Starting phenix.real_space_refine on Sat Feb 7 16:36:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pn7_17777/02_2026/8pn7_17777.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pn7_17777/02_2026/8pn7_17777.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8pn7_17777/02_2026/8pn7_17777.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pn7_17777/02_2026/8pn7_17777.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8pn7_17777/02_2026/8pn7_17777.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pn7_17777/02_2026/8pn7_17777.map" } resolution = 2.03 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= 0.029 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: 5 Type Number sf(0) Gaussians P 18 5.49 5 S 150 5.16 5 C 21030 2.51 5 N 5934 2.21 5 O 7740 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34872 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 3909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3909 Classifications: {'peptide': 506} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 484} Chain: "B" Number of atoms: 3909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3909 Classifications: {'peptide': 506} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 484} Chain: "C" Number of atoms: 3909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3909 Classifications: {'peptide': 506} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 484} Chain: "D" Number of atoms: 3909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3909 Classifications: {'peptide': 506} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 484} Chain: "E" Number of atoms: 3909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3909 Classifications: {'peptide': 506} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 484} Chain: "F" Number of atoms: 3909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3909 Classifications: {'peptide': 506} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 484} Chain: "G" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1594 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 13, 'TRANS': 198} Chain: "H" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1594 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 13, 'TRANS': 198} Chain: "I" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1594 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 13, 'TRANS': 198} Chain: "J" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1594 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 13, 'TRANS': 198} Chain: "K" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1594 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 13, 'TRANS': 198} Chain: "L" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1594 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 13, 'TRANS': 198} Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 216 Classifications: {'water': 216} Link IDs: {None: 215} Chain: "B" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 225 Classifications: {'water': 225} Link IDs: {None: 224} Chain: "C" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 231 Classifications: {'water': 231} Link IDs: {None: 230} Chain: "D" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 226 Classifications: {'water': 226} Link IDs: {None: 225} Chain: "E" Number of atoms: 223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 223 Classifications: {'water': 223} Link IDs: {None: 222} Chain: "F" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 213 Classifications: {'water': 213} Link IDs: {None: 212} Chain: "G" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "H" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "I" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "J" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "K" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "L" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Time building chain proxies: 8.69, per 1000 atoms: 0.25 Number of scatterers: 34872 At special positions: 0 Unit cell: (149.823, 154.008, 138.942, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 150 16.00 P 18 15.00 O 7740 8.00 N 5934 7.00 C 21030 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.95 Conformation dependent library (CDL) restraints added in 1.5 seconds 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7824 Finding SS restraints... Secondary structure from input PDB file: 182 helices and 48 sheets defined 41.7% alpha, 25.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.72 Creating SS restraints... Processing helix chain 'A' and resid 5 through 16 removed outlier: 3.530A pdb=" N GLU A 9 " --> pdb=" O LEU A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 30 Processing helix chain 'A' and resid 34 through 43 Processing helix chain 'A' and resid 63 through 67 Processing helix chain 'A' and resid 95 through 99 Processing helix chain 'A' and resid 101 through 119 Processing helix chain 'A' and resid 132 through 135 Processing helix chain 'A' and resid 136 through 154 removed outlier: 3.962A pdb=" N LEU A 140 " --> pdb=" O GLY A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 177 Processing helix chain 'A' and resid 194 through 203 Processing helix chain 'A' and resid 207 through 213 Processing helix chain 'A' and resid 213 through 220 Processing helix chain 'A' and resid 230 through 245 Processing helix chain 'A' and resid 266 through 272 Processing helix chain 'A' and resid 282 through 291 removed outlier: 3.778A pdb=" N LEU A 286 " --> pdb=" O ASP A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 294 No H-bonds generated for 'chain 'A' and resid 292 through 294' Processing helix chain 'A' and resid 328 through 332 Processing helix chain 'A' and resid 334 through 351 Processing helix chain 'A' and resid 367 through 373 Processing helix chain 'A' and resid 374 through 389 removed outlier: 3.639A pdb=" N LEU A 382 " --> pdb=" O HIS A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 409 Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 431 through 440 Processing helix chain 'A' and resid 441 through 444 removed outlier: 3.840A pdb=" N ILE A 444 " --> pdb=" O ARG A 441 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 441 through 444' Processing helix chain 'A' and resid 446 through 462 Processing helix chain 'A' and resid 464 through 470 Processing helix chain 'A' and resid 478 through 480 No H-bonds generated for 'chain 'A' and resid 478 through 480' Processing helix chain 'A' and resid 481 through 494 Processing helix chain 'B' and resid 6 through 16 Processing helix chain 'B' and resid 20 through 30 Processing helix chain 'B' and resid 34 through 43 Processing helix chain 'B' and resid 60 through 67 removed outlier: 4.460A pdb=" N GLY B 63 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N GLU B 65 " --> pdb=" O PHE B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 99 Processing helix chain 'B' and resid 101 through 119 Processing helix chain 'B' and resid 132 through 135 Processing helix chain 'B' and resid 136 through 154 removed outlier: 3.966A pdb=" N LEU B 140 " --> pdb=" O GLY B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 177 Processing helix chain 'B' and resid 194 through 203 Processing helix chain 'B' and resid 207 through 213 Processing helix chain 'B' and resid 213 through 220 Processing helix chain 'B' and resid 230 through 245 removed outlier: 3.716A pdb=" N PHE B 244 " --> pdb=" O ARG B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 272 Processing helix chain 'B' and resid 282 through 291 removed outlier: 3.815A pdb=" N LEU B 286 " --> pdb=" O ASP B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 295 Processing helix chain 'B' and resid 328 through 332 Processing helix chain 'B' and resid 334 through 351 Processing helix chain 'B' and resid 367 through 373 Processing helix chain 'B' and resid 374 through 389 removed outlier: 3.638A pdb=" N LEU B 382 " --> pdb=" O HIS B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 409 Processing helix chain 'B' and resid 411 through 415 Processing helix chain 'B' and resid 431 through 440 Processing helix chain 'B' and resid 441 through 444 removed outlier: 3.567A pdb=" N ILE B 444 " --> pdb=" O ARG B 441 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 441 through 444' Processing helix chain 'B' and resid 447 through 462 removed outlier: 3.632A pdb=" N ALA B 451 " --> pdb=" O ALA B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 470 Processing helix chain 'B' and resid 478 through 480 No H-bonds generated for 'chain 'B' and resid 478 through 480' Processing helix chain 'B' and resid 481 through 494 Processing helix chain 'C' and resid 6 through 16 Processing helix chain 'C' and resid 20 through 30 Processing helix chain 'C' and resid 34 through 43 Processing helix chain 'C' and resid 63 through 67 Processing helix chain 'C' and resid 95 through 99 Processing helix chain 'C' and resid 101 through 119 Processing helix chain 'C' and resid 132 through 135 Processing helix chain 'C' and resid 136 through 154 removed outlier: 3.945A pdb=" N LEU C 140 " --> pdb=" O GLY C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 177 Processing helix chain 'C' and resid 194 through 203 Processing helix chain 'C' and resid 207 through 213 Processing helix chain 'C' and resid 213 through 220 Processing helix chain 'C' and resid 230 through 245 Processing helix chain 'C' and resid 266 through 272 Processing helix chain 'C' and resid 282 through 291 removed outlier: 3.739A pdb=" N LEU C 286 " --> pdb=" O ASP C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 294 No H-bonds generated for 'chain 'C' and resid 292 through 294' Processing helix chain 'C' and resid 328 through 332 Processing helix chain 'C' and resid 334 through 351 Processing helix chain 'C' and resid 367 through 373 Processing helix chain 'C' and resid 374 through 389 removed outlier: 3.614A pdb=" N LEU C 382 " --> pdb=" O HIS C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 409 Processing helix chain 'C' and resid 411 through 415 Processing helix chain 'C' and resid 431 through 440 Processing helix chain 'C' and resid 441 through 444 removed outlier: 3.674A pdb=" N ILE C 444 " --> pdb=" O ARG C 441 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 441 through 444' Processing helix chain 'C' and resid 447 through 462 removed outlier: 3.698A pdb=" N ALA C 451 " --> pdb=" O ALA C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 470 Processing helix chain 'C' and resid 478 through 480 No H-bonds generated for 'chain 'C' and resid 478 through 480' Processing helix chain 'C' and resid 481 through 494 Processing helix chain 'D' and resid 6 through 16 Processing helix chain 'D' and resid 20 through 30 Processing helix chain 'D' and resid 34 through 43 Processing helix chain 'D' and resid 60 through 67 removed outlier: 4.433A pdb=" N GLY D 63 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N GLU D 65 " --> pdb=" O PHE D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 99 Processing helix chain 'D' and resid 101 through 119 Processing helix chain 'D' and resid 132 through 135 Processing helix chain 'D' and resid 136 through 154 removed outlier: 3.948A pdb=" N LEU D 140 " --> pdb=" O GLY D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 177 Processing helix chain 'D' and resid 194 through 203 Processing helix chain 'D' and resid 207 through 213 Processing helix chain 'D' and resid 213 through 220 Processing helix chain 'D' and resid 230 through 245 Processing helix chain 'D' and resid 266 through 272 Processing helix chain 'D' and resid 282 through 291 removed outlier: 3.796A pdb=" N LEU D 286 " --> pdb=" O ASP D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 294 No H-bonds generated for 'chain 'D' and resid 292 through 294' Processing helix chain 'D' and resid 328 through 332 Processing helix chain 'D' and resid 334 through 351 Processing helix chain 'D' and resid 367 through 373 Processing helix chain 'D' and resid 374 through 389 removed outlier: 3.652A pdb=" N LEU D 382 " --> pdb=" O HIS D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 409 Processing helix chain 'D' and resid 411 through 415 Processing helix chain 'D' and resid 431 through 440 Processing helix chain 'D' and resid 441 through 444 removed outlier: 4.131A pdb=" N ILE D 444 " --> pdb=" O ARG D 441 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 441 through 444' Processing helix chain 'D' and resid 447 through 462 Processing helix chain 'D' and resid 464 through 470 Processing helix chain 'D' and resid 478 through 480 No H-bonds generated for 'chain 'D' and resid 478 through 480' Processing helix chain 'D' and resid 481 through 494 Processing helix chain 'E' and resid 6 through 16 Processing helix chain 'E' and resid 20 through 30 Processing helix chain 'E' and resid 34 through 43 Processing helix chain 'E' and resid 60 through 67 removed outlier: 4.458A pdb=" N GLY E 63 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N GLU E 65 " --> pdb=" O PHE E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 99 Processing helix chain 'E' and resid 101 through 119 Processing helix chain 'E' and resid 132 through 135 Processing helix chain 'E' and resid 136 through 154 removed outlier: 3.967A pdb=" N LEU E 140 " --> pdb=" O GLY E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 177 Processing helix chain 'E' and resid 194 through 203 Processing helix chain 'E' and resid 207 through 213 Processing helix chain 'E' and resid 213 through 220 Processing helix chain 'E' and resid 230 through 245 Processing helix chain 'E' and resid 266 through 272 Processing helix chain 'E' and resid 282 through 291 removed outlier: 3.789A pdb=" N LEU E 286 " --> pdb=" O ASP E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 295 Processing helix chain 'E' and resid 328 through 332 Processing helix chain 'E' and resid 334 through 351 Processing helix chain 'E' and resid 367 through 373 Processing helix chain 'E' and resid 374 through 389 removed outlier: 3.639A pdb=" N LEU E 382 " --> pdb=" O HIS E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 409 Processing helix chain 'E' and resid 431 through 440 Processing helix chain 'E' and resid 447 through 462 Processing helix chain 'E' and resid 464 through 470 Processing helix chain 'E' and resid 478 through 480 No H-bonds generated for 'chain 'E' and resid 478 through 480' Processing helix chain 'E' and resid 481 through 494 Processing helix chain 'F' and resid 6 through 16 Processing helix chain 'F' and resid 20 through 30 Processing helix chain 'F' and resid 34 through 43 Processing helix chain 'F' and resid 63 through 67 Processing helix chain 'F' and resid 95 through 99 Processing helix