc_start: 0.8720 (ttm) cc_final: 0.8273 (ttm) REVERT: B 109 MET cc_start: 0.8653 (mmm) cc_final: 0.7966 (mmm) REVERT: B 233 GLU cc_start: 0.8815 (mt-10) cc_final: 0.8595 (tt0) REVERT: B 248 LYS cc_start: 0.9335 (mttt) cc_final: 0.9002 (mptt) REVERT: B 261 LYS cc_start: 0.8732 (tttm) cc_final: 0.8362 (tppt) REVERT: D 177 MET cc_start: 0.7989 (mtp) cc_final: 0.7085 (ttm) REVERT: D 226 ILE cc_start: 0.8419 (tt) cc_final: 0.7665 (mt) REVERT: D 254 GLU cc_start: 0.8920 (mt-10) cc_final: 0.8684 (mt-10) REVERT: D 274 TYR cc_start: 0.7879 (m-80) cc_final: 0.7633 (m-10) REVERT: E 35 ASP cc_start: 0.9109 (m-30) cc_final: 0.8829 (p0) REVERT: E 56 LYS cc_start: 0.9137 (mmtt) cc_final: 0.8915 (tppp) REVERT: E 104 ASN cc_start: 0.8455 (t0) cc_final: 0.8203 (t0) REVERT: E 109 MET cc_start: 0.9268 (mmt) cc_final: 0.8897 (tpp) REVERT: E 211 TYR cc_start: 0.9297 (m-80) cc_final: 0.8915 (m-10) REVERT: E 299 ASN cc_start: 0.9124 (m-40) cc_final: 0.8898 (m110) REVERT: G 1 MET cc_start: 0.8638 (ttm) cc_final: 0.8434 (ttp) REVERT: G 11 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8528 (mt-10) REVERT: G 57 MET cc_start: 0.8989 (ttm) cc_final: 0.8767 (mtp) REVERT: G 78 GLU cc_start: 0.8842 (mt-10) cc_final: 0.8472 (mp0) REVERT: G 248 LYS cc_start: 0.9033 (mttt) cc_final: 0.8783 (mttp) REVERT: G 261 LYS cc_start: 0.8520 (tttt) cc_final: 0.8204 (tppt) REVERT: K 33 TRP cc_start: 0.8712 (m100) cc_final: 0.8237 (m100) REVERT: K 36 MET cc_start: 0.4614 (ptp) cc_final: 0.4406 (ptp) REVERT: L 18 ASP cc_start: 0.9130 (m-30) cc_final: 0.8804 (m-30) REVERT: L 32 ASP cc_start: 0.7097 (t0) cc_final: 0.6109 (t0) REVERT: L 72 GLN cc_start: 0.8522 (mt0) cc_final: 0.8235 (mt0) REVERT: M 33 TRP cc_start: 0.8048 (m100) cc_final: 0.7507 (m100) REVERT: M 51 ARG cc_start: 0.8471 (mtt-85) cc_final: 0.8194 (mtt-85) REVERT: M 63 ASP cc_start: 0.9021 (p0) cc_final: 0.8810 (p0) REVERT: M 79 PHE cc_start: 0.7326 (t80) cc_final: 0.6974 (t80) REVERT: N 32 ASP cc_start: 0.8655 (t0) cc_final: 0.8207 (t0) REVERT: N 33 TRP cc_start: 0.8577 (m100) cc_final: 0.8134 (m100) REVERT: O 45 TYR cc_start: 0.8255 (m-80) cc_final: 0.7696 (m-80) REVERT: O 48 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8656 (mt) REVERT: O 92 TYR cc_start: 0.8323 (t80) cc_final: 0.8093 (t80) REVERT: O 93 ARG cc_start: 0.8701 (tpp-160) cc_final: 0.8206 (tpp-160) REVERT: O 106 LEU cc_start: 0.9094 (mt) cc_final: 0.8847 (mt) REVERT: A 263 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7493 (tm-30) REVERT: A 315 TYR cc_start: 0.6091 (m-80) cc_final: 0.5711 (m-10) REVERT: A 482 TYR cc_start: 0.7435 (t80) cc_final: 0.7057 (t80) REVERT: A 519 MET cc_start: 0.8032 (tmm) cc_final: 0.7771 (tmm) REVERT: A 537 LEU cc_start: 0.1228 (mt) cc_final: 0.0902 (tt) REVERT: C 1 MET cc_start: 0.7570 (ttp) cc_final: 0.6965 (ttp) REVERT: C 17 TYR cc_start: 0.8220 (t80) cc_final: 0.7951 (t80) REVERT: C 34 GLU cc_start: 0.8584 (pt0) cc_final: 0.8165 (pp20) REVERT: C 60 GLN cc_start: 0.8582 (tp40) cc_final: 0.8366 (tp40) REVERT: C 184 MET cc_start: 0.9516 (mmt) cc_final: 0.9171 (mmm) REVERT: F 122 MET cc_start: 0.9435 (mmm) cc_final: 0.8323 (mmm) REVERT: F 208 GLN cc_start: 0.7877 (mm110) cc_final: 0.7431 (mm-40) REVERT: F 248 LYS cc_start: 0.9091 (mttt) cc_final: 0.8838 (mttm) REVERT: H 57 MET cc_start: 0.9238 (ttm) cc_final: 0.8959 (mtp) REVERT: H 104 ASN cc_start: 0.8520 (t0) cc_final: 0.8270 (t0) REVERT: H 174 ILE cc_start: 0.8812 (mt) cc_final: 0.8514 (mm) REVERT: H 207 GLN cc_start: 0.8445 (tp40) cc_final: 0.7887 (tp40) REVERT: H 210 LEU cc_start: 0.8546 (pp) cc_final: 0.8277 (pp) REVERT: H 286 ASN cc_start: 0.8970 (m-40) cc_final: 0.8632 (m-40) REVERT: H 291 GLN cc_start: 0.9066 (tt0) cc_final: 0.8696 (tp-100) REVERT: I 1 MET cc_start: 0.8270 (tpp) cc_final: 0.8054 (tpp) REVERT: I 17 TYR cc_start: 0.8452 (t80) cc_final: 0.8024 (t80) REVERT: I 40 GLU cc_start: 0.7537 (mm-30) cc_final: 0.7084 (mm-30) REVERT: I 159 ASP cc_start: 0.8389 (t0) cc_final: 0.7731 (t0) REVERT: I 247 ASP cc_start: 0.8452 (p0) cc_final: 0.7926 (p0) REVERT: I 291 GLN cc_start: 0.9553 (tt0) cc_final: 0.9212 (mt0) REVERT: J 18 ASP cc_start: 0.8689 (m-30) cc_final: 0.8335 (t0) REVERT: J 51 ARG cc_start: 0.8409 (mmp80) cc_final: 0.8061 (mmm160) REVERT: J 57 LYS cc_start: 0.8877 (mttt) cc_final: 0.8536 (tppt) REVERT: J 62 LEU cc_start: 0.9070 (tt) cc_final: 0.8611 (tp) REVERT: J 99 GLU cc_start: 0.8804 (tt0) cc_final: 0.8513 (mt-10) outliers start: 54 outliers final: 35 residues processed: 403 average time/residue: 0.2205 time to fit residues: 136.3065 Evaluate side-chains 348 residues out of total 3117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 312 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 225 ASN Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 80 ILE Chi-restraints excluded: chain M residue 59 SER Chi-restraints excluded: chain N residue 40 VAL Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain C residue 277 HIS Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain I residue 92 ILE Chi-restraints excluded: chain I residue 151 LEU Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain J residue 27 ILE Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 97 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: [46, 29, 94, 67, 217, 148, 241, 81, 211, 89, 106] chunk 46 optimal weight: 9.9990 chunk 29 optimal weight: 0.2980 chunk 94 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 217 optimal weight: 5.9990 chunk 148 optimal weight: 0.7980 chunk 241 optimal weight: 10.0000 chunk 81 optimal weight: 0.9980 chunk 211 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 208 GLN ** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 208 GLN H 47 ASN ** I 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.106859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.067391 restraints weight = 74186.445| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 3.39 r_work: 0.2884 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30499 Z= 0.132 Angle : 0.549 8.448 41502 Z= 0.292 Chirality : 0.043 0.210 4828 Planarity : 0.004 0.048 4868 Dihedral : 15.294 177.317 4910 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.73 % Allowed : 10.62 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.09 (0.14), residues: 3500 helix: 2.23 (0.13), residues: 1622 sheet: -0.33 (0.22), residues: 536 loop : -0.70 (0.16), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 232 TYR 0.029 0.001 TYR J 117 PHE 0.017 0.001 PHE D 124 TRP 0.014 0.001 TRP O 33 HIS 0.007 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (30494) covalent geometry : angle 0.54852 / 0.29 (41494) SS BOND : bond 0.00111 / 0.06 ( 1) SS BOND : angle 0.19277 / 0.10 ( 2) hydrogen bonds : bond 0.04207 / 2.88 ( 1551) hydrogen bonds : angle 4.79211 / 3.39 ( 4401) metal coordination : bond 0.00369 / 0.18 ( 4) metal coordination : angle 2.43669 / 1.14 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 3117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 353 time to evaluate : 1.107 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: B 1 MET cc_start: 0.8666 (ttm) cc_final: 0.8096 (ttt) REVERT: B 47 ASN cc_start: 0.8789 (OUTLIER) cc_final: 0.8478 (t0) REVERT: B 109 MET cc_start: 0.8684 (mmm) cc_final: 0.8123 (mmm) REVERT: B 233 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8213 (tt0) REVERT: B 248 LYS cc_start: 0.9279 (mttt) cc_final: 0.8861 (mptt) REVERT: B 261 LYS cc_start: 0.8658 (tttm) cc_final: 0.8305 (tppt) REVERT: D 171 LEU cc_start: 0.7397 (OUTLIER) cc_final: 0.6655 (tt) REVERT: D 177 MET cc_start: 0.8119 (mtp) cc_final: 0.7297 (ttm) REVERT: D 226 ILE cc_start: 0.8193 (tt) cc_final: 0.7801 (mt) REVERT: D 245 ARG cc_start: 0.7379 (OUTLIER) cc_final: 0.6864 (tpt90) REVERT: D 254 GLU cc_start: 0.8979 (mt-10) cc_final: 0.8699 (mt-10) REVERT: D 274 TYR cc_start: 0.7834 (m-80) cc_final: 0.7577 (m-10) REVERT: E 35 ASP cc_start: 0.9111 (m-30) cc_final: 