Starting phenix.real_space_refine on Sun Jun 29 13:43:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pn8_17778/06_2025/8pn8_17778.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pn8_17778/06_2025/8pn8_17778.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pn8_17778/06_2025/8pn8_17778.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pn8_17778/06_2025/8pn8_17778.map" model { file = "/net/cci-nas-00/data/ceres_data/8pn8_17778/06_2025/8pn8_17778.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pn8_17778/06_2025/8pn8_17778.cif" } resolution = 2.31 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.032 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 21066 2.51 5 N 5928 2.21 5 O 7136 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 34298 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 3904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3904 Classifications: {'peptide': 506} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 484} Chain: "B" Number of atoms: 3904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3904 Classifications: {'peptide': 506} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 484} Chain: "C" Number of atoms: 3904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3904 Classifications: {'peptide': 506} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 484} Chain: "D" Number of atoms: 3904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3904 Classifications: {'peptide': 506} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 484} Chain: "E" Number of atoms: 3904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3904 Classifications: {'peptide': 506} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 484} Chain: "F" Number of atoms: 3904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3904 Classifications: {'peptide': 506} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 484} Chain: "G" Number of atoms: 1605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1605 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 13, 'TRANS': 199} Chain: "H" Number of atoms: 1605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1605 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 13, 'TRANS': 199} Chain: "I" Number of atoms: 1605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1605 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 13, 'TRANS': 199} Chain: "J" Number of atoms: 1605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1605 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 13, 'TRANS': 199} Chain: "K" Number of atoms: 1605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1605 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 13, 'TRANS': 199} Chain: "L" Number of atoms: 1605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1605 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 13, 'TRANS': 199} 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: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 131 Classifications: {'water': 131} Link IDs: {None: 130} Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 126 Classifications: {'water': 126} Link IDs: {None: 125} Chain: "C" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 138 Classifications: {'water': 138} Link IDs: {None: 137} Chain: "D" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Chain: "E" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 122 Classifications: {'water': 122} Link IDs: {None: 121} Chain: "F" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 136 Classifications: {'water': 136} Link IDs: {None: 135} Chain: "G" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "H" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "I" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "J" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "K" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "L" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Time building chain proxies: 19.57, per 1000 atoms: 0.57 Number of scatterers: 34298 At special positions: 0 Unit cell: (151.497, 152.334, 138.105, 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 7136 8.00 N 5928 7.00 C 21066 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: 8.34 Conformation dependent library (CDL) restraints added in 4.1 seconds 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 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: 174 helices and 48 sheets defined 40.8% alpha, 25.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.47 Creating SS restraints... Processing helix chain 'A' and resid 5 through 17 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 removed outlier: 3.502A pdb=" N LYS A 66 " --> pdb=" O GLY A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 99 Processing helix chain 'A' and resid 101 through 119 Processing helix chain 'A' and resid 136 through 154 removed outlier: 3.919A pdb=" N LEU A 140 " --> pdb=" O GLY A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 177 removed outlier: 3.836A pdb=" N MET A 177 " --> pdb=" O TYR A 173 " (cutoff:3.500A) 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: 3.876A 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: 3.896A pdb=" N LEU A 382 " --> pdb=" O HIS A 378 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 383 " --> pdb=" O GLY A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 409 removed outlier: 3.580A pdb=" N ILE A 407 " --> pdb=" O GLY A 403 " (cutoff:3.500A) 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: 3.708A 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 17 Processing helix chain 'B' and resid 20 through 30 Processing helix chain 'B' and resid 34 through 43 Processing helix chain 'B' and resid 63 through 67 Processing helix chain 'B' and resid 95 through 99 Processing helix chain 'B' and resid 101 through 119 Processing helix chain 'B' and resid 136 through 154 removed outlier: 3.916A pdb=" N LEU B 140 " --> pdb=" O GLY B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 177 removed outlier: 3.826A pdb=" N MET B 177 " --> pdb=" O TYR B 173 " (cutoff:3.500A) 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 243 removed outlier: 3.500A pdb=" N ASP B 243 " --> pdb=" O ARG B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 272 Processing helix chain 'B' and resid 282 through 291 removed outlier: 3.799A pdb=" N LEU B 286 " --> pdb=" O ASP B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 294 No H-bonds generated for 'chain 'B' and resid 292 through 294' 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: 3.671A 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 447 through 462 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 17 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 136 through 154 removed outlier: 3.989A pdb=" N LEU C 140 " --> pdb=" O GLY C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 177 removed outlier: 3.880A pdb=" N MET C 177 " --> pdb=" O TYR C 173 " (cutoff:3.500A) 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 243 Processing helix chain 'C' and resid 266 through 272 Processing helix chain 'C' and resid 282 through 291 removed outlier: 3.850A 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 removed outlier: 3.523A pdb=" N GLU C 371 " --> pdb=" O GLY C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 389 removed outlier: 3.678A pdb=" N LEU C 382 " --> pdb=" O HIS C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 409 removed outlier: 3.568A pdb=" N ILE C 407 " --> pdb=" O GLY C 403 " (cutoff:3.500A) 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: 3.860A 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 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 17 Processing helix chain 'D' and resid 20 through 30 Processing helix chain 'D' and resid 34 through 43 Processing helix chain 'D' and resid 63 through 67 Processing helix chain 'D' and resid 95 through 99 Processing helix chain 'D' and resid 101 through 119 Processing helix chain 'D' and resid 136 through 154 removed outlier: 3.968A pdb=" N LEU D 140 " --> pdb=" O GLY D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 177 removed outlier: 3.798A pdb=" N MET D 177 " --> pdb=" O TYR D 173 " (cutoff:3.500A) 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: 3.792A 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 removed outlier: 3.535A pdb=" N GLU D 371 " --> pdb=" O GLY D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 389 removed outlier: 3.657A pdb=" N LEU D 382 " --> pdb=" O HIS D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 409 removed outlier: 3.625A pdb=" N ILE D 407 " --> pdb=" O GLY D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 415 Processing helix chain 'D' and resid 431 through 440 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 17 Processing helix chain 'E' and resid 20 through 30 Processing helix chain 'E' and resid 34 through 43 Processing helix chain 'E' and resid 95 through 99 Processing helix chain 'E' and resid 101 through 119 Processing helix chain 'E' and resid 136 through 154 removed outlier: 4.062A pdb=" N LEU E 140 " --> pdb=" O GLY E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 177 removed outlier: 3.796A pdb=" N MET E 177 " --> pdb=" O TYR E 173 " (cutoff:3.500A) 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: 3.832A pdb=" N LEU E 286 " --> pdb=" O ASP E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 294 No H-bonds generated for 'chain 'E' and resid 292 through 294' 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: 3.646A pdb=" N LEU E 382 " --> pdb=" O HIS E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 409 removed outlier: 3.601A pdb=" N ILE E 407 " --> pdb=" O GLY E 403 " (cutoff:3.500A) Processing helix chain 'E' and resid 411 through 415 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 17 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: 4.117A pdb=" N LEU F 140 " --> pdb=" O GLY F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 177 removed outlier: 3.837A pdb=" N MET F 177 " --> pdb=" O TYR F 173 " (cutoff:3.500A) 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 243 Processing helix chain 'F' and resid 266 through 272 Processing helix chain 'F' and resid 282 through 291 removed outlier: 3.822A 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: 3.907A pdb=" N LEU F 382 " --> pdb=" O HIS F 378 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU F 383 " --> pdb=" O GLY F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 403 through 409 removed outlier: 3.587A pdb=" N ILE F 407 " --> pdb=" O GLY F 403 " (cutoff:3.500A) Processing helix chain 'F' and resid 411 through 415 Processing helix chain 'F' and resid 431 through 440 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 460 through 483 Processing helix chain 'G' and resid 579 through 588 removed outlier: 3.654A pdb=" N LEU G 588 " --> pdb=" O GLU G 584 " (cutoff:3.500A) Processing helix chain 'H' and resid 460 through 483 Processing helix chain 'H' and resid 491 through 495 Processing helix chain 'H' and resid 579 through 588 removed outlier: 3.640A pdb=" N LEU H 588 " --> pdb=" O GLU H 584 " (cutoff:3.500A) Processing helix chain 'I' and resid 460 through 483 Processing helix chain 'I' and resid 491 through 495 Processing helix chain 'I' and resid 579 through 588 removed outlier: 3.656A pdb=" N LEU I 588 " --> pdb=" O GLU I 584 " (cutoff:3.500A) Processing helix chain 'J' and resid 460 through 483 removed outlier: 3.537A pdb=" N ALA J 464 " --> pdb=" O GLU J 460 " (cutoff:3.500A) Processing helix chain 'J' and resid 491 through 495 Processing helix chain 'J' and resid 579 through 588 removed outlier: 3.660A pdb=" N LEU J 588 " --> pdb=" O GLU J 584 " (cutoff:3.500A) Processing helix chain 'K' and resid 460 through 483 removed outlier: 3.536A pdb=" N ALA K 464 " --> pdb=" O GLU K 460 " (cutoff:3.500A) Processing helix chain 'K' and resid 491 through 495 Processing helix chain 'K' and resid 579 through 587 Processing helix chain 'L' and resid 460 through 483 Processing helix chain 'L' and resid 579 through 588 removed outlier: 3.640A pdb=" N LEU L 588 " --> pdb=" O GLU L 584 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 51 removed outlier: 4.406A pdb=" N THR A 76 " --> pdb=" O PHE A 51 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N ILE A 123 " --> pdb=" O THR A 85 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N PHE A 87 " --> pdb=" O ILE A 123 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ILE A 125 " --> pdb=" O PHE A 87 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N PHE A 89 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE A 122 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N VAL A 162 " --> pdb=" O ILE A 122 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLY A 124 " --> pdb=" O VAL A 162 " (cutoff:3.500A) removed outlier: 3.653A 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: 6.457A 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: 4.359A pdb=" N THR A 309 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N VAL A 356 " --> pdb=" O THR A 318 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N GLY A 320 " --> pdb=" O VAL A 356 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N PHE A 358 " --> pdb=" O GLY A 320 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL A 322 " --> pdb=" O PHE A 358 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ASP A 360 " --> pdb=" O VAL A 322 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ASN A 324 " --> pdb=" O ASP A 360 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE A 355 " --> pdb=" O VAL A 394 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N ILE A 396 " --> pdb=" O ILE A 355 