chain 'F' and resid 101 through 119 Processing helix chain 'F' and resid 132 through 134 No H-bonds generated for 'chain 'F' and resid 132 through 134' Processing helix chain 'F' and resid 135 through 154 removed outlier: 3.863A pdb=" N LEU F 140 " --> pdb=" O GLY F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 177 Processing helix chain 'F' and resid 194 through 203 Processing helix chain 'F' and resid 207 through 213 Processing helix chain 'F' and resid 213 through 220 Processing helix chain 'F' and resid 230 through 245 Processing helix chain 'F' and resid 266 through 272 Processing helix chain 'F' and resid 282 through 291 removed outlier: 3.778A pdb=" N LEU F 286 " --> pdb=" O ASP F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 294 No H-bonds generated for 'chain 'F' and resid 292 through 294' Processing helix chain 'F' and resid 328 through 332 Processing helix chain 'F' and resid 334 through 351 Processing helix chain 'F' and resid 367 through 373 Processing helix chain 'F' and resid 374 through 389 removed outlier: 3.633A pdb=" N LEU F 382 " --> pdb=" O HIS F 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 403 through 409 Processing helix chain 'F' and resid 411 through 415 Processing helix chain 'F' and resid 431 through 440 Processing helix chain 'F' and resid 441 through 444 removed outlier: 3.755A pdb=" N ILE F 444 " --> pdb=" O ARG F 441 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 441 through 444' Processing helix chain 'F' and resid 447 through 462 Processing helix chain 'F' and resid 464 through 470 Processing helix chain 'F' and resid 478 through 480 No H-bonds generated for 'chain 'F' and resid 478 through 480' Processing helix chain 'F' and resid 481 through 494 Processing helix chain 'G' and resid 461 through 483 Processing helix chain 'G' and resid 579 through 588 removed outlier: 3.686A pdb=" N LEU G 588 " --> pdb=" O GLU G 584 " (cutoff:3.500A) Processing helix chain 'H' and resid 461 through 483 Processing helix chain 'H' and resid 491 through 495 Processing helix chain 'H' and resid 579 through 587 Processing helix chain 'I' and resid 461 through 483 Processing helix chain 'I' and resid 491 through 495 Processing helix chain 'I' and resid 579 through 588 removed outlier: 3.624A pdb=" N LEU I 588 " --> pdb=" O GLU I 584 " (cutoff:3.500A) Processing helix chain 'J' and resid 461 through 483 Processing helix chain 'J' and resid 491 through 495 Processing helix chain 'J' and resid 579 through 588 removed outlier: 3.617A pdb=" N LEU J 588 " --> pdb=" O GLU J 584 " (cutoff:3.500A) Processing helix chain 'K' and resid 461 through 483 Processing helix chain 'K' and resid 491 through 495 Processing helix chain 'K' and resid 579 through 587 Processing helix chain 'L' and resid 461 through 483 Processing helix chain 'L' and resid 579 through 588 Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 51 removed outlier: 4.413A pdb=" N THR A 76 " --> pdb=" O PHE A 51 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N ILE A 123 " --> pdb=" O THR A 85 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N PHE A 87 " --> pdb=" O ILE A 123 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N ILE A 125 " --> pdb=" O PHE A 87 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N PHE A 89 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE A 122 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N VAL A 162 " --> pdb=" O ILE A 122 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLY A 124 " --> pdb=" O VAL A 162 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY A 226 " --> pdb=" O ILE A 181 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 166 through 168 removed outlier: 6.496A pdb=" N CYS A 167 " --> pdb=" O PHE A 191 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 296 through 299 removed outlier: 4.325A pdb=" N THR A 309 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N VAL A 356 " --> pdb=" O THR A 318 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N GLY A 320 " --> pdb=" O VAL A 356 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N PHE A 358 " --> pdb=" O GLY A 320 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL A 322 " --> pdb=" O PHE A 358 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ASP A 360 " --> pdb=" O VAL A 322 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ASN A 324 " --> pdb=" O ASP A 360 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N VAL A 361 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N LYS A 400 " --> pdb=" O VAL A 361 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 296 through 299 removed outlier: 4.325A pdb=" N THR A 309 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N VAL A 356 " --> pdb=" O THR A 318 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N GLY A 320 " --> pdb=" O VAL A 356 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N PHE A 358 " --> pdb=" O GLY A 320 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL A 322 " --> pdb=" O PHE A 358 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ASP A 360 " --> pdb=" O VAL A 322 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ASN A 324 " --> pdb=" O ASP A 360 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N VAL A 361 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N LYS A 400 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU A 393 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N TYR A 420 " --> pdb=" O LEU A 393 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N THR A 395 " --> pdb=" O TYR A 420 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU A 475 " --> pdb=" O ASN A 419 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 49 through 51 removed outlier: 4.400A pdb=" N THR B 76 " --> pdb=" O PHE B 51 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE B 122 " --> pdb=" O ILE B 160 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N VAL B 162 " --> pdb=" O ILE B 122 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLY B 124 " --> pdb=" O VAL B 162 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY B 226 " --> pdb=" O ILE B 181 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 166 through 168 removed outlier: 6.487A pdb=" N CYS B 167 " --> pdb=" O PHE B 191 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 297 through 299 removed outlier: 4.309A pdb=" N THR B 309 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N VAL B 356 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLY B 320 " --> pdb=" O VAL B 356 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N PHE B 358 " --> pdb=" O GLY B 320 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL B 322 " --> pdb=" O PHE B 358 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ASP B 360 " --> pdb=" O VAL B 322 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ASN B 324 " --> pdb=" O ASP B 360 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE B 355 " --> pdb=" O VAL B 394 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N ILE B 396 " --> pdb=" O ILE B 355 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR B 357 " --> pdb=" O ILE B 396 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N THR B 398 " --> pdb=" O THR B 357 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N VAL B 359 " --> pdb=" O THR B 398 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LYS B 400 " --> pdb=" O VAL B 359 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 297 through 299 removed outlier: 4.309A pdb=" N THR B 309 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N VAL B 356 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLY B 320 " --> pdb=" O VAL B 356 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N PHE B 358 " --> pdb=" O GLY B 320 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL B 322 " --> pdb=" O PHE B 358 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ASP B 360 " --> pdb=" O VAL B 322 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ASN B 324 " --> pdb=" O ASP B 360 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE B 355 " --> pdb=" O VAL B 394 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N ILE B 396 " --> pdb=" O ILE B 355 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR B 357 " --> pdb=" O ILE B 396 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N THR B 398 " --> pdb=" O THR B 357 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N VAL B 359 " --> pdb=" O THR B 398 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LYS B 400 " --> pdb=" O VAL B 359 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU B 393 " --> pdb=" O LEU B 418 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N TYR B 420 " --> pdb=" O LEU B 393 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N THR B 395 " --> pdb=" O TYR B 420 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU B 475 " --> pdb=" O ASN B 419 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 49 through 51 removed outlier: 4.384A pdb=" N THR C 76 " --> pdb=" O PHE C 51 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE C 122 " --> pdb=" O ILE C 160 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N VAL C 162 " --> pdb=" O ILE C 122 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLY C 124 " --> pdb=" O VAL C 162 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY C 226 " --> pdb=" O ILE C 181 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 166 through 168 removed outlier: 6.482A pdb=" N CYS C 167 " --> pdb=" O PHE C 191 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 296 through 299 removed outlier: 4.288A pdb=" N THR C 309 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N VAL C 356 " --> pdb=" O THR C 318 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N GLY C 320 " --> pdb=" O VAL C 356 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N PHE C 358 " --> pdb=" O GLY C 320 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL C 322 " --> pdb=" O PHE C 358 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N ASP C 360 " --> pdb=" O VAL C 322 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ASN C 324 " --> pdb=" O ASP C 360 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE C 355 " --> pdb=" O VAL C 394 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ILE C 396 " --> pdb=" O ILE C 355 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N THR C 357 " --> pdb=" O ILE C 396 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N THR C 398 " --> pdb=" O THR C 357 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N VAL C 359 " --> pdb=" O THR C 398 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LYS C 400 " --> pdb=" O VAL C 359 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 296 through 299 removed outlier: 4.288A pdb=" N THR C 309 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N VAL C 356 " --> pdb=" O THR C 318 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N GLY C 320 " --> pdb=" O VAL C 356 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N PHE C 358 " --> pdb=" O GLY C 320 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL C 322 " --> pdb=" O PHE C 358 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N ASP C 360 " --> pdb=" O VAL C 322 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ASN C 324 " --> pdb=" O ASP C 360 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE C 355 " --> pdb=" O VAL C 394 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ILE C 396 " --> pdb=" O ILE C 355 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N THR C 357 " --> pdb=" O ILE C 396 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N THR C 398 " --> pdb=" O THR C 357 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N VAL C 359 " --> pdb=" O THR C 398 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LYS C 400 " --> pdb=" O VAL C 359 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU C 393 " --> pdb=" O LEU C 418 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N TYR C 420 " --> pdb=" O LEU C 393 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N THR C 395 " --> pdb=" O TYR C 420 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU C 475 " --> pdb=" O ASN C 419 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 49 through 51 removed outlier: 4.382A pdb=" N THR D 76 " --> pdb=" O PHE D 51 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N ILE D 123 " --> pdb=" O THR D 85 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N PHE D 87 " --> pdb=" O ILE D 123 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N ILE D 125 " --> pdb=" O PHE D 87 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N PHE D 89 " --> pdb=" O ILE D 125 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE D 122 " --> pdb=" O ILE D 160 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N VAL D 162 " --> pdb=" O ILE D 122 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLY D 124 " --> pdb=" O VAL D 162 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY D 226 " --> pdb=" O ILE D 181 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 166 through 168 removed outlier: 6.444A pdb=" N CYS D 167 " --> pdb=" O PHE D 191 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 296 through 299 removed outlier: 4.288A pdb=" N THR D 309 " --> pdb=" O ILE D 299 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N VAL D 356 " --> pdb=" O THR D 318 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N GLY D 320 " --> pdb=" O VAL D 356 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N PHE D 358 " --> pdb=" O GLY D 320 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL D 322 " --> pdb=" O PHE D 358 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ASP D 360 " --> pdb=" O VAL D 322 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ASN D 324 " --> pdb=" O ASP D 360 " (cutoff:3.500A) removed outlier: 8.726A pdb=" N VAL D 361 " --> pdb=" O THR D 398 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N LYS D 400 " --> pdb=" O VAL D 361 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 296 through 299 removed outlier: 4.288A pdb=" N THR D 309 " --> pdb=" O ILE D 299 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N VAL D 356 " --> pdb=" O THR D 318 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N GLY D 320 " --> pdb=" O VAL D 356 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N PHE D 358 " --> pdb=" O GLY D 320 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL D 322 " --> pdb=" O PHE D 358 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ASP D 360 " --> pdb=" O VAL D 322 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ASN D 324 " --> pdb=" O ASP D 360 " (cutoff:3.500A) removed outlier: 8.726A pdb=" N VAL D 361 " --> pdb=" O THR D 398 