0.8868 (p0) REVERT: E 56 LYS cc_start: 0.9146 (mmtt) cc_final: 0.8933 (tppp) REVERT: E 104 ASN cc_start: 0.8450 (t0) cc_final: 0.8179 (t0) REVERT: E 109 MET cc_start: 0.9194 (mmt) cc_final: 0.8860 (tpp) REVERT: E 211 TYR cc_start: 0.9269 (m-80) cc_final: 0.8854 (m-10) REVERT: E 299 ASN cc_start: 0.9106 (m-40) cc_final: 0.8691 (m110) REVERT: G 11 GLU cc_start: 0.8771 (mt-10) cc_final: 0.8470 (mt-10) REVERT: G 57 MET cc_start: 0.8951 (ttm) cc_final: 0.8674 (mtp) REVERT: G 78 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8452 (mp0) REVERT: G 112 TYR cc_start: 0.7372 (OUTLIER) cc_final: 0.6463 (m-80) REVERT: G 248 LYS cc_start: 0.8913 (mttt) cc_final: 0.8563 (mmtm) REVERT: G 261 LYS cc_start: 0.8555 (tttt) cc_final: 0.8230 (tppt) REVERT: K 33 TRP cc_start: 0.8405 (m100) cc_final: 0.8047 (m100) REVERT: L 18 ASP cc_start: 0.9113 (m-30) cc_final: 0.8774 (m-30) REVERT: L 32 ASP cc_start: 0.6975 (t0) cc_final: 0.6126 (t0) REVERT: M 51 ARG cc_start: 0.8451 (mtt-85) cc_final: 0.8220 (mtt-85) REVERT: M 63 ASP cc_start: 0.8982 (p0) cc_final: 0.8684 (p0) REVERT: M 79 PHE cc_start: 0.7103 (t80) cc_final: 0.6766 (t80) REVERT: N 17 GLU cc_start: 0.8184 (mp0) cc_final: 0.7875 (tm-30) REVERT: N 32 ASP cc_start: 0.8666 (t0) cc_final: 0.8250 (t0) REVERT: O 45 TYR cc_start: 0.8231 (m-80) cc_final: 0.7628 (m-80) REVERT: O 48 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8650 (mt) REVERT: O 92 TYR cc_start: 0.8432 (t80) cc_final: 0.8180 (t80) REVERT: O 93 ARG cc_start: 0.8731 (tpp-160) cc_final: 0.8220 (tpp-160) REVERT: O 106 LEU cc_start: 0.9129 (mt) cc_final: 0.8877 (mt) REVERT: O 109 TYR cc_start: 0.8388 (m-10) cc_final: 0.7909 (m-10) REVERT: A 263 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7438 (tm-30) REVERT: A 315 TYR cc_start: 0.6050 (m-80) cc_final: 0.5670 (m-10) REVERT: A 482 TYR cc_start: 0.7583 (t80) cc_final: 0.7197 (t80) REVERT: C 1 MET cc_start: 0.7474 (ttp) cc_final: 0.6881 (ttp) REVERT: C 17 TYR cc_start: 0.8092 (t80) cc_final: 0.7687 (t80) REVERT: C 34 GLU cc_start: 0.8538 (pt0) cc_final: 0.8137 (pp20) REVERT: C 60 GLN cc_start: 0.8562 (tp40) cc_final: 0.8338 (tp40) REVERT: F 122 MET cc_start: 0.9417 (mmm) cc_final: 0.8309 (mmm) REVERT: F 187 LYS cc_start: 0.9245 (tppt) cc_final: 0.8942 (ttpp) REVERT: F 208 GLN cc_start: 0.7917 (mm110) cc_final: 0.7455 (mm-40) REVERT: F 210 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.9050 (pp) REVERT: H 57 MET cc_start: 0.9233 (ttm) cc_final: 0.8908 (mtp) REVERT: H 104 ASN cc_start: 0.8510 (t0) cc_final: 0.8243 (t0) REVERT: H 174 ILE cc_start: 0.8813 (mt) cc_final: 0.8575 (mm) REVERT: H 207 GLN cc_start: 0.8378 (tp40) cc_final: 0.8027 (tp-100) REVERT: H 231 MET cc_start: 0.9132 (mtp) cc_final: 0.8877 (mtm) REVERT: H 291 GLN cc_start: 0.9075 (tt0) cc_final: 0.8663 (tp-100) REVERT: I 17 TYR cc_start: 0.8446 (t80) cc_final: 0.8175 (t80) REVERT: I 40 GLU cc_start: 0.7514 (mm-30) cc_final: 0.7178 (mm-30) REVERT: I 159 ASP cc_start: 0.8281 (t0) cc_final: 0.7698 (t0) REVERT: I 211 TYR cc_start: 0.7661 (m-80) cc_final: 0.7387 (m-80) REVERT: I 247 ASP cc_start: 0.8464 (p0) cc_final: 0.7935 (p0) REVERT: I 285 ASP cc_start: 0.8851 (m-30) cc_final: 0.8643 (m-30) REVERT: I 291 GLN cc_start: 0.9558 (tt0) cc_final: 0.9207 (mt0) REVERT: J 18 ASP cc_start: 0.8595 (m-30) cc_final: 0.8311 (t0) REVERT: J 51 ARG cc_start: 0.8481 (mmp80) cc_final: 0.8195 (mmm160) REVERT: J 57 LYS cc_start: 0.8896 (mttt) cc_final: 0.8571 (tppt) outliers start: 54 outliers final: 30 residues processed: 390 average time/residue: 0.2065 time to fit residues: 126.5768 Evaluate side-chains 353 residues out of total 3117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 317 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 47 ASN Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 225 ASN Chi-restraints excluded: chain D residue 245 ARG Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain G residue 109 MET Chi-restraints excluded: chain G residue 112 TYR Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain M residue 41 HIS Chi-restraints excluded: chain M residue 59 SER Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 277 HIS Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 210 LEU Chi-restraints excluded: chain F residue 289 ASP Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain I residue 57 MET Chi-restraints excluded: chain I residue 92 ILE Chi-restraints excluded: chain I residue 151 LEU Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 97 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: [124, 322, 274, 236, 106, 59, 68, 91, 157, 275, 182] chunk 124 optimal weight: 5.9990 chunk 322 optimal weight: 7.9990 chunk 274 optimal weight: 0.3980 chunk 236 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 68 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 157 optimal weight: 1.9990 chunk 275 optimal weight: 0.6980 chunk 182 optimal weight: 50.0000 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 191 ASN ** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.105264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.065752 restraints weight = 73805.644| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 3.36 r_work: 0.2849 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 30499 Z= 0.209 Angle : 0.579 9.344 41502 Z= 0.303 Chirality : 0.044 0.220 4828 Planarity : 0.004 0.065 4868 Dihedral : 15.280 178.881 4910 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.09 % Allowed : 11.93 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.07 (0.14), residues: 3500 helix: 2.21 (0.13), residues: 1617 sheet: -0.41 (0.21), residues: 573 loop : -0.67 (0.16), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 170 TYR 0.023 0.001 TYR D 172 PHE 0.016 0.001 PHE D 36 TRP 0.011 0.001 TRP K 33 HIS 0.007 0.001 HIS L 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.21 (30494) covalent geometry : angle 0.57834 / 0.30 (41494) SS BOND : bond 0.00182 / 0.10 ( 1) SS BOND : angle 0.22830 / 0.12 ( 2) hydrogen bonds : bond 0.04306 / 2.96 ( 1551) hydrogen bonds : angle 4.73379 / 3.35 ( 4401) metal coordination : bond 0.00451 / 0.22 ( 4) metal coordination : angle 2.39800 / 1.17 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 3117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 321 time to evaluate : 0.906 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: B 1 MET cc_start: 0.8701 (ttm) cc_final: 0.8284 (ttm) REVERT: B 47 ASN cc_start: 0.8912 (OUTLIER) cc_final: 0.8581 (t0) REVERT: B 233 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8573 (tt0) REVERT: B 248 LYS cc_start: 0.9305 (mttt) cc_final: 0.8974 (mptt) REVERT: B 261 LYS cc_start: 0.8718 (tttm) cc_final: 0.8405 (tttp) REVERT: B 303 ARG cc_start: 0.5474 (mmp80) cc_final: 0.5059 (mmp80) REVERT: D 24 SER cc_start: 0.7720 (m) cc_final: 0.7471 (p) REVERT: D 177 MET cc_start: 0.8078 (mtp) cc_final: 0.7148 (ttm) REVERT: D 245 ARG cc_start: 0.7395 (OUTLIER) cc_final: 0.6493 (tpt90) REVERT: D 254 GLU cc_start: 0.8938 (mt-10) cc_final: 0.8680 (mt-10) REVERT: D 274 TYR cc_start: 0.7903 (m-80) cc_final: 0.7613 (m-10) REVERT: E 35 ASP cc_start: 0.9132 (m-30) cc_final: 0.8819 (p0) REVERT: E 104 ASN cc_start: 0.8435 (t0) cc_final: 0.8163 (t0) REVERT: E 122 MET cc_start: 0.9112 (mmm) cc_final: 0.8868 (mtp) REVERT: E 211 TYR cc_start: 0.9297 (m-80) cc_final: 0.8928 (m-10) REVERT: G 78 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8473 (mp0) REVERT: G 112 TYR cc_start: 0.7475 (OUTLIER) cc_final: 0.6649 (m-80) REVERT: G 248 LYS cc_start: 0.8986 (mttt) cc_final: 0.8634 (mmtm) REVERT: G 261 LYS cc_start: 0.8600 (tttt) cc_final: 0.8260 (tppt) REVERT: K 28 ASP cc_start: 0.9086 (t0) cc_final: 0.8819 (t0) REVERT: K 33 TRP cc_start: 0.8562 (m100) cc_final: 0.8329 (m100) REVERT: K 117 TYR cc_start: 0.7896 (OUTLIER) cc_final: 0.7528 (t80) REVERT: L 18 ASP cc_start: 0.9116 (m-30) cc_final: 0.8786 (m-30) REVERT: L 32 ASP cc_start: 0.6894 (t0) cc_final: 0.6185 (t0) REVERT: L 36 MET cc_start: 0.5271 (mmm) cc_final: 0.5002 (mmm) REVERT: M 63 ASP cc_start: 0.8950 (p0) cc_final: 0.8704 (p0) REVERT: M 79 PHE cc_start: 0.7373 (t80) cc_final: 0.6988 (t80) REVERT: N 17 GLU cc_start: 0.8231 (mp0) cc_final: 0.7932 (tm-30) REVERT: N 32 ASP cc_start: 0.8556 (t0) cc_final: 0.8169 (t0) REVERT: O 45 TYR cc_start: 0.8326 (m-80) cc_final: 0.7756 (m-80) REVERT: O 48 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8629 (mt) REVERT: O 93 ARG cc_start: 0.8791 (tpp-160) cc_final: 0.8285 (tpp-160) REVERT: O 106 LEU cc_start: 0.9115 (mt) cc_final: 0.8857 (mt) REVERT: O 109 TYR cc_start: 0.8422 (m-10) cc_final: 0.7907 (m-10) REVERT: A 263 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7428 (tm-30) REVERT: A 315 TYR cc_start: 0.6033 (m-80) cc_final: 0.5656 (m-10) REVERT: A 482 TYR cc_start: 0.7639 (t80) cc_final: 0.7182 (t80) REVERT: C 1 MET cc_start: 0.7553 (ttp) cc_final: 0.6934 (ttp) REVERT: C 17 TYR cc_start: 0.8188 (t80) cc_final: 0.7800 (t80) REVERT: C 34 GLU cc_start: 0.8608 (pt0) cc_final: 0.8194 (pp20) REVERT: C 60 GLN cc_start: 0.8592 (tp40) cc_final: 0.8343 (tp40) REVERT: F 122 MET cc_start: 0.9435 (mmm) cc_final: 0.8430 (mmm) REVERT: F 208 GLN cc_start: 0.8130 (mm110) cc_final: 0.7652 (mm-40) REVERT: F 210 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.9023 (pp) REVERT: H 57 MET cc_start: 0.9278 (ttm) cc_final: 0.8948 (mtp) REVERT: H 63 GLU cc_start: 0.9137 (tt0) cc_final: 0.8613 (tp30) REVERT: H 104 ASN cc_start: 0.8552 (t0) cc_final: 0.8296 (t0) REVERT: H 174 ILE cc_start: 0.8811 (mt) cc_final: 0.8610 (mm) REVERT: H 207 GLN cc_start: 0.8389 (tp40) cc_final: 0.7953 (tp40) REVERT: H 291 GLN cc_start: 0.9111 (tt0) cc_final: 0.8723 (tp-100) REVERT: I 17 TYR cc_start: 0.8440 (t80) cc_final: 0.7991 (t80) REVERT: I 40 GLU cc_start: 0.7545 (mm-30) cc_final: 0.7062 (mm-30) REVERT: I 159 ASP cc_start: 0.8350 (t0) cc_final: 0.7782 (t0) REVERT: I 173 LEU cc_start: 0.8582 (tp) cc_final: 0.8285 (mp) REVERT: I 247 ASP cc_start: 0.8439 (p0) cc_final: 0.7901 (p0) REVERT: I 291 GLN cc_start: 0.9569 (tt0) cc_final: 0.9223 (mt0) REVERT: J 18 ASP cc_start: 0.8513 (m-30) cc_final: 0.8266 (t70) REVERT: J 51 ARG cc_start: 0.8551 (mmp80) cc_final: 0.8296 (mmm160) REVERT: J 57 LYS cc_start: 0.8825 (mttt) cc_final: 0.8545 (tppt) outliers start: 65 outliers final: 40 residues processed: 366 average time/residue: 0.1981 time to fit residues: 115.7290 Evaluate side-chains 342 residues out of total 3117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 296 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 47 ASN Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 225 ASN Chi-restraints excluded: chain D residue 245 ARG Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain G residue 109 MET Chi-restraints excluded: chain G residue 112 TYR Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 117 TYR Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 80 ILE Chi-restraints excluded: chain M residue 59 SER Chi-restraints excluded: chain M residue 80 ILE Chi-restraints excluded: chain M residue 109 TYR Chi-restraints excluded: chain N residue 80 ILE Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 277 HIS Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 210 LEU Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain I residue 57 MET Chi-restraints excluded: chain I residue 92 ILE Chi-restraints excluded: chain I residue 151 LEU Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain I residue 228 ILE Chi-restraints excluded: chain I residue 231 MET Chi-restraints excluded: chain J residue 73 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: [41, 21, 32, 146, 223, 69, 175, 302, 255, 75, 246] chunk 41 optimal weight: 8.9990 chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 146 optimal weight: 3.9990 chunk 223 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 175 optimal weight: 10.0000 chunk 302 optimal weight: 0.7980 chunk 255 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 246 optimal weight: 0.7980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 47 ASN ** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 ASN ** I 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.104732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.065259 restraints weight = 74144.324| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 3.36 r_work: 0.2837 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 30499 Z= 0.216 Angle : 0.591 10.226 41502 Z= 0.309 Chirality : 0.044 0.225 4828 Planarity : 0.004 0.074 4868 Dihedral : 15.297 179.266 4910 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.12 % Allowed : 13.35 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.03 (0.14), residues: 3500 helix: 2.18 (0.13), residues: 1617 sheet: -0.40 (0.21), residues: 575 loop : -0.70 (0.16), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 284 TYR 0.030 0.001 TYR J 117 PHE 0.016 0.001 PHE D 36 TRP 0.010 0.001 TRP K 33 HIS 0.008 0.001 HIS J 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.22 (30494) covalent geometry : angle 0.58993 / 0.31 (41494) SS BOND : bond 0.00196 / 0.10 ( 1) SS BOND : angle 0.19839 / 0.11 ( 2) hydrogen bonds : bond 0.04321 / 2.97 ( 1551) hydrogen bonds : angle 4.67644 / 3.31 ( 4401) metal coordination : bond 0.00490 / 0.24 ( 4) metal coordination : angle 2.34119 / 1.16 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 3117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 304 time to evaluate : 1.199 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: B 1 MET cc_start: 0.8737 (ttm) cc_final: 0.8333 (ttm) REVERT: B 47 ASN cc_start: 0.8910 (OUTLIER) cc_final: 0.8582 (t0) REVERT: B 109 MET cc_start: 0.8567 (mmm) cc_final: 0.7963 (mmm) REVERT: B 233 GLU cc_start: 0.8810 (mt-10) cc_final: 0.8580 (tt0) REVERT: B 248 LYS cc_start: 0.9299 (mttt) cc_final: 0.8917 (mptt) REVERT: B 261 LYS cc_start: 0.8697 (tttm) cc_final: 0.8313 (tppt) REVERT: D 24 SER cc_start: 0.7774 (m) cc_final: 0.7549 (p) REVERT: D 51 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.8260 (ptm160) REVERT: D 177 MET cc_start: 0.8060 (mtp) cc_final: 0.7157 (ttm) REVERT: D 245 ARG cc_start: 0.7498 (OUTLIER) cc_final: 0.6937 (mmm-85) REVERT: D 254 GLU cc_start: 0.8949 (mt-10) cc_final: 0.8691 (mt-10) REVERT: D 274 TYR cc_start: 0.7913 (m-80) cc_final: 0.7617 (m-10) REVERT: E 35 ASP cc_start: 0.9192 (m-30) cc_final: 0.8868 (p0) REVERT: E 104 ASN cc_start: 0.8442 (t0) cc_final: 0.8172 (t0) REVERT: E 211 TYR cc_start: 0.9295 (m-80) cc_final: 0.8952 (m-10) REVERT: G 11 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8482 (mt-10) REVERT: G 78 GLU cc_start: 0.8874 (mt-10) cc_final: 0.8487 (mp0) REVERT: G 112 TYR cc_start: 0.7512 (OUTLIER) cc_final: 0.6625 (m-80) REVERT: G 248 LYS cc_start: 0.8981 (mttt) cc_final: 0.8626 (mmtm) REVERT: G 261 LYS cc_start: 0.8597 (tttt) cc_final: 0.8232 (tppt) REVERT: K 28 ASP cc_start: 0.9128 (t0) cc_final: 0.8918 (t0) REVERT: K 117 TYR cc_start: 0.8008 (OUTLIER) cc_final: 0.7578 (t80) REVERT: L 18 ASP cc_start: 0.9117 (m-30) cc_final: 0.8781 (m-30) REVERT: L 32 ASP cc_start: 0.7229 (t0) cc_final: 0.6618 (t0) REVERT: M 63 ASP cc_start: 0.8912 (p0) cc_final: 0.8709 (p0) REVERT: M 79 PHE cc_start: 0.7343 (t80) cc_final: 0.6981 (t80) REVERT: N 17 GLU cc_start: 0.8245 (mp0) cc_final: 0.7933 (tm-30) REVERT: N 32 ASP cc_start: 0.8559 (t0) cc_final: 0.8174 (t0) REVERT: O 45 TYR cc_start: 0.8346 (m-80) cc_final: 0.7794 (m-80) REVERT: O 48 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8619 (mt) REVERT: O 92 TYR cc_start: 0.8023 (t80) cc_final: 0.7763 (t80) REVERT: O 93 ARG cc_start: 0.8767 (tpp-160) cc_final: 0.8235 (tpp-160) REVERT: O 106 LEU cc_start: 0.9104 (mt) cc_final: 0.8867 (mt) REVERT: A 263 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7429 (tm-30) REVERT: A 315 TYR cc_start: 0.6051 (m-80) cc_final: 0.5677 (m-10) REVERT: A 482 