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N THR A 357 " --> pdb=" O ILE A 396 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N THR A 398 " --> pdb=" O THR A 357 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N VAL A 359 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LYS A 400 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 296 through 299 removed outlier: 4.359A pdb=" N THR A 309 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N VAL A 356 " --> pdb=" O THR A 318 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N GLY A 320 " --> pdb=" O VAL A 356 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N PHE A 358 " --> pdb=" O GLY A 320 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL A 322 " --> pdb=" O PHE A 358 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ASP A 360 " --> pdb=" O VAL A 322 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ASN A 324 " --> pdb=" O ASP A 360 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE A 355 " --> pdb=" O VAL A 394 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N ILE A 396 " --> pdb=" O ILE A 355 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N THR A 357 " --> pdb=" O ILE A 396 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N THR A 398 " --> pdb=" O THR A 357 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N VAL A 359 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LYS A 400 " --> pdb=" O VAL A 359 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU A 393 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N TYR A 420 " --> pdb=" O LEU A 393 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N THR A 395 " --> pdb=" O TYR A 420 " (cutoff:3.500A) removed outlier: 3.775A 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: 4.404A pdb=" N THR B 76 " --> pdb=" O PHE B 51 " (cutoff:3.500A) removed outlier: 8.686A pdb=" N ILE B 123 " --> pdb=" O THR B 85 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N PHE B 87 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N ILE B 125 " --> pdb=" O PHE B 87 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N PHE B 89 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE B 122 " --> pdb=" O ILE B 160 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N VAL B 162 " --> pdb=" O ILE B 122 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLY B 124 " --> pdb=" O VAL B 162 " (cutoff:3.500A) removed outlier: 3.645A 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: 6.455A 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 296 through 299 removed outlier: 4.357A pdb=" N THR B 309 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N VAL B 356 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLY B 320 " --> pdb=" O VAL B 356 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N PHE B 358 " --> pdb=" O GLY B 320 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL B 322 " --> pdb=" O PHE B 358 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N ASP B 360 " --> pdb=" O VAL B 322 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ASN B 324 " --> pdb=" O ASP B 360 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ILE B 355 " --> pdb=" O VAL B 394 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N ILE B 396 " --> pdb=" O ILE B 355 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N THR B 357 " --> pdb=" O ILE B 396 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N THR B 398 " --> pdb=" O THR B 357 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N VAL B 359 " --> pdb=" O THR B 398 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LYS B 400 " --> pdb=" O VAL B 359 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE B 402 " --> pdb=" O VAL B 361 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 296 through 299 removed outlier: 4.357A pdb=" N THR B 309 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N VAL B 356 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLY B 320 " --> pdb=" O VAL B 356 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N PHE B 358 " --> pdb=" O GLY B 320 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL B 322 " --> pdb=" O PHE B 358 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N ASP B 360 " --> pdb=" O VAL B 322 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ASN B 324 " --> pdb=" O ASP B 360 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ILE B 355 " --> pdb=" O VAL B 394 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N ILE B 396 " --> pdb=" O ILE B 355 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N THR B 357 " --> pdb=" O ILE B 396 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N THR B 398 " --> pdb=" O THR B 357 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N VAL B 359 " --> pdb=" O THR B 398 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LYS B 400 " --> pdb=" O VAL B 359 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE B 402 " --> pdb=" O VAL B 361 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU B 393 " --> pdb=" O LEU B 418 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N TYR B 420 " --> pdb=" O LEU B 393 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N THR B 395 " --> pdb=" O TYR B 420 " (cutoff:3.500A) removed outlier: 3.754A 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: 4.427A pdb=" N THR C 76 " --> pdb=" O PHE C 51 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N ILE C 123 " --> pdb=" O THR C 85 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N PHE C 87 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ILE C 125 " --> pdb=" O PHE C 87 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N PHE C 89 " --> pdb=" O ILE C 125 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE C 122 " --> pdb=" O ILE C 160 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N VAL C 162 " --> pdb=" O ILE C 122 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLY C 124 " --> pdb=" O VAL C 162 " (cutoff:3.500A) removed outlier: 3.704A 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: 6.503A 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: 4.347A pdb=" N THR C 309 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N VAL C 356 " --> pdb=" O THR C 318 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N GLY C 320 " --> pdb=" O VAL C 356 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N PHE C 358 " --> pdb=" O GLY C 320 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL C 322 " --> pdb=" O PHE C 358 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N ASP C 360 " --> pdb=" O VAL C 322 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N ASN C 324 " --> pdb=" O ASP C 360 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE C 355 " --> pdb=" O VAL C 394 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N ILE C 396 " --> pdb=" O ILE C 355 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N THR C 357 " --> pdb=" O ILE C 396 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N THR C 398 " --> pdb=" O THR C 357 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N VAL C 359 " --> pdb=" O THR C 398 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LYS C 400 " --> pdb=" O VAL C 359 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N ALA C 428 " --> pdb=" O ARG C 399 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ALA C 401 " --> pdb=" O ALA C 428 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 296 through 299 removed outlier: 4.347A pdb=" N THR C 309 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N VAL C 356 " --> pdb=" O THR C 318 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N GLY C 320 " --> pdb=" O VAL C 356 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N PHE C 358 " --> pdb=" O GLY C 320 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL C 322 " --> pdb=" O PHE C 358 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N ASP C 360 " --> pdb=" O VAL C 322 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N ASN C 324 " --> pdb=" O ASP C 360 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE C 355 " --> pdb=" O VAL C 394 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N ILE C 396 " --> pdb=" O ILE C 355 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N THR C 357 " --> pdb=" O ILE C 396 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N THR C 398 " --> pdb=" O THR C 357 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N VAL C 359 " --> pdb=" O THR C 398 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LYS C 400 " --> pdb=" O VAL C 359 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU C 393 " --> pdb=" O LEU C 418 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N TYR C 420 " --> pdb=" O LEU C 393 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N THR C 395 " --> pdb=" O TYR C 420 " (cutoff:3.500A) removed outlier: 3.754A 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: 4.421A pdb=" N THR D 76 " --> pdb=" O PHE D 51 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N ILE D 123 " --> pdb=" O THR D 85 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N PHE D 87 " --> pdb=" O ILE D 123 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ILE D 125 " --> pdb=" O PHE D 87 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N PHE D 89 " --> pdb=" O ILE D 125 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE D 122 " --> pdb=" O ILE D 160 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N VAL D 162 " --> pdb=" O ILE D 122 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N GLY D 124 " --> pdb=" O VAL D 162 " (cutoff:3.500A) removed outlier: 3.674A 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: 6.486A 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: 4.400A pdb=" N THR D 309 " --> pdb=" O ILE D 299 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N VAL D 356 " --> pdb=" O THR D 318 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLY D 320 " --> pdb=" O VAL D 356 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N PHE D 358 " --> pdb=" O GLY D 320 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL D 322 " --> pdb=" O PHE D 358 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N ASP D 360 " --> pdb=" O VAL D 322 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ASN D 324 " --> pdb=" O ASP D 360 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE D 355 " --> pdb=" O VAL D 394 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N ILE D 396 " --> pdb=" O ILE D 355 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N THR D 357 " --> pdb=" O ILE D 396 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N THR D 398 " --> pdb=" O THR D 357 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N VAL D 359 " --> pdb=" O THR D 398 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LYS D 400 " --> pdb=" O VAL D 359 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N ALA D 428 " --> pdb=" O ARG D 399 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ALA D 401 " --> pdb=" O ALA D 428 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 296 through 299 removed outlier: 4.400A pdb=" N THR D 309 " --> pdb=" O ILE D 299 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N VAL D 356 " --> pdb=" O THR D 318 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLY D 320 " --> pdb=" O VAL D 356 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N PHE D 358 " --> pdb=" O GLY D 320 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL D 322 " --> pdb=" O PHE D 358 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N ASP D 360 " --> pdb=" O VAL D 322 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ASN D 324 " --> pdb=" O ASP D 360 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE D 355 " --> pdb=" O VAL D 394 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N ILE D 396 " --> pdb=" O ILE D 355 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N THR D 357 " --> pdb=" O ILE D 396 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N THR D 398 " --> pdb=" O THR D 357 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N VAL D 359 " --> pdb=" O THR D 398 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LYS D 400 " --> pdb=" O VAL D 359 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU D 393 " --> pdb=" O LEU D 418 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N TYR D 420 " --> pdb=" O LEU D 393 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N THR D 395 " --> pdb=" O TYR D 420 " (cutoff:3.500A) removed outlier: 3.748A 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: 4.423A pdb=" N THR E 76 " --> pdb=" O PHE E 51 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N ILE E 123 " --> pdb=" O THR E 85 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N PHE E 87 " --> pdb=" O ILE E 123 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N ILE E 125 " --> pdb=" O PHE E 87 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N PHE E 89 " --> pdb=" O ILE E 125 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE E 122 " --> pdb=" O ILE E 160 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N VAL E 162 " --> pdb=" O ILE E 122 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N GLY E 124 " --> pdb=" O VAL E 162 " (cutoff:3.500A) removed outlier: 3.678A 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: 6.467A 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 296 through 299 removed outlier: 4.396A pdb=" N THR E 309 " --> pdb=" O ILE E 299 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N VAL E 356 " --> pdb=" O THR E 318 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N GLY E 320 " --> pdb=" O VAL E 356 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N PHE E 358 " --> pdb=" O GLY E 320 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL E 322 " --> pdb=" O PHE E 358 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ASP E 360 " --> pdb=" O VAL E 322 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ASN E 324 " --> pdb=" O ASP E 360 " (cutoff:3.500A) removed outlier: 6.570A 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: 6.382A pdb=" N THR E 357 " --> pdb=" O ILE E 396 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N THR E 398 " --> pdb=" O THR E 357 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N VAL E 359 " --> pdb=" O THR E 398 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LYS E 400 " --> pdb=" O VAL E 359 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N ALA E 428 " --> pdb=" O ARG E 399 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ALA E 401 " --> pdb=" O ALA E 428 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 296 through 299 removed outlier: 4.396A pdb=" N THR E 309 " --> pdb=" O ILE E 299 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N VAL E 356 " --> pdb=" O THR E 318 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N GLY E 320 " --> pdb=" O VAL E 356 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N PHE E 358 " --> pdb=" O GLY E 320 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL E 322 " --> pdb=" O PHE E 358 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ASP E 360 " --> pdb=" O VAL E 322 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ASN E 324 " --> pdb=" O ASP E 360 " (cutoff:3.500A) removed outlier: 6.570A 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: 6.382A pdb=" N THR E 357 " --> pdb=" O ILE E 396 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N THR E 398 " --> pdb=" O THR E 357 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N VAL E 359 " --> pdb=" O THR E 398 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LYS E 400 " --> pdb=" O VAL E 359 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU E 393 " --> pdb=" O LEU E 418 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N TYR E 420 " --> pdb=" O LEU E 393 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N THR E 395 " --> pdb=" O TYR E 420 " (cutoff:3.500A) removed outlier: 3.772A 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: 4.432A pdb=" N THR F 76 " --> pdb=" O PHE F 51 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N ILE F 123 " --> pdb=" O THR F 85 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N PHE F 87 " --> pdb=" O ILE F 123 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N ILE F 125 " --> pdb=" O PHE F 87 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N PHE F 89 " --> pdb=" O ILE F 125 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE F 122 " --> pdb=" O ILE F 160 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N VAL F 162 " --> pdb=" O ILE F 122 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLY F 124 " --> pdb=" O VAL F 162 " (cutoff:3.500A) removed outlier: 3.657A 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: 6.482A 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: 4.348A pdb=" N THR F 309 " --> pdb=" O ILE F 299 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N VAL F 356 " --> pdb=" O THR F 318 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N GLY F 320 " --> pdb=" O VAL F 356 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N PHE F 358 " --> pdb=" O GLY F 320 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL F 322 " --> pdb=" O PHE F 358 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ASP F 360 " --> pdb=" O VAL F 322 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N ASN F 324 " --> pdb=" O ASP F 360 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE F 355 " --> pdb=" O VAL F 394 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N ILE F 396 " --> pdb=" O ILE F 355 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N THR F 357 " --> pdb=" O ILE F 396 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N THR F 398 " --> pdb=" O THR F 357 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N VAL F 359 " --> pdb=" O THR F 398 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LYS F 400 " --> pdb=" O VAL F 359 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ALA F 428 " --> pdb=" O ARG F 399 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ALA F 401 " --> pdb=" O ALA F 428 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 296 through 299 removed outlier: 4.348A pdb=" N THR F 309 " --> pdb=" O ILE F 299 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N VAL F 356 " --> pdb=" O THR F 318 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N GLY F 320 " --> pdb=" O VAL F 356 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N PHE F 358 " --> pdb=" O GLY F 320 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL F 322 " --> pdb=" O PHE F 358 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ASP F 360 " --> pdb=" O VAL F 322 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N ASN F 324 " --> pdb=" O ASP F 360 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE F 355 " --> pdb=" O VAL F 394 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N ILE F 396 " --> pdb=" O ILE F 355 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N THR F 357 " --> pdb=" O ILE F 396 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N THR F 398 " --> pdb=" O THR F 357 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N VAL F 359 " --> pdb=" O THR F 398 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LYS F 400 " --> pdb=" O VAL F 359 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU F 393 " --> pdb=" O LEU F 418 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N TYR F 420 " --> pdb=" O LEU F 393 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N THR F 395 " --> pdb=" O TYR F 420 " (cutoff:3.500A) removed outlier: 3.760A 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: 3.843A pdb=" N GLN G 551 " --> pdb=" O VAL G 548 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 600 through 602 removed outlier: 3.599A pdb=" N LEU G 664 " --> pdb=" O LEU G 601 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS G 648 " --> pdb=" O GLU G 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 635 through 639 removed outlier: 6.011A pdb=" N ASN G 636 " --> pdb=" O ILE G 628 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ILE G 628 " --> pdb=" O ASN G 636 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU G 638 " --> pdb=" O LEU G 626 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE G 628 " --> pdb=" O LYS G 610 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 619 through 620 removed outlier: 4.293A pdb=" N VAL G 620 " --> pdb=" O GLY G 644 " (cutoff:3.500A) removed outlier: 3.827A 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 removed outlier: 3.869A pdb=" N GLN H 551 " --> pdb=" O VAL H 548 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 600 through 603 removed outlier: 6.884A pdb=" N LEU H 601 " --> pdb=" O ILE H 663 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA H 661 " --> pdb=" O CYS H 603 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 635 through 639 removed outlier: 3.926A pdb=" N ALA H 627 " --> pdb=" O LEU H 638 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N LEU H 626 " --> pdb=" O ILE H 612 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ILE H 612 " --> pdb=" O LEU H 626 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE H 628 " --> pdb=" O LYS H 610 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 619 through 620 removed outlier: 3.526A pdb=" N GLY H 644 " --> pdb=" O VAL H 620 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 500 through 505 removed outlier: 3.872A 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: 7.079A pdb=" N LEU I 601 " --> pdb=" O ILE I 663 " (cutoff:3.500A) removed outlier: 3.673A 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: 3.710A pdb=" N ALA I 627 " --> pdb=" O LEU I 638 " (cutoff:3.500A) removed outlier: 6.585A 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 removed outlier: 3.841A pdb=" N GLN J 551 " --> pdb=" O VAL J 548 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 600 through 602 removed outlier: 3.917A pdb=" N LEU J 664 " --> pdb=" O LEU J 601 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS J 648 " --> pdb=" O GLU J 665 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 635 through 639 removed outlier: 3.852A pdb=" N ALA J 627 " --> pdb=" O LEU J 638 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N LEU J 626 " --> pdb=" O ILE J 612 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ILE J 612 " --> pdb=" O LEU J 626 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE J 628 " --> pdb=" O LYS J 610 " (cutoff:3.500A) removed outlier: 3.643A 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 removed outlier: 3.649A pdb=" N GLY J 644 " --> pdb=" O VAL J 620 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 500 through 505 removed outlier: 3.853A pdb=" N GLN K 551 " --> pdb=" O VAL K 548 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 634 through 639 removed outlier: 6.226A pdb=" N MET K 634 " --> pdb=" O GLU K 630 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N GLU K 630 " --> pdb=" O MET K 634 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N ASN K 636 " --> pdb=" O ILE K 628 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ILE K 628 " --> pdb=" O ASN K 636 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEU K 638 " --> pdb=" O LEU K 626 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N LEU K 626 " --> pdb=" O ILE K 612 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE K 612 " --> pdb=" O LEU K 626 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE K 628 " --> pdb=" O LYS K 610 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 619 through 620 Processing sheet with id=AE8, first strand: chain 'K' and resid 648 through 649 removed outlier: 3.789A pdb=" N LYS K 648 " --> pdb=" O GLU K 665 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'L' and resid 500 through 505 removed outlier: 3.881A pdb=" N GLN L 551 " --> pdb=" O VAL L 548 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 600 through 602 removed outlier: 6.806A 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: 3.880A pdb=" N ALA L 627 " --> pdb=" O LEU L 638 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N LEU L 626 " --> pdb=" O ILE L 612 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ILE L 612 " --> pdb=" O LEU L 626 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE L 628 " --> pdb=" O LYS L 610 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 618 through 620 removed outlier: 3.609A pdb=" N GLN L 618 " --> pdb=" O ILE L 646 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL L 620 " --> pdb=" O GLY L 644 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLY L 644 " --> pdb=" O VAL L 620 " (cutoff:3.500A) 1628 hydrogen bonds defined for protein. 4476 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 16.16 Time building geometry restraints manager: 9.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9531 1.33 - 1.45: 5289 1.45 - 1.58: 18894 1.58 - 1.70: 60 1.70 - 1.82: 276 Bond restraints: 34050 Sorted by residual: bond pdb=" O5A COA F 601 " pdb=" P2A COA F 601 " ideal model delta sigma weight residual 1.491 1.610 -0.119 2.00e-02 2.50e+03 3.55e+01 bond pdb=" O5A COA E 601 " pdb=" P2A COA E 601 " ideal model delta sigma weight residual 1.491 1.610 -0.119 2.00e-02 2.50e+03 3.52e+01 bond pdb=" O5A COA D 601 " pdb=" P2A COA D 601 " ideal model delta sigma weight residual 1.491 1.610 -0.119 2.00e-02 2.50e+03 3.52e+01 bond pdb=" O5A COA C 601 " pdb=" P2A COA C 601 " ideal model delta sigma weight residual 1.491 1.609 -0.118 2.00e-02 2.50e+03 3.50e+01 bond pdb=" O5A COA A 601 " pdb=" P2A COA A 601 " ideal model delta sigma weight residual 1.491 1.609 -0.118 2.00e-02 2.50e+03 3.48e+01 ... (remaining 34045 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.95: 45943 4.95 - 9.90: 82 9.90 - 14.85: 31 14.85 - 19.80: 0 19.80 - 24.75: 6 Bond angle restraints: 46062 Sorted by residual: angle pdb=" P1A COA D 601 " pdb=" O3A COA D 601 " pdb=" P2A COA D 601 " ideal model delta sigma weight residual 135.11 110.36 24.75 3.00e+00 1.11e-01 6.81e+01 angle pdb=" P1A COA B 601 " pdb=" O3A COA B 601 " pdb=" P2A COA B 601 " ideal model delta sigma weight residual 135.11 110.37 24.74 3.00e+00 1.11e-01 6.80e+01 angle pdb=" P1A COA C 601 " pdb=" O3A COA C 601 " pdb=" P2A COA C 601 " ideal model delta sigma weight residual 135.11 110.38 24.73 3.00e+00 1.11e-01 6.80e+01 angle pdb=" P1A COA F 601 " pdb=" O3A COA F 601 " pdb=" P2A COA F 601 " ideal model delta sigma weight residual 135.11 110.40 24.71 3.00e+00 1.11e-01 6.78e+01 angle pdb=" P1A COA A 601 " pdb=" O3A COA A 601 " pdb=" P2A COA A 601 " ideal model delta sigma weight residual 135.11 110.41 24.70 3.00e+00 1.11e-01 6.78e+01 ... (remaining 46057 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.83: 19783 16.83 - 33.66: 800 33.66 - 50.49: 171 50.49 - 67.32: 83 67.32 - 84.15: 13 Dihedral angle restraints: 20850 sinusoidal: 8664 harmonic: 12186 Sorted by residual: dihedral pdb=" CA PHE J 578 " pdb=" C PHE J 578 " pdb=" N THR J 579 " pdb=" CA THR J 579 " ideal model delta harmonic sigma weight residual 180.00 160.37 19.63 0 5.00e+00 4.00e-02 1.54e+01 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 180.00 160.51 19.49 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA ARG D 460 " pdb=" C ARG D 460 " pdb=" N PHE D 461 " pdb=" CA PHE D 461 " ideal model delta harmonic sigma weight residual -180.00 -162.60 -17.40 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 