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N LYS D 400 " --> pdb=" O VAL D 361 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU D 393 " --> pdb=" O LEU D 418 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N TYR D 420 " --> pdb=" O LEU D 393 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N THR D 395 " --> pdb=" O TYR D 420 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU D 475 " --> pdb=" O ASN D 419 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 49 through 51 removed outlier: 4.399A pdb=" N THR E 76 " --> pdb=" O PHE E 51 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N ILE E 123 " --> pdb=" O THR E 85 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N PHE E 87 " --> pdb=" O ILE E 123 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N ILE E 125 " --> pdb=" O PHE E 87 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N PHE E 89 " --> pdb=" O ILE E 125 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE E 122 " --> pdb=" O ILE E 160 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N VAL E 162 " --> pdb=" O ILE E 122 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLY E 124 " --> pdb=" O VAL E 162 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY E 226 " --> pdb=" O ILE E 181 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 166 through 168 removed outlier: 6.486A pdb=" N CYS E 167 " --> pdb=" O PHE E 191 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'E' and resid 297 through 299 removed outlier: 4.307A pdb=" N THR E 309 " --> pdb=" O ILE E 299 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N VAL E 356 " --> pdb=" O THR E 318 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N GLY E 320 " --> pdb=" O VAL E 356 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N PHE E 358 " --> pdb=" O GLY E 320 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL E 322 " --> pdb=" O PHE E 358 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ASP E 360 " --> pdb=" O VAL E 322 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ASN E 324 " --> pdb=" O ASP E 360 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE E 355 " --> pdb=" O VAL E 394 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N ILE E 396 " --> pdb=" O ILE E 355 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N THR E 357 " --> pdb=" O ILE E 396 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N THR E 398 " --> pdb=" O THR E 357 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N VAL E 359 " --> pdb=" O THR E 398 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LYS E 400 " --> pdb=" O VAL E 359 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 297 through 299 removed outlier: 4.307A pdb=" N THR E 309 " --> pdb=" O ILE E 299 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N VAL E 356 " --> pdb=" O THR E 318 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N GLY E 320 " --> pdb=" O VAL E 356 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N PHE E 358 " --> pdb=" O GLY E 320 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL E 322 " --> pdb=" O PHE E 358 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ASP E 360 " --> pdb=" O VAL E 322 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ASN E 324 " --> pdb=" O ASP E 360 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE E 355 " --> pdb=" O VAL E 394 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N ILE E 396 " --> pdb=" O ILE E 355 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N THR E 357 " --> pdb=" O ILE E 396 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N THR E 398 " --> pdb=" O THR E 357 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N VAL E 359 " --> pdb=" O THR E 398 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LYS E 400 " --> pdb=" O VAL E 359 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU E 393 " --> pdb=" O LEU E 418 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N TYR E 420 " --> pdb=" O LEU E 393 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N THR E 395 " --> pdb=" O TYR E 420 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU E 475 " --> pdb=" O ASN E 419 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 49 through 51 removed outlier: 4.400A pdb=" N THR F 76 " --> pdb=" O PHE F 51 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N ILE F 123 " --> pdb=" O THR F 85 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N PHE F 87 " --> pdb=" O ILE F 123 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N ILE F 125 " --> pdb=" O PHE F 87 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N PHE F 89 " --> pdb=" O ILE F 125 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY F 226 " --> pdb=" O ILE F 181 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 166 through 168 removed outlier: 6.479A pdb=" N CYS F 167 " --> pdb=" O PHE F 191 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'F' and resid 296 through 299 removed outlier: 4.331A pdb=" N THR F 309 " --> pdb=" O ILE F 299 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N VAL F 356 " --> pdb=" O THR F 318 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N GLY F 320 " --> pdb=" O VAL F 356 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N PHE F 358 " --> pdb=" O GLY F 320 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL F 322 " --> pdb=" O PHE F 358 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ASP F 360 " --> pdb=" O VAL F 322 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ASN F 324 " --> pdb=" O ASP F 360 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE F 355 " --> pdb=" O VAL F 394 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N ILE F 396 " --> pdb=" O ILE F 355 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N THR F 357 " --> pdb=" O ILE F 396 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N THR F 398 " --> pdb=" O THR F 357 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N VAL F 359 " --> pdb=" O THR F 398 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LYS F 400 " --> pdb=" O VAL F 359 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 296 through 299 removed outlier: 4.331A pdb=" N THR F 309 " --> pdb=" O ILE F 299 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N VAL F 356 " --> pdb=" O THR F 318 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N GLY F 320 " --> pdb=" O VAL F 356 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N PHE F 358 " --> pdb=" O GLY F 320 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL F 322 " --> pdb=" O PHE F 358 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ASP F 360 " --> pdb=" O VAL F 322 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ASN F 324 " --> pdb=" O ASP F 360 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE F 355 " --> pdb=" O VAL F 394 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N ILE F 396 " --> pdb=" O ILE F 355 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N THR F 357 " --> pdb=" O ILE F 396 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N THR F 398 " --> pdb=" O THR F 357 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N VAL F 359 " --> pdb=" O THR F 398 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LYS F 400 " --> pdb=" O VAL F 359 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU F 393 " --> pdb=" O LEU F 418 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N TYR F 420 " --> pdb=" O LEU F 393 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N THR F 395 " --> pdb=" O TYR F 420 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU F 475 " --> pdb=" O ASN F 419 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 500 through 505 removed outlier: 3.721A pdb=" N ASP G 520 " --> pdb=" O ASP G 517 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 600 through 602 removed outlier: 4.081A pdb=" N LEU G 664 " --> pdb=" O LEU G 601 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 634 through 639 removed outlier: 5.967A pdb=" N MET G 634 " --> pdb=" O GLU G 630 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLU G 630 " --> pdb=" O MET G 634 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ASN G 636 " --> pdb=" O ILE G 628 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE G 628 " --> pdb=" O ASN G 636 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU G 638 " --> pdb=" O LEU G 626 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN G 611 " --> pdb=" O ILE G 628 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N GLU G 630 " --> pdb=" O VAL G 609 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N VAL G 609 " --> pdb=" O GLU G 630 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 619 through 620 removed outlier: 4.009A pdb=" N VAL G 620 " --> pdb=" O GLY G 644 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY G 644 " --> pdb=" O VAL G 620 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'H' and resid 500 through 505 Processing sheet with id=AD3, first strand: chain 'H' and resid 600 through 602 removed outlier: 4.098A pdb=" N LEU H 664 " --> pdb=" O LEU H 601 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 608 through 612 removed outlier: 6.521A pdb=" N ILE H 628 " --> pdb=" O LYS H 610 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N ILE H 612 " --> pdb=" O LEU H 626 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N LEU H 626 " --> pdb=" O ILE H 612 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU H 638 " --> pdb=" O LEU H 626 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ILE H 628 " --> pdb=" O ASN H 636 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ASN H 636 " --> pdb=" O ILE H 628 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLU H 630 " --> pdb=" O MET H 634 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N MET H 634 " --> pdb=" O GLU H 630 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 619 through 620 Processing sheet with id=AD6, first strand: chain 'I' and resid 500 through 505 removed outlier: 3.656A pdb=" N GLN I 551 " --> pdb=" O VAL I 548 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 600 through 602 removed outlier: 7.249A pdb=" N LEU I 601 " --> pdb=" O ILE I 663 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS I 648 " --> pdb=" O GLU I 665 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 634 through 639 removed outlier: 5.927A pdb=" N MET I 634 " --> pdb=" O GLU I 630 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLU I 630 " --> pdb=" O MET I 634 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ASN I 636 " --> pdb=" O ILE I 628 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ILE I 628 " --> pdb=" O ASN I 636 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU I 638 " --> pdb=" O LEU I 626 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N LEU I 626 " --> pdb=" O ILE I 612 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N ILE I 612 " --> pdb=" O LEU I 626 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE I 628 " --> pdb=" O LYS I 610 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 619 through 620 Processing sheet with id=AE1, first strand: chain 'J' and resid 500 through 505 Processing sheet with id=AE2, first strand: chain 'J' and resid 600 through 602 removed outlier: 4.287A pdb=" N LEU J 664 " --> pdb=" O LEU J 601 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS J 648 " --> pdb=" O GLU J 665 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 634 through 639 removed outlier: 5.844A pdb=" N MET J 634 " --> pdb=" O GLU J 630 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLU J 630 " --> pdb=" O MET J 634 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ASN J 636 " --> pdb=" O ILE J 628 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ILE J 628 " --> pdb=" O ASN J 636 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU J 638 " --> pdb=" O LEU J 626 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N LEU J 626 " --> pdb=" O ILE J 612 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N ILE J 612 " --> pdb=" O LEU J 626 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE J 628 " --> pdb=" O LYS J 610 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY J 607 " --> pdb=" O LEU J 657 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 619 through 620 Processing sheet with id=AE5, first strand: chain 'K' and resid 500 through 505 removed outlier: 4.017A pdb=" N ASP K 520 " --> pdb=" O ASP K 517 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 634 through 639 removed outlier: 5.937A pdb=" N MET K 634 " --> pdb=" O GLU K 630 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLU K 630 " --> pdb=" O MET K 634 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ASN K 636 " --> pdb=" O ILE K 628 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ILE K 628 " --> pdb=" O ASN K 636 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU K 638 " --> pdb=" O LEU K 626 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N LEU K 626 " --> pdb=" O ILE K 612 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ILE K 612 " --> pdb=" O LEU K 626 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE K 628 " --> pdb=" O LYS K 610 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 618 through 620 removed outlier: 3.615A pdb=" N GLN K 618 " --> pdb=" O ILE K 646 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 648 through 649 Processing sheet with id=AE9, first strand: chain 'L' and resid 500 through 505 Processing sheet with id=AF1, first strand: chain 'L' and resid 600 through 602 removed outlier: 6.994A pdb=" N LEU L 601 " --> pdb=" O ILE L 663 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 635 through 639 removed outlier: 6.025A pdb=" N ASN L 636 " --> pdb=" O ILE L 628 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ILE L 628 " --> pdb=" O ASN L 636 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU L 638 " --> pdb=" O LEU L 626 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N LEU L 626 " --> pdb=" O ILE L 612 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ILE L 612 " --> pdb=" O LEU L 626 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE L 628 " --> pdb=" O LYS L 610 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY L 607 " --> pdb=" O LEU L 657 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 618 through 620 removed outlier: 4.537A pdb=" N GLN L 618 " --> pdb=" O ILE L 646 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE L 646 " --> pdb=" O GLN L 618 " (cutoff:3.500A) 1667 hydrogen bonds defined for protein. 4533 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.65 Time building geometry restraints manager: 3.