TYR cc_start: 0.7719 (t80) cc_final: 0.7217 (t80) REVERT: C 17 TYR cc_start: 0.8327 (t80) cc_final: 0.7795 (t80) REVERT: C 34 GLU cc_start: 0.8655 (pt0) cc_final: 0.8279 (pp20) REVERT: C 60 GLN cc_start: 0.8603 (tp40) cc_final: 0.8371 (tp40) REVERT: F 57 MET cc_start: 0.9118 (ttm) cc_final: 0.8891 (ttm) REVERT: F 122 MET cc_start: 0.9439 (mmm) cc_final: 0.8440 (mmm) REVERT: F 187 LYS cc_start: 0.9174 (tppt) cc_final: 0.8883 (ttpp) REVERT: F 208 GLN cc_start: 0.8231 (mm110) cc_final: 0.7780 (mm-40) REVERT: F 210 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.9016 (pp) REVERT: H 57 MET cc_start: 0.9295 (ttm) cc_final: 0.9090 (mtp) REVERT: H 63 GLU cc_start: 0.9134 (tt0) cc_final: 0.8607 (tp30) REVERT: H 104 ASN cc_start: 0.8582 (t0) cc_final: 0.8327 (t0) REVERT: H 207 GLN cc_start: 0.8377 (tp40) cc_final: 0.7938 (tp40) REVERT: H 291 GLN cc_start: 0.9150 (tt0) cc_final: 0.8662 (tp-100) REVERT: I 17 TYR cc_start: 0.8425 (t80) cc_final: 0.8045 (t80) REVERT: I 40 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7418 (mm-30) REVERT: I 159 ASP cc_start: 0.8442 (t0) cc_final: 0.8123 (t0) REVERT: I 247 ASP cc_start: 0.8422 (p0) cc_final: 0.7898 (p0) REVERT: J 18 ASP cc_start: 0.8456 (m-30) cc_final: 0.8240 (t70) REVERT: J 51 ARG cc_start: 0.8594 (mmp80) cc_final: 0.8358 (mmm160) REVERT: J 57 LYS cc_start: 0.8794 (mttt) cc_final: 0.8507 (tppt) outliers start: 66 outliers final: 47 residues processed: 347 average time/residue: 0.1990 time to fit residues: 108.6141 Evaluate side-chains 345 residues out of total 3117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 291 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 47 ASN Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 51 ARG Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 245 ARG Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain G residue 92 ILE Chi-restraints excluded: chain G residue 109 MET Chi-restraints excluded: chain G residue 112 TYR Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 117 TYR Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 80 ILE Chi-restraints excluded: chain M residue 59 SER Chi-restraints excluded: chain M residue 80 ILE Chi-restraints excluded: chain M residue 109 TYR Chi-restraints excluded: chain N residue 31 ILE Chi-restraints excluded: chain N residue 80 ILE Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 277 HIS Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 210 LEU Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain I residue 47 ASN Chi-restraints excluded: chain I residue 92 ILE Chi-restraints excluded: chain I residue 151 LEU Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain I residue 228 ILE Chi-restraints excluded: chain I residue 231 MET Chi-restraints excluded: chain J residue 27 ILE Chi-restraints excluded: chain J residue 73 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: [116, 304, 44, 260, 155, 232, 312, 270, 333, 198, 187] chunk 116 optimal weight: 0.9990 chunk 304 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 260 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 232 optimal weight: 4.9990 chunk 312 optimal weight: 0.0770 chunk 270 optimal weight: 0.8980 chunk 333 optimal weight: 3.9990 chunk 198 optimal weight: 30.0000 chunk 187 optimal weight: 20.0000 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 47 ASN A 131 ASN ** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 277 HIS H 281 ASN I 74 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.106445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.067192 restraints weight = 73275.154| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 3.36 r_work: 0.2878 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30499 Z= 0.124 Angle : 0.536 9.536 41502 Z= 0.284 Chirality : 0.043 0.200 4828 Planarity : 0.004 0.060 4868 Dihedral : 15.253 177.864 4910 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.80 % Allowed : 14.37 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.05 (0.14), residues: 3500 helix: 2.18 (0.13), residues: 1623 sheet: -0.37 (0.21), residues: 567 loop : -0.68 (0.16), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 284 TYR 0.036 0.001 TYR J 117 PHE 0.016 0.001 PHE N 79 TRP 0.037 0.001 TRP K 33 HIS 0.004 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (30494) covalent geometry : angle 0.53566 / 0.28 (41494) SS BOND : bond 0.00107 / 0.06 ( 1) SS BOND : angle 0.21805 / 0.12 ( 2) hydrogen bonds : bond 0.03955 / 2.71 ( 1551) hydrogen bonds : angle 4.53609 / 3.21 ( 4401) metal coordination : bond 0.00384 / 0.19 ( 4) metal coordination : angle 2.29315 / 1.10 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 313 time to evaluate : 1.064 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: B 1 MET cc_start: 0.8673 (ttm) cc_final: 0.8248 (ttm) REVERT: B 47 ASN cc_start: 0.8792 (OUTLIER) cc_final: 0.8508 (t0) REVERT: B 233 GLU cc_start: 0.8719 (mt-10) cc_final: 0.8173 (tt0) REVERT: B 248 LYS cc_start: 0.9243 (mttt) cc_final: 0.8828 (mptt) REVERT: B 261 LYS cc_start: 0.8520 (tttm) cc_final: 0.8177 (tppt) REVERT: D 24 SER cc_start: 0.7798 (m) cc_final: 0.7531 (p) REVERT: D 51 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8276 (ptm160) REVERT: D 177 MET cc_start: 0.8088 (mtp) cc_final: 0.7469 (ttm) REVERT: D 208 MET cc_start: 0.9468 (mtt) cc_final: 0.9167 (ttm) REVERT: D 245 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.7027 (mmm-85) REVERT: D 254 GLU cc_start: 0.8954 (mt-10) cc_final: 0.8683 (mt-10) REVERT: D 274 TYR cc_start: 0.7903 (m-80) cc_final: 0.7608 (m-10) REVERT: E 35 ASP cc_start: 0.9168 (m-30) cc_final: 0.8920 (p0) REVERT: E 104 ASN cc_start: 0.8432 (t0) cc_final: 0.8155 (t0) REVERT: E 109 MET cc_start: 0.9209 (mmt) cc_final: 0.8674 (mmm) REVERT: E 211 TYR cc_start: 0.9237 (m-80) cc_final: 0.8923 (m-10) REVERT: G 78 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8457 (mp0) REVERT: G 112 TYR cc_start: 0.7371 (OUTLIER) cc_final: 0.6554 (m-80) REVERT: G 248 LYS cc_start: 0.8881 (mttt) cc_final: 0.8530 (mmtm) REVERT: G 261 LYS cc_start: 0.8585 (tttt) cc_final: 0.8261 (tppt) REVERT: K 28 ASP cc_start: 0.9205 (t0) cc_final: 0.8947 (t0) REVERT: K 117 TYR cc_start: 0.7988 (OUTLIER) cc_final: 0.7599 (t80) REVERT: L 18 ASP cc_start: 0.9092 (m-30) cc_final: 0.8746 (m-30) REVERT: L 32 ASP cc_start: 0.6938 (t0) cc_final: 0.6492 (t0) REVERT: L 72 GLN cc_start: 0.8767 (mm110) cc_final: 0.8276 (mp10) REVERT: M 63 ASP cc_start: 0.8847 (p0) cc_final: 0.8609 (p0) REVERT: M 79 PHE cc_start: 0.7324 (t80) cc_final: 0.6958 (t80) REVERT: N 17 GLU cc_start: 0.8213 (mp0) cc_final: 0.7855 (tm-30) REVERT: N 32 ASP cc_start: 0.8575 (t0) cc_final: 0.8265 (t0) REVERT: N 67 GLU cc_start: 0.8477 (tp30) cc_final: 0.8263 (tp30) REVERT: O 45 TYR cc_start: 0.8303 (m-80) cc_final: 0.7745 (m-80) REVERT: O 48 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8611 (mt) REVERT: O 92 TYR cc_start: 0.8040 (t80) cc_final: 0.7805 (t80) REVERT: O 93 ARG cc_start: 0.8814 (tpp-160) cc_final: 0.8307 (tpp-160) REVERT: O 106 LEU cc_start: 0.9091 (mt) cc_final: 0.8865 (mt) REVERT: O 109 TYR cc_start: 0.8403 (m-10) cc_final: 0.8096 (m-10) REVERT: A 263 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7382 (tm-30) REVERT: A 315 TYR cc_start: 0.6180 (m-80) cc_final: 0.5824 (m-10) REVERT: A 450 MET cc_start: 0.7397 (mmm) cc_final: 0.7179 (mmm) REVERT: A 482 TYR cc_start: 0.7788 (t80) cc_final: 0.7297 (t80) REVERT: C 17 TYR cc_start: 0.8072 (t80) cc_final: 0.7656 (t80) REVERT: C 34 GLU cc_start: 0.8579 (pt0) cc_final: 0.8216 (pp20) REVERT: C 60 GLN cc_start: 0.8566 (tp40) cc_final: 0.8327 (tp40) REVERT: F 57 MET cc_start: 0.9096 (ttm) cc_final: 0.8860 (ttm) REVERT: F 122 MET cc_start: 0.9408 (mmm) cc_final: 0.8311 (mmm) REVERT: F 187 LYS cc_start: 0.9191 (tppt) cc_final: 0.8887 (ttpp) REVERT: F 208 GLN cc_start: 0.8156 (mm-40) cc_final: 0.7688 (mm-40) REVERT: F 210 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.9016 (pp) REVERT: H 63 GLU cc_start: 0.9122 (tt0) cc_final: 0.8588 (tp30) REVERT: H 104 ASN cc_start: 0.8553 (t0) cc_final: 0.8286 (t0) REVERT: H 207 GLN cc_start: 0.8301 (tp40) cc_final: 0.8030 (tp-100) REVERT: H 291 GLN cc_start: 0.9129 (tt0) cc_final: 0.8617 (tp-100) REVERT: I 17 TYR cc_start: 0.8380 (t80) cc_final: 0.8131 (t80) REVERT: I 40 GLU cc_start: 0.7636 (mm-30) cc_final: 0.7342 (mm-30) REVERT: I 47 ASN cc_start: 0.8195 (t160) cc_final: 0.7876 (t0) REVERT: I 159 ASP cc_start: 0.8475 (t0) cc_final: 0.8138 (t0) REVERT: I 173 LEU cc_start: 0.8565 (tp) cc_final: 0.8230 (mp) REVERT: I 247 ASP cc_start: 0.8382 (p0) cc_final: 0.7879 (p0) REVERT: J 51 ARG cc_start: 0.8571 (mmp80) cc_final: 0.8360 (mmm160) REVERT: J 57 LYS cc_start: 0.8763 (mttt) cc_final: 0.8470 (tppt) outliers start: 56 outliers final: 34 residues processed: 351 average time/residue: 0.2018 time to fit residues: 112.0533 Evaluate side-chains 338 residues out of total 3117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 297 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 47 ASN Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 51 ARG Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 245 ARG Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain G residue 112 TYR Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 117 TYR Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 80 ILE Chi-restraints excluded: chain M residue 41 HIS Chi-restraints excluded: chain M residue 59 SER Chi-restraints excluded: chain M residue 109 TYR Chi-restraints excluded: chain O residue 18 ASP Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 277 HIS Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 210 LEU Chi-restraints excluded: chain F residue 289 ASP Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain I residue 57 MET Chi-restraints excluded: chain I residue 92 ILE Chi-restraints excluded: chain I residue 151 LEU Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain I residue 228 ILE Chi-restraints excluded: chain J residue 73 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: [130, 24, 27, 49, 199, 293, 167, 91, 203, 53, 301] chunk 130 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 49 optimal weight: 0.0570 chunk 199 optimal weight: 20.0000 chunk 293 optimal weight: 0.0270 chunk 167 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 203 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 301 optimal weight: 0.6980 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 41 HIS ** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.106760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.067449 restraints weight = 73478.164| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 3.37 r_work: 0.2885 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 30499 Z= 0.120 Angle : 0.536 14.080 41502 Z= 0.281 Chirality : 0.043 0.196 4828 Planarity : 0.004 0.060 4868 Dihedral : 15.209 177.790 4910 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.48 % Allowed : 14.98 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.09 (0.14), residues: 3500 helix: 2.20 (0.13), residues: 1625 sheet: -0.32 (0.21), residues: 560 loop : -0.67 (0.16), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 303 TYR 0.030 0.001 TYR J 117 PHE 0.016 0.001 PHE L 79 TRP 0.032 0.001 TRP A 257 HIS 0.004 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (30494) covalent geometry : angle 0.53559 / 0.28 (41494) SS BOND : bond 0.00119 / 0.06 ( 1) SS BOND : angle 0.19073 / 0.11 ( 2) hydrogen bonds : bond 0.03852 / 2.64 ( 1551) hydrogen bonds : angle 4.44562 / 3.14 ( 4401) metal coordination : bond 0.00364 / 0.18 ( 4) metal coordination : angle 2.52003 / 1.16 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 3117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 316 time to evaluate : 1.125 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: B 1 MET cc_start: 0.8633 (ttm) cc_final: 0.8216 (ttm) REVERT: B 47 ASN cc_start: 0.8778 (OUTLIER) cc_final: 0.8506 (t0) REVERT: B 109 MET cc_start: 0.8455 (mmm) cc_final: 0.8048 (mmm) REVERT: B 122 MET cc_start: 0.9187 (mmm) cc_final: 0.8836 (mmm) REVERT: B 233 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8148 (tt0) REVERT: B 248 LYS cc_start: 0.9238 (mttt) cc_final: 0.8820 (mptt) REVERT: B 261 LYS cc_start: 0.8513 (tttm) cc_final: 0.8166 (tppt) REVERT: B 303 ARG cc_start: 0.5873 (mmp80) cc_final: 0.5377 (mmp80) REVERT: D 1 MET cc_start: 0.8859 (tpt) cc_final: 0.8635 (tpp) REVERT: D 24 SER cc_start: 0.7785 (m) cc_final: 0.7514 (p) REVERT: D 51 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.8287 (ptm160) REVERT: D 177 MET cc_start: 0.8049 (mtp) cc_final: 0.7299 (ttm) REVERT: D 245 ARG cc_start: 0.7417 (OUTLIER) cc_final: 0.6998 (mmm-85) REVERT: D 274 TYR cc_start: 0.7897 (m-80) cc_final: 0.7607 (m-10) REVERT: D 282 TRP cc_start: 0.8205 (t60) cc_final: 0.7553 (t-100) REVERT: E 35 ASP cc_start: 0.9169 (m-30) cc_final: 0.8939 (p0) REVERT: E 104 ASN cc_start: 0.8438 (t0) cc_final: 0.8148 (t0) REVERT: E 211 TYR cc_start: 0.9206 (m-80) cc_final: 0.8902 (m-10) REVERT: G 11 GLU cc_start: 0.8731 (mt-10) cc_final: 0.8422 (mt-10) REVERT: G 57 MET cc_start: 0.8954 (ttm) cc_final: 0.8655 (mtp) REVERT: G 78 GLU cc_start: 0.8864 (mt-10) cc_final: 0.8456 (mp0) REVERT: G 109 MET cc_start: 0.9015 (tpp) cc_final: 0.8561 (tpp) REVERT: G 112 TYR cc_start: 0.7243 (OUTLIER) cc_final: 0.6329 (m-80) REVERT: G 248 LYS cc_start: 0.8830 (mttt) cc_final: 0.8490 (mmtm) REVERT: G 261 LYS cc_start: 0.8574 (tttt) cc_final: 0.8255 (tppt) REVERT: K 28 ASP cc_start: 0.9238 (t0) cc_final: 0.8894 (t0) REVERT: K 117 TYR cc_start: 0.7957 (OUTLIER) cc_final: 0.7461 (t80) REVERT: L 18 ASP cc_start: 0.9050 (m-30) cc_final: 0.8718 (m-30) REVERT: L 32 ASP cc_start: 0.7064 (t0) cc_final: 0.6639 (t0) REVERT: L 72 GLN cc_start: 0.8793 (mm110) cc_final: 0.8267 (mp10) REVERT: M 63 ASP cc_start: 0.8827 (p0) cc_final: 0.8593 (p0) REVERT: M 79 PHE cc_start: 0.7321 (t80) cc_final: 0.6974 (t80) REVERT: N 17 GLU cc_start: 0.8210 (mp0) cc_final: 0.7844 (tm-30) REVERT: N 32 ASP cc_start: 0.8539 (t0) cc_final: 0.8246 (t0) REVERT: N 67 GLU cc_start: 0.8475 (tp30) cc_final: 0.8218 (tp30) REVERT: O 45 TYR cc_start: 0.8317 (m-80) cc_final: 0.7777 (m-80) REVERT: O 48 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8609 (mt) REVERT: O 92 TYR cc_start: 0.8069 (t80) cc_final: 0.7858 (t80) REVERT: O 93 ARG cc_start: 0.8800 (tpp-160) cc_final: 0.8282 (tpp-160) REVERT: O 106 LEU cc_start: 0.9086 (mt) cc_final: 0.8851 (mt) REVERT: O 109 TYR cc_start: 0.8444 (m-10) cc_final: 0.8164 (m-10) REVERT: A 263 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7360 (tm-30) REVERT: A 315 TYR cc_start: 0.6170 (m-80) cc_final: 0.5818 (m-10) REVERT: A 482 TYR cc_start: 0.7828 (t80) cc_final: 0.7365 (t80) REVERT: C 17 TYR cc_start: 0.8038 (t80) cc_final: 0.7622 (t80) REVERT: C 34 GLU cc_start: 0.8565 (pt0) cc_final: 0.8184 (pp20) REVERT: C 60 GLN cc_start: 0.8598 (tp40) cc_final: 0.8390 (tp40) REVERT: C 141 TYR cc_start: 0.9127 (m-10) cc_final: 0.8776 (m-10) REVERT: C 284 ARG cc_start: 0.7483 (mtm110) cc_final: 0.7136 (ptt180) REVERT: F 122 MET cc_start: 0.9406 (mmm) cc_final: 0.8393 (mmm) REVERT: F 208 GLN cc_start: 0.8153 (mm-40) cc_final: 0.7686 (mm-40) REVERT: F 210 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.9027 (pp) REVERT: H 63 GLU cc_start: 0.9128 (tt0) cc_final: 0.8597 (tp30) REVERT: H 104 ASN cc_start: 0.8564 (t0) cc_final: 0.8286 (t0) REVERT: H 207 GLN cc_start: 0.8347 (tp40) cc_final: 0.8109 (tp-100) REVERT: H 291 GLN cc_start: 0.9123 (tt0) cc_final: 0.8696 (tp-100) REVERT: I 17 TYR cc_start: 0.8385 (t80) cc_final: 0.8036 (t80) REVERT: I 40 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7314 (mm-30) REVERT: I 47 ASN cc_start: 0.8201 (t160) cc_final: 0.7872 (t0) REVERT: I 159 ASP cc_start: 0.8498 (t0) cc_final: 0.8160 (t0) REVERT: I 173 LEU cc_start: 