20847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 4538 0.071 - 0.142: 590 0.142 - 0.213: 8 0.213 - 0.284: 6 0.284 - 0.355: 6 Chirality restraints: 5148 Sorted by residual: chirality pdb=" C2B COA B 601 " pdb=" C1B COA B 601 " pdb=" C3B COA B 601 " pdb=" O2B COA B 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.76 0.36 2.00e-01 2.50e+01 3.16e+00 chirality pdb=" C2B COA D 601 " pdb=" C1B COA D 601 " pdb=" C3B COA D 601 " pdb=" O2B COA D 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.76 0.35 2.00e-01 2.50e+01 3.14e+00 chirality pdb=" C2B COA E 601 " pdb=" C1B COA E 601 " pdb=" C3B COA E 601 " pdb=" O2B COA E 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.76 0.35 2.00e-01 2.50e+01 3.14e+00 ... (remaining 5145 not shown) Planarity restraints: 6048 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 365 " -0.019 5.00e-02 4.00e+02 2.88e-02 1.32e+00 pdb=" N PRO B 366 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO B 366 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 366 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN F 500 " 0.018 5.00e-02 4.00e+02 2.77e-02 1.23e+00 pdb=" N PRO F 501 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO F 501 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO F 501 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG K 538 " -0.018 5.00e-02 4.00e+02 2.76e-02 1.21e+00 pdb=" N PRO K 539 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO K 539 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO K 539 " -0.015 5.00e-02 4.00e+02 ... (remaining 6045 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 5313 2.76 - 3.29: 32667 3.29 - 3.83: 61434 3.83 - 4.36: 75543 4.36 - 4.90: 125725 Nonbonded interactions: 300682 Sorted by model distance: nonbonded pdb=" OD2 ASP F 72 " pdb=" OG SER F 101 " model vdw 2.224 3.040 nonbonded pdb=" OD2 ASP H 491 " pdb=" OG SER H 493 " model vdw 2.233 3.040 nonbonded pdb=" OD2 ASP A 72 " pdb=" OG SER A 101 " model vdw 2.234 3.040 nonbonded pdb=" OD2 ASP E 225 " pdb=" O HOH E 701 " model vdw 2.235 3.040 nonbonded pdb=" OD2 ASP D 72 " pdb=" OG SER D 101 " model vdw 2.238 3.040 ... (remaining 300677 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: 0.04 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: 6.990 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: 0.050 Extract box with map and model: 1.380 Check model and map are aligned: 0.260 Set scattering table: 0.310 Process input model: 79.230 Find NCS groups from input model: 1.590 Set up NCS constraints: 0.200 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:11.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 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 : 0.004 0.119 34056 Z= 0.209 Angle : 0.696 24.749 46062 Z= 0.291 Chirality : 0.046 0.355 5148 Planarity : 0.003 0.029 6048 Dihedral : 10.663 84.152 13026 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 0.43 % Allowed : 3.51 % Favored : 96.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.13), residues: 4290 helix: 1.15 (0.13), residues: 1548 sheet: 1.69 (0.18), residues: 750 loop : -0.10 (0.14), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP L 537 HIS 0.008 0.001 HIS B 104 PHE 0.013 0.001 PHE I 578 TYR 0.007 0.001 TYR B 173 ARG 0.002 0.000 ARG D 317 Details of bonding type rmsd hydrogen bonds : bond 0.16924 ( 1551) hydrogen bonds : angle 7.41425 ( 4476) covalent geometry : bond 0.00430 (34050) covalent geometry : angle 0.69633 (46062) Misc. bond : bond 0.00040 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 648 time to evaluate : 3.500 Fit side-chains REVERT: A 6 GLU cc_start: 0.7515 (mt-10) cc_final: 0.7272 (mt-10) REVERT: A 21 GLU cc_start: 0.7724 (mm-30) cc_final: 0.6981 (mp0) REVERT: A 29 LYS cc_start: 0.8196 (tppt) cc_final: 0.7887 (mmmt) REVERT: A 171 ASP cc_start: 0.8675 (m-30) cc_final: 0.8017 (t0) REVERT: A 190 MET cc_start: 0.9030 (mtp) cc_final: 0.8780 (mtp) REVERT: A 267 LYS cc_start: 0.8509 (mmtt) cc_final: 0.8157 (mmtp) REVERT: A 317 ARG cc_start: 0.8428 (mtt-85) cc_final: 0.7993 (mtt-85) REVERT: A 400 LYS cc_start: 0.8406 (mttt) cc_final: 0.8138 (mtmp) REVERT: B 6 GLU cc_start: 0.7485 (mt-10) cc_final: 0.7200 (mt-10) REVERT: B 21 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7385 (mt-10) REVERT: B 22 LYS cc_start: 0.7810 (tttt) cc_final: 0.7523 (ttpt) REVERT: B 171 ASP cc_start: 0.8707 (m-30) cc_final: 0.7998 (t0) REVERT: B 190 MET cc_start: 0.8977 (mtp) cc_final: 0.8712 (mtp) REVERT: B 220 LYS cc_start: 0.8843 (mtpp) cc_final: 0.8601 (mtmm) REVERT: B 289 ARG cc_start: 0.8415 (mmt180) cc_final: 0.8129 (mtp85) REVERT: B 317 ARG cc_start: 0.8517 (mtt-85) cc_final: 0.8005 (mtt-85) REVERT: B 400 LYS cc_start: 0.8439 (mttt) cc_final: 0.8198 (mtmp) REVERT: B 449 LYS cc_start: 0.7778 (tptt) cc_final: 0.7518 (tptm) REVERT: B 502 ARG cc_start: 0.8079 (mtp85) cc_final: 0.7682 (ttm110) REVERT: C 6 GLU cc_start: 0.7421 (mt-10) cc_final: 0.6549 (pm20) REVERT: C 22 LYS cc_start: 0.7819 (ttmm) cc_final: 0.7604 (ttpt) REVERT: C 171 ASP cc_start: 0.8532 (m-30) cc_final: 0.8146 (t0) REVERT: C 266 ASP cc_start: 0.8346 (t0) cc_final: 0.7996 (t0) REVERT: C 289 ARG cc_start: 0.8501 (mtt-85) cc_final: 0.8299 (mtp85) REVERT: C 449 LYS cc_start: 0.7824 (tptt) cc_final: 0.7448 (tptm) REVERT: C 452 GLU cc_start: 0.7703 (tt0) cc_final: 0.7252 (tt0) REVERT: C 453 ARG cc_start: 0.6586 (mtt-85) cc_final: 0.6362 (mmt90) REVERT: C 456 GLU cc_start: 0.7276 (pt0) cc_final: 0.7060 (pt0) REVERT: C 458 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7456 (tp30) REVERT: C 502 ARG cc_start: 0.8065 (mtp85) cc_final: 0.7722 (ttm170) REVERT: D 6 GLU cc_start: 0.7463 (mt-10) cc_final: 0.7200 (mt-10) REVERT: D 21 GLU cc_start: 0.7684 (mm-30) cc_final: 0.6992 (mp0) REVERT: D 22 LYS cc_start: 0.7971 (tttm) cc_final: 0.7657 (ttpt) REVERT: D 171 ASP cc_start: 0.8676 (m-30) cc_final: 0.8080 (t0) REVERT: D 400 LYS cc_start: 0.8347 (mttt) cc_final: 0.8099 (mtmp) REVERT: D 449 LYS cc_start: 0.7796 (tptt) cc_final: 0.7580 (tptm) REVERT: D 453 ARG cc_start: 0.6775 (mtt-85) cc_final: 0.6176 (mtt180) REVERT: D 475 GLU cc_start: 0.8414 (tp30) cc_final: 0.7739 (tp30) REVERT: D 502 ARG cc_start: 0.8102 (mtp85) cc_final: 0.7660 (ttm110) REVERT: E 22 LYS cc_start: 0.7971 (tttt) cc_final: 0.7474 (ttpt) REVERT: E 66 LYS cc_start: 0.8698 (ptpt) cc_final: 0.8497 (ptpp) REVERT: E 67 GLN cc_start: 0.8369 (pt0) cc_final: 0.8169 (pt0) REVERT: E 220 LYS cc_start: 0.8846 (mtpp) cc_final: 0.8591 (mtmm) REVERT: E 268 SER cc_start: 0.9015 (m) cc_final: 0.8795 (t) REVERT: E 400 LYS cc_start: 0.8336 (mttt) cc_final: 0.8077 (mtmp) REVERT: E 452 GLU cc_start: 0.7622 (tt0) cc_final: 0.7147 (tt0) REVERT: F 6 GLU cc_start: 0.7387 (mt-10) cc_final: 0.6527 (pm20) REVERT: F 21 GLU cc_start: 0.7538 (mm-30) cc_final: 0.6814 (mp0) REVERT: F 22 LYS cc_start: 0.7747 (ptmt) cc_final: 0.7182 (pptt) REVERT: F 29 LYS cc_start: 0.8286 (mmtp) cc_final: 0.8072 (mmmt) REVERT: F 30 ARG cc_start: 0.8104 (mtt90) cc_final: 0.7834 (mtm-85) REVERT: F 171 ASP cc_start: 0.8501 (m-30) cc_final: 0.8112 (t0) REVERT: F 189 TYR cc_start: 0.8710 (p90) cc_final: 0.8509 (p90) REVERT: F 266 ASP cc_start: 0.8565 (t0) cc_final: 0.8359 (t0) REVERT: F 400 LYS cc_start: 0.8343 (mttt) cc_final: 0.8117 (mtmp) REVERT: F 453 ARG cc_start: 0.7365 (mmt180) cc_final: 0.6417 (mtt180) REVERT: F 458 GLU cc_start: 0.7603 (tt0) cc_final: 0.7162 (tp30) REVERT: F 502 ARG cc_start: 0.8081 (mtp85) cc_final: 0.7706 (ttm170) REVERT: G 483 ARG cc_start: 0.8237 (mtp85) cc_final: 0.7931 (mmm160) REVERT: G 490 ARG cc_start: 0.8364 (ptp90) cc_final: 0.8006 (ptp-170) REVERT: G 635 GLU cc_start: 0.6127 (mt-10) cc_final: 0.4682 (pt0) REVERT: H 483 ARG cc_start: 0.8240 (mtp85) cc_final: 0.7823 (mmm160) REVERT: H 490 ARG cc_start: 0.8288 (ptp90) cc_final: 0.8049 (ptp-170) REVERT: H 520 ASP cc_start: 0.7002 (p0) cc_final: 0.6637 (p0) REVERT: H 534 ARG cc_start: 0.8087 (ttm110) cc_final: 0.7724 (mtp85) REVERT: H 580 ARG cc_start: 0.8602 (mmm-85) cc_final: 0.8179 (mmt-90) REVERT: H 630 GLU cc_start: 0.7022 (tt0) cc_final: 0.6733 (tt0) REVERT: H 635 GLU cc_start: 0.6065 (mt-10) cc_final: 0.5308 (pt0) REVERT: I 483 ARG cc_start: 0.8088 (mtp85) cc_final: 0.7588 (mmm160) REVERT: I 489 MET cc_start: 0.8883 (ttp) cc_final: 0.8672 (ttp) REVERT: I 630 GLU cc_start: 0.7009 (tt0) cc_final: 0.6676 (tt0) REVERT: J 483 ARG cc_start: 0.8330 (mtt-85) cc_final: 0.8025 (mmm160) REVERT: J 490 ARG cc_start: 0.8322 (ptp90) cc_final: 0.7965 (ptp-170) REVERT: K 483 ARG cc_start: 0.8218 (mtt180) cc_final: 0.7818 (mmm160) REVERT: K 490 ARG cc_start: 0.8295 (ptp90) cc_final: 0.7979 (ptp-170) REVERT: K 534 ARG cc_start: 0.7760 (mtt90) cc_final: 0.7409 (ttm110) REVERT: K 613 MET cc_start: 0.5061 (mpp) cc_final: 0.2645 (tmt) REVERT: K 635 GLU cc_start: 0.5736 (mt-10) cc_final: 0.4529 (pt0) REVERT: K 665 GLU cc_start: 0.5004 (mt-10) cc_final: 0.4591 (mm-30) REVERT: L 483 ARG cc_start: 0.8162 (mtp85) cc_final: 0.7619 (mmm160) REVERT: L 632 MET cc_start: 0.6827 (mtm) cc_final: 0.6290 (mtm) REVERT: L 635 GLU cc_start: 0.6008 (mt-10) cc_final: 0.4863 (pt0) outliers start: 15 outliers final: 6 residues processed: 660 average time/residue: 1.9590 time to fit residues: 1482.3561 Evaluate side-chains 525 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 519 time to evaluate : 3.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 143 HIS Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 143 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 359 optimal weight: 10.0000 chunk 322 optimal weight: 0.9990 chunk 179 optimal weight: 0.4980 chunk 110 optimal weight: 1.9990 chunk 217 optimal weight: 0.9990 chunk 172 optimal weight: 2.9990 chunk 333 optimal weight: 0.9980 chunk 129 optimal weight: 0.9980 chunk 203 optimal weight: 1.9990 chunk 248 optimal weight: 1.9990 chunk 386 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 278 ASN G 479 ASN G 556 GLN H 479 ASN H 556 GLN I 476 HIS I 479 ASN I 556 GLN J 479 ASN J 556 GLN K 479 ASN K 556 GLN L 556 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.138947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.086566 restraints weight = 34236.900| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.80 r_work: 0.2935 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 34056 Z= 0.127 Angle : 0.497 5.464 46062 Z= 0.267 Chirality : 0.045 0.154 5148 Planarity : 0.004 0.032 6048 Dihedral : 8.266 57.979 5158 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.00 % Allowed : 8.41 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.13), residues: 4290 helix: 1.45 (0.14), residues: 1500 sheet: 1.41 (0.17), residues: 792 loop : 0.18 (0.14), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 544 HIS 0.009 0.001 HIS C 104 PHE 0.012 0.001 PHE E 384 TYR 0.008 0.001 TYR F 173 ARG 0.009 0.000 ARG D 148 Details of bonding type rmsd hydrogen bonds : bond 0.04550 ( 1551) hydrogen bonds : angle 5.53541 ( 4476) covalent geometry : bond 0.00284 (34050) covalent geometry : angle 0.49707 (46062) Misc. bond : bond 0.00007 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 502 time to evaluate : 3.653 Fit side-chains REVERT: A 21 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7114 (mp0) REVERT: A 29 LYS cc_start: 0.8289 (tppt) cc_final: 0.7938 (mmmt) REVERT: A 171 ASP cc_start: 0.8821 (m-30) cc_final: 0.8242 (t0) REVERT: A 257 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.8022 (tt0) REVERT: A 317 ARG cc_start: 0.8441 (mtt-85) cc_final: 0.8048 (mtp85) REVERT: A 400 LYS cc_start: 0.8303 (mttt) cc_final: 0.8094 (mtmp) REVERT: B 21 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7458 (mt-10) REVERT: B 22 LYS cc_start: 0.7939 (tttt) cc_final: 0.7446 (ttpt) REVERT: B 30 ARG cc_start: 0.8119 (mtt90) cc_final: 0.7837 (mtm-85) REVERT: B 171 ASP cc_start: 0.8773 (m-30) cc_final: 0.8136 (t0) REVERT: B 220 LYS cc_start: 0.8879 (mtpp) cc_final: 0.8591 (mtmm) REVERT: B 257 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.8011 (tt0) REVERT: B 266 ASP cc_start: 0.8258 (t70) cc_final: 0.7799 (t0) REVERT: B 289 ARG cc_start: 0.8707 (mmt180) cc_final: 0.8404 (mtp85) REVERT: B 317 ARG cc_start: 0.8474 (mtt-85) cc_final: 0.8206 (mtt-85) REVERT: B 400 LYS cc_start: 0.8426 (mttt) cc_final: 0.8193 (mtmp) REVERT: B 430 MET cc_start: 0.9187 (ptp) cc_final: 0.8959 (ptm) REVERT: B 502 ARG cc_start: 0.8487 (mtp85) cc_final: 0.7986 (ttm110) REVERT: C 6 GLU cc_start: 0.7595 (mt-10) cc_final: 0.6492 (pm20) REVERT: C 9 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7447 (mm-30) REVERT: C 22 LYS cc_start: 0.7881 (ttmm) cc_final: 0.7632 (ttpt) REVERT: C 49 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8449 (tt0) REVERT: C 171 ASP cc_start: 0.8604 (m-30) cc_final: 0.8283 (t0) REVERT: C 257 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7923 (tm-30) REVERT: C 266 ASP cc_start: 0.8555 (t0) cc_final: 0.8055 (t0) REVERT: C 449 LYS cc_start: 0.7611 (tptt) cc_final: 0.7307 (tptm) REVERT: C 452 GLU cc_start: 0.7848 (tt0) cc_final: 0.7354 (tt0) REVERT: C 453 ARG cc_start: 0.6576 (mtt-85) cc_final: 0.6049 (mtt90) REVERT: C 455 LYS cc_start: 0.7822 (OUTLIER) cc_final: 0.7136 (tmmm) REVERT: C 456 GLU cc_start: 0.7476 (pt0) cc_final: 0.7223 (pt0) REVERT: C 458 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7278 (tp30) REVERT: C 475 GLU cc_start: 0.8498 (tp30) cc_final: 0.8114 (tp30) REVERT: C 497 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7664 (pt0) REVERT: C 502 ARG cc_start: 0.8511 (mtp85) cc_final: 0.7996 (ttm170) REVERT: D 21 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7087 (mp0) REVERT: D 22 LYS cc_start: 0.8066 (tttm) cc_final: 0.7731 (ttpt) REVERT: D 148 ARG cc_start: 0.8833 (OUTLIER) cc_final: 0.8265 (ttm170) REVERT: D 171 ASP cc_start: 0.8758 (m-30) cc_final: 0.8128 (t0) REVERT: D 257 