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 5725 1.31 - 1.44: 8303 1.44 - 1.57: 19668 1.57 - 1.69: 36 1.69 - 1.82: 276 Bond restraints: 34008 Sorted by residual: bond pdb=" C9P COA E 601 " pdb=" N8P COA E 601 " ideal model delta sigma weight residual 1.340 1.484 -0.144 2.00e-02 2.50e+03 5.21e+01 bond pdb=" C9P COA C 601 " pdb=" N8P COA C 601 " ideal model delta sigma weight residual 1.340 1.484 -0.144 2.00e-02 2.50e+03 5.19e+01 bond pdb=" C9P COA F 601 " pdb=" N8P COA F 601 " ideal model delta sigma weight residual 1.340 1.484 -0.144 2.00e-02 2.50e+03 5.16e+01 bond pdb=" C9P COA A 601 " pdb=" N8P COA A 601 " ideal model delta sigma weight residual 1.340 1.484 -0.144 2.00e-02 2.50e+03 5.16e+01 bond pdb=" C9P COA B 601 " pdb=" N8P COA B 601 " ideal model delta sigma weight residual 1.340 1.484 -0.144 2.00e-02 2.50e+03 5.16e+01 ... (remaining 34003 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.84: 45753 3.84 - 7.69: 165 7.69 - 11.53: 58 11.53 - 15.37: 14 15.37 - 19.21: 12 Bond angle restraints: 46002 Sorted by residual: angle pdb=" O1A COA F 601 " pdb=" P1A COA F 601 " pdb=" O2A COA F 601 " ideal model delta sigma weight residual 120.41 101.20 19.21 3.00e+00 1.11e-01 4.10e+01 angle pdb=" O1A COA C 601 " pdb=" P1A COA C 601 " pdb=" O2A COA C 601 " ideal model delta sigma weight residual 120.41 101.21 19.20 3.00e+00 1.11e-01 4.10e+01 angle pdb=" O1A COA D 601 " pdb=" P1A COA D 601 " pdb=" O2A COA D 601 " ideal model delta sigma weight residual 120.41 101.21 19.20 3.00e+00 1.11e-01 4.10e+01 angle pdb=" O1A COA A 601 " pdb=" P1A COA A 601 " pdb=" O2A COA A 601 " ideal model delta sigma weight residual 120.41 101.21 19.20 3.00e+00 1.11e-01 4.10e+01 angle pdb=" O1A COA B 601 " pdb=" P1A COA B 601 " pdb=" O2A COA B 601 " ideal model delta sigma weight residual 120.41 101.22 19.19 3.00e+00 1.11e-01 4.09e+01 ... (remaining 45997 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 19669 18.00 - 36.00: 886 36.00 - 54.00: 191 54.00 - 72.00: 67 72.00 - 90.00: 43 Dihedral angle restraints: 20856 sinusoidal: 8676 harmonic: 12180 Sorted by residual: dihedral pdb=" CA PHE L 578 " pdb=" C PHE L 578 " pdb=" N THR L 579 " pdb=" CA THR L 579 " ideal model delta harmonic sigma weight residual 180.00 158.95 21.05 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA PHE G 578 " pdb=" C PHE G 578 " pdb=" N THR G 579 " pdb=" CA THR G 579 " ideal model delta harmonic sigma weight residual 180.00 159.04 20.96 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA PHE H 578 " pdb=" C PHE H 578 " pdb=" N THR H 579 " pdb=" CA THR H 579 " ideal model delta harmonic sigma weight residual 180.00 159.29 20.71 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 20853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 3614 0.039 - 0.077: 973 0.077 - 0.116: 478 0.116 - 0.154: 71 0.154 - 0.193: 12 Chirality restraints: 5148 Sorted by residual: chirality pdb=" C2 BTI K 700 " pdb=" C4 BTI K 700 " pdb=" C7 BTI K 700 " pdb=" S1 BTI K 700 " both_signs ideal model delta sigma weight residual False 3.11 3.30 -0.19 2.00e-01 2.50e+01 9.29e-01 chirality pdb=" C3B COA F 601 " pdb=" C2B COA F 601 " pdb=" C4B COA F 601 " pdb=" O3B COA F 601 " both_signs ideal model delta sigma weight residual False -2.73 -2.53 -0.19 2.00e-01 2.50e+01 9.23e-01 chirality pdb=" C2 BTI G 700 " pdb=" C4 BTI G 700 " pdb=" C7 BTI G 700 " pdb=" S1 BTI G 700 " both_signs ideal model delta sigma weight residual False 3.11 3.30 -0.19 2.00e-01 2.50e+01 9.21e-01 ... (remaining 5145 not shown) Planarity restraints: 6036 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 365 " -0.023 5.00e-02 4.00e+02 3.40e-02 1.85e+00 pdb=" N PRO C 366 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO C 366 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 366 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 365 " 0.023 5.00e-02 4.00e+02 3.40e-02 1.85e+00 pdb=" N PRO D 366 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO D 366 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 366 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 365 " -0.022 5.00e-02 4.00e+02 3.29e-02 1.73e+00 pdb=" N PRO A 366 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 366 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 366 " -0.018 5.00e-02 4.00e+02 ... (remaining 6033 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 8465 2.80 - 3.32: 34158 3.32 - 3.85: 65528 3.85 - 4.37: 78113 4.37 - 4.90: 125638 Nonbonded interactions: 311902 Sorted by model distance: nonbonded pdb=" OE1 GLU F 49 " pdb=" O HOH F 701 " model vdw 2.272 3.040 nonbonded pdb=" OD2 ASP B 72 " pdb=" OG SER B 101 " model vdw 2.281 3.040 nonbonded pdb=" OD2 ASP A 72 " pdb=" OG SER A 101 " model vdw 2.283 3.040 nonbonded pdb=" OD2 ASP F 72 " pdb=" OG SER F 101 " model vdw 2.283 3.040 nonbonded pdb=" OD2 ASP E 72 " pdb=" OG SER E 101 " model vdw 2.288 3.040 ... (remaining 311897 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 8.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 37.120 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.211 34014 Z= 0.333 Angle : 0.748 19.213 46002 Z= 0.321 Chirality : 0.045 0.193 5148 Planarity : 0.004 0.034 6036 Dihedral : 12.299 89.996 13032 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.35 % Allowed : 5.22 % Favored : 94.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.20 (0.13), residues: 4284 helix: 1.50 (0.14), residues: 1500 sheet: 1.44 (0.18), residues: 792 loop : 0.05 (0.14), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 38 TYR 0.011 0.001 TYR E 173 PHE 0.015 0.001 PHE D 384 TRP 0.004 0.001 TRP J 544 HIS 0.008 0.001 HIS C 104 Details of bonding type rmsd covalent geometry : bond 0.00533 (34008) covalent geometry : angle 0.74756 (46002) hydrogen bonds : bond 0.16226 ( 1583) hydrogen bonds : angle 6.97667 ( 4533) Misc. bond : bond 0.14981 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 550 time to evaluate : 1.336 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: A 9 GLU cc_start: 0.6537 (tp30) cc_final: 0.6027 (tp30) REVERT: A 23 ARG cc_start: 0.7536 (mtt-85) cc_final: 0.7273 (mtp85) REVERT: A 25 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7267 (tm-30) REVERT: A 499 GLU cc_start: 0.7232 (tt0) cc_final: 0.6926 (mp0) REVERT: A 502 ARG cc_start: 0.7769 (ttm-80) cc_final: 0.7555 (ttm-80) REVERT: B 9 GLU cc_start: 0.6536 (tp30) cc_final: 0.5913 (tp30) REVERT: B 22 LYS cc_start: 0.7481 (tttm) cc_final: 0.6698 (tmtm) REVERT: B 25 GLU cc_start: 0.7441 (mm-30) cc_final: 0.6843 (tm-30) REVERT: B 30 ARG cc_start: 0.8338 (mtt90) cc_final: 0.8063 (mtt180) REVERT: B 279 LYS cc_start: 0.8328 (tptt) cc_final: 0.7977 (mtpt) REVERT: B 285 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7516 (mm-30) REVERT: B 430 MET cc_start: 0.8745 (ptp) cc_final: 0.8418 (ptp) REVERT: B 453 ARG cc_start: 0.6923 (mmt180) cc_final: 0.6493 (mmt-90) REVERT: B 502 ARG cc_start: 0.7709 (ttm-80) cc_final: 0.7479 (tpt170) REVERT: C 9 GLU cc_start: 0.6633 (mm-30) cc_final: 0.5837 (tp30) REVERT: C 183 MET cc_start: 0.9287 (mtp) cc_final: 0.8931 (mtp) REVERT: C 492 MET cc_start: 0.8898 (tmm) cc_final: 0.8167 (tmm) REVERT: C 497 GLU cc_start: 0.8008 (tp30) cc_final: 0.7755 (mt-10) REVERT: C 498 MET cc_start: 0.8032 (ptp) cc_final: 0.7450 (ptm) REVERT: C 499 GLU cc_start: 0.7158 (tt0) cc_final: 0.6926 (mp0) REVERT: C 502 ARG cc_start: 0.7700 (ttm-80) cc_final: 0.7425 (tmt170) REVERT: D 9 GLU cc_start: 0.6839 (mm-30) cc_final: 0.6055 (tp30) REVERT: D 183 MET cc_start: 0.9438 (mtp) cc_final: 0.9096 (mtp) REVERT: D 453 ARG cc_start: 0.6908 (mtt180) cc_final: 0.6137 (mtt-85) REVERT: D 475 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.8031 (tp30) REVERT: D 492 MET cc_start: 0.9131 (tmm) cc_final: 0.8502 (tmm) REVERT: D 498 MET cc_start: 0.8398 (ptm) cc_final: 0.8020 (ptp) REVERT: E 9 GLU cc_start: 0.6931 (mm-30) cc_final: 0.6599 (tp30) REVERT: E 22 LYS cc_start: 0.7669 (tttm) cc_final: 0.6860 (tmtm) REVERT: E 25 GLU cc_start: 0.7461 (mm-30) cc_final: 0.6973 (tm-30) REVERT: E 29 LYS cc_start: 0.8113 (mmpt) cc_final: 0.7899 (mmpt) REVERT: E 430 MET cc_start: 0.8782 (ptp) cc_final: 0.8496 (ptp) REVERT: E 502 ARG cc_start: 0.7805 (ttm-80) cc_final: 0.7570 (ttm-80) REVERT: F 9 GLU cc_start: 0.6502 (tp30) cc_final: 0.5979 (tp30) REVERT: F 25 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7259 (tm-30) REVERT: F 499 GLU cc_start: 0.7228 (tt0) cc_final: 0.6867 (mp0) REVERT: F 502 ARG cc_start: 0.7816 (tpp-160) cc_final: 0.7590 (ttm-80) REVERT: G 534 ARG cc_start: 0.7857 (mtt90) cc_final: 0.7627 (ptp90) REVERT: G 589 MET cc_start: 0.9176 (mmp) cc_final: 0.8931 (mmp) REVERT: H 521 LEU cc_start: 0.8551 (mt) cc_final: 0.8344 (mm) REVERT: I 489 MET cc_start: 0.8631 (ttp) cc_final: 0.8356 (ttt) REVERT: I 491 ASP cc_start: 0.8240 (t0) cc_final: 0.8022 (t70) REVERT: K 589 MET cc_start: 0.9163 (mmp) cc_final: 0.8930 (mmp) REVERT: L 632 MET cc_start: 0.7575 (mtm) cc_final: 0.7283 (mtm) REVERT: L 653 GLU cc_start: 0.7415 (mp0) cc_final: 0.7190 (mp0) outliers start: 12 outliers final: 0 residues processed: 556 average time/residue: 0.9428 time to fit residues: 599.6621 Evaluate side-chains 483 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 480 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain D residue 475 GLU Chi-restraints excluded: chain F residue 25 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 6.9990 chunk 401 optimal weight: 2.9990 chunk 424 optimal weight: 0.9990 chunk 155 optimal weight: 6.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 263 ASN E 263 ASN G 476 HIS H 568 HIS I 556 GLN L 600 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.151841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.087607 restraints weight = 30964.638| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 1.76 r_work: 0.2876 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.0914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 34014 Z= 0.129 Angle : 0.530 6.209 46002 Z= 0.289 Chirality : 0.046 0.154 5148 Planarity : 0.004 0.032 6036 Dihedral : 8.432 81.578 5157 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.86 % Allowed : 7.28 % Favored : 90.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.02 (0.13), residues: 4284 helix: 1.33 (0.13), residues: 1572 sheet: 1.31 (0.18), residues: 792 loop : -0.07 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 453 TYR 0.011 0.002 TYR A 173 PHE 0.014 0.002 PHE B 384 TRP 0.008 0.001 TRP I 544 HIS 0.009 0.001 HIS B 104 Details of bonding type rmsd covalent geometry : bond 0.00273 (34008) covalent geometry : angle 0.52994 (46002) hydrogen bonds : bond 0.05111 ( 1583) hydrogen bonds : angle 5.40646 ( 4533) Misc. bond : bond 0.00058 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 488 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.6638 (tp30) cc_final: 0.5986 (tp30) REVERT: A 14 GLN cc_start: 0.7452 (OUTLIER) cc_final: 0.6745 (tm130) REVERT: A 23 ARG cc_start: 0.7219 (mtt-85) cc_final: 0.6976 (mtp85) REVERT: A 25 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.7170 (tm-30) REVERT: A 257 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7707 (tt0) REVERT: A 499 GLU cc_start: 0.7543 (tt0) cc_final: 0.6949 (mp0) REVERT: A 502 ARG cc_start: 0.8138 (ttm-80) cc_final: 0.7856 (ttm-80) REVERT: B 9 GLU cc_start: 0.6547 (tp30) cc_final: 0.5845 (tp30) REVERT: B 22 LYS cc_start: 0.7532 (tttm) cc_final: 0.6684 (tmtm) REVERT: B 30 ARG cc_start: 0.8167 (mtt90) cc_final: 0.7928 (mtm-85) REVERT: B 279 LYS cc_start: 0.8167 (tptt) cc_final: 0.7626 (mtpt) REVERT: B 285 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7593 (mm-30) REVERT: B 430 MET cc_start: 0.8560 (ptp) cc_final: 0.8280 (ptp) REVERT: B 453 ARG cc_start: 0.6787 (mmt180) cc_final: 0.6386 (mmt-90) REVERT: B 499 GLU cc_start: 0.7321 (tp30) cc_final: 0.6786 (mp0) REVERT: B 502 ARG cc_start: 0.8126 (ttm-80) cc_final: 0.7854 (ttm-80) REVERT: C 9 GLU cc_start: 0.6678 (mm-30) cc_final: 0.5892 (tp30) REVERT: C 14 GLN cc_start: 0.7606 (OUTLIER) cc_final: 0.6725 (tm130) REVERT: C 25 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.7066 (mm-30) REVERT: C 183 MET cc_start: 0.9303 (mtp) cc_final: 0.9031 (mtp) REVERT: C 430 MET cc_start: 0.8713 (ptp) cc_final: 0.8377 (ptm) REVERT: C 492 MET cc_start: 0.8876 (tmm) cc_final: 0.8142 (tmm) REVERT: C 497 GLU cc_start: 0.8251 (tp30) cc_final: 0.7864 (mt-10) REVERT: C 498 MET cc_start: 0.8088 (ptp) cc_final: 0.7571 (ptm) REVERT: C 499 GLU cc_start: 0.7540 (tt0) cc_final: 0.7031 (mp0) REVERT: C 502 ARG cc_start: 0.8143 (ttm-80) cc_final: 0.7397 (tpt170) REVERT: D 9 GLU cc_start: 0.6676 (mm-30) cc_final: 0.5874 (tp30) REVERT: D 14 GLN cc_start: 0.7592 (OUTLIER) cc_final: 0.6752 (tm130) REVERT: D 183 MET cc_start: 0.9304 (mtp) cc_final: 0.9049 (mtp) REVERT: D 453 ARG cc_start: 0.6499 (mtt180) cc_final: 0.5806 (mtt-85) REVERT: D 492 MET cc_start: 0.8868 (tmm) cc_final: 0.8147 (tmm) REVERT: D 498 MET cc_start: 0.8098 (ptm) cc_final: 0.7862 (ptp) REVERT: E 9 GLU cc_start: 0.6831 (mm-30) cc_final: 0.6499 (tp30) REVERT: E 22 LYS cc_start: 0.7523 (tttm) cc_final: 0.6637 (tmtm) REVERT: E 25 GLU cc_start: 0.7342 (mm-30) cc_final: 0.6778 (tm-30) REVERT: E 29 LYS cc_start: 0.7892 (mmpt) cc_final: 0.7617 (mmpt) REVERT: E 215 LYS cc_start: 0.8410 (tptp) cc_final: 0.8209 (tptm) REVERT: E 430 MET cc_start: 0.8588 (ptp) cc_final: 0.8260 (ptp) REVERT: E 475 GLU cc_start: 0.8091 (tp30) cc_final: 0.7627 (tp30) REVERT: E 499 GLU cc_start: 0.7378 (tp30) cc_final: 0.6836 (mp0) REVERT: E 502 ARG cc_start: 0.8137 (ttm-80) cc_final: 0.7864 (ttm-80) REVERT: F 9 GLU cc_start: 0.6511 (tp30) cc_final: 0.5940 (tp30) REVERT: F 14 GLN cc_start: 0.7445 (OUTLIER) cc_final: 0.6732 (tm130) REVERT: F 25 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.7116 (tm-30) REVERT: F 257 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7696 (tt0) REVERT: F 499 GLU cc_start: 0.7599 (tt0) cc_final: 0.6948 (mp0) REVERT: F 502 ARG cc_start: 0.8229 (tpp-160) cc_final: 0.7916 (ttm-80) REVERT: G 491 ASP cc_start: 0.7854 (t0) cc_final: 0.7512 (t0) REVERT: H 521 LEU cc_start: 0.8157 (mt) cc_final: 0.7670 (mm) REVERT: H 534 ARG cc_start: 0.7395 (ttm110) cc_final: 0.7054 (ttm-80) REVERT: H 580 ARG cc_start: 0.7140 (mtm110) cc_final: 0.6814 (mtt-85) REVERT: I 489 MET cc_start: 0.8398 (ttp) cc_final: 0.7978 (ttp) REVERT: I 580 ARG cc_start: 0.7571 (mtp180) cc_final: 0.7249 (mtt90) REVERT: J 580 ARG cc_start: 0.7460 (mtp180) cc_final: 0.6497 (mtm110) REVERT: K 458 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7093 (mt-10) REVERT: L 653 GLU cc_start: 0.6998 (mp0) cc_final: 0.6624 (mp0) outliers start: 64 outliers final: 14 residues processed: 514 average time/residue: 0.9395 time to fit residues: 553.4846 Evaluate side-chains 487 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 464 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain C residue 14 GLN Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain D residue 14 GLN Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain E residue 251 GLU Chi-restraints excluded: chain F residue 14 GLN Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 171 ASP Chi-restraints excluded: chain F residue 257 GLU Chi-restraints excluded: chain F residue 279 LYS Chi-restraints excluded: chain G residue 522 LEU Chi-restraints excluded: chain I residue 587 ASP Chi-restraints excluded: chain J residue 587 ASP Chi-restraints excluded: chain K residue 524 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 383 optimal weight: 40.0000 chunk 263 optimal weight: 9.9990 chunk 2 optimal weight: 0.7980 chunk 227 optimal weight: 2.9990 chunk 354 optimal weight: 8.9990 chunk 85 optimal weight: 5.9990 chunk 394 optimal weight: 1.9990 chunk 295 optimal weight: 0.9990 chunk 122 optimal weight: 6.9990 chunk 316 optimal weight: 0.4980 chunk 412 optimal weight: 8.