0.8598 (tp) cc_final: 0.8246 (mp) REVERT: I 247 ASP cc_start: 0.8391 (p0) cc_final: 0.7885 (p0) REVERT: J 57 LYS cc_start: 0.8763 (mttt) cc_final: 0.8437 (tppt) outliers start: 46 outliers final: 31 residues processed: 348 average time/residue: 0.1992 time to fit residues: 109.4858 Evaluate side-chains 337 residues out of total 3117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 299 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 47 ASN Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 51 ARG Chi-restraints excluded: chain D residue 245 ARG Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain G residue 112 TYR Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 117 TYR Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 80 ILE Chi-restraints excluded: chain M residue 41 HIS Chi-restraints excluded: chain M residue 59 SER Chi-restraints excluded: chain M residue 109 TYR Chi-restraints excluded: chain N residue 31 ILE Chi-restraints excluded: chain O residue 18 ASP Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 277 HIS Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 210 LEU Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain I residue 92 ILE Chi-restraints excluded: chain I residue 151 LEU Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain I residue 228 ILE Chi-restraints excluded: chain J residue 73 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: [128, 261, 3, 231, 228, 82, 229, 44, 76, 138, 290] chunk 128 optimal weight: 3.9990 chunk 261 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 231 optimal weight: 7.9990 chunk 228 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 chunk 229 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 138 optimal weight: 0.9980 chunk 290 optimal weight: 4.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.105593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.066270 restraints weight = 73642.657| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 3.36 r_work: 0.2861 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 30499 Z= 0.177 Angle : 0.570 13.612 41502 Z= 0.296 Chirality : 0.043 0.257 4828 Planarity : 0.004 0.069 4868 Dihedral : 15.187 178.767 4910 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.57 % Allowed : 15.59 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.07 (0.14), residues: 3500 helix: 2.22 (0.13), residues: 1624 sheet: -0.35 (0.21), residues: 558 loop : -0.72 (0.16), residues: 1318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J 51 TYR 0.029 0.001 TYR J 117 PHE 0.019 0.001 PHE L 79 TRP 0.068 0.002 TRP A 257 HIS 0.004 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.18 (30494) covalent geometry : angle 0.56964 / 0.30 (41494) SS BOND : bond 0.00173 / 0.09 ( 1) SS BOND : angle 0.19509 / 0.11 ( 2) hydrogen bonds : bond 0.03969 / 2.72 ( 1551) hydrogen bonds : angle 4.46271 / 3.16 ( 4401) metal coordination : bond 0.00488 / 0.24 ( 4) metal coordination : angle 2.36885 / 1.15 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 3117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 300 time to evaluate : 0.872 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: B 1 MET cc_start: 0.8647 (ttm) cc_final: 0.8233 (ttm) REVERT: B 47 ASN cc_start: 0.8839 (OUTLIER) cc_final: 0.8539 (t0) REVERT: B 122 MET cc_start: 0.9219 (mmm) cc_final: 0.8925 (mmm) REVERT: B 231 MET cc_start: 0.8560 (mtp) cc_final: 0.8254 (ttp) REVERT: B 233 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8219 (tt0) REVERT: B 261 LYS cc_start: 0.8590 (tttm) cc_final: 0.8228 (tppt) REVERT: D 1 MET cc_start: 0.8866 (tpt) cc_final: 0.8648 (tpp) REVERT: D 24 SER cc_start: 0.7735 (m) cc_final: 0.7470 (p) REVERT: D 51 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.8320 (ptm160) REVERT: D 177 MET cc_start: 0.8041 (mtp) cc_final: 0.7321 (ttm) REVERT: D 245 ARG cc_start: 0.7509 (OUTLIER) cc_final: 0.7027 (mmm-85) REVERT: D 254 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7608 (pt0) REVERT: D 274 TYR cc_start: 0.7913 (m-80) cc_final: 0.7618 (m-10) REVERT: E 35 ASP cc_start: 0.9197 (m-30) cc_final: 0.8941 (p0) REVERT: E 104 ASN cc_start: 0.8447 (t0) cc_final: 0.8157 (t0) REVERT: E 211 TYR cc_start: 0.9218 (m-80) cc_final: 0.8936 (m-10) REVERT: G 11 GLU cc_start: 0.8733 (mt-10) cc_final: 0.8481 (mt-10) REVERT: G 78 GLU cc_start: 0.8868 (mt-10) cc_final: 0.8466 (mp0) REVERT: G 109 MET cc_start: 0.9105 (tpp) cc_final: 0.8618 (tpp) REVERT: G 112 TYR cc_start: 0.7384 (OUTLIER) cc_final: 0.6500 (m-80) REVERT: G 248 LYS cc_start: 0.8909 (mttt) cc_final: 0.8549 (mmtm) REVERT: G 261 LYS cc_start: 0.8572 (tttt) cc_final: 0.8262 (tppt) REVERT: K 28 ASP cc_start: 0.9235 (t0) cc_final: 0.8926 (t0) REVERT: K 117 TYR cc_start: 0.7964 (OUTLIER) cc_final: 0.7483 (t80) REVERT: L 18 ASP cc_start: 0.9061 (m-30) cc_final: 0.8726 (m-30) REVERT: L 32 ASP cc_start: 0.7120 (t0) cc_final: 0.6716 (t0) REVERT: M 79 PHE cc_start: 0.7382 (t80) cc_final: 0.7073 (t80) REVERT: N 17 GLU cc_start: 0.8253 (mp0) cc_final: 0.7908 (tm-30) REVERT: N 32 ASP cc_start: 0.8542 (t0) cc_final: 0.8250 (t0) REVERT: O 45 TYR cc_start: 0.8373 (m-80) cc_final: 0.7856 (m-80) REVERT: O 48 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8628 (mt) REVERT: O 93 ARG cc_start: 0.8829 (tpp-160) cc_final: 0.8334 (tpp-160) REVERT: O 106 LEU cc_start: 0.9083 (mt) cc_final: 0.8843 (mt) REVERT: O 109 TYR cc_start: 0.8419 (m-10) cc_final: 0.8060 (m-10) REVERT: A 257 TRP cc_start: 0.4548 (m100) cc_final: 0.3963 (m100) REVERT: A 315 TYR cc_start: 0.6148 (m-80) cc_final: 0.5796 (m-10) REVERT: A 482 TYR cc_start: 0.7868 (t80) cc_final: 0.7377 (t80) REVERT: C 17 TYR cc_start: 0.8141 (t80) cc_final: 0.7740 (t80) REVERT: C 34 GLU cc_start: 0.8616 (pt0) cc_final: 0.8226 (pp20) REVERT: C 60 GLN cc_start: 0.8604 (tp40) cc_final: 0.8353 (tp40) REVERT: C 122 MET cc_start: 0.9332 (mmm) cc_final: 0.8887 (mmm) REVERT: C 141 TYR cc_start: 0.9187 (m-10) cc_final: 0.8829 (m-10) REVERT: C 284 ARG cc_start: 0.7414 (mtm110) cc_final: 0.7140 (ptt180) REVERT: F 57 MET cc_start: 0.9080 (ttm) cc_final: 0.8817 (ttm) REVERT: F 122 MET cc_start: 0.9407 (mmm) cc_final: 0.8332 (mmm) REVERT: F 187 LYS cc_start: 0.9086 (tppt) cc_final: 0.8718 (ptmm) REVERT: F 208 GLN cc_start: 0.8235 (mm-40) cc_final: 0.7791 (mm-40) REVERT: F 210 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.9013 (pp) REVERT: H 63 GLU cc_start: 0.9132 (tt0) cc_final: 0.8592 (tp30) REVERT: H 104 ASN cc_start: 0.8580 (t0) cc_final: 0.8303 (t0) REVERT: H 207 GLN cc_start: 0.8365 (tp40) cc_final: 0.8112 (tp-100) REVERT: H 291 GLN cc_start: 0.9142 (tt0) cc_final: 0.8693 (tp-100) REVERT: I 17 TYR cc_start: 0.8398 (t80) cc_final: 0.8063 (t80) REVERT: I 40 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7421 (mm-30) REVERT: I 47 ASN cc_start: 0.8288 (t160) cc_final: 0.7945 (t0) REVERT: I 159 ASP cc_start: 0.8481 (t0) cc_final: 0.8143 (t0) REVERT: I 247 ASP cc_start: 0.8389 (p0) cc_final: 0.7877 (p0) REVERT: J 57 LYS cc_start: 0.8763 (mttt) cc_final: 0.8476 (tppt) outliers start: 49 outliers final: 36 residues processed: 334 average time/residue: 0.1988 time to fit residues: 106.2375 Evaluate side-chains 334 residues out of total 3117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 290 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 47 ASN Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 51 ARG Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 245 ARG Chi-restraints excluded: chain D residue 254 GLU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain G residue 112 TYR Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 117 TYR Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 80 ILE Chi-restraints excluded: chain M residue 41 HIS Chi-restraints excluded: chain M residue 59 SER Chi-restraints excluded: chain M residue 109 TYR Chi-restraints excluded: chain N residue 31 ILE Chi-restraints excluded: chain O residue 18 