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7915 (tm-30) REVERT: D 400 LYS cc_start: 0.8260 (mttt) cc_final: 0.8022 (mtmp) REVERT: D 453 ARG cc_start: 0.6876 (mtt-85) cc_final: 0.6232 (mtt180) REVERT: D 475 GLU cc_start: 0.8478 (tp30) cc_final: 0.7933 (tp30) REVERT: D 502 ARG cc_start: 0.8507 (mtp85) cc_final: 0.8000 (ttm110) REVERT: E 22 LYS cc_start: 0.8075 (tttt) cc_final: 0.7567 (ttpt) REVERT: E 67 GLN cc_start: 0.8390 (pt0) cc_final: 0.8172 (pt0) REVERT: E 171 ASP cc_start: 0.8802 (OUTLIER) cc_final: 0.8214 (t0) REVERT: E 220 LYS cc_start: 0.8938 (mtpp) cc_final: 0.8674 (mtmm) REVERT: E 266 ASP cc_start: 0.8627 (t0) cc_final: 0.8398 (t0) REVERT: E 285 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7710 (tt0) REVERT: E 400 LYS cc_start: 0.8276 (mttt) cc_final: 0.8026 (mtmp) REVERT: F 6 GLU cc_start: 0.7585 (mt-10) cc_final: 0.6451 (pm20) REVERT: F 9 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7405 (mm-30) REVERT: F 21 GLU cc_start: 0.7714 (mm-30) cc_final: 0.6955 (mp0) REVERT: F 22 LYS cc_start: 0.7842 (ptmt) cc_final: 0.7255 (pptt) REVERT: F 29 LYS cc_start: 0.8436 (mmtp) cc_final: 0.8131 (mmmt) REVERT: F 30 ARG cc_start: 0.8112 (mtt90) cc_final: 0.7787 (mtm-85) REVERT: F 49 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8538 (tt0) REVERT: F 171 ASP cc_start: 0.8619 (m-30) cc_final: 0.8285 (t0) REVERT: F 189 TYR cc_start: 0.8739 (p90) cc_final: 0.8432 (p90) REVERT: F 257 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7832 (tm-30) REVERT: F 453 ARG cc_start: 0.7211 (mmt180) cc_final: 0.6262 (mtt180) REVERT: F 458 GLU cc_start: 0.7679 (tt0) cc_final: 0.7175 (tp30) REVERT: F 502 ARG cc_start: 0.8492 (mtp85) cc_final: 0.7962 (ttm170) REVERT: G 483 ARG cc_start: 0.8141 (mtp85) cc_final: 0.7156 (mmm160) REVERT: G 490 ARG cc_start: 0.8215 (ptp90) cc_final: 0.7968 (ptp-170) REVERT: G 534 ARG cc_start: 0.7704 (mtp85) cc_final: 0.7043 (mtp-110) REVERT: G 630 GLU cc_start: 0.6471 (OUTLIER) cc_final: 0.4990 (tm-30) REVERT: G 635 GLU cc_start: 0.5446 (mt-10) cc_final: 0.4489 (pt0) REVERT: H 483 ARG cc_start: 0.8074 (mtp85) cc_final: 0.6987 (mmm160) REVERT: H 490 ARG cc_start: 0.8192 (ptp90) cc_final: 0.7881 (ptp-170) REVERT: H 517 ASP cc_start: 0.6887 (p0) cc_final: 0.6407 (p0) REVERT: H 521 LEU cc_start: 0.7991 (tp) cc_final: 0.7790 (tp) REVERT: H 534 ARG cc_start: 0.8141 (ttm110) cc_final: 0.7884 (ttp-110) REVERT: H 580 ARG cc_start: 0.8295 (mmm-85) cc_final: 0.7707 (mmt-90) REVERT: H 630 GLU cc_start: 0.6440 (tt0) cc_final: 0.6201 (tt0) REVERT: H 635 GLU cc_start: 0.5876 (mt-10) cc_final: 0.5286 (pt0) REVERT: I 483 ARG cc_start: 0.8053 (mtp85) cc_final: 0.7052 (mmm160) REVERT: I 520 ASP cc_start: 0.5758 (m-30) cc_final: 0.5419 (m-30) REVERT: I 521 LEU cc_start: 0.7901 (mt) cc_final: 0.7601 (tp) REVERT: I 527 ASP cc_start: 0.7995 (OUTLIER) cc_final: 0.7583 (p0) REVERT: I 534 ARG cc_start: 0.7939 (ttm170) cc_final: 0.7154 (mtp85) REVERT: I 630 GLU cc_start: 0.6420 (tt0) cc_final: 0.6114 (tt0) REVERT: J 483 ARG cc_start: 0.8328 (mtt-85) cc_final: 0.7343 (mmm160) REVERT: J 490 ARG cc_start: 0.8196 (ptp90) cc_final: 0.7747 (ptp-170) REVERT: J 630 GLU cc_start: 0.6449 (OUTLIER) cc_final: 0.4977 (tm-30) REVERT: K 483 ARG cc_start: 0.8347 (mtt180) cc_final: 0.7219 (mmm160) REVERT: K 490 ARG cc_start: 0.8165 (ptp90) cc_final: 0.7745 (ptp-170) REVERT: K 534 ARG cc_start: 0.7534 (mtt90) cc_final: 0.7020 (ttm110) REVERT: K 613 MET cc_start: 0.4643 (mpp) cc_final: 0.2544 (tmt) REVERT: K 630 GLU cc_start: 0.6624 (OUTLIER) cc_final: 0.5531 (tm-30) REVERT: K 635 GLU cc_start: 0.5610 (mt-10) cc_final: 0.4418 (pt0) REVERT: K 665 GLU cc_start: 0.4658 (mt-10) cc_final: 0.4372 (mm-30) REVERT: L 483 ARG cc_start: 0.8109 (mtp85) cc_final: 0.7067 (mmm160) REVERT: L 534 ARG cc_start: 0.8012 (ttm-80) cc_final: 0.7746 (ttm-80) REVERT: L 630 GLU cc_start: 0.6055 (OUTLIER) cc_final: 0.5185 (tm-30) REVERT: L 635 GLU cc_start: 0.5528 (mt-10) cc_final: 0.4621 (pt0) outliers start: 69 outliers final: 22 residues processed: 533 average time/residue: 2.0143 time to fit residues: 1237.6341 Evaluate side-chains 519 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 480 time to evaluate : 4.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 499 GLU Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 143 HIS Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain C residue 497 GLU Chi-restraints excluded: chain D residue 148 ARG Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 285 GLU Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 143 HIS Chi-restraints excluded: chain F residue 257 GLU Chi-restraints excluded: chain G residue 552 SER Chi-restraints excluded: chain G residue 630 GLU Chi-restraints excluded: chain H residue 552 SER Chi-restraints excluded: chain I residue 527 ASP Chi-restraints excluded: chain I residue 552 SER Chi-restraints excluded: chain J residue 552 SER Chi-restraints excluded: chain J residue 630 GLU Chi-restraints excluded: chain K residue 509 ARG Chi-restraints excluded: chain K residue 630 GLU Chi-restraints excluded: chain L residue 482 LYS Chi-restraints excluded: chain L residue 630 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 310 optimal weight: 3.9990 chunk 308 optimal weight: 0.2980 chunk 9 optimal weight: 0.9990 chunk 369 optimal weight: 7.9990 chunk 115 optimal weight: 0.3980 chunk 396 optimal weight: 0.9990 chunk 299 optimal weight: 0.7980 chunk 377 optimal weight: 5.9990 chunk 323 optimal weight: 0.7980 chunk 373 optimal weight: 6.9990 chunk 268 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 276 ASN E 276 ASN F 278 ASN G 479 ASN G 556 GLN H 479 ASN I 479 ASN I 556 GLN J 479 ASN K 476 HIS K 479 ASN K 556 GLN L 556 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.140013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.087761 restraints weight = 34468.451| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 1.80 r_work: 0.2958 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 34056 Z= 0.104 Angle : 0.465 5.573 46062 Z= 0.249 Chirality : 0.044 0.144 5148 Planarity : 0.004 0.030 6048 Dihedral : 7.669 55.618 5158 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.77 % Allowed : 9.42 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.13), residues: 4290 helix: 1.50 (0.14), residues: 1512 sheet: 1.33 (0.17), residues: 792 loop : 0.17 (0.14), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 544 HIS 0.007 0.001 HIS E 104 PHE 0.010 0.001 PHE B 351 TYR 0.008 0.001 TYR F 173 ARG 0.007 0.000 ARG H 499 Details of bonding type rmsd hydrogen bonds : bond 0.03939 ( 1551) hydrogen bonds : angle 5.18799 ( 4476) covalent geometry : bond 0.00227 (34050) covalent geometry : angle 0.46483 (46062) Misc. bond : bond 0.00007 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 494 time to evaluate : 3.581 Fit side-chains REVERT: A 21 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7102 (mp0) REVERT: A 29 LYS cc_start: 0.8306 (tppt) cc_final: 0.7973 (mmmt) REVERT: A 171 ASP cc_start: 0.8838 (m-30) cc_final: 0.8295 (t0) REVERT: A 257 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.8030 (tt0) REVERT: A 317 ARG cc_start: 0.8458 (mtt-85) cc_final: 0.8089 (mtp85) REVERT: A 478 MET cc_start: 0.9157 (mmt) cc_final: 0.8933 (mmt) REVERT: B 21 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7186 (mp0) REVERT: B 22 LYS cc_start: 0.7898 (tttt) cc_final: 0.7412 (ttpt) REVERT: B 30 ARG cc_start: 0.8101 (mtt90) cc_final: 0.7837 (mtm-85) REVERT: B 171 ASP cc_start: 0.8784 (m-30) cc_final: 0.8172 (t0) REVERT: B 220 LYS cc_start: 0.8873 (mtpp) cc_final: 0.8588 (mtmm) REVERT: B 257 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.8050 (tt0) REVERT: B 266 ASP cc_start: 0.8234 (t70) cc_final: 0.7745 (t0) REVERT: B 289 ARG cc_start: 0.8690 (mmt180) cc_final: 0.8481 (mtp85) REVERT: B 317 ARG cc_start: 0.8541 (mtt-85) cc_final: 0.7899 (mtm180) REVERT: B 502 ARG cc_start: 0.8440 (mtp85) cc_final: 0.7968 (ttm110) REVERT: C 9 GLU cc_start: 0.7660 (mm-30) cc_final: 0.7177 (mm-30) REVERT: C 22 LYS cc_start: 0.7916 (ttmm) cc_final: 0.7669 (ttpt) REVERT: C 49 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8522 (tt0) REVERT: C 171 ASP cc_start: 0.8613 (m-30) cc_final: 0.8337 (t0) REVERT: C 189 TYR cc_start: 0.8757 (p90) cc_final: 0.8403 (p90) REVERT: C 257 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7914 (tm-30) REVERT: C 266 ASP cc_start: 0.8592 (t0) cc_final: 0.8264 (t0) REVERT: C 449 LYS cc_start: 0.7606 (tptt) cc_final: 0.7296 (tptm) REVERT: C 452 GLU cc_start: 0.7842 (tt0) cc_final: 0.7356 (tt0) REVERT: C 453 ARG cc_start: 0.6570 (mtt-85) cc_final: 0.6040 (mtt90) REVERT: C 455 LYS cc_start: 0.7823 (OUTLIER) cc_final: 0.7138 (tmmm) REVERT: C 456 GLU cc_start: 0.7448 (pt0) cc_final: 0.7203 (pt0) REVERT: C 458 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7311 (tp30) REVERT: C 475 GLU cc_start: 0.8459 (tp30) cc_final: 0.8083 (tp30) REVERT: C 497 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7601 (pt0) REVERT: C 502 ARG cc_start: 0.8504 (mtp85) cc_final: 0.8000 (ttm170) REVERT: D 21 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7082 (mp0) REVERT: D 22 LYS cc_start: 0.8084 (tttm) cc_final: 0.7759 (ttpt) REVERT: D 66 LYS cc_start: 0.8417 (mtpt) cc_final: 0.8199 (mtmm) REVERT: D 171 ASP cc_start: 0.8769 (m-30) cc_final: 0.8168 (t0) REVERT: D 453 ARG cc_start: 0.6831 (mtt-85) cc_final: 0.6278 (mtt180) REVERT: D 475 GLU cc_start: 0.8489 (tp30) cc_final: 0.7953 (tp30) REVERT: D 502 ARG cc_start: 0.8514 (mtp85) cc_final: 0.8020 (ttm110) REVERT: E 22 LYS cc_start: 0.8072 (tttt) cc_final: 0.7564 (ttpt) REVERT: E 29 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8173 (mtmt) REVERT: E 171 ASP cc_start: 0.8831 (OUTLIER) cc_final: 0.8259 (t0) REVERT: E 220 LYS cc_start: 0.8916 (mtpp) cc_final: 0.8643 (mtmm) REVERT: E 400 LYS cc_start: 0.8231 (mttt) cc_final: 0.8023 (mtmp) REVERT: F 9 GLU cc_start: 0.7649 (mm-30) cc_final: 0.7170 (mm-30) REVERT: F 21 GLU cc_start: 0.7726 (mm-30) cc_final: 0.6984 (mp0) REVERT: F 22 LYS cc_start: 0.7855 (ptmt) cc_final: 0.7270 (pptt) REVERT: F 29 LYS cc_start: 0.8406 (mmtp) cc_final: 0.8118 (mmmt) REVERT: F 30 ARG cc_start: 0.8102 (mtt90) cc_final: 0.7865 (mtm-85) REVERT: F 49 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8516 (tt0) REVERT: F 171 ASP cc_start: 0.8663 (m-30) cc_final: 0.8372 (t0) REVERT: F 189 TYR cc_start: 0.8770 (p90) cc_final: 0.8421 (p90) REVERT: F 453 ARG cc_start: 0.7241 (mmt180) cc_final: 0.6329 (mtt180) REVERT: F 458 GLU cc_start: 0.7671 (tt0) cc_final: 0.7122 (tp30) REVERT: G 483 ARG cc_start: 0.8164 (mtp85) cc_final: 0.7191 (mmm160) REVERT: G 489 MET cc_start: 0.8843 (ttp) cc_final: 0.8528 (ttp) REVERT: G 490 ARG cc_start: 0.8199 (ptp90) cc_final: 0.7941 (ptp-170) REVERT: G 527 ASP cc_start: 0.7899 (OUTLIER) cc_final: 0.7525 (p0) REVERT: G 534 ARG cc_start: 0.7432 (mtp85) cc_final: 0.7177 (mtp180) REVERT: G 613 MET cc_start: 0.4920 (pmm) cc_final: 0.2267 (tmt) REVERT: G 630 GLU cc_start: 0.6453 (OUTLIER) cc_final: 0.4969 (tm-30) REVERT: G 635 GLU cc_start: 0.5473 (mt-10) cc_final: 0.4473 (pt0) REVERT: H 483 ARG cc_start: 0.8087 (mtp85) cc_final: 0.7059 (mmm160) REVERT: H 490 ARG cc_start: 0.8137 (ptp90) cc_final: 0.7901 (ptp-170) REVERT: H 520 ASP cc_start: 0.6169 (p0) cc_final: 0.5857 (p0) REVERT: H 534 ARG cc_start: 0.8091 (ttm110) cc_final: 0.7409 (mtp85) REVERT: H 580 ARG cc_start: 0.8280 (mmm-85) cc_final: 0.7696 (mmt-90) REVERT: H 630 GLU cc_start: 0.6407 (tt0) cc_final: 0.6107 (tt0) REVERT: H 635 GLU cc_start: 0.5872 (mt-10) cc_final: 0.5251 (pt0) REVERT: I 483 ARG cc_start: 0.8050 (mtp85) cc_final: 0.7103 (mmm160) REVERT: I 521 LEU cc_start: 0.8046 (mt) cc_final: 0.7687 (tp) REVERT: I 527 ASP cc_start: 0.8043 (OUTLIER) cc_final: 0.7612 (p0) REVERT: I 534 ARG cc_start: 0.7952 (ttm170) cc_final: 0.7739 (ttm-80) REVERT: I 630 GLU cc_start: 0.6444 (tt0) cc_final: 0.6183 (tt0) REVERT: J 483 ARG cc_start: 0.8308 (mtt-85) cc_final: 0.7301 (mmm160) REVERT: J 490 ARG cc_start: 0.8169 (ptp90) cc_final: 0.7944 (ptp-170) REVERT: J 534 ARG cc_start: 0.7930 (mtp85) cc_final: 0.7603 (mtt-85) REVERT: J 630 GLU cc_start: 0.6541 (OUTLIER) cc_final: 0.5057 (tm-30) REVERT: K 483 ARG cc_start: 0.8360 (mtt180) cc_final: 0.7268 (mmm160) REVERT: K 490 ARG cc_start: 0.8170 (ptp90) cc_final: 0.7785 (ptp-170) REVERT: K 613 MET cc_start: 0.4421 (mpp) cc_final: 0.2538 (tmt) REVERT: K 630 GLU cc_start: 0.6596 (OUTLIER) cc_final: 0.5465 (tm-30) REVERT: K 635 GLU cc_start: 0.5672 (mt-10) cc_final: 0.4520 (pt0) REVERT: K 665 GLU cc_start: 0.4579 (mt-10) cc_final: 0.4324 (mm-30) REVERT: L 483 ARG cc_start: 0.8086 (mtp85) cc_final: 0.7088 (mmm160) REVERT: L 534 ARG cc_start: 0.8016 (ttm-80) cc_final: 0.7694 (ttm-80) REVERT: L 630 GLU cc_start: 0.6097 (OUTLIER) cc_final: 0.5260 (tm-30) REVERT: L 635 GLU cc_start: 0.5548 (mt-10) cc_final: 0.4617 (pt0) outliers start: 61 outliers final: 21 residues processed: 520 average time/residue: 2.0216 time to fit residues: 1208.2476 Evaluate side-chains 512 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 476 time to evaluate : 4.