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 263 ASN C 378 HIS E 263 ASN H 568 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.150921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.086403 restraints weight = 30727.904| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 1.76 r_work: 0.2857 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 34014 Z= 0.148 Angle : 0.545 7.259 46002 Z= 0.297 Chirality : 0.046 0.148 5148 Planarity : 0.004 0.036 6036 Dihedral : 8.310 80.081 5154 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.51 % Allowed : 8.58 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.92 (0.13), residues: 4284 helix: 1.25 (0.13), residues: 1572 sheet: 1.21 (0.18), residues: 792 loop : -0.11 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 453 TYR 0.010 0.002 TYR D 173 PHE 0.014 0.002 PHE E 384 TRP 0.010 0.001 TRP I 544 HIS 0.009 0.001 HIS E 104 Details of bonding type rmsd covalent geometry : bond 0.00321 (34008) covalent geometry : angle 0.54480 (46002) hydrogen bonds : bond 0.05380 ( 1583) hydrogen bonds : angle 5.27607 ( 4533) Misc. bond : bond 0.00021 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 477 time to evaluate : 1.418 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: A 9 GLU cc_start: 0.6668 (tp30) cc_final: 0.6045 (tp30) REVERT: A 14 GLN cc_start: 0.7471 (OUTLIER) cc_final: 0.6809 (tm130) REVERT: A 25 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.7178 (tm-30) REVERT: A 29 LYS cc_start: 0.7881 (mmpt) cc_final: 0.7533 (tttm) REVERT: A 257 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7698 (tt0) REVERT: A 499 GLU cc_start: 0.7594 (tt0) cc_final: 0.6973 (mp0) REVERT: A 502 ARG cc_start: 0.8139 (ttm-80) cc_final: 0.7860 (ttm-80) REVERT: B 9 GLU cc_start: 0.6576 (tp30) cc_final: 0.5873 (tp30) REVERT: B 22 LYS cc_start: 0.7560 (tttm) cc_final: 0.6694 (tmtm) REVERT: B 30 ARG cc_start: 0.8223 (mtt90) cc_final: 0.8004 (mtm-85) REVERT: B 257 GLU cc_start: 0.8238 (tt0) cc_final: 0.7786 (tm-30) REVERT: B 279 LYS cc_start: 0.8132 (tptt) cc_final: 0.7614 (mtpt) REVERT: B 285 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7574 (mm-30) REVERT: B 430 MET cc_start: 0.8571 (ptp) cc_final: 0.8314 (ptp) REVERT: B 453 ARG cc_start: 0.6804 (mmt180) cc_final: 0.6544 (mmt-90) REVERT: B 484 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8364 (ttpp) REVERT: B 499 GLU cc_start: 0.7423 (tp30) cc_final: 0.6844 (mp0) REVERT: B 502 ARG cc_start: 0.8139 (ttm-80) cc_final: 0.7875 (ttm-80) REVERT: C 9 GLU cc_start: 0.6750 (mm-30) cc_final: 0.5962 (tp30) REVERT: C 14 GLN cc_start: 0.7599 (OUTLIER) cc_final: 0.6778 (tm130) REVERT: C 25 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.7100 (mm-30) REVERT: C 183 MET cc_start: 0.9332 (mtp) cc_final: 0.9004 (mtp) REVERT: C 257 GLU cc_start: 0.8139 (tt0) cc_final: 0.7643 (tm-30) REVERT: C 492 MET cc_start: 0.8872 (tmm) cc_final: 0.8114 (tmm) REVERT: C 497 GLU cc_start: 0.8260 (tp30) cc_final: 0.7877 (mt-10) REVERT: C 498 MET cc_start: 0.8059 (ptp) cc_final: 0.7544 (ptm) REVERT: C 499 GLU cc_start: 0.7615 (tt0) cc_final: 0.7041 (mp0) REVERT: C 502 ARG cc_start: 0.8137 (ttm-80) cc_final: 0.7376 (tpt170) REVERT: D 9 GLU cc_start: 0.6794 (mm-30) cc_final: 0.5973 (tp30) REVERT: D 14 GLN cc_start: 0.7604 (OUTLIER) cc_final: 0.6771 (tm130) REVERT: D 183 MET cc_start: 0.9328 (mtp) cc_final: 0.9026 (mtp) REVERT: D 257 GLU cc_start: 0.8157 (tt0) cc_final: 0.7681 (tm-30) REVERT: D 453 ARG cc_start: 0.6493 (mtt180) cc_final: 0.5803 (mtt-85) REVERT: D 492 MET cc_start: 0.8876 (tmm) cc_final: 0.8264 (tmm) REVERT: D 498 MET cc_start: 0.8159 (ptm) cc_final: 0.7943 (ptp) REVERT: E 9 GLU cc_start: 0.6866 (mm-30) cc_final: 0.6532 (tp30) REVERT: E 22 LYS cc_start: 0.7552 (tttm) cc_final: 0.6668 (tmtm) REVERT: E 25 GLU cc_start: 0.7352 (mm-30) cc_final: 0.6789 (tm-30) REVERT: E 29 LYS cc_start: 0.7883 (mmpt) cc_final: 0.7604 (mmpt) REVERT: E 215 LYS cc_start: 0.8427 (tptp) cc_final: 0.8196 (tptp) REVERT: E 257 GLU cc_start: 0.8234 (tt0) cc_final: 0.7791 (tm-30) REVERT: E 430 MET cc_start: 0.8598 (ptp) cc_final: 0.8301 (ptp) REVERT: E 453 ARG cc_start: 0.6782 (mmt-90) cc_final: 0.6541 (mtt-85) REVERT: E 475 GLU cc_start: 0.8088 (tp30) cc_final: 0.7606 (tp30) REVERT: E 499 GLU cc_start: 0.7441 (tp30) cc_final: 0.6859 (mp0) REVERT: E 502 ARG cc_start: 0.8146 (ttm-80) cc_final: 0.7877 (ttm-80) REVERT: F 9 GLU cc_start: 0.6648 (tp30) cc_final: 0.5994 (tp30) REVERT: F 14 GLN cc_start: 0.7462 (OUTLIER) cc_final: 0.6799 (tm130) REVERT: F 25 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.7125 (tm-30) REVERT: F 257 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7672 (tt0) REVERT: F 499 GLU cc_start: 0.7624 (tt0) cc_final: 0.6958 (mp0) REVERT: F 502 ARG cc_start: 0.8200 (tpp-160) cc_final: 0.7905 (ttm-80) REVERT: G 491 ASP cc_start: 0.7905 (t0) cc_final: 0.7500 (t70) REVERT: G 534 ARG cc_start: 0.7339 (mtt90) cc_final: 0.6669 (ttm110) REVERT: G 593 GLU cc_start: 0.7043 (pm20) cc_final: 0.6796 (mm-30) REVERT: H 521 LEU cc_start: 0.8297 (mt) cc_final: 0.7801 (mm) REVERT: H 534 ARG cc_start: 0.7402 (ttm110) cc_final: 0.7051 (ttm-80) REVERT: H 580 ARG cc_start: 0.7163 (mtm110) cc_final: 0.6875 (mtt-85) REVERT: I 534 ARG cc_start: 0.7362 (ttm110) cc_final: 0.7135 (ttm-80) REVERT: I 580 ARG cc_start: 0.7588 (mtp180) cc_final: 0.6855 (mmt90) REVERT: J 534 ARG cc_start: 0.7502 (ttm-80) cc_final: 0.6948 (ttm110) REVERT: J 555 ILE cc_start: 0.7760 (mt) cc_final: 0.7532 (mt) REVERT: J 568 HIS cc_start: 0.8770 (t-90) cc_final: 0.8513 (t-90) REVERT: J 580 ARG cc_start: 0.7471 (mtp180) cc_final: 0.6494 (mtm110) REVERT: J 653 GLU cc_start: 0.6490 (OUTLIER) cc_final: 0.5587 (mm-30) REVERT: K 534 ARG cc_start: 0.7341 (ttm-80) cc_final: 0.6876 (ttm110) REVERT: L 605 MET cc_start: 0.6125 (pmm) cc_final: 0.5796 (pmm) REVERT: L 653 GLU cc_start: 0.7067 (mp0) cc_final: 0.6684 (mp0) outliers start: 52 outliers final: 15 residues processed: 499 average time/residue: 0.9774 time to fit residues: 558.3542 Evaluate side-chains 492 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 466 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 484 LYS Chi-restraints excluded: chain C residue 14 GLN Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain D residue 14 GLN Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain E residue 251 GLU Chi-restraints excluded: chain F residue 14 GLN Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 171 ASP Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 257 GLU Chi-restraints excluded: chain G residue 522 LEU Chi-restraints excluded: chain G residue 524 THR Chi-restraints excluded: chain G residue 589 MET Chi-restraints excluded: chain J residue 482 LYS Chi-restraints excluded: chain J residue 524 THR Chi-restraints excluded: chain J residue 653 GLU Chi-restraints excluded: chain K residue 524 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 81 optimal weight: 2.9990 chunk 193 optimal weight: 3.9990 chunk 240 optimal weight: 7.9990 chunk 373 optimal weight: 0.0040 chunk 84 optimal weight: 0.9990 chunk 215 optimal weight: 6.9990 chunk 311 optimal weight: 5.9990 chunk 419 optimal weight: 20.0000 chunk 65 optimal weight: 2.9990 chunk 298 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 overall best weight: 1.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 263 ASN E 263 ASN H 568 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.151129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.086565 restraints weight = 30670.609| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 1.76 r_work: 0.2860 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 34014 Z= 0.142 Angle : 0.538 8.134 46002 Z= 0.292 Chirality : 0.046 0.147 5148 Planarity : 0.004 0.038 6036 Dihedral : 8.228 79.534 5154 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.65 % Allowed : 9.13 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.91 (0.13), residues: 4284 helix: 1.27 (0.13), residues: 1572 sheet: 1.15 (0.18), residues: 792 loop : -0.12 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 453 TYR 0.011 0.002 TYR A 173 PHE 0.013 0.002 PHE E 384 TRP 0.010 0.001 TRP I 544 HIS 0.008 0.001 HIS E 104 Details of bonding type rmsd covalent geometry : bond 0.00307 (34008) covalent geometry : angle 0.53843 (46002) hydrogen bonds : bond 0.05169 ( 1583) hydrogen bonds : angle 5.16995 ( 4533) Misc. bond : bond 0.00014 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 487 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.6717 (tp30) cc_final: 0.6045 (tp30) REVERT: A 14 GLN cc_start: 0.7457 (OUTLIER) cc_final: 0.6789 (tm130) REVERT: A 23 ARG cc_start: 0.7261 (mtt-85) cc_final: 0.7004 (mtp85) REVERT: A 29 LYS cc_start: 0.7892 (mmpt) cc_final: 0.7549 (tttm) REVERT: A 257 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7706 (tt0) REVERT: A 499 GLU cc_start: 0.7629 (tt0) cc_final: 0.6989 (mp0) REVERT: A 502 ARG cc_start: 0.8130 (ttm-80) cc_final: 0.7856 (ttm-80) REVERT: B 9 GLU cc_start: 0.6584 (tp30) cc_final: 0.5879 (tp30) REVERT: B 22 LYS cc_start: 0.7556 (tttm) cc_final: 0.6673 (tmtm) REVERT: B 29 LYS cc_start: 0.7858 (mmpt) cc_final: 0.7550 (tttm) REVERT: B 30 ARG cc_start: 0.8214 (mtt90) cc_final: 0.7968 (mtm-85) REVERT: B 257 GLU cc_start: 0.8226 (tt0) cc_final: 0.7761 (tm-30) REVERT: B 279 LYS cc_start: 0.8136 (tptt) cc_final: 0.7622 (mtpt) REVERT: B 285 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7605 (mm-30) REVERT: B 453 ARG cc_start: 0.6841 (mmt180) cc_final: 0.6589 (mmt-90) REVERT: B 484 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8392 (ttpp) REVERT: B 499 GLU cc_start: 0.7419 (tp30) cc_final: 0.6858 (mp0) REVERT: B 502 ARG cc_start: 0.8134 (ttm-80) cc_final: 0.7876 (ttm-80) REVERT: C 9 GLU cc_start: 0.6797 (mm-30) cc_final: 0.5993 (tp30) REVERT: C 14 GLN cc_start: 0.7603 (OUTLIER) cc_final: 0.6758 (tm130) REVERT: C 25 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.7105 (mm-30) REVERT: C 183 MET cc_start: 0.9345 (mtp) cc_final: 0.8994 (mtp) REVERT: C 257 GLU cc_start: 0.8148 (tt0) cc_final: 0.7036 (pm20) REVERT: C 492 MET cc_start: 0.8889 (tmm) cc_final: 0.8126 (tmm) REVERT: C 497 GLU cc_start: 0.8258 (tp30) cc_final: 0.7896 (mt-10) REVERT: C 499 GLU cc_start: 0.7611 (tt0) cc_final: 0.7049 (mp0) REVERT: C 502 ARG cc_start: 0.8124 (ttm-80) cc_final: 0.7387 (tpt170) REVERT: D 9 GLU cc_start: 0.6844 (mm-30) cc_final: 0.6020 (tp30) REVERT: D 14 GLN cc_start: 0.7597 (OUTLIER) cc_final: 0.6743 (tm130) REVERT: D 183 MET cc_start: 0.9340 (mtp) cc_final: 0.9019 (mtp) REVERT: D 257 GLU cc_start: 0.8177 (tt0) cc_final: 0.7112 (pm20) REVERT: D 453 ARG cc_start: 0.6520 (mtt180) cc_final: 0.5826 (mtt-85) REVERT: D 492 MET cc_start: 0.8901 (tmm) cc_final: 0.8291 (tmm) REVERT: D 498 MET cc_start: 0.8112 (ptm) cc_final: 0.7912 (ptp) REVERT: E 9 GLU cc_start: 0.6863 (mm-30) cc_final: 0.6531 (tp30) REVERT: E 22 LYS cc_start: 0.7558 (tttm) cc_final: 0.6671 (tmtm) REVERT: E 25 GLU cc_start: 0.7384 (mm-30) cc_final: 0.6785 (tm-30) REVERT: E 29 LYS cc_start: 0.7900 (mmpt) cc_final: 0.7616 (mmpt) REVERT: E 215 LYS cc_start: 0.8467 (tttp) cc_final: 0.8246 (tptp) REVERT: E 257 GLU cc_start: 0.8226 (tt0) cc_final: 0.7768 (tm-30) REVERT: E 430 MET cc_start: 0.8598 (ptp) cc_final: 0.8314 (ptp) REVERT: E 453 ARG cc_start: 0.6822 (mmt-90) cc_final: 0.6588 (mtt-85) REVERT: E 475 GLU cc_start: 0.8094 (tp30) cc_final: 0.7609 (tp30) REVERT: E 499 GLU cc_start: 0.7442 (tp30) cc_final: 0.6873 (mp0) REVERT: E 502 ARG cc_start: 0.8140 (ttm-80) cc_final: 0.7876 (ttm-80) REVERT: F 9 GLU cc_start: 0.6696 (tp30) cc_final: 0.6033 (tp30) REVERT: F 14 GLN cc_start: 0.7443 (OUTLIER) cc_final: 0.6776 (tm130) REVERT: F 25 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.7125 (tm-30) REVERT: F 257 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7678 (tt0) REVERT: F 499 GLU cc_start: 0.7652 (tt0) cc_final: 0.6979 (mp0) REVERT: F 502 ARG cc_start: 0.8192 (tpp-160) cc_final: 0.7905 (ttm-80) REVERT: G 458 GLU cc_start: 0.7449 (mt-10) cc_final: 0.6808 (mt-10) REVERT: G 491 ASP cc_start: 0.8003 (t0) cc_final: 0.7632 (t70) REVERT: G 534 ARG cc_start: 0.7222 (mtt90) cc_final: 0.6846 (ttm110) REVERT: H 521 LEU cc_start: 0.8302 (mt) cc_final: 0.7800 (mm) REVERT: H 534 ARG cc_start: 0.7427 (ttm110) cc_final: 0.7090 (ttm-80) REVERT: H 580 ARG cc_start: 0.7141 (mtm110) cc_final: 0.6865 (mtt-85) REVERT: I 491 ASP cc_start: 0.7935 (t0) cc_final: 0.7552 (t70) REVERT: I 520 ASP cc_start: 0.5945 (m-30) cc_final: 0.5716 (m-30) REVERT: I 534 ARG cc_start: 0.7326 (ttm110) cc_final: 0.6975 (ttm-80) REVERT: I 580 ARG cc_start: 0.7613 (mtp180) cc_final: 0.6874 (mmt90) REVERT: J 580 ARG cc_start: 0.7478 (mtp180) cc_final: 0.6507 (mtm110) REVERT: J 653 GLU cc_start: 0.6545 (OUTLIER) cc_final: 0.5657 (mm-30) REVERT: K 534 ARG cc_start: 0.7304 (ttm-80) cc_final: 0.6834 (ttm110) REVERT: L 489 MET cc_start: 0.7988 (ttm) cc_final: 0.7708 (ttp) REVERT: L 605 MET cc_start: 0.6155 (pmm) cc_final: 0.5824 (pmm) REVERT: L 653 GLU cc_start: 0.7067 (mp0) cc_final: 0.6676 (mp0) outliers start: 57 outliers final: 18 residues processed: 508 average time/residue: 0.9688 time to fit residues: 564.3812 Evaluate side-chains 502 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 474 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 484 LYS Chi-restraints excluded: chain C residue 14 GLN Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain D residue 14 GLN Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 251 GLU Chi-restraints excluded: chain E residue 279 LYS Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain F residue 14 GLN Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 171 ASP Chi-restraints excluded: chain F residue 257 GLU Chi-restraints excluded: chain G residue 522 LEU Chi-restraints excluded: chain G