ASP Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 277 HIS Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 210 LEU Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain I residue 57 MET Chi-restraints excluded: chain I residue 69 LEU Chi-restraints excluded: chain I residue 92 ILE Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain I residue 228 ILE Chi-restraints excluded: chain I residue 289 ASP Chi-restraints excluded: chain J residue 73 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: [93, 233, 162, 25, 165, 206, 309, 315, 14, 15, 133] chunk 93 optimal weight: 2.9990 chunk 233 optimal weight: 3.9990 chunk 162 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 165 optimal weight: 0.0370 chunk 206 optimal weight: 2.9990 chunk 309 optimal weight: 5.9990 chunk 315 optimal weight: 0.8980 chunk 14 optimal weight: 0.0980 chunk 15 optimal weight: 2.9990 chunk 133 optimal weight: 8.9990 overall best weight: 1.4062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 208 GLN ** F 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.105856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.066553 restraints weight = 73312.213| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 3.34 r_work: 0.2867 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30499 Z= 0.152 Angle : 0.569 13.402 41502 Z= 0.295 Chirality : 0.043 0.302 4828 Planarity : 0.004 0.079 4868 Dihedral : 15.179 178.687 4910 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.64 % Allowed : 15.75 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.05 (0.14), residues: 3500 helix: 2.19 (0.13), residues: 1624 sheet: -0.38 (0.21), residues: 561 loop : -0.71 (0.16), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG J 51 TYR 0.028 0.001 TYR J 117 PHE 0.019 0.001 PHE L 79 TRP 0.046 0.002 TRP A 257 HIS 0.003 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (30494) covalent geometry : angle 0.56813 / 0.30 (41494) SS BOND : bond 0.00149 / 0.08 ( 1) SS BOND : angle 0.18954 / 0.11 ( 2) hydrogen bonds : bond 0.03885 / 2.66 ( 1551) hydrogen bonds : angle 4.44816 / 3.14 ( 4401) metal coordination : bond 0.00476 / 0.23 ( 4) metal coordination : angle 2.28939 / 1.09 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 3117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 295 time to evaluate : 1.122 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: B 1 MET cc_start: 0.8639 (ttm) cc_final: 0.8232 (ttm) REVERT: B 47 ASN cc_start: 0.8827 (OUTLIER) cc_final: 0.8532 (t0) REVERT: B 109 MET cc_start: 0.8490 (mmm) cc_final: 0.7997 (mmm) REVERT: B 231 MET cc_start: 0.8570 (mtp) cc_final: 0.8250 (ttp) REVERT: B 233 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8211 (tt0) REVERT: B 261 LYS cc_start: 0.8558 (tttm) cc_final: 0.8184 (tppt) REVERT: D 24 SER cc_start: 0.7712 (m) cc_final: 0.7453 (p) REVERT: D 51 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.8368 (ptm160) REVERT: D 177 MET cc_start: 0.8040 (mtp) cc_final: 0.7323 (ttm) REVERT: D 245 ARG cc_start: 0.7492 (OUTLIER) cc_final: 0.7023 (mmm-85) REVERT: D 274 TYR cc_start: 0.7918 (m-80) cc_final: 0.7619 (m-10) REVERT: D 282 TRP cc_start: 0.8188 (t60) cc_final: 0.7541 (t-100) REVERT: E 35 ASP cc_start: 0.9219 (m-30) cc_final: 0.8955 (p0) REVERT: E 104 ASN cc_start: 0.8441 (t0) cc_final: 0.8147 (t0) REVERT: E 109 MET cc_start: 0.9104 (tpp) cc_final: 0.8755 (tpp) REVERT: E 211 TYR cc_start: 0.9207 (m-80) cc_final: 0.8929 (m-10) REVERT: G 11 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8453 (mt-10) REVERT: G 112 TYR cc_start: 0.7400 (OUTLIER) cc_final: 0.6498 (m-80) REVERT: G 248 LYS cc_start: 0.8889 (mttt) cc_final: 0.8533 (mmtm) REVERT: G 261 LYS cc_start: 0.8555 (tttt) cc_final: 0.8258 (tppt) REVERT: K 28 ASP cc_start: 0.9208 (t0) cc_final: 0.8906 (t0) REVERT: K 117 TYR cc_start: 0.7986 (OUTLIER) cc_final: 0.7498 (t80) REVERT: L 18 ASP cc_start: 0.9054 (m-30) cc_final: 0.8717 (m-30) REVERT: L 32 ASP cc_start: 0.7125 (t0) cc_final: 0.6733 (t0) REVERT: M 79 PHE cc_start: 0.7394 (t80) cc_final: 0.7131 (t80) REVERT: N 17 GLU cc_start: 0.8255 (mp0) cc_final: 0.7909 (tm-30) REVERT: N 32 ASP cc_start: 0.8542 (t0) cc_final: 0.8256 (t0) REVERT: O 45 TYR cc_start: 0.8341 (m-80) cc_final: 0.7900 (m-80) REVERT: O 48 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8619 (mt) REVERT: O 68 LYS cc_start: 0.9100 (mmtt) cc_final: 0.8778 (mttm) REVERT: O 93 ARG cc_start: 0.8795 (tpp-160) cc_final: 0.8318 (tpp-160) REVERT: O 109 TYR cc_start: 0.8315 (m-10) cc_final: 0.8015 (m-10) REVERT: A 257 TRP cc_start: 0.4505 (m100) cc_final: 0.3930 (m100) REVERT: A 315 TYR cc_start: 0.6167 (m-80) cc_final: 0.5811 (m-10) REVERT: A 482 TYR cc_start: 0.7893 (t80) cc_final: 0.7395 (t80) REVERT: C 17 TYR cc_start: 0.8157 (t80) cc_final: 0.7752 (t80) REVERT: C 34 GLU cc_start: 0.8601 (pt0) cc_final: 0.8231 (pp20) REVERT: C 60 GLN cc_start: 0.8606 (tp40) cc_final: 0.8360 (tp40) REVERT: C 122 MET cc_start: 0.9347 (mmm) cc_final: 0.8959 (mmm) REVERT: C 141 TYR cc_start: 0.9192 (m-10) cc_final: 0.8836 (m-10) REVERT: C 284 ARG cc_start: 0.7373 (mtm110) cc_final: 0.7135 (ptt-90) REVERT: F 57 MET cc_start: 0.9072 (ttm) cc_final: 0.8866 (ttp) REVERT: F 122 MET cc_start: 0.9410 (mmm) cc_final: 0.8430 (mmm) REVERT: F 208 GLN cc_start: 0.8250 (mm-40) cc_final: 0.7824 (mm-40) REVERT: F 210 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.9007 (pp) REVERT: H 63 GLU cc_start: 0.9127 (tt0) cc_final: 0.8710 (tm-30) REVERT: H 104 ASN cc_start: 0.8630 (t0) cc_final: 0.8342 (t0) REVERT: H 207 GLN cc_start: 0.8357 (tp40) cc_final: 0.8129 (tp-100) REVERT: H 291 GLN cc_start: 0.9124 (tt0) cc_final: 0.8608 (tp-100) REVERT: I 17 TYR cc_start: 0.8392 (t80) cc_final: 0.8065 (t80) REVERT: I 40 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7392 (mm-30) REVERT: I 47 ASN cc_start: 0.8323 (t160) cc_final: 0.7987 (t0) REVERT: I 247 ASP cc_start: 0.8384 (p0) cc_final: 0.7883 (p0) REVERT: J 57 LYS cc_start: 0.8781 (mttt) cc_final: 0.8522 (tppt) outliers start: 51 outliers final: 35 residues processed: 332 average time/residue: 0.1982 time to fit residues: 104.8014 Evaluate side-chains 332 residues out of total 3117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 290 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 47 ASN Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 51 ARG Chi-restraints excluded: chain D residue 245 ARG Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain G residue 112 TYR Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 117 TYR Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 80 ILE Chi-restraints excluded: chain M residue 41 HIS Chi-restraints excluded: chain M residue 59 SER Chi-restraints excluded: chain M residue 109 TYR Chi-restraints excluded: chain O residue 18 ASP Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 277 HIS Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 210 LEU Chi-restraints excluded: chain F residue 289 ASP Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain I residue 57 MET Chi-restraints excluded: chain I residue 69 LEU Chi-restraints excluded: chain I residue 92 ILE Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain I residue 228 ILE Chi-restraints excluded: chain J residue 73 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: [197, 210, 127, 189, 245, 272, 136, 148, 132, 45, 253] chunk 197 optimal weight: 20.0000 chunk 210 optimal weight: 5.9990 chunk 127 optimal weight: 6.9990 chunk 189 optimal weight: 20.0000 chunk 245 optimal weight: 3.9990 chunk 272 optimal weight: 0.6980 chunk 136 optimal weight: 10.0000 chunk 148 optimal weight: 0.6980 chunk 132 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 253 optimal weight: 1.