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 499 GLU Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 143 HIS Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain C residue 497 GLU Chi-restraints excluded: chain E residue 29 LYS Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 268 SER Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 143 HIS Chi-restraints excluded: chain G residue 527 ASP Chi-restraints excluded: chain G residue 630 GLU Chi-restraints excluded: chain H residue 552 SER Chi-restraints excluded: chain I residue 527 ASP Chi-restraints excluded: chain I residue 552 SER Chi-restraints excluded: chain J residue 552 SER Chi-restraints excluded: chain J residue 630 GLU Chi-restraints excluded: chain K residue 552 SER Chi-restraints excluded: chain K residue 591 VAL Chi-restraints excluded: chain K residue 630 GLU Chi-restraints excluded: chain L residue 552 SER Chi-restraints excluded: chain L residue 630 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 57 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 172 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 117 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 240 optimal weight: 2.9990 chunk 352 optimal weight: 6.9990 chunk 388 optimal weight: 4.9990 chunk 208 optimal weight: 4.9990 chunk 228 optimal weight: 0.9980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 67 GLN F 278 ASN G 479 ASN G 556 GLN H 479 ASN H 556 GLN I 556 GLN J 479 ASN J 556 GLN K 479 ASN K 556 GLN L 556 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.137302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.083105 restraints weight = 34139.085| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 1.84 r_work: 0.2841 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 34056 Z= 0.156 Angle : 0.509 6.585 46062 Z= 0.274 Chirality : 0.046 0.151 5148 Planarity : 0.004 0.033 6048 Dihedral : 7.658 55.569 5158 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.12 % Allowed : 9.68 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.13), residues: 4290 helix: 1.40 (0.13), residues: 1506 sheet: 1.28 (0.17), residues: 792 loop : 0.08 (0.14), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 537 HIS 0.010 0.001 HIS B 104 PHE 0.012 0.001 PHE D 384 TYR 0.011 0.002 TYR B 173 ARG 0.006 0.000 ARG A 453 Details of bonding type rmsd hydrogen bonds : bond 0.04684 ( 1551) hydrogen bonds : angle 5.21662 ( 4476) covalent geometry : bond 0.00362 (34050) covalent geometry : angle 0.50855 (46062) Misc. bond : bond 0.00003 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 487 time to evaluate : 3.532 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7093 (mp0) REVERT: A 29 LYS cc_start: 0.8282 (tppt) cc_final: 0.7913 (mmmt) REVERT: A 49 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8497 (tt0) REVERT: A 171 ASP cc_start: 0.8831 (m-30) cc_final: 0.8300 (t0) REVERT: A 317 ARG cc_start: 0.8360 (mtt-85) cc_final: 0.7951 (mtp85) REVERT: B 21 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7052 (mp0) REVERT: B 22 LYS cc_start: 0.7844 (tttt) cc_final: 0.7332 (ttpt) REVERT: B 30 ARG cc_start: 0.8067 (mtt90) cc_final: 0.7783 (mtm-85) REVERT: B 49 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8508 (tt0) REVERT: B 171 ASP cc_start: 0.8770 (m-30) cc_final: 0.8150 (t0) REVERT: B 220 LYS cc_start: 0.8817 (mtpp) cc_final: 0.8509 (mtmm) REVERT: B 257 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.8002 (tt0) REVERT: B 266 ASP cc_start: 0.8307 (t70) cc_final: 0.7758 (t0) REVERT: B 289 ARG cc_start: 0.8658 (mmt180) cc_final: 0.8382 (mtp85) REVERT: B 317 ARG cc_start: 0.8430 (mtt-85) cc_final: 0.7740 (mtm180) REVERT: B 502 ARG cc_start: 0.8465 (mtp85) cc_final: 0.7930 (ttm110) REVERT: C 9 GLU cc_start: 0.7539 (mm-30) cc_final: 0.7036 (mm-30) REVERT: C 22 LYS cc_start: 0.7846 (ttmm) cc_final: 0.7573 (ttpt) REVERT: C 49 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8488 (tt0) REVERT: C 171 ASP cc_start: 0.8588 (m-30) cc_final: 0.8324 (t0) REVERT: C 257 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7885 (tm-30) REVERT: C 266 ASP cc_start: 0.8577 (t0) cc_final: 0.8207 (t0) REVERT: C 449 LYS cc_start: 0.7485 (tptt) cc_final: 0.7234 (tptm) REVERT: C 452 GLU cc_start: 0.7759 (tt0) cc_final: 0.7256 (tt0) REVERT: C 453 ARG cc_start: 0.6331 (mtt-85) cc_final: 0.5839 (mtt90) REVERT: C 455 LYS cc_start: 0.7637 (OUTLIER) cc_final: 0.6973 (tmmm) REVERT: C 456 GLU cc_start: 0.7396 (pt0) cc_final: 0.7158 (pt0) REVERT: C 458 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7146 (tp30) REVERT: C 475 GLU cc_start: 0.8392 (tp30) cc_final: 0.7957 (tp30) REVERT: C 497 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7587 (pt0) REVERT: C 502 ARG cc_start: 0.8537 (mtp85) cc_final: 0.7972 (ttm170) REVERT: D 21 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7085 (mp0) REVERT: D 22 LYS cc_start: 0.8143 (tttm) cc_final: 0.7765 (ttpt) REVERT: D 66 LYS cc_start: 0.8316 (mtpt) cc_final: 0.8101 (mtmm) REVERT: D 117 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8138 (ttmm) REVERT: D 171 ASP cc_start: 0.8767 (m-30) cc_final: 0.8213 (t0) REVERT: D 257 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7624 (tm-30) REVERT: D 285 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7946 (tm-30) REVERT: D 452 GLU cc_start: 0.7996 (tt0) cc_final: 0.7731 (pt0) REVERT: D 453 ARG cc_start: 0.6694 (mtt-85) cc_final: 0.6029 (mtt180) REVERT: D 475 GLU cc_start: 0.8441 (tp30) cc_final: 0.7870 (tp30) REVERT: D 497 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.8046 (mt-10) REVERT: E 22 LYS cc_start: 0.8031 (tttt) cc_final: 0.7494 (ttpt) REVERT: E 29 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8151 (mtmt) REVERT: E 143 HIS cc_start: 0.8488 (OUTLIER) cc_final: 0.8047 (m170) REVERT: E 171 ASP cc_start: 0.8842 (OUTLIER) cc_final: 0.8280 (t0) REVERT: E 220 LYS cc_start: 0.8888 (mtpp) cc_final: 0.8608 (mtmm) REVERT: E 257 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7597 (tm-30) REVERT: E 400 LYS cc_start: 0.8186 (mttt) cc_final: 0.7912 (mtmp) REVERT: E 498 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.8043 (ttp) REVERT: F 9 GLU cc_start: 0.7418 (mm-30) cc_final: 0.6925 (mm-30) REVERT: F 21 GLU cc_start: 0.7656 (mm-30) cc_final: 0.6861 (mp0) REVERT: F 22 LYS cc_start: 0.7778 (ptmt) cc_final: 0.7146 (pptt) REVERT: F 29 LYS cc_start: 0.8309 (mmtp) cc_final: 0.7995 (mmmt) REVERT: F 30 ARG cc_start: 0.8012 (mtt90) cc_final: 0.7741 (mtm-85) REVERT: F 49 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8502 (tt0) REVERT: F 171 ASP cc_start: 0.8620 (m-30) cc_final: 0.8381 (t0) REVERT: F 257 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7861 (tt0) REVERT: F 453 ARG cc_start: 0.7029 (mmt180) cc_final: 0.6126 (mtt180) REVERT: F 458 GLU cc_start: 0.7624 (tt0) cc_final: 0.7038 (tp30) REVERT: G 483 ARG cc_start: 0.8048 (mtp85) cc_final: 0.6925 (mmm160) REVERT: G 489 MET cc_start: 0.8725 (ttp) cc_final: 0.8413 (ttp) REVERT: G 490 ARG cc_start: 0.8175 (ptp90) cc_final: 0.7913 (ptp-170) REVERT: G 527 ASP cc_start: 0.7901 (OUTLIER) cc_final: 0.7525 (p0) REVERT: G 613 MET cc_start: 0.5012 (OUTLIER) cc_final: 0.2338 (tmt) REVERT: G 630 GLU cc_start: 0.6264 (OUTLIER) cc_final: 0.4860 (tm-30) REVERT: G 635 GLU cc_start: 0.5295 (mt-10) cc_final: 0.4339 (pt0) REVERT: H 483 ARG cc_start: 0.8003 (mtp85) cc_final: 0.6877 (mmm160) REVERT: H 490 ARG cc_start: 0.8108 (ptp90) cc_final: 0.7841 (ptp-170) REVERT: H 534 ARG cc_start: 0.8027 (ttm110) cc_final: 0.7662 (ttm110) REVERT: H 580 ARG cc_start: 0.8209 (mmm-85) cc_final: 0.7623 (mmt-90) REVERT: H 599 LYS cc_start: 0.5369 (OUTLIER) cc_final: 0.4828 (tmmt) REVERT: H 630 GLU cc_start: 0.6282 (tt0) cc_final: 0.5921 (tt0) REVERT: H 635 GLU cc_start: 0.5652 (mt-10) cc_final: 0.5021 (pt0) REVERT: I 483 ARG cc_start: 0.7998 (mtp85) cc_final: 0.6930 (mmm160) REVERT: I 527 ASP cc_start: 0.8086 (OUTLIER) cc_final: 0.7651 (p0) REVERT: I 630 GLU cc_start: 0.6485 (tt0) cc_final: 0.6175 (tt0) REVERT: J 483 ARG cc_start: 0.8231 (mtt-85) cc_final: 0.7155 (mmm160) REVERT: J 490 ARG cc_start: 0.8098 (ptp90) cc_final: 0.7624 (ptp-170) REVERT: J 534 ARG cc_start: 0.7906 (mtp85) cc_final: 0.7536 (mtt-85) REVERT: J 630 GLU cc_start: 0.6326 (OUTLIER) cc_final: 0.4833 (tm-30) REVERT: K 483 ARG cc_start: 0.8289 (mtt180) cc_final: 0.7152 (mmm160) REVERT: K 490 ARG cc_start: 0.8151 (ptp90) cc_final: 0.7903 (ptp-170) REVERT: K 630 GLU cc_start: 0.6406 (OUTLIER) cc_final: 0.5249 (tm-30) REVERT: K 635 GLU cc_start: 0.5523 (mt-10) cc_final: 0.4343 (pt0) REVERT: L 483 ARG cc_start: 0.8045 (mtp85) cc_final: 0.6957 (mmm160) REVERT: L 534 ARG cc_start: 0.7937 (ttm-80) cc_final: 0.7649 (ttm-80) REVERT: L 630 GLU cc_start: 0.5922 (OUTLIER) cc_final: 0.5133 (tm-30) outliers start: 73 outliers final: 22 residues processed: 517 average time/residue: 2.0578 time to fit residues: 1226.5110 Evaluate side-chains 523 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 475 time to evaluate : 3.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 143 HIS Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain C residue 497 GLU Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain D residue 497 GLU Chi-restraints excluded: chain E residue 29 LYS Chi-restraints excluded: chain E residue 143 HIS Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 257 GLU Chi-restraints excluded: chain E residue 268 SER Chi-restraints excluded: chain E residue 498 MET Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 143 HIS Chi-restraints excluded: chain F residue 251 GLU Chi-restraints excluded: chain F residue 257 GLU Chi-restraints excluded: chain G residue 527 ASP Chi-restraints excluded: chain G residue 552 SER Chi-restraints excluded: chain G residue 613 MET Chi-restraints excluded: chain G residue 630 GLU Chi-restraints excluded: chain H residue 552 SER Chi-restraints excluded: chain H residue 599 LYS Chi-restraints excluded: chain I residue 482 LYS Chi-restraints excluded: chain I residue 527 ASP Chi-restraints excluded: chain I residue 552 SER Chi-restraints excluded: chain J residue 552 SER Chi-restraints excluded: chain J residue 613 MET Chi-restraints excluded: chain J residue 630 GLU Chi-restraints excluded: chain K residue 552 SER Chi-restraints excluded: chain K residue 591 VAL Chi-restraints excluded: chain K residue 630 GLU Chi-restraints excluded: chain L residue 552 SER Chi-restraints excluded: chain L residue 630 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 123 optimal weight: 0.5980 chunk 247 optimal weight: 3.9990 chunk 425 optimal weight: 8.9990 chunk 386 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 333 optimal weight: 0.6980 chunk 367 optimal weight: 7.9990 chunk 294 optimal weight: 6.9990 chunk 328 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 67 GLN E 67 GLN F 278 ASN G 479 ASN G 556 GLN H 479 ASN J 479 ASN J 556 GLN K 479 ASN K 556 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.139342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.085476 restraints weight = 33967.832| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 1.84 r_work: 0.2879 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 34056 Z= 0.106 Angle : 0.467 7.702 46062 Z= 0.250 Chirality : 0.044 0.142 5148 Planarity : 0.003 0.034 6048 Dihedral : 7.384 54.519 5158 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.88 % Allowed : 10.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.13), residues: 4290 helix: 1.51 (0.14), residues: 1512 sheet: 1.23 (0.17), residues: 792 loop : 0.12 (0.14), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 544 HIS 0.007 0.001 HIS E 104 PHE 0.011 0.001 PHE F 351 TYR 0.008 0.001 TYR C 173 ARG 0.010 0.000 ARG K 534 Details of bonding type rmsd hydrogen bonds : bond 0.03867 ( 1551) hydrogen bonds : angle 5.05710 ( 4476) covalent geometry : bond 0.00235 (34050) covalent geometry : angle 0.46662 (46062) Misc. bond : bond 0.00005 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 484 time to evaluate : 4.016 Fit side-chains REVERT: A 21 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7044 (mp0) REVERT: A 29 LYS cc_start: 0.8294 (tppt) cc_final: 0.7916 (mmmt) REVERT: A 49 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8439 (tt0) REVERT: A 171 ASP cc_start: 0.8816 (m-30) cc_final: 0.8269 (t0) REVERT: A 257 GLU cc_start: 0.8283 (tt0) cc_final: 0.7723 (tm-30) REVERT: A 317 ARG cc_start: 0.8357 (mtt-85) cc_final: 0.7957 (mtp85) REVERT: A 430 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.7377 (pmm) REVERT: A 478 MET cc_start: 0.9143 (mmt) cc_final: 0.8897 (mmt) REVERT: B 21 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7035 (mp0) REVERT: B 22 LYS cc_start: 0.7818 (tttt) cc_final: 0.7309 (ttpt) REVERT: B 30 ARG cc_start: 0.7990 (mtt90) cc_final: 0.7695 (mtm-85) REVERT: B 49 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8395 (tt0) REVERT: B 171 ASP cc_start: 0.8763 (m-30) cc_final: 0.8130 (t0) REVERT: B 220 LYS cc_start: 0.8819 (mtpp) cc_final: 0.8498 (mtmm) REVERT: B 257 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.8002 (tt0) REVERT: B 266 ASP cc_start: 0.8262 (t70) cc_final: 0.7695 (t0) REVERT: B 267 LYS cc_start: 0.8409 (mmtm) cc_final: 0.8161 (mmtp) REVERT: B 289 ARG cc_start: 0.8624 (mmt180) cc_final: 0.8422 (mtp85) REVERT: B 317 ARG cc_start: 0.8427 (mtt-85) cc_final: 0.7740 (mtm180) REVERT: B 502 ARG cc_start: 0.8453 (mtp85) cc_final: 0.7926 (ttm110) REVERT: C 9 GLU cc_start: 0.7527 (mm-30) cc_final: 0.7022 (mm-30) REVERT: C 22 LYS cc_start: 0.7835 (ttmm) cc_final: 0.7555 (ttpt) REVERT: C 49 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8467 (tt0) REVERT: C 171 ASP cc_start: 0.8601 (m-30) cc_final: 0.8310 (t0) REVERT: C 189 TYR cc_start: 0.8725 (p90) cc_final: 0.8348 (p90) REVERT: C 257 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7890 (tm-30) REVERT: C 266 ASP cc_start: 0.8579 (t0) cc_final: 0.8177 (t0) REVERT: C 449 LYS cc_start: 0.7454 (tptt) cc_final: 0.7124 (tptm) REVERT: C 452 GLU cc_start: 0.7740 (tt0) cc_final: 0.7238 (tt0) REVERT: C 453 ARG cc_start: 0.6312 (mtt-85) cc_final: 0.5783 (mtt90) REVERT: C 455 LYS cc_start: 0.7617 (OUTLIER) cc_final: 0.6953 (tmmm) REVERT: C 456 GLU cc_start: 0.7295 (pt0) cc_final: 0.7028 (pt0) REVERT: C 458 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7116 (tp30) REVERT: C 475 GLU cc_start: 0.8385 (tp30) cc_final: 0.7969 (tp30) REVERT: C 497 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7529 (pt0) REVERT: C 502 ARG cc_start: 0.8484 (mtp85) cc_final: 0.7916 (ttm170) REVERT: D 21 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7078 (mp0) REVERT: D 22 LYS cc_start: 0.8133 (tttm) cc_final: 0.7761 (ttpt) REVERT: D 171 ASP cc_start: 0.8749 (m-30) cc_final: 0.8189 (t0) REVERT: D 453 ARG cc_start: 0.6703 (mtt-85) cc_final: 0.6068 (mtt180) REVERT: D 475 GLU cc_start: 0.8443 (tp30) cc_final: 0.7879 (tp30) REVERT: D 502 ARG cc_start: 0.8502 (mtp85) cc_final: 0.7963 (ttm110) REVERT: E 22 LYS cc_start: 0.8005 (tttt) cc_final: 0.7464 (ttpt) REVERT: E 29 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.8115 (mtmt) REVERT: E 171 ASP cc_start: 0.8809 (OUTLIER) cc_final: 0.8248 (t0) REVERT: E 220 LYS cc_start: 0.8861 (mtpp) cc_final: 0.8566 (mtmm) REVERT: E 498 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7996 (ttp) REVERT: F 9 GLU cc_start: 0.7392 (mm-30) cc_final: 0.6905 (mm-30) REVERT: F 21 GLU cc_start: 0.7686 (mm-30) cc_final: 0.6901 (mp0) REVERT: F 22 LYS cc_start: 0.7782 (ptmt) cc_final: 0.7150 (pptt) REVERT: F 29 LYS cc_start: 0.8297 (mmtp) cc_final: 0.7981 (mmmt) REVERT: F 30 ARG cc_start: 0.7926 (mtt90) cc_final: 0.7625 (mtm-85) REVERT: F 49 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8471 (tt0) REVERT: F 171 ASP cc_start: 0.8587 (m-30) cc_final: 0.8358 (t0) REVERT: F 257 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7839 (tm-30) REVERT: F 453 ARG cc_start: 0.7019 (mmt180) cc_final: 0.6114 (mtt180) REVERT: F 458 GLU cc_start: 0.7563 (tt0) cc_final: 0.6970 (tp30) REVERT: G 483 ARG cc_start: 0.8041 (mtp85) cc_final: 0.6928 (mmm160) REVERT: G 489 MET cc_start: 0.8739 (ttp) cc_final: 0.8404 (ttp) REVERT: G 490 ARG cc_start: 0.8128 (ptp90) cc_final: 0.7647 (ptp-170) REVERT: G 527 ASP cc_start: 0.7866 (OUTLIER) cc_final: 0.7493 (p0) REVERT: G 613 MET cc_start: 0.4995 (OUTLIER) cc_final: 0.2341 (tmt) REVERT: G 630 GLU cc_start: 0.6252 (OUTLIER) cc_final: 0.4843 (tm-30) REVERT: G 635 GLU cc_start: 0.5276 (mt-10) cc_final: 0.4322 (pt0) REVERT: H 483 ARG cc_start: 0.7981 (mtp85) cc_final: 0.6865 (mmm160) REVERT: H 490 ARG cc_start: 0.8080 (ptp90) cc_final: 0.7620 (ptp-170) REVERT: H 534 ARG cc_start: 0.7990 (ttm110) cc_final: 0.7294 (mtp85) REVERT: H 580 ARG cc_start: 0.8161 (mmm-85) cc_final: 0.7566 (mmt-90) REVERT: H 630 GLU cc_start: 0.6269 (tt0) cc_final: 0.6011 (tt0) REVERT: H 635 GLU cc_start: 0.5742 (mt-10) cc_final: 0.5018 (pt0) REVERT: I 483 ARG cc_start: 0.7977 (mtp85) cc_final: 0.6914 (mmm160) REVERT: I 527 ASP cc_start: 0.8081 (OUTLIER) cc_final: 0.7660 (p0) REVERT: I 534 ARG cc_start: 0.7865 (ttm170) cc_final: 0.7513 (ttm170) REVERT: I 630 GLU cc_start: 0.6441 (tt0) cc_final: 0.6159 (tt0) REVERT: J 483 ARG cc_start: 0.8166 (mtt-85) cc_final: 0.7114 (mmm160) REVERT: J 490 ARG cc_start: 0.8093 (ptp90) cc_final: 0.7623 (ptp-170) REVERT: J 534 ARG cc_start: 0.7854 (mtp85) cc_final: 0.7517 (mtt-85) REVERT: J 630 GLU cc_start: 0.6318 (OUTLIER) cc_final: 0.4843 (tm-30) REVERT: K 483 ARG cc_start: 0.8264 (mtt180) cc_final: 0.7145 (mmm160) REVERT: K 490 ARG cc_start: 0.8127 (ptp90) cc_final: 0.7681 (ptp-170) REVERT: K 630 GLU cc_start: 0.6375 (OUTLIER) cc_final: 0.5245 (tm-30) REVERT: K 635 GLU cc_start: 0.5500 (mt-10) cc_final: 0.4332 (pt0) REVERT: K 665 GLU cc_start: 0.4474 (mt-10) cc_final: 0.4268 (mm-30) REVERT: L 483 ARG cc_start: 0.8001 (mtp85) cc_final: 0.6936 (mmm160) REVERT: L 520 ASP cc_start: 0.5313 (m-30) cc_final: 0.4855 (m-30) REVERT: L 534 ARG cc_start: 0.7871 (ttm-80) cc_final: 0.7622 (ttm-80) outliers start: 65 outliers final: 24 residues processed: 513 average time/residue: 1.9474 time to fit residues: 1149.0133 Evaluate side-chains 528 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 485 time to evaluate : 3.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 499 GLU Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 143 HIS Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain C residue 497 GLU Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 29 LYS Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 268 SER Chi-restraints excluded: chain E residue 498 MET Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 143 HIS Chi-restraints excluded: chain F residue 251 GLU Chi-restraints excluded: chain F residue 257 GLU Chi-restraints excluded: chain G residue 527 ASP Chi-restraints excluded: chain G residue 552 SER Chi-restraints excluded: chain G residue 613 MET Chi-restraints excluded: chain G residue 630 GLU Chi-restraints excluded: chain H residue 552 SER Chi-restraints excluded: chain I residue 527 ASP Chi-restraints excluded: chain I residue 552 SER Chi-restraints excluded: chain J residue 552 SER Chi-restraints excluded: chain J residue 630 GLU Chi-restraints excluded: chain K residue 509 ARG Chi-restraints excluded: chain K residue 552 SER Chi-restraints excluded: chain K residue 630 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 206 optimal weight: 5.9990 chunk 140 optimal weight: 3.9990 chunk 186 optimal weight: 4.9990 chunk 147 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 403 optimal weight: 20.0000 chunk 36 optimal weight: 0.1980 chunk 191 optimal weight: 1.9990 chunk 245 optimal weight: 3.9990 chunk 202 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 67 GLN E 67 GLN F 278 ASN G 479 ASN H 479 ASN H 556 GLN J 479 ASN ** J 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 479 ASN K 556 GLN L 556 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.136099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.081863 restraints weight = 34005.610| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 1.83 r_work: 0.2818 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 34056 Z= 0.212 Angle : 0.546 8.526 46062 Z= 0.293 Chirality : 0.048 0.156 5148 Planarity : 0.004 0.035 6048 Dihedral : 7.663 55.624 5158 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.26 % Allowed : 10.12 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.13), residues: 4290 helix: 1.36 (0.13), residues: 1494 sheet: 1.23 (0.17), residues: 792 loop : 0.06 (0.14), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP K 537 HIS 0.011 0.002 HIS E 104 PHE 0.014 0.002 PHE E 384 TYR 0.012 0.002 TYR A 173 ARG 0.006 0.000 ARG A 453 Details of bonding type rmsd hydrogen bonds : bond 0.05120 ( 1551) hydrogen bonds : angle 5.24812 ( 4476) covalent geometry : bond 0.00508 (34050) covalent geometry : angle 0.54637 (46062) Misc. bond : bond 0.00007 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 480 time to evaluate : 3.719 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7084 (mp0) REVERT: A 29 LYS cc_start: 0.8314 (tppt) cc_final: 0.7923 (mmmt) REVERT: A 49 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8496 (tt0) REVERT: A 171 ASP cc_start: 0.8839 (m-30) cc_final: 0.8318 (t0) REVERT: A 257 GLU cc_start: 0.8212 (tt0) cc_final: 0.7657 (tm-30) REVERT: A 285 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7780 (tt0) REVERT: A 317 ARG cc_start: 0.8392 (mtt-85) cc_final: 0.7902 (mtp85) REVERT: A 430 MET cc_start: 0.8910 (OUTLIER) cc_final: 0.7833 (pmm) REVERT: A 478 MET cc_start: 0.9187 (mmt) cc_final: 0.8909 (mmt) REVERT: B 21 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7042 (mp0) REVERT: B 22 LYS cc_start: 0.7857 (tttt) cc_final: 0.7346 (ttpt) REVERT: B 30 ARG cc_start: 0.8067 (mtt90) cc_final: 0.7786 (mtm-85) REVERT: B 49 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8464 (tt0) REVERT: B 171 ASP cc_start: 0.8818 (m-30) cc_final: 0.8225 (t0) REVERT: B 220 LYS cc_start: 0.8809 (mtpp) cc_final: 0.8493 (mtmm) REVERT: B 266 ASP cc_start: 0.8365 (t70) cc_final: 0.7807 (t0) REVERT: B 289 ARG cc_start: 0.8616 (mmt180) cc_final: 0.8362 (mtp85) REVERT: B 317 ARG cc_start: 0.8432 (mtt-85) cc_final: 0.7853 (mtp85) REVERT: C 9 GLU cc_start: 0.7475 (mm-30) cc_final: 0.6962 (mm-30) REVERT: C 22 LYS cc_start: 0.7920 (ttmm) cc_final: 0.7566 (ttpt) REVERT: C 49 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8489 (tt0) REVERT: C 171 ASP cc_start: 0.8616 (m-30) cc_final: 0.8374 (t0) REVERT: C 257 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7878 (tm-30) REVERT: C 266 ASP cc_start: 0.8641 (t0) cc_final: 0.8284 (t0) REVERT: C 449 LYS cc_start: 0.7518 (tptt) cc_final: 0.7256 (tptm) REVERT: C 452 GLU cc_start: 0.7751 (tt0) cc_final: 0.7290 (tt0) REVERT: C 453 ARG cc_start: 0.6282 (mtt-85) cc_final: 0.5771 (mtt90) REVERT: C 455 LYS cc_start: 0.7641 (OUTLIER) cc_final: 0.6976 (tmmm) REVERT: C 456 GLU cc_start: 0.7389 (pt0) cc_final: 0.7121 (pt0) REVERT: C 458 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7176 (tp30) REVERT: C 475 GLU cc_start: 0.8394 (tp30) cc_final: 0.7968 (tp30) REVERT: C 497 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7569 (pt0) REVERT: C 502 ARG cc_start: 0.8559 (mtp85) cc_final: 0.7975 (ttm170) REVERT: D 21 GLU cc_start: 0.7806 (mm-30) cc_final: 0.6998 (mp0) REVERT: D 22 LYS cc_start: 0.8181 (tttm) cc_final: 0.7822 (ttpt) REVERT: D 117 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8170 (ttmm) REVERT: D 171 ASP cc_start: 0.8781 (m-30) cc_final: 0.8315 (t0) REVERT: D 257 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7625 (tm-30) REVERT: D 452 GLU cc_start: 0.8024 (tt0) cc_final: 0.7764 (pt0) REVERT: D 453 ARG cc_start: 0.6756 (mtt-85) cc_final: 0.6072 (mtt180) REVERT: D 475 GLU cc_start: 0.8462 (tp30) cc_final: 0.7912 (tp30) REVERT: E 22 LYS cc_start: 0.8066 (tttt) cc_final: 0.7528 (ttpt) REVERT: E 29 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8152 (mtmt) REVERT: E 171 ASP cc_start: 0.8859 (OUTLIER) cc_final: 0.8366 (t0) REVERT: E 220 LYS cc_start: 0.8913 (mtpp) cc_final: 0.8627 (mtmm) REVERT: E 257 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7542 (tm-30) REVERT: F 9 GLU cc_start: 0.7423 (mm-30) cc_final: 0.6916 (mm-30) REVERT: F 21 GLU cc_start: 0.7669 (mm-30) cc_final: 0.6903 (mp0) REVERT: F 22 LYS cc_start: 0.7888 (ptmt) cc_final: 0.7221 (pptt) REVERT: F 29 LYS cc_start: 0.8322 (mmtp) cc_final: 0.7993 (mmmt) REVERT: F 30 ARG cc_start: 0.8041 (mtt90) cc_final: 0.7723 (mtm-85) REVERT: F 49 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8498 (tt0) REVERT: F 453 ARG cc_start: 0.7057 (mmt180) cc_final: 0.6088 (mtt180) REVERT: F 458 GLU cc_start: 0.7673 (tt0) cc_final: 0.7097 (tp30) REVERT: F 502 ARG cc_start: 0.8541 (mtp85) cc_final: 0.7926 (ttm170) REVERT: G 483 ARG cc_start: 0.8064 (mtp85) cc_final: 0.6929 (mmm160) REVERT: G 489 MET cc_start: 0.8738 (ttp) cc_final: 0.8450 (ttp) REVERT: G 490 ARG cc_start: 0.8136 (ptp90) cc_final: 0.7885 (ptp-170) REVERT: G 527 ASP cc_start: 0.7933 (OUTLIER) cc_final: 0.7540 (p0) REVERT: G 630 GLU cc_start: 0.6313 (OUTLIER) cc_final: 0.4894 (tm-30) REVERT: G 635 GLU cc_start: 0.5398 (mt-10) cc_final: 0.4360 (pt0) REVERT: H 483 ARG cc_start: 0.8018 (mtp85) cc_final: 0.6875 (mmm160) REVERT: H 490 ARG cc_start: 0.8094 (ptp90) cc_final: 0.7831 (ptp-170) REVERT: H 580 ARG cc_start: 0.8203 (mmm-85) cc_final: 0.7607 (mmt-90) REVERT: H 599 LYS cc_start: 0.5333 (OUTLIER) cc_final: 0.4800 (tmmt) REVERT: H 630 GLU cc_start: 0.6400 (tt0) cc_final: 0.6102 (tt0) REVERT: H 635 GLU cc_start: 0.5623 (mt-10) cc_final: 0.4970 (pt0) REVERT: I 483 ARG cc_start: 0.7991 (mtp85) cc_final: 0.6922 (mmm160) REVERT: I 521 LEU cc_start: 0.8027 (mt) cc_final: 0.7548 (tp) REVERT: I 527 ASP cc_start: 0.8118 (OUTLIER) cc_final: 0.7688 (p0) REVERT: I 630 GLU cc_start: 0.6491 (tt0) cc_final: 0.6191 (tt0) REVERT: J 483 ARG cc_start: 0.8221 (mtt-85) cc_final: 0.7115 (mmm160) REVERT: J 490 ARG cc_start: 0.8113 (ptp90) cc_final: 0.7599 (ptp-170) REVERT: J 534 ARG cc_start: 0.7928 (mtp85) cc_final: 0.7530 (mtt-85) REVERT: J 630 GLU cc_start: 0.6343 (OUTLIER) cc_final: 0.4860 (tm-30) REVERT: K 483 ARG cc_start: 0.8324 (mtt180) cc_final: 0.7175 (mmm160) REVERT: K 490 ARG cc_start: 0.8116 (ptp90) cc_final: 0.7867 (ptp-170) REVERT: K 630 GLU cc_start: 0.6374 (OUTLIER) cc_final: 0.5171 (tm-30) REVERT: K 635 GLU cc_start: 0.5503 (mt-10) cc_final: 0.4324 (pt0) REVERT: K 665 GLU cc_start: 0.4453 (mt-10) cc_final: 0.4236 (mm-30) REVERT: L 483 ARG cc_start: 0.8026 (mtp85) cc_final: 0.6943 (mmm160) REVERT: L 534 ARG cc_start: 0.7902 (ttm-80) cc_final: 0.7604 (ttm-80) REVERT: L 635 GLU cc_start: 0.5370 (mt-10) cc_final: 0.4450 (pt0) outliers start: 78 outliers final: 26 residues processed: 512 average time/residue: 1.9802 time to fit residues: 1169.3990 Evaluate side-chains 521 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 475 time to evaluate : 4.