residue 589 MET Chi-restraints excluded: chain I residue 524 THR Chi-restraints excluded: chain J residue 482 LYS Chi-restraints excluded: chain J residue 524 THR Chi-restraints excluded: chain J residue 653 GLU Chi-restraints excluded: chain K residue 524 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 112 optimal weight: 0.6980 chunk 113 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 358 optimal weight: 7.9990 chunk 332 optimal weight: 0.7980 chunk 385 optimal weight: 0.9990 chunk 221 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 292 optimal weight: 0.6980 chunk 262 optimal weight: 5.9990 chunk 182 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 263 ASN E 263 ASN H 568 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.155544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.092950 restraints weight = 31376.326| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.72 r_work: 0.3028 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 34014 Z= 0.111 Angle : 0.502 7.300 46002 Z= 0.271 Chirality : 0.044 0.145 5148 Planarity : 0.004 0.039 6036 Dihedral : 8.003 78.946 5151 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.30 % Allowed : 10.03 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.99 (0.13), residues: 4284 helix: 1.40 (0.13), residues: 1572 sheet: 1.12 (0.18), residues: 792 loop : -0.10 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 453 TYR 0.010 0.001 TYR F 173 PHE 0.013 0.001 PHE F 351 TRP 0.010 0.001 TRP I 544 HIS 0.007 0.001 HIS B 104 Details of bonding type rmsd covalent geometry : bond 0.00234 (34008) covalent geometry : angle 0.50193 (46002) hydrogen bonds : bond 0.04455 ( 1583) hydrogen bonds : angle 5.02166 ( 4533) Misc. bond : bond 0.00012 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 481 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.6866 (tp30) cc_final: 0.6210 (tp30) REVERT: A 29 LYS cc_start: 0.8106 (mmpt) cc_final: 0.7754 (tttm) REVERT: A 100 SER cc_start: 0.8646 (t) cc_final: 0.8160 (p) REVERT: A 257 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7785 (tt0) REVERT: A 499 GLU cc_start: 0.7713 (tt0) cc_final: 0.7131 (mp0) REVERT: A 502 ARG cc_start: 0.8214 (ttm-80) cc_final: 0.7975 (ttm-80) REVERT: B 9 GLU cc_start: 0.6736 (tp30) cc_final: 0.6064 (tp30) REVERT: B 22 LYS cc_start: 0.7724 (tttm) cc_final: 0.6868 (tmtm) REVERT: B 30 ARG cc_start: 0.8376 (mtt90) cc_final: 0.8140 (mtm-85) REVERT: B 257 GLU cc_start: 0.8338 (tt0) cc_final: 0.7940 (tm-30) REVERT: B 279 LYS cc_start: 0.8251 (tptt) cc_final: 0.7787 (mtpt) REVERT: B 285 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7795 (mm-30) REVERT: B 430 MET cc_start: 0.8718 (ptp) cc_final: 0.8489 (ptp) REVERT: B 453 ARG cc_start: 0.7055 (mmt180) cc_final: 0.6824 (mmt-90) REVERT: B 484 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8581 (ttpp) REVERT: B 499 GLU cc_start: 0.7273 (tp30) cc_final: 0.6965 (mp0) REVERT: B 502 ARG cc_start: 0.8191 (ttm-80) cc_final: 0.7964 (ttm-80) REVERT: C 9 GLU cc_start: 0.6965 (mm-30) cc_final: 0.6163 (tp30) REVERT: C 25 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.7264 (mm-30) REVERT: C 183 MET cc_start: 0.9385 (mtp) cc_final: 0.9026 (mtp) REVERT: C 257 GLU cc_start: 0.8212 (tt0) cc_final: 0.7813 (tm-30) REVERT: C 492 MET cc_start: 0.9032 (tmm) cc_final: 0.8347 (tmm) REVERT: C 497 GLU cc_start: 0.8289 (tp30) cc_final: 0.8050 (mt-10) REVERT: C 499 GLU cc_start: 0.7638 (tt0) cc_final: 0.7198 (mp0) REVERT: C 502 ARG cc_start: 0.8219 (ttm-80) cc_final: 0.7525 (tpt170) REVERT: D 9 GLU cc_start: 0.6939 (mm-30) cc_final: 0.6121 (tp30) REVERT: D 183 MET cc_start: 0.9378 (mtp) cc_final: 0.9059 (mtp) REVERT: D 257 GLU cc_start: 0.8218 (tt0) cc_final: 0.7814 (tm-30) REVERT: D 453 ARG cc_start: 0.6864 (mtt180) cc_final: 0.6081 (mtt-85) REVERT: D 492 MET cc_start: 0.9046 (tmm) cc_final: 0.8376 (tmm) REVERT: E 9 GLU cc_start: 0.7005 (mm-30) cc_final: 0.6672 (tp30) REVERT: E 22 LYS cc_start: 0.7717 (tttm) cc_final: 0.6842 (tmtm) REVERT: E 25 GLU cc_start: 0.7560 (mm-30) cc_final: 0.6996 (tm-30) REVERT: E 29 LYS cc_start: 0.8041 (mmpt) cc_final: 0.7795 (mmpt) REVERT: E 257 GLU cc_start: 0.8312 (tt0) cc_final: 0.7919 (tm-30) REVERT: E 430 MET cc_start: 0.8717 (ptp) cc_final: 0.8457 (ptp) REVERT: E 453 ARG cc_start: 0.7031 (mmt-90) cc_final: 0.6808 (mtt-85) REVERT: E 475 GLU cc_start: 0.8160 (tp30) cc_final: 0.7811 (tp30) REVERT: E 499 GLU cc_start: 0.7306 (tp30) cc_final: 0.6982 (mp0) REVERT: E 502 ARG cc_start: 0.8216 (ttm-80) cc_final: 0.7651 (tpt170) REVERT: F 9 GLU cc_start: 0.6853 (tp30) cc_final: 0.6199 (tp30) REVERT: F 25 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7385 (tm-30) REVERT: F 257 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7744 (tt0) REVERT: F 453 ARG cc_start: 0.6980 (mtt-85) cc_final: 0.6372 (mmt90) REVERT: F 499 GLU cc_start: 0.7728 (tt0) cc_final: 0.7117 (mp0) REVERT: F 502 ARG cc_start: 0.8260 (tpp-160) cc_final: 0.8024 (ttm-80) REVERT: G 458 GLU cc_start: 0.7476 (mt-10) cc_final: 0.6848 (mt-10) REVERT: G 491 ASP cc_start: 0.8033 (t0) cc_final: 0.7677 (t70) REVERT: G 534 ARG cc_start: 0.7283 (mtt90) cc_final: 0.6826 (ttm110) REVERT: H 521 LEU cc_start: 0.8398 (mt) cc_final: 0.7877 (mm) REVERT: H 580 ARG cc_start: 0.7361 (mtm110) cc_final: 0.7047 (mtt-85) REVERT: H 605 MET cc_start: 0.6289 (pmm) cc_final: 0.6026 (pmm) REVERT: I 580 ARG cc_start: 0.7753 (mtp180) cc_final: 0.7094 (mmt90) REVERT: J 534 ARG cc_start: 0.7605 (ttm-80) cc_final: 0.7298 (ttm110) REVERT: J 568 HIS cc_start: 0.8809 (t-90) cc_final: 0.8545 (t-90) REVERT: J 580 ARG cc_start: 0.7665 (mtp180) cc_final: 0.6713 (mtm110) REVERT: J 653 GLU cc_start: 0.6496 (OUTLIER) cc_final: 0.5892 (mp0) REVERT: K 534 ARG cc_start: 0.7309 (ttm-80) cc_final: 0.6856 (ttm110) REVERT: L 489 MET cc_start: 0.8060 (ttm) cc_final: 0.7813 (ttp) REVERT: L 580 ARG cc_start: 0.7212 (mtp-110) cc_final: 0.6991 (mmt90) REVERT: L 605 MET cc_start: 0.6202 (pmm) cc_final: 0.5804 (pmm) REVERT: L 653 GLU cc_start: 0.7089 (mp0) cc_final: 0.6696 (mp0) outliers start: 45 outliers final: 20 residues processed: 504 average time/residue: 0.9259 time to fit residues: 537.1744 Evaluate side-chains 491 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 465 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 484 LYS Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 251 GLU Chi-restraints excluded: chain E residue 279 LYS Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 171 ASP Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 257 GLU Chi-restraints excluded: chain G residue 524 THR Chi-restraints excluded: chain G residue 589 MET Chi-restraints excluded: chain H residue 465 HIS Chi-restraints excluded: chain J residue 524 THR Chi-restraints excluded: chain J residue 653 GLU Chi-restraints excluded: chain K residue 524 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 38 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 325 optimal weight: 4.9990 chunk 411 optimal weight: 5.9990 chunk 51 optimal weight: 0.0970 chunk 142 optimal weight: 2.9990 chunk 261 optimal weight: 3.9990 chunk 183 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 354 optimal weight: 6.9990 chunk 92 optimal weight: 0.0770 overall best weight: 1.4140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 GLN B 263 ASN C 300 GLN E 263 ASN H 568 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.154149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.091244 restraints weight = 31124.442| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.71 r_work: 0.3000 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 34014 Z= 0.145 Angle : 0.540 8.516 46002 Z= 0.293 Chirality : 0.046 0.146 5148 Planarity : 0.004 0.038 6036 Dihedral : 8.055 78.799 5151 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.30 % Allowed : 10.46 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.92 (0.13), residues: 4284 helix: 1.31 (0.13), residues: 1572 sheet: 1.12 (0.18), residues: 792 loop : -0.12 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 453 TYR 0.011 0.002 TYR F 173 PHE 0.014 0.002 PHE F 351 TRP 0.010 0.001 TRP I 544 HIS 0.008 0.001 HIS E 104 Details of bonding type rmsd covalent geometry : bond 0.00317 (34008) covalent geometry : angle 0.54050 (46002) hydrogen bonds : bond 0.05198 ( 1583) hydrogen bonds : angle 5.10060 ( 4533) Misc. bond : bond 0.00016 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 472 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.6872 (tp30) cc_final: 0.6209 (tp30) REVERT: A 14 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.6920 (tm130) REVERT: A 23 ARG cc_start: 0.7539 (mtt-85) cc_final: 0.7277 (mtp85) REVERT: A 257 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7766 (tt0) REVERT: A 499 GLU cc_start: 0.7717 (tt0) cc_final: 0.7132 (mp0) REVERT: A 502 ARG cc_start: 0.8214 (ttm-80) cc_final: 0.7973 (ttm-80) REVERT: B 9 GLU cc_start: 0.6808 (tp30) cc_final: 0.6115 (tp30) REVERT: B 22 LYS cc_start: 0.7731 (tttm) cc_final: 0.6877 (tmtm) REVERT: B 30 ARG cc_start: 0.8430 (mtt90) cc_final: 0.8207 (mtm-85) REVERT: B 257 GLU cc_start: 0.8315 (tt0) cc_final: 0.7917 (tm-30) REVERT: B 279 LYS cc_start: 0.8271 (tptt) cc_final: 0.7820 (mtpt) REVERT: B 285 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7788 (mm-30) REVERT: B 430 MET cc_start: 0.8702 (ptp) cc_final: 0.8429 (ptp) REVERT: B 453 ARG cc_start: 0.7017 (mmt180) cc_final: 0.6783 (mmt-90) REVERT: B 484 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8613 (ttpp) REVERT: B 499 GLU cc_start: 0.7380 (tp30) cc_final: 0.6973 (mp0) REVERT: B 502 ARG cc_start: 0.8219 (ttm-80) cc_final: 0.7993 (ttm-80) REVERT: C 9 GLU cc_start: 0.7003 (mm-30) cc_final: 0.6200 (tp30) REVERT: C 14 GLN cc_start: 0.7724 (OUTLIER) cc_final: 0.6876 (tm130) REVERT: C 25 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7271 (mm-30) REVERT: C 183 MET cc_start: 0.9414 (mtp) cc_final: 0.9048 (mtp) REVERT: C 257 GLU cc_start: 0.8253 (tt0) cc_final: 0.7859 (tm-30) REVERT: C 492 MET cc_start: 0.9040 (tmm) cc_final: 0.8310 (tmm) REVERT: C 497 GLU cc_start: 0.8314 (tp30) cc_final: 0.8049 (mt-10) REVERT: C 499 GLU cc_start: 0.7687 (tt0) cc_final: 0.7191 (mp0) REVERT: C 502 ARG cc_start: 0.8217 (ttm-80) cc_final: 0.7520 (tpt170) REVERT: D 9 GLU cc_start: 0.7062 (mm-30) cc_final: 0.6236 (tp30) REVERT: D 14 GLN cc_start: 0.7728 (OUTLIER) cc_final: 0.6881 (tm130) REVERT: D 183 MET cc_start: 0.9408 (mtp) cc_final: 0.9076 (mtp) REVERT: D 257 GLU cc_start: 0.8250 (tt0) cc_final: 0.7850 (tm-30) REVERT: D 453 ARG cc_start: 0.6854 (mtt180) cc_final: 0.6065 (mtt-85) REVERT: D 492 MET cc_start: 0.9043 (tmm) cc_final: 0.8459 (tmm) REVERT: E 9 GLU cc_start: 0.7038 (mm-30) cc_final: 0.6703 (tp30) REVERT: E 22 LYS cc_start: 0.7724 (tttm) cc_final: 0.6859 (tmtm) REVERT: E 25 GLU cc_start: 0.7576 (mm-30) cc_final: 0.6994 (tm-30) REVERT: E 29 LYS cc_start: 0.8078 (mmpt) cc_final: 0.7817 (mmpt) REVERT: E 257 GLU cc_start: 0.8292 (tt0) cc_final: 0.7901 (tm-30) REVERT: E 430 MET cc_start: 0.8736 (ptp) cc_final: 0.8476 (ptp) REVERT: E 453 ARG cc_start: 0.7005 (mmt-90) cc_final: 0.6766 (mtt-85) REVERT: E 475 GLU cc_start: 0.8178 (tp30) cc_final: 0.7798 (tp30) REVERT: E 499 GLU cc_start: 0.7392 (tp30) cc_final: 0.6993 (mp0) REVERT: E 502 ARG cc_start: 0.8196 (ttm-80) cc_final: 0.7849 (ttm-80) REVERT: F 9 GLU cc_start: 0.6840 (tp30) cc_final: 0.6182 (tp30) REVERT: F 14 GLN cc_start: 0.7616 (OUTLIER) cc_final: 0.6909 (tm130) REVERT: F 25 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7369 (tm-30) REVERT: F 257 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7741 (tt0) REVERT: F 453 ARG cc_start: 0.7011 (mtt-85) cc_final: 0.6351 (mmt90) REVERT: F 499 GLU cc_start: 0.7737 (tt0) cc_final: 0.7107 (mp0) REVERT: F 502 ARG cc_start: 0.8237 (tpp-160) cc_final: 0.8002 (ttm-80) REVERT: G 491 ASP cc_start: 0.8045 (t0) cc_final: 0.7689 (t70) REVERT: G 534 ARG cc_start: 0.7238 (mtt90) cc_final: 0.6698 (ttp-110) REVERT: H 509 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.7429 (mtm180) REVERT: H 521 LEU cc_start: 0.8395 (mt) cc_final: 0.7886 (mm) REVERT: H 580 ARG cc_start: 0.7331 (mtm110) cc_final: 0.7048 (mtt-85) REVERT: I 534 ARG cc_start: 0.7490 (ttm-80) cc_final: 0.7170 (ttm110) REVERT: I 580 ARG cc_start: 0.7792 (mtp180) cc_final: 0.7357 (mtt90) REVERT: J 580 ARG cc_start: 0.7666 (mtp180) cc_final: 0.6721 (mtm110) REVERT: J 653 GLU cc_start: 0.6470 (OUTLIER) cc_final: 0.5850 (mp0) REVERT: K 534 ARG cc_start: 0.7368 (ttm-80) cc_final: 0.6918 (ttm110) REVERT: L 489 MET cc_start: 0.8076 (ttm) cc_final: 0.7794 (ttp) REVERT: L 605 MET cc_start: 0.6108 (pmm) cc_final: 0.5708 (pmm) REVERT: L 653 GLU cc_start: 0.7097 (mp0) cc_final: 0.6701 (mp0) outliers start: 45 outliers final: 23 residues processed: 493 average time/residue: 0.9596 time to fit residues: 542.2716 Evaluate side-chains 496 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 462 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 484 LYS Chi-restraints excluded: chain C residue 14 GLN Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain D residue 14 GLN Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 251 GLU Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain F residue 14 GLN Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 171 ASP Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 257 GLU Chi-restraints excluded: chain G residue 522 LEU Chi-restraints excluded: chain G residue 524 THR Chi-restraints excluded: chain G residue 589 MET Chi-restraints excluded: chain H residue 465 HIS Chi-restraints excluded: chain H residue 509 ARG Chi-restraints excluded: chain I residue 524 THR Chi-restraints excluded: chain J residue 482 LYS Chi-restraints excluded: chain J residue 524 THR Chi-restraints excluded: chain J residue 653 GLU Chi-restraints excluded: chain K residue 524 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 235 optimal weight: 0.9980 chunk 355 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 388 optimal weight: 9.9990 chunk 213 optimal weight: 0.9990 chunk 150 optimal weight: 10.0000 chunk 418 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 293 optimal weight: 9.9990 chunk 347 optimal weight: 0.0270 overall best weight: 1.0044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 263 ASN D 300 GLN E 263 ASN H 568 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.154961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.092494 restraints weight = 31247.938| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.71 r_work: 0.3018 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 34014 Z= 0.121 Angle : 0.516 8.661 46002 Z= 0.278 Chirality : 0.045 0.146 5148 Planarity : 0.004 0.037 6036 Dihedral : 7.976 78.491 5151 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.36 % Allowed : 10.70 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.97 (0.13), residues: 4284 helix: 1.38 (0.13), residues: 1572 sheet: 1.10 (0.18), residues: 792 loop : -0.11 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 453 TYR 0.010 0.001 TYR F 173 PHE 0.013 0.001 PHE F 351 TRP 0.010 0.001 TRP I 544 HIS 0.008 0.001 HIS B 104 Details of bonding type rmsd covalent geometry : bond 0.00260 (34008) covalent geometry : angle 0.51557 (46002) hydrogen bonds : bond 0.04674 ( 1583) hydrogen bonds : angle 5.01225 ( 4533) Misc. bond : bond 0.00011 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 469 time to evaluate : 1.419 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: A 9 GLU cc_start: 0.6835 (tp30) cc_final: 0.6098 (tp30) REVERT: A 14 GLN cc_start: 0.7623 (OUTLIER) cc_final: 0.6920 (tm130) REVERT: A 23 ARG cc_start: 0.7516 (mtt-85) cc_final: 0.7252 (mtp85) REVERT: A 25 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7197 (tm-30) REVERT: A 100 SER cc_start: 0.8650 (t) cc_final: 0.8159 (p) REVERT: A 257 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7770 (tt0) REVERT: A 499 GLU cc_start: 0.7724 (tt0) cc_final: 0.7131 (mp0) REVERT: A 502 ARG cc_start: 0.8209 (ttm-80) cc_final: 0.7973 (ttm-80) REVERT: B 9 GLU cc_start: 0.6799 (tp30) cc_final: 0.6102 (tp30) REVERT: B 22 LYS cc_start: 0.7710 (tttm) cc_final: 0.6860 (tmtm) REVERT: B 29 LYS cc_start: 0.8011 (mmpt) cc_final: 0.7730 (tttm) REVERT: B 30 ARG cc_start: 0.8364 (mtt90) cc_final: 0.8142 (mtm-85) REVERT: B 257 GLU cc_start: 0.8321 (tt0) cc_final: 0.7925 (tm-30) REVERT: B 279 LYS cc_start: 0.8237 (tptt) cc_final: 0.7778 (mtpt) REVERT: B 285 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7795 (mm-30) REVERT: B 430 MET cc_start: 0.8700 (ptp) cc_final: 0.8424 (ptp) REVERT: B 453 ARG cc_start: 0.7007 (mmt180) cc_final: 0.6789 (mmt-90) REVERT: B 484 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8597 (ttpp) REVERT: B 499 GLU cc_start: 0.7349 (tp30) cc_final: 0.6981 (mp0) REVERT: B 502 ARG cc_start: 0.8207 (ttm-80) cc_final: 0.7984 (ttm-80) REVERT: C 9 GLU cc_start: 0.6993 (mm-30) cc_final: 0.6189 (tp30) REVERT: C 25 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7267 (mm-30) REVERT: C 183 MET cc_start: 0.9404 (mtp) cc_final: 0.9037 (mtp) REVERT: C 257 GLU cc_start: 0.8223 (tt0) cc_final: 0.7823 (tm-30) REVERT: C 492 MET cc_start: 0.9041 (tmm) cc_final: 0.8338 (tmm) REVERT: C 497 GLU cc_start: 0.8299 (tp30) cc_final: 0.8039 (mt-10) REVERT: C 499 GLU cc_start: 0.7690 (tt0) cc_final: 0.7187 (mp0) REVERT: C 502 ARG cc_start: 0.8213 (ttm-80) cc_final: 0.7517 (tpt170) REVERT: D 9 GLU cc_start: 0.7052 (mm-30) cc_final: 0.6226 (tp30) REVERT: D 183 MET cc_start: 0.9390 (mtp) cc_final: 0.9056 (mtp) REVERT: D 257 GLU cc_start: 0.8222 (tt0) cc_final: 0.7819 (tm-30) REVERT: D 453 ARG cc_start: 0.6832 (mtt180) cc_final: 0.6042 (mtt-85) REVERT: D 492 MET cc_start: 0.9045 (tmm) cc_final: 0.8361 (tmm) REVERT: E 9 GLU cc_start: 0.7015 (mm-30) cc_final: 0.6681 (tp30) REVERT: E 22 LYS cc_start: 0.7699 (tttm) cc_final: 0.6831 (tmtm) REVERT: E 25 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7015 (tm-30) REVERT: E 29 LYS cc_start: 0.8091 (mmpt) cc_final: 0.7841 (mmpt) REVERT: E 257 GLU cc_start: 0.8300 (tt0) cc_final: 0.7905 (tm-30) REVERT: E 430 MET cc_start: 0.8716 (ptp) cc_final: 0.8461 (ptp) REVERT: E 453 ARG cc_start: 0.6993 (mmt-90) cc_final: 0.6776 (mtt-85) REVERT: E 475 GLU cc_start: 0.8165 (tp30) cc_final: 0.7813 (tp30) REVERT: E 499 GLU cc_start: 0.7301 (tp30) cc_final: 0.6988 (mp0) REVERT: E 502 ARG cc_start: 0.8189 (ttm-80) cc_final: 0.7628 (tpt170) REVERT: F 9 GLU cc_start: 0.6811 (tp30) cc_final: 0.6082 (tp30) REVERT: F 14 GLN cc_start: 0.7608 (OUTLIER) cc_final: 0.6904 (tm130) REVERT: F 25 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7363 (tm-30) REVERT: F 257 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7748 (tt0) REVERT: F 453 ARG cc_start: 0.7002 (mtt-85) cc_final: 0.6342 (mmt90) REVERT: F 499 GLU cc_start: 0.7733 (tt0) cc_final: 0.7111 (mp0) REVERT: F 502 ARG cc_start: 0.8244 (tpp-160) cc_final: 0.8011 (ttm-80) REVERT: G 458 GLU cc_start: 0.7425 (mt-10) cc_final: 0.6801 (mt-10) REVERT: G 491 ASP cc_start: 0.8041 (t0) cc_final: 0.7678 (t70) REVERT: G 534 ARG cc_start: 0.7199 (mtt90) cc_final: 0.6755 (ttm110) REVERT: H 521 LEU cc_start: 0.8400 (mt) cc_final: 0.7888 (mm) REVERT: H 580 ARG cc_start: 0.7339 (mtm110) cc_final: 0.7032 (mtt-85) REVERT: H 605 MET cc_start: 0.6114 (pmm) cc_final: 0.5805 (pmm) REVERT: I 534 ARG cc_start: 0.7450 (ttm-80) cc_final: 0.7144 (ttm110) REVERT: I 580 ARG cc_start: 0.7764 (mtp180) cc_final: 0.7088 (mmt90) REVERT: J 568 HIS cc_start: 0.8823 (t-170) cc_final: 0.8588 (t-90) REVERT: J 580 ARG cc_start: 0.7669 (mtp180) cc_final: 0.6718 (mtm110) REVERT: J 613 MET cc_start: 0.6341 (mpt) cc_final: 0.5995 (mpp) REVERT: J 653 GLU cc_start: 0.6457 (OUTLIER) cc_final: 0.5824 (mp0) REVERT: K 534 ARG cc_start: 0.7294 (ttm-80) cc_final: 0.6854 (ttm110) REVERT: L 489 MET cc_start: 0.8055 (ttm) cc_final: 0.7830 (ttp) REVERT: L 605 MET cc_start: 0.6088 (pmm) cc_final: 0.5696 (pmm) outliers start: 47 outliers final: 29 residues processed: 492 average time/residue: 0.9668 time to fit residues: 545.4030 Evaluate side-chains 500 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 463 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 484 LYS Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 251 GLU Chi-restraints excluded: chain E residue 279 LYS Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain F residue 14 GLN Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 171 ASP Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 257 GLU Chi-restraints excluded: chain F residue 279 LYS Chi-restraints excluded: chain G residue 522 LEU Chi-restraints excluded: chain G residue 589 MET Chi-restraints excluded: chain H residue 465 HIS Chi-restraints excluded: chain I residue 524 THR Chi-restraints excluded: chain J residue 482 LYS Chi-restraints excluded: chain J residue 524 THR Chi-restraints excluded: chain J residue 587 ASP Chi-restraints excluded: chain J residue 653 GLU Chi-restraints excluded: chain K residue 524 THR Chi-restraints excluded: chain L residue 665 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 369 optimal weight: 5.9990 chunk 385 optimal weight: 0.8980 chunk 423 optimal weight: 9.9990 chunk 240 optimal weight: 0.9980 chunk 234 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 183 optimal weight: 0.9980 chunk 299 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 368 optimal weight: 0.4980 chunk 117 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 263 ASN E 263 ASN H 568 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.155885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.093735 restraints weight = 31388.262| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.71 r_work: 0.3037 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 34014 Z= 0.107 Angle : 0.500 9.167 46002 Z= 0.269 Chirality : 0.044 0.143 5148 Planarity : 0.004 0.048 6036 Dihedral : 7.862 78.176 5151 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.30 % Allowed : 10.93 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.02 (0.13), residues: 4284 helix: 1.46 (0.13), residues: 1572 sheet: 1.10 (0.18), residues: 792 loop : -0.09 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG L 534 TYR 0.009 0.001 TYR F 173 PHE 0.012 0.001 PHE F 351 TRP 0.011 0.001 TRP I 544 HIS 0.007 0.001 HIS B 104 Details of bonding type rmsd covalent geometry : bond 0.00225 (34008) covalent geometry : angle 0.50010 (46002) hydrogen bonds : bond 0.04288 ( 1583) hydrogen bonds : angle 4.92011 ( 4533) Misc. bond : bond 0.00009 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 469 time to evaluate : 1.404 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: A 9 GLU cc_start: 0.6848 (tp30) cc_final: 0.6108 (tp30) REVERT: A 14 GLN cc_start: 0.7647 (OUTLIER) cc_final: 0.6892 (tm130) REVERT: A 25 GLU cc_start: 0.7675 (mm-30) cc_final: 0.7170 (tm-30) REVERT: A 100 SER cc_start: 0.8614 (t) cc_final: 0.8198 (p) REVERT: A 257 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7779 (tt0) REVERT: A 499 GLU cc_start: 0.7727 (tt0) cc_final: 0.7135 (mp0) REVERT: A 502 ARG cc_start: 0.8210 (ttm-80) cc_final: 0.7977 (ttm-80) REVERT: B 9 GLU cc_start: 0.6775 (tp30) cc_final: 0.6076 (tp30) REVERT: B 22 LYS cc_start: 0.7710 (tttm) cc_final: 0.6857 (tmtm) REVERT: B 29 LYS cc_start: 0.8052 (mmpt) cc_final: 0.7723 (tttm) REVERT: B 30 ARG cc_start: 0.8365 (mtt90) cc_final: 0.8134 (mtm-85) REVERT: B 100 SER cc_start: 0.8616 (t) cc_final: 0.8123 (p) REVERT: B 257 GLU cc_start: 0.8316 (tt0) cc_final: 0.7913 (tm-30) REVERT: B 279 LYS cc_start: 0.8240 (tptt) cc_final: 0.7790 (mtpt) REVERT: B 285 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7781 (mm-30) REVERT: B 430 MET cc_start: 0.8691 (ptp) cc_final: 0.8423 (ptp) REVERT: B 453 ARG cc_start: 0.7019 (mmt180) cc_final: 0.6807 (mmt-90) REVERT: B 484 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8575 (ttpp) REVERT: B 499 GLU cc_start: 0.7255 (tp30) cc_final: 0.6989 (mp0) REVERT: B 502 ARG cc_start: 0.8202 (ttm-80) cc_final: 0.7979 (ttm-80) REVERT: C 9 GLU cc_start: 0.6988 (mm-30) cc_final: 0.6181 (tp30) REVERT: C 14 GLN cc_start: 0.7750 (OUTLIER) cc_final: 0.6802 (tm130) REVERT: C 25 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7326 (mm-30) REVERT: C 183 MET cc_start: 0.9384 (mtp) cc_final: 0.9113 (mtp) REVERT: C 257 GLU cc_start: 0.8225 (tt0) cc_final: 0.7823 (tm-30) REVERT: C 492 MET cc_start: 0.9022 (tmm) cc_final: 0.8353 (tmm) REVERT: C 497 GLU cc_start: 0.8296 (tp30) cc_final: 0.8045 (mt-10) REVERT: C 499 GLU cc_start: 0.7626 (tt0) cc_final: 0.7191 (mp0) REVERT: C 502 ARG cc_start: 0.8215 (ttm-80) cc_final: 0.7544 (tpt170) REVERT: D 9 GLU cc_start: 0.7041 (mm-30) cc_final: 0.6214 (tp30) REVERT: D 183 MET cc_start: 0.9382 (mtp) cc_final: 0.9052 (mtp) REVERT: D 257 GLU cc_start: 0.8222 (tt0) cc_final: 0.7816 (tm-30) REVERT: D 453 ARG cc_start: 0.6763 (mtt180) cc_final: 0.6019 (mtt-85) REVERT: D 492 MET cc_start: 0.9033 (tmm) cc_final: 0.8377 (tmm) REVERT: E 9 GLU cc_start: 0.6999 (mm-30) cc_final: 0.6662 (tp30) REVERT: E 22 LYS cc_start: 0.7697 (tttm) cc_final: 0.6822 (tmtm) REVERT: E 25 GLU cc_start: 0.7554 (mm-30) cc_final: 0.6988 (tm-30) REVERT: E 29 LYS cc_start: 0.8083 (mmpt) cc_final: 0.7843 (mmpt) REVERT: E 100 SER cc_start: 0.8610 (t) cc_final: 0.8131 (p) REVERT: E 257 GLU cc_start: 0.8298 (tt0) cc_final: 0.7899 (tm-30) REVERT: E 430 MET cc_start: 0.8696 (ptp) cc_final: 0.8448 (ptp) REVERT: E 453 ARG cc_start: 0.7025 (mmt-90) cc_final: 0.6815 (mtt-85) REVERT: E 475 GLU cc_start: 0.8160 (tp30) cc_final: 0.7816 (tp30) REVERT: E 499 GLU cc_start: 0.7294 (tp30) cc_final: 0.7005 (mp0) REVERT: E 502 ARG cc_start: 0.8177 (ttm-80) cc_final: 0.7958 (ttm-80) REVERT: F 9 GLU cc_start: 0.6797 (tp30) cc_final: 0.6064 (tp30) REVERT: F 14 GLN cc_start: 0.7609 (OUTLIER) cc_final: 0.6854 (tm130) REVERT: F 25 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7394 (tm-30) REVERT: F 100 SER cc_start: 0.8641 (t) cc_final: 0.8143 (p) REVERT: F 257 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7748 (tt0) REVERT: F 499 GLU cc_start: 0.7730 (tt0) cc_final: 0.7127 (mp0) REVERT: F 502 ARG cc_start: 0.8246 (tpp-160) cc_final: 0.8012 (ttm-80) REVERT: G 458 GLU cc_start: 0.7463 (mt-10) cc_final: 0.6828 (mt-10) REVERT: G 491 ASP cc_start: 0.8034 (t0) cc_final: 0.7662 (t70) REVERT: G 534 ARG cc_start: 0.7210 (mtt90) cc_final: 0.6627 (ttp-110) REVERT: H 521 LEU cc_start: 0.8397 (mt) cc_final: 0.7879 (mm) REVERT: H 580 ARG cc_start: 0.7399 (mtm110) cc_final: 0.7067 (mtt-85) REVERT: H 605 MET cc_start: 0.6196 (pmm) cc_final: 0.5865 (pmm) REVERT: H 632 MET cc_start: 0.7066 (mtm) cc_final: 0.6734 (mtm) REVERT: I 534 ARG cc_start: 0.7350 (ttm-80) cc_final: 0.7059 (ttm110) REVERT: I 580 ARG cc_start: 0.7762 (mtp180) cc_final: 0.7063 (mmt90) REVERT: J 568 HIS cc_start: 0.8790 (t-90) cc_final: 0.8545 (t-90) REVERT: J 580 ARG cc_start: 0.7631 (mtp180) cc_final: 0.6664 (mtm110) REVERT: J 613 MET cc_start: 0.6279 (OUTLIER) cc_final: 0.5962 (mpp) REVERT: J 653 GLU cc_start: 0.6471 (OUTLIER) cc_final: 0.5810 (mp0) REVERT: K 534 ARG cc_start: 0.7273 (ttm-80) cc_final: 0.6843 (ttm110) REVERT: L 489 MET cc_start: 0.8011 (ttm) cc_final: 0.7795 (ttp) REVERT: L 534 ARG cc_start: 0.7735 (ttm110) cc_final: 0.7361 (ttm110) REVERT: L 580 ARG cc_start: 0.7207 (OUTLIER) cc_final: 0.7005 (mmt90) REVERT: L 605 MET cc_start: 0.6114 (pmm) cc_final: 0.5722 (pmm) outliers start: 45 outliers final: 27 residues processed: 490 average time/residue: 0.9496 time to fit residues: 533.3254 Evaluate side-chains 501 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 463 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 484 LYS Chi-restraints excluded: chain C residue 14 GLN Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 251 GLU Chi-restraints excluded: chain E residue 279 LYS Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain F residue 14 GLN Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 171 ASP Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 257 GLU Chi-restraints excluded: chain F residue 279 LYS Chi-restraints excluded: chain G residue 522 LEU Chi-restraints excluded: chain G residue 589 MET Chi-restraints excluded: chain H residue 465 HIS Chi-restraints excluded: chain I residue 524 THR Chi-restraints excluded: chain I residue 587 ASP Chi-restraints excluded: chain J residue 482 LYS Chi-restraints excluded: chain J residue 587 ASP Chi-restraints excluded: chain J residue 613 MET Chi-restraints excluded: chain J residue 653 GLU Chi-restraints excluded: chain K residue 524 THR Chi-restraints excluded: chain L residue 580 ARG Chi-restraints excluded: chain L residue 665 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 27 optimal weight: 2.9990 chunk 348 optimal weight: 5.9990 chunk 391 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 424 optimal weight: 40.0000 chunk 363 optimal weight: 0.0270 chunk 85 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 358 optimal weight: 10.0000 overall best weight: 2.