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 286 ASN ** F 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.104741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.065296 restraints weight = 73510.319| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 3.33 r_work: 0.2910 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 30499 Z= 0.214 Angle : 0.609 12.342 41502 Z= 0.314 Chirality : 0.045 0.352 4828 Planarity : 0.004 0.064 4868 Dihedral : 15.190 179.980 4910 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.41 % Allowed : 16.14 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 0.98 (0.14), residues: 3500 helix: 2.16 (0.13), residues: 1624 sheet: -0.45 (0.21), residues: 571 loop : -0.74 (0.16), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 51 TYR 0.029 0.001 TYR J 117 PHE 0.023 0.001 PHE O 65 TRP 0.041 0.002 TRP A 257 HIS 0.004 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.21 (30494) covalent geometry : angle 0.60864 / 0.31 (41494) SS BOND : bond 0.00217 / 0.11 ( 1) SS BOND : angle 0.15749 / 0.09 ( 2) hydrogen bonds : bond 0.04157 / 2.85 ( 1551) hydrogen bonds : angle 4.54010 / 3.21 ( 4401) metal coordination : bond 0.00577 / 0.28 ( 4) metal coordination : angle 2.24220 / 1.10 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7000 Ramachandran restraints generated. 3500 Oldfield, 0 Emsley, 3500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 3117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 282 time to evaluate : 0.976 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: B 1 MET cc_start: 0.8760 (ttm) cc_final: 0.8365 (ttm) REVERT: B 47 ASN cc_start: 0.8937 (OUTLIER) cc_final: 0.8634 (t0) REVERT: B 109 MET cc_start: 0.8657 (mmm) cc_final: 0.8053 (mmm) REVERT: B 231 MET cc_start: 0.8613 (mtp) cc_final: 0.8311 (ttp) REVERT: B 233 GLU cc_start: 0.8798 (mt-10) cc_final: 0.8331 (tt0) REVERT: B 261 LYS cc_start: 0.8655 (tttm) cc_final: 0.8286 (tppt) REVERT: D 24 SER cc_start: 0.7812 (m) cc_final: 0.7582 (p) REVERT: D 51 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.8541 (ptm160) REVERT: D 177 MET cc_start: 0.8075 (mtp) cc_final: 0.7380 (ttm) REVERT: D 274 TYR cc_start: 0.7957 (m-80) cc_final: 0.7550 (m-10) REVERT: E 35 ASP cc_start: 0.9236 (m-30) cc_final: 0.8836 (p0) REVERT: E 57 MET cc_start: 0.9211 (ttm) cc_final: 0.8999 (ttp) REVERT: E 104 ASN cc_start: 0.8536 (t0) cc_final: 0.8281 (t0) REVERT: E 109 MET cc_start: 0.9297 (tpp) cc_final: 0.8947 (tpp) REVERT: E 211 TYR cc_start: 0.9281 (m-80) cc_final: 0.9003 (m-10) REVERT: G 11 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8453 (mt-10) REVERT: G 74 GLN cc_start: 0.8701 (mm-40) cc_final: 0.8288 (mp10) REVERT: G 112 TYR cc_start: 0.7681 (OUTLIER) cc_final: 0.6686 (m-80) REVERT: G 248 LYS cc_start: 0.8956 (mttt) cc_final: 0.8644 (mmtm) REVERT: G 261 LYS cc_start: 0.8656 (tttt) cc_final: 0.8381 (tppt) REVERT: K 28 ASP cc_start: 0.9232 (t0) cc_final: 0.8971 (t0) REVERT: K 117 TYR cc_start: 0.8156 (OUTLIER) cc_final: 0.7706 (t80) REVERT: L 18 ASP cc_start: 0.9079 (m-30) cc_final: 0.8746 (m-30) REVERT: L 32 ASP cc_start: 0.7155 (t0) cc_final: 0.6786 (t0) REVERT: M 79 PHE cc_start: 0.7407 (t80) cc_final: 0.7151 (t80) REVERT: N 17 GLU cc_start: 0.8272 (mp0) cc_final: 0.7929 (tm-30) REVERT: N 32 ASP cc_start: 0.8533 (t0) cc_final: 0.8249 (t0) REVERT: N 93 ARG cc_start: 0.8823 (mtp-110) cc_final: 0.8510 (ttm110) REVERT: O 45 TYR cc_start: 0.8461 (m-80) cc_final: 0.7844 (m-80) REVERT: O 48 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8616 (mt) REVERT: O 68 LYS cc_start: 0.9091 (mmtt) cc_final: 0.8774 (mttm) REVERT: O 93 ARG cc_start: 0.8812 (tpp-160) cc_final: 0.8357 (tpp-160) REVERT: O 109 TYR cc_start: 0.8355 (m-10) cc_final: 0.8008 (m-10) REVERT: A 257 TRP cc_start: 0.4579 (m100) cc_final: 0.4036 (m100) REVERT: A 315 TYR cc_start: 0.6218 (m-80) cc_final: 0.5883 (m-10) REVERT: A 482 TYR cc_start: 0.7948 (t80) cc_final: 0.7476 (t80) REVERT: C 17 TYR cc_start: 0.8263 (t80) cc_final: 0.7901 (t80) REVERT: C 34 GLU cc_start: 0.8678 (pt0) cc_final: 0.8343 (pp20) REVERT: C 60 GLN cc_start: 0.8677 (tp40) cc_final: 0.8450 (tp40) REVERT: C 122 MET cc_start: 0.9371 (mmm) cc_final: 0.8957 (mmm) REVERT: C 284 ARG cc_start: 0.7366 (mtm110) cc_final: 0.7069 (ptt180) REVERT: F 57 MET cc_start: 0.9162 (ttm) cc_final: 0.8903 (ttm) REVERT: F 122 MET cc_start: 0.9398 (mmm) cc_final: 0.8474 (mmm) REVERT: F 208 GLN cc_start: 0.8403 (mm-40) cc_final: 0.8007 (mm-40) REVERT: H 104 ASN cc_start: 0.8706 (t0) cc_final: 0.8441 (t0) REVERT: H 207 GLN cc_start: 0.8430 (tp40) cc_final: 0.8191 (tp-100) REVERT: H 291 GLN cc_start: 0.9156 (tt0) cc_final: 0.8654 (tp-100) REVERT: I 17 TYR cc_start: 0.8460 (t80) cc_final: 0.8121 (t80) REVERT: I 40 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7354 (mm-30) REVERT: I 47 ASN cc_start: 0.8521 (t160) cc_final: 0.8189 (t0) REVERT: I 159 ASP cc_start: 0.8660 (t0) cc_final: 0.8448 (t0) REVERT: I 211 TYR cc_start: 0.7890 (m-80) cc_final: 0.7524 (m-80) REVERT: I 247 ASP cc_start: 0.8418 (p0) cc_final: 0.7886 (p0) REVERT: I 252 ARG cc_start: 0.8190 (mmm-85) cc_final: 0.7833 (mmt180) REVERT: J 57 LYS cc_start: 0.8795 (mttt) cc_final: 0.8544 (tppt) outliers start: 44 outliers final: 35 residues processed: 313 average time/residue: 0.1987 time to fit residues: 99.6389 Evaluate side-chains 312 residues out of total 3117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 272 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 ASN Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 51 ARG Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain G residue 112 TYR Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 117 TYR Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 80 ILE Chi-restraints excluded: chain M residue 41 HIS Chi-restraints excluded: chain M residue 59 SER Chi-restraints excluded: chain M residue 109 TYR Chi-restraints excluded: chain O residue 18 ASP Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 277 HIS Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 289 ASP Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 283 ILE Chi-restraints excluded: chain I residue 57 MET Chi-restraints excluded: chain I residue 69 LEU Chi-restraints excluded: chain I residue 92 ILE Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain I residue 228 ILE Chi-restraints excluded: chain I residue 289 ASP Chi-restraints excluded: chain J residue 73 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: [31, 336, 301, 271, 65, 193, 152, 149, 11, 29, 89] chunk 31 optimal weight: 0.9980 chunk 336 optimal weight: 1.9990 chunk 301 optimal weight: 0.5980 chunk 271 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 193 optimal weight: 0.9990 chunk 152 optimal weight: 0.7980 chunk 149 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.106164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.066909 restraints weight = 73489.568| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 3.35 r_work: 0.2944 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30499 Z= 0.126 Angle : 0.568 12.967 41502 Z= 0.294 Chirality : 0.043 0.350 4828 Planarity : 0.004 0.072 4868 Dihedral : 15.170 178.325 4910 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.25 % Allowed : 16.27 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % 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: 1.00 (0.14), residues: 3500 helix: 2.14 (0.13), residues: 1629 sheet: -0.40 (0.21), residues: 563 loop : -0.72 (0.16), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG J 51 TYR 0.028 0.001 TYR J 117 PHE 0.020 0.001 PHE L 79 TRP 0.037 0.002 TRP A 257 HIS 0.003 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 (30494) covalent geometry : angle 0.56713 / 0.29 (41494) SS BOND : bond 0.00134 / 0.07 ( 1) SS BOND : angle 0.18901 / 0.11 ( 2) hydrogen bonds : bond 0.03820 / 2.61 ( 1551) hydrogen bonds : angle 4.43491 / 3.13 ( 4401) metal coordination : bond 0.00447 / 0.22 ( 4) metal coordination : angle 2.24338 / 1.02 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8112.17 seconds wall clock time: 139 minutes 22.82 seconds (8362.82 seconds total)