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 263 ASN E 263 ASN H 568 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.152588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.089370 restraints weight = 30897.130| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.71 r_work: 0.2968 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 34014 Z= 0.220 Angle : 0.616 9.565 46002 Z= 0.336 Chirality : 0.050 0.177 5148 Planarity : 0.005 0.042 6036 Dihedral : 8.182 78.415 5151 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.33 % Allowed : 10.99 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.79 (0.13), residues: 4284 helix: 1.12 (0.13), residues: 1572 sheet: 1.10 (0.18), residues: 792 loop : -0.14 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 534 TYR 0.014 0.003 TYR F 173 PHE 0.017 0.002 PHE E 384 TRP 0.009 0.002 TRP J 544 HIS 0.010 0.002 HIS C 104 Details of bonding type rmsd covalent geometry : bond 0.00500 (34008) covalent geometry : angle 0.61643 (46002) hydrogen bonds : bond 0.06247 ( 1583) hydrogen bonds : angle 5.24844 ( 4533) Misc. bond : bond 0.00023 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 478 time to evaluate : 1.070 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: A 9 GLU cc_start: 0.6861 (tp30) cc_final: 0.6129 (tp30) REVERT: A 14 GLN cc_start: 0.7621 (OUTLIER) cc_final: 0.6945 (tm130) REVERT: A 23 ARG cc_start: 0.7553 (mtt-85) cc_final: 0.7288 (mtp85) REVERT: A 25 GLU cc_start: 0.7644 (mm-30) cc_final: 0.7221 (tm-30) REVERT: A 257 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7766 (tt0) REVERT: A 499 GLU cc_start: 0.7762 (tt0) cc_final: 0.7133 (mp0) REVERT: A 502 ARG cc_start: 0.8236 (ttm-80) cc_final: 0.7991 (ttm-80) REVERT: B 9 GLU cc_start: 0.6816 (tp30) cc_final: 0.6103 (tp30) REVERT: B 22 LYS cc_start: 0.7744 (tttm) cc_final: 0.6875 (tmtm) REVERT: B 29 LYS cc_start: 0.8099 (mmpt) cc_final: 0.7757 (tttm) REVERT: B 257 GLU cc_start: 0.8343 (tt0) cc_final: 0.8012 (tm-30) REVERT: B 279 LYS cc_start: 0.8300 (tptt) cc_final: 0.7873 (mtpt) REVERT: B 285 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7857 (mm-30) REVERT: B 453 ARG cc_start: 0.7005 (mmt180) cc_final: 0.6754 (mmt-90) REVERT: B 484 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8683 (ttpp) REVERT: B 499 GLU cc_start: 0.7474 (tp30) cc_final: 0.6986 (mp0) REVERT: B 502 ARG cc_start: 0.8242 (ttm-80) cc_final: 0.8011 (ttm-80) REVERT: C 9 GLU cc_start: 0.7051 (mm-30) cc_final: 0.6244 (tp30) REVERT: C 14 GLN cc_start: 0.7773 (OUTLIER) cc_final: 0.6963 (tm130) REVERT: C 25 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7285 (mm-30) REVERT: C 257 GLU cc_start: 0.8269 (tt0) cc_final: 0.7875 (tm-30) REVERT: C 430 MET cc_start: 0.8820 (ptp) cc_final: 0.8513 (ptm) REVERT: C 492 MET cc_start: 0.9034 (tmm) cc_final: 0.8413 (tmm) REVERT: C 497 GLU cc_start: 0.8324 (tp30) cc_final: 0.8061 (mt-10) REVERT: C 499 GLU cc_start: 0.7680 (tt0) cc_final: 0.7117 (mp0) REVERT: C 502 ARG cc_start: 0.8232 (ttm-80) cc_final: 0.7516 (tpt170) REVERT: D 9 GLU cc_start: 0.7079 (mm-30) cc_final: 0.6248 (tp30) REVERT: D 14 GLN cc_start: 0.7705 (OUTLIER) cc_final: 0.6853 (tm130) REVERT: D 183 MET cc_start: 0.9427 (mtp) cc_final: 0.9089 (mtp) REVERT: D 257 GLU cc_start: 0.8273 (tt0) cc_final: 0.7875 (tm-30) REVERT: D 453 ARG cc_start: 0.6735 (mtt180) cc_final: 0.6006 (mtt-85) REVERT: D 492 MET cc_start: 0.9042 (tmm) cc_final: 0.8405 (tmm) REVERT: E 9 GLU cc_start: 0.7083 (mm-30) cc_final: 0.6736 (tp30) REVERT: E 22 LYS cc_start: 0.7724 (tttm) cc_final: 0.6850 (tmtm) REVERT: E 25 GLU cc_start: 0.7618 (mm-30) cc_final: 0.7074 (tm-30) REVERT: E 29 LYS cc_start: 0.8112 (mmpt) cc_final: 0.7866 (mmpt) REVERT: E 257 GLU cc_start: 0.8326 (tt0) cc_final: 0.8000 (tm-30) REVERT: E 430 MET cc_start: 0.8729 (ptp) cc_final: 0.8464 (ptp) REVERT: E 453 ARG cc_start: 0.6962 (mmt-90) cc_final: 0.6704 (mtt-85) REVERT: E 499 GLU cc_start: 0.7492 (tp30) cc_final: 0.7002 (mp0) REVERT: E 502 ARG cc_start: 0.8227 (ttm-80) cc_final: 0.7998 (ttm-80) REVERT: F 9 GLU cc_start: 0.6857 (tp30) cc_final: 0.6125 (tp30) REVERT: F 14 GLN cc_start: 0.7609 (OUTLIER) cc_final: 0.6970 (tm130) REVERT: F 25 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7304 (tm-30) REVERT: F 257 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7747 (tt0) REVERT: F 499 GLU cc_start: 0.7796 (tt0) cc_final: 0.7126 (mp0) REVERT: F 502 ARG cc_start: 0.8233 (tpp-160) cc_final: 0.7994 (ttm-80) REVERT: G 491 ASP cc_start: 0.8069 (t0) cc_final: 0.7693 (t70) REVERT: G 534 ARG cc_start: 0.7336 (mtt90) cc_final: 0.6801 (ttm110) REVERT: H 509 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.7384 (mtm180) REVERT: H 521 LEU cc_start: 0.8408 (mt) cc_final: 0.7912 (mm) REVERT: H 605 MET cc_start: 0.6198 (pmm) cc_final: 0.5819 (pmm) REVERT: I 491 ASP cc_start: 0.7991 (t0) cc_final: 0.7621 (t70) REVERT: I 580 ARG cc_start: 0.7806 (mtp180) cc_final: 0.7064 (mmt90) REVERT: J 580 ARG cc_start: 0.7628 (mtp180) cc_final: 0.6700 (mtm110) REVERT: J 613 MET cc_start: 0.6115 (OUTLIER) cc_final: 0.5630 (mpp) REVERT: J 653 GLU cc_start: 0.6560 (OUTLIER) cc_final: 0.5827 (mp0) REVERT: K 534 ARG cc_start: 0.7403 (ttm-80) cc_final: 0.6956 (ttm110) REVERT: L 489 MET cc_start: 0.8119 (ttm) cc_final: 0.7813 (ttp) outliers start: 46 outliers final: 22 residues processed: 498 average time/residue: 1.0069 time to fit residues: 578.2238 Evaluate side-chains 507 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 473 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 484 LYS Chi-restraints excluded: chain C residue 14 GLN Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain D residue 14 GLN Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain E residue 251 GLU Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain F residue 14 GLN Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 171 ASP Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 257 GLU Chi-restraints excluded: chain G residue 522 LEU Chi-restraints excluded: chain H residue 509 ARG Chi-restraints excluded: chain I residue 524 THR Chi-restraints excluded: chain J residue 482 LYS Chi-restraints excluded: chain J residue 524 THR Chi-restraints excluded: chain J residue 587 ASP Chi-restraints excluded: chain J residue 613 MET Chi-restraints excluded: chain J residue 653 GLU Chi-restraints excluded: chain K residue 524 THR Chi-restraints excluded: chain L residue 580 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 252 optimal weight: 6.9990 chunk 264 optimal weight: 0.0570 chunk 128 optimal weight: 0.9990 chunk 314 optimal weight: 30.0000 chunk 316 optimal weight: 0.0670 chunk 12 optimal weight: 0.1980 chunk 413 optimal weight: 3.9990 chunk 354 optimal weight: 2.9990 chunk 75 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 overall best weight: 0.8640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 263 ASN E 263 ASN H 568 HIS I 568 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.155137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.092853 restraints weight = 31294.520| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.70 r_work: 0.3024 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 34014 Z= 0.116 Angle : 0.525 10.358 46002 Z= 0.281 Chirality : 0.045 0.144 5148 Planarity : 0.004 0.056 6036 Dihedral : 7.993 78.166 5151 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.04 % Allowed : 11.45 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.93 (0.13), residues: 4284 helix: 1.36 (0.13), residues: 1572 sheet: 1.06 (0.18), residues: 792 loop : -0.12 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG L 534 TYR 0.011 0.001 TYR B 173 PHE 0.014 0.001 PHE A 351 TRP 0.011 0.001 TRP L 544 HIS 0.007 0.001 HIS B 104 Details of bonding type rmsd covalent geometry : bond 0.00249 (34008) covalent geometry : angle 0.52492 (46002) hydrogen bonds : bond 0.04522 ( 1583) hydrogen bonds : angle 5.00324 ( 4533) Misc. bond : bond 0.00012 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 467 time to evaluate : 1.408 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: A 9 GLU cc_start: 0.6848 (tp30) cc_final: 0.6115 (tp30) REVERT: A 14 GLN cc_start: 0.7615 (OUTLIER) cc_final: 0.6868 (tm130) REVERT: A 23 ARG cc_start: 0.7513 (mtt-85) cc_final: 0.7250 (mtp85) REVERT: A 25 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7186 (tm-30) REVERT: A 100 SER cc_start: 0.8570 (t) cc_final: 0.8079 (p) REVERT: A 257 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7781 (tt0) REVERT: A 499 GLU cc_start: 0.7699 (tt0) cc_final: 0.7114 (mp0) REVERT: A 502 ARG cc_start: 0.8218 (ttm-80) cc_final: 0.7976 (ttm-80) REVERT: B 9 GLU cc_start: 0.6779 (tp30) cc_final: 0.6088 (tp30) REVERT: B 22 LYS cc_start: 0.7706 (tttm) cc_final: 0.6844 (tmtm) REVERT: B 29 LYS cc_start: 0.8099 (mmpt) cc_final: 0.7756 (tttm) REVERT: B 30 ARG cc_start: 0.8408 (mtt90) cc_final: 0.8184 (mtm-85) REVERT: B 100 SER cc_start: 0.8576 (t) cc_final: 0.8075 (p) REVERT: B 257 GLU cc_start: 0.8304 (tt0) cc_final: 0.7906 (tm-30) REVERT: B 279 LYS cc_start: 0.8258 (tptt) cc_final: 0.7808 (mtpt) REVERT: B 285 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7775 (mm-30) REVERT: B 453 ARG cc_start: 0.7021 (mmt180) cc_final: 0.6795 (mmt-90) REVERT: B 484 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8593 (ttpp) REVERT: B 499 GLU cc_start: 0.7350 (tp30) cc_final: 0.6994 (mp0) REVERT: B 502 ARG cc_start: 0.8212 (ttm-80) cc_final: 0.7987 (ttm-80) REVERT: C 9 GLU cc_start: 0.6948 (mm-30) cc_final: 0.6187 (tp30) REVERT: C 14 GLN cc_start: 0.7719 (OUTLIER) cc_final: 0.6798 (tm130) REVERT: C 25 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7274 (mm-30) REVERT: C 257 GLU cc_start: 0.8260 (tt0) cc_final: 0.7857 (tm-30) REVERT: C 492 MET cc_start: 0.9020 (tmm) cc_final: 0.8323 (tmm) REVERT: C 497 GLU cc_start: 0.8292 (tp30) cc_final: 0.8045 (mt-10) REVERT: C 499 GLU cc_start: 0.7675 (tt0) cc_final: 0.7151 (mp0) REVERT: C 502 ARG cc_start: 0.8202 (ttm-80) cc_final: 0.7510 (tpt170) REVERT: D 9 GLU cc_start: 0.7060 (mm-30) cc_final: 0.6230 (tp30) REVERT: D 14 GLN cc_start: 0.7712 (OUTLIER) cc_final: 0.6835 (tm130) REVERT: D 183 MET cc_start: 0.9398 (mtp) cc_final: 0.9059 (mtp) REVERT: D 257 GLU cc_start: 0.8245 (tt0) cc_final: 0.7840 (tm-30) REVERT: D 453 ARG cc_start: 0.6802 (mtt180) cc_final: 0.6065 (mtt-85) REVERT: D 492 MET cc_start: 0.9048 (tmm) cc_final: 0.8367 (tmm) REVERT: E 9 GLU cc_start: 0.7002 (mm-30) cc_final: 0.6670 (tp30) REVERT: E 22 LYS cc_start: 0.7705 (tttm) cc_final: 0.6848 (tmtm) REVERT: E 25 GLU cc_start: 0.7596 (mm-30) cc_final: 0.7035 (tm-30) REVERT: E 29 LYS cc_start: 0.8144 (mmpt) cc_final: 0.7883 (mmpt) REVERT: E 100 SER cc_start: 0.8611 (t) cc_final: 0.8113 (p) REVERT: E 257 GLU cc_start: 0.8290 (tt0) cc_final: 0.7890 (tm-30) REVERT: E 430 MET cc_start: 0.8718 (ptp) cc_final: 0.8470 (ptp) REVERT: E 475 GLU cc_start: 0.8163 (tp30) cc_final: 0.7792 (tp30) REVERT: E 499 GLU cc_start: 0.7376 (tp30) cc_final: 0.7006 (mp0) REVERT: E 502 ARG cc_start: 0.8202 (ttm-80) cc_final: 0.7977 (ttm-80) REVERT: F 9 GLU cc_start: 0.6818 (tp30) cc_final: 0.6088 (tp30) REVERT: F 14 GLN cc_start: 0.7606 (OUTLIER) cc_final: 0.6859 (tm130) REVERT: F 25 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7375 (tm-30) REVERT: F 100 SER cc_start: 0.8647 (t) cc_final: 0.8130 (p) REVERT: F 257 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7739 (tt0) REVERT: F 499 GLU cc_start: 0.7737 (tt0) cc_final: 0.7118 (mp0) REVERT: F 502 ARG cc_start: 0.8256 (tpp-160) cc_final: 0.8016 (ttm-80) REVERT: G 491 ASP cc_start: 0.8012 (t0) cc_final: 0.7643 (t70) REVERT: G 534 ARG cc_start: 0.7299 (mtt90) cc_final: 0.6704 (ttp-110) REVERT: H 521 LEU cc_start: 0.8417 (mt) cc_final: 0.7914 (mm) REVERT: H 580 ARG cc_start: 0.7377 (mtm110) cc_final: 0.7000 (mtm-85) REVERT: H 605 MET cc_start: 0.6195 (pmm) cc_final: 0.5842 (pmm) REVERT: I 580 ARG cc_start: 0.7773 (mtp180) cc_final: 0.7091 (mmt90) REVERT: J 568 HIS cc_start: 0.8850 (t-170) cc_final: 0.8580 (t-90) REVERT: J 580 ARG cc_start: 0.7672 (mtp180) cc_final: 0.6731 (mtm110) REVERT: J 613 MET cc_start: 0.6010 (OUTLIER) cc_final: 0.5665 (mpp) REVERT: J 653 GLU cc_start: 0.6481 (OUTLIER) cc_final: 0.5804 (mp0) REVERT: K 534 ARG cc_start: 0.7362 (ttm-80) cc_final: 0.6942 (ttm110) REVERT: L 489 MET cc_start: 0.8068 (ttm) cc_final: 0.7775 (ttp) REVERT: L 534 ARG cc_start: 0.7754 (ttm110) cc_final: 0.7459 (ttm110) REVERT: L 580 ARG cc_start: 0.7226 (OUTLIER) cc_final: 0.7009 (mmt90) REVERT: L 605 MET cc_start: 0.6104 (pmm) cc_final: 0.5754 (pmm) outliers start: 36 outliers final: 19 residues processed: 486 average time/residue: 0.9715 time to fit residues: 539.6641 Evaluate side-chains 494 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 463 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 484 LYS Chi-restraints excluded: chain C residue 14 GLN Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain D residue 14 GLN Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 251 GLU Chi-restraints excluded: chain E residue 279 LYS Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain F residue 14 GLN Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 171 ASP Chi-restraints excluded: chain F residue 257 GLU Chi-restraints excluded: chain G residue 522 LEU Chi-restraints excluded: chain I residue 524 THR Chi-restraints excluded: chain J residue 482 LYS Chi-restraints excluded: chain J residue 524 THR Chi-restraints excluded: chain J residue 587 ASP Chi-restraints excluded: chain J residue 613 MET Chi-restraints excluded: chain J residue 653 GLU Chi-restraints excluded: chain K residue 524 THR Chi-restraints excluded: chain L residue 580 ARG Chi-restraints excluded: chain L residue 665 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 371 optimal weight: 2.9990 chunk 281 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 238 optimal weight: 0.8980 chunk 277 optimal weight: 0.0980 chunk 178 optimal weight: 0.9980 chunk 315 optimal weight: 0.9980 chunk 300 optimal weight: 0.2980 chunk 425 optimal weight: 0.8980 chunk 301 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 263 ASN E 263 ASN H 568 HIS I 568 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.156327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.094383 restraints weight = 31279.048| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.70 r_work: 0.3049 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 34014 Z= 0.104 Angle : 0.507 9.870 46002 Z= 0.270 Chirality : 0.044 0.142 5148 Planarity : 0.004 0.053 6036 Dihedral : 7.801 77.497 5151 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.90 % Allowed : 11.68 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.13), residues: 4284 helix: 1.47 (0.13), residues: 1572 sheet: 1.09 (0.18), residues: 792 loop : -0.09 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG L 534 TYR 0.011 0.001 TYR B 173 PHE 0.012 0.001 PHE F 351 TRP 0.011 0.001 TRP L 544 HIS 0.007 0.001 HIS B 104 Details of bonding type rmsd covalent geometry : bond 0.00220 (34008) covalent geometry : angle 0.50682 (46002) hydrogen bonds : bond 0.04137 ( 1583) hydrogen bonds : angle 4.86824 ( 4533) Misc. bond : bond 0.00008 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22741.12 seconds wall clock time: 385 minutes 45.89 seconds (23145.89 seconds total)