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 143 HIS Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain C residue 497 GLU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 29 LYS Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 257 GLU Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 143 HIS Chi-restraints excluded: chain F residue 251 GLU Chi-restraints excluded: chain G residue 527 ASP Chi-restraints excluded: chain G residue 552 SER Chi-restraints excluded: chain G residue 630 GLU Chi-restraints excluded: chain H residue 552 SER Chi-restraints excluded: chain H residue 599 LYS Chi-restraints excluded: chain I residue 527 ASP Chi-restraints excluded: chain I residue 552 SER Chi-restraints excluded: chain J residue 552 SER Chi-restraints excluded: chain J residue 630 GLU Chi-restraints excluded: chain K residue 509 ARG Chi-restraints excluded: chain K residue 552 SER Chi-restraints excluded: chain K residue 591 VAL Chi-restraints excluded: chain K residue 630 GLU Chi-restraints excluded: chain L residue 460 GLU Chi-restraints excluded: chain L residue 482 LYS Chi-restraints excluded: chain L residue 552 SER Chi-restraints excluded: chain L residue 613 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 179 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 238 optimal weight: 1.9990 chunk 202 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 412 optimal weight: 5.9990 chunk 104 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 183 optimal weight: 0.6980 chunk 336 optimal weight: 0.5980 chunk 309 optimal weight: 0.0670 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 67 GLN E 67 GLN F 278 ASN G 479 ASN H 479 ASN H 556 GLN J 479 ASN J 556 GLN K 479 ASN K 556 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.139243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.085535 restraints weight = 34068.394| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 1.84 r_work: 0.2880 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 34056 Z= 0.101 Angle : 0.469 8.650 46062 Z= 0.250 Chirality : 0.044 0.139 5148 Planarity : 0.003 0.035 6048 Dihedral : 7.318 53.758 5158 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.36 % Allowed : 11.28 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.13), residues: 4290 helix: 1.49 (0.14), residues: 1512 sheet: 1.23 (0.17), residues: 792 loop : 0.11 (0.14), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 544 HIS 0.007 0.001 HIS C 104 PHE 0.011 0.001 PHE B 351 TYR 0.007 0.001 TYR C 173 ARG 0.006 0.000 ARG A 453 Details of bonding type rmsd hydrogen bonds : bond 0.03813 ( 1551) hydrogen bonds : angle 5.03669 ( 4476) covalent geometry : bond 0.00221 (34050) covalent geometry : angle 0.46912 (46062) Misc. bond : bond 0.00007 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 491 time to evaluate : 3.783 Fit side-chains REVERT: A 21 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7061 (mp0) REVERT: A 29 LYS cc_start: 0.8311 (tppt) cc_final: 0.7917 (mmmt) REVERT: A 49 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8440 (tt0) REVERT: A 171 ASP cc_start: 0.8816 (m-30) cc_final: 0.8271 (t0) REVERT: A 257 GLU cc_start: 0.8186 (tt0) cc_final: 0.7657 (tm-30) REVERT: A 317 ARG cc_start: 0.8383 (mtt-85) cc_final: 0.7925 (mtp85) REVERT: A 430 MET cc_start: 0.8899 (OUTLIER) cc_final: 0.7373 (pmm) REVERT: B 21 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7030 (mp0) REVERT: B 22 LYS cc_start: 0.7828 (tttt) cc_final: 0.7324 (ttpt) REVERT: B 30 ARG cc_start: 0.8008 (mtt90) cc_final: 0.7726 (mtm-85) REVERT: B 49 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8404 (tt0) REVERT: B 171 ASP cc_start: 0.8801 (m-30) cc_final: 0.8202 (t0) REVERT: B 220 LYS cc_start: 0.8798 (mtpp) cc_final: 0.8527 (mtmm) REVERT: B 257 GLU cc_start: 0.8287 (tt0) cc_final: 0.7718 (tm-30) REVERT: B 266 ASP cc_start: 0.8309 (t70) cc_final: 0.7789 (t0) REVERT: B 317 ARG cc_start: 0.8423 (mtt-85) cc_final: 0.7743 (mtm180) REVERT: B 502 ARG cc_start: 0.8455 (mtp85) cc_final: 0.7930 (ttm110) REVERT: C 9 GLU cc_start: 0.7519 (mm-30) cc_final: 0.7008 (mm-30) REVERT: C 22 LYS cc_start: 0.7873 (ttmm) cc_final: 0.7577 (ttpt) REVERT: C 49 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8460 (tt0) REVERT: C 171 ASP cc_start: 0.8605 (m-30) cc_final: 0.8311 (t0) REVERT: C 257 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7883 (tm-30) REVERT: C 266 ASP cc_start: 0.8581 (t0) cc_final: 0.8226 (t0) REVERT: C 449 LYS cc_start: 0.7508 (tptt) cc_final: 0.7172 (tptm) REVERT: C 452 GLU cc_start: 0.7737 (tt0) cc_final: 0.7230 (tt0) REVERT: C 453 ARG cc_start: 0.6333 (mtt-85) cc_final: 0.5795 (mtt90) REVERT: C 456 GLU cc_start: 0.7321 (pt0) cc_final: 0.7039 (pt0) REVERT: C 458 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7121 (tp30) REVERT: C 475 GLU cc_start: 0.8413 (tp30) cc_final: 0.7995 (tp30) REVERT: C 497 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7518 (pt0) REVERT: C 502 ARG cc_start: 0.8515 (mtp85) cc_final: 0.7942 (ttm170) REVERT: D 21 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7048 (mp0) REVERT: D 22 LYS cc_start: 0.8153 (tttm) cc_final: 0.7799 (ttpt) REVERT: D 117 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8124 (ttmm) REVERT: D 171 ASP cc_start: 0.8760 (m-30) cc_final: 0.8243 (t0) REVERT: D 453 ARG cc_start: 0.6709 (mtt-85) cc_final: 0.6073 (mtt180) REVERT: D 475 GLU cc_start: 0.8441 (tp30) cc_final: 0.7904 (tp30) REVERT: E 22 LYS cc_start: 0.8003 (tttt) cc_final: 0.7471 (ttpt) REVERT: E 171 ASP cc_start: 0.8834 (OUTLIER) cc_final: 0.8322 (t0) REVERT: E 220 LYS cc_start: 0.8863 (mtpp) cc_final: 0.8576 (mtmm) REVERT: F 9 GLU cc_start: 0.7396 (mm-30) cc_final: 0.6905 (mm-30) REVERT: F 21 GLU cc_start: 0.7653 (mm-30) cc_final: 0.6893 (mp0) REVERT: F 22 LYS cc_start: 0.7814 (ptmt) cc_final: 0.7165 (pptt) REVERT: F 29 LYS cc_start: 0.8284 (mmtp) cc_final: 0.7952 (mmmt) REVERT: F 30 ARG cc_start: 0.7959 (mtt90) cc_final: 0.7735 (mtm-85) REVERT: F 49 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8483 (tt0) REVERT: F 257 GLU cc_start: 0.8130 (tt0) cc_final: 0.7638 (tm-30) REVERT: F 453 ARG cc_start: 0.7054 (mmt180) cc_final: 0.6112 (mtt180) REVERT: F 458 GLU cc_start: 0.7597 (tt0) cc_final: 0.7019 (tp30) REVERT: F 502 ARG cc_start: 0.8528 (mtp85) cc_final: 0.7917 (ttm170) REVERT: G 483 ARG cc_start: 0.8064 (mtp85) cc_final: 0.6951 (mmm160) REVERT: G 489 MET cc_start: 0.8753 (ttp) cc_final: 0.8426 (ttp) REVERT: G 490 ARG cc_start: 0.8152 (ptp90) cc_final: 0.7666 (ptp-170) REVERT: G 527 ASP cc_start: 0.7865 (OUTLIER) cc_final: 0.7497 (p0) REVERT: G 630 GLU cc_start: 0.6292 (OUTLIER) cc_final: 0.4900 (tm-30) REVERT: G 635 GLU cc_start: 0.5381 (mt-10) cc_final: 0.4330 (pt0) REVERT: H 483 ARG cc_start: 0.7965 (mtp85) cc_final: 0.6866 (mmm160) REVERT: H 490 ARG cc_start: 0.8093 (ptp90) cc_final: 0.7866 (ptp-170) REVERT: H 534 ARG cc_start: 0.8011 (ttm110) cc_final: 0.7570 (ttp-110) REVERT: H 580 ARG cc_start: 0.8220 (mmm-85) cc_final: 0.7633 (mmt-90) REVERT: H 599 LYS cc_start: 0.5286 (OUTLIER) cc_final: 0.4740 (tmmt) REVERT: H 630 GLU cc_start: 0.6344 (tt0) cc_final: 0.6000 (tt0) REVERT: H 635 GLU cc_start: 0.5679 (mt-10) cc_final: 0.4983 (pt0) REVERT: I 483 ARG cc_start: 0.7967 (mtp85) cc_final: 0.6902 (mmm160) REVERT: I 520 ASP cc_start: 0.5668 (m-30) cc_final: 0.5199 (m-30) REVERT: I 521 LEU cc_start: 0.8026 (mt) cc_final: 0.7584 (tp) REVERT: I 527 ASP cc_start: 0.8113 (OUTLIER) cc_final: 0.7696 (p0) REVERT: I 534 ARG cc_start: 0.7755 (ttm-80) cc_final: 0.6971 (mtp85) REVERT: I 630 GLU cc_start: 0.6457 (tt0) cc_final: 0.6081 (tt0) REVERT: J 483 ARG cc_start: 0.8201 (mtt-85) cc_final: 0.7128 (mmm160) REVERT: J 490 ARG cc_start: 0.8070 (ptp90) cc_final: 0.7574 (ptp-170) REVERT: J 534 ARG cc_start: 0.7879 (mtp85) cc_final: 0.7511 (mtt-85) REVERT: J 630 GLU cc_start: 0.6348 (OUTLIER) cc_final: 0.4869 (tm-30) REVERT: K 483 ARG cc_start: 0.8280 (mtt180) cc_final: 0.7168 (mmm160) REVERT: K 490 ARG cc_start: 0.8131 (ptp90) cc_final: 0.7898 (ptp-170) REVERT: K 630 GLU cc_start: 0.6391 (OUTLIER) cc_final: 0.5242 (tm-30) REVERT: K 635 GLU cc_start: 0.5464 (mt-10) cc_final: 0.4379 (pt0) REVERT: L 483 ARG cc_start: 0.8003 (mtp85) cc_final: 0.6940 (mmm160) REVERT: L 500 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7838 (mp0) REVERT: L 534 ARG cc_start: 0.7879 (ttm-80) cc_final: 0.7502 (ttm-80) REVERT: L 635 GLU cc_start: 0.5291 (mt-10) cc_final: 0.4502 (pt0) outliers start: 47 outliers final: 25 residues processed: 515 average time/residue: 1.9080 time to fit residues: 1132.9496 Evaluate side-chains 523 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 483 time to evaluate : 4.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 499 GLU Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 143 HIS Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 497 GLU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 29 LYS Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 268 SER Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 143 HIS Chi-restraints excluded: chain F residue 251 GLU Chi-restraints excluded: chain G residue 527 ASP Chi-restraints excluded: chain G residue 552 SER Chi-restraints excluded: chain G residue 630 GLU Chi-restraints excluded: chain H residue 552 SER Chi-restraints excluded: chain H residue 599 LYS Chi-restraints excluded: chain I residue 527 ASP Chi-restraints excluded: chain I residue 552 SER Chi-restraints excluded: chain J residue 552 SER Chi-restraints excluded: chain J residue 630 GLU Chi-restraints excluded: chain K residue 552 SER Chi-restraints excluded: chain K residue 591 VAL Chi-restraints excluded: chain K residue 630 GLU Chi-restraints excluded: chain L residue 552 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 424 optimal weight: 0.9980 chunk 422 optimal weight: 0.6980 chunk 397 optimal weight: 10.0000 chunk 264 optimal weight: 3.9990 chunk 333 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 chunk 187 optimal weight: 1.9990 chunk 356 optimal weight: 10.0000 chunk 380 optimal weight: 9.9990 chunk 304 optimal weight: 10.0000 chunk 220 optimal weight: 0.5980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 67 GLN E 67 GLN G 479 ASN G 556 GLN H 479 ASN H 556 GLN J 479 ASN ** J 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 479 ASN K 556 GLN L 556 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.136456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.082317 restraints weight = 34034.031| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 1.83 r_work: 0.2826 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 34056 Z= 0.183 Angle : 0.533 9.290 46062 Z= 0.286 Chirality : 0.047 0.168 5148 Planarity : 0.004 0.035 6048 Dihedral : 7.516 54.296 5158 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.80 % Allowed : 11.01 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.13), residues: 4290 helix: 1.40 (0.13), residues: 1494 sheet: 1.21 (0.17), residues: 792 loop : 0.09 (0.14), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 537 HIS 0.010 0.002 HIS B 104 PHE 0.013 0.002 PHE D 384 TYR 0.011 0.002 TYR C 173 ARG 0.008 0.000 ARG A 453 Details of bonding type rmsd hydrogen bonds : bond 0.04885 ( 1551) hydrogen bonds : angle 5.19033 ( 4476) covalent geometry : bond 0.00434 (34050) covalent geometry : angle 0.53329 (46062) Misc. bond : bond 0.00003 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 486 time to evaluate : 3.813 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7016 (mp0) REVERT: A 29 LYS cc_start: 0.8323 (tppt) cc_final: 0.7935 (mmmt) REVERT: A 49 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8435 (tt0) REVERT: A 171 ASP cc_start: 0.8850 (m-30) cc_final: 0.8318 (t0) REVERT: A 257 GLU cc_start: 0.8144 (tt0) cc_final: 0.7664 (tm-30) REVERT: A 285 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7789 (tt0) REVERT: A 317 ARG cc_start: 0.8396 (mtt-85) cc_final: 0.7919 (mtp85) REVERT: A 430 MET cc_start: 0.8885 (OUTLIER) cc_final: 0.7722 (pmm) REVERT: B 21 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7010 (mp0) REVERT: B 22 LYS cc_start: 0.7843 (tttt) cc_final: 0.7333 (ttpt) REVERT: B 30 ARG cc_start: 0.8067 (mtt90) cc_final: 0.7780 (mtm-85) REVERT: B 49 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8402 (tt0) REVERT: B 171 ASP cc_start: 0.8822 (m-30) cc_final: 0.8234 (t0) REVERT: B 220 LYS cc_start: 0.8791 (mtpp) cc_final: 0.8482 (mtmm) REVERT: B 257 GLU cc_start: 0.8225 (tt0) cc_final: 0.7680 (tm-30) REVERT: B 266 ASP cc_start: 0.8279 (t70) cc_final: 0.8021 (t0) REVERT: B 317 ARG cc_start: 0.8432 (mtt-85) cc_final: 0.7738 (mtm180) REVERT: C 9 GLU cc_start: 0.7474 (mm-30) cc_final: 0.6963 (mm-30) REVERT: C 22 LYS cc_start: 0.7923 (ttmm) cc_final: 0.7562 (ttpt) REVERT: C 49 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.8482 (tt0) REVERT: C 171 ASP cc_start: 0.8604 (m-30) cc_final: 0.8339 (t0) REVERT: C 257 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7876 (tm-30) REVERT: C 266 ASP cc_start: 0.8613 (t0) cc_final: 0.8253 (t0) REVERT: C 449 LYS cc_start: 0.7511 (tptt) cc_final: 0.7245 (tptm) REVERT: C 452 GLU cc_start: 0.7746 (tt0) cc_final: 0.7299 (tt0) REVERT: C 453 ARG cc_start: 0.6268 (mtt-85) cc_final: 0.5767 (mtt90) REVERT: C 456 GLU cc_start: 0.7374 (pt0) cc_final: 0.7098 (pt0) REVERT: C 458 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7177 (tp30) REVERT: C 475 GLU cc_start: 0.8400 (tp30) cc_final: 0.7970 (tp30) REVERT: C 497 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7548 (pt0) REVERT: C 502 ARG cc_start: 0.8568 (mtp85) cc_final: 0.7979 (ttm170) REVERT: D 21 GLU cc_start: 0.7798 (mm-30) cc_final: 0.6991 (mp0) REVERT: D 22 LYS cc_start: 0.8172 (tttm) cc_final: 0.7811 (ttpt) REVERT: D 117 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8152 (ttmm) REVERT: D 171 ASP cc_start: 0.8758 (m-30) cc_final: 0.8287 (t0) REVERT: D 257 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7584 (tm-30) REVERT: D 452 GLU cc_start: 0.8029 (tt0) cc_final: 0.7782 (pt0) REVERT: D 453 ARG cc_start: 0.6719 (mtt-85) cc_final: 0.6062 (mtt180) REVERT: D 475 GLU cc_start: 0.8449 (tp30) cc_final: 0.7897 (tp30) REVERT: E 22 LYS cc_start: 0.8056 (tttt) cc_final: 0.7520 (ttpt) REVERT: E 29 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8152 (mtmt) REVERT: E 143 HIS cc_start: 0.8476 (OUTLIER) cc_final: 0.8037 (m170) REVERT: E 171 ASP cc_start: 0.8849 (OUTLIER) cc_final: 0.8342 (t0) REVERT: E 220 LYS cc_start: 0.8886 (mtpp) cc_final: 0.8602 (mtmm) REVERT: E 257 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7560 (tm-30) REVERT: F 9 GLU cc_start: 0.7426 (mm-30) cc_final: 0.6919 (mm-30) REVERT: F 21 GLU cc_start: 0.7636 (mm-30) cc_final: 0.6863 (mp0) REVERT: F 22 LYS cc_start: 0.7853 (ptmt) cc_final: 0.7172 (pptt) REVERT: F 29 LYS cc_start: 0.8301 (mmtp) cc_final: 0.7961 (mmmt) REVERT: F 30 ARG cc_start: 0.8025 (mtt90) cc_final: 0.7710 (mtm-85) REVERT: F 49 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8482 (tt0) REVERT: F 257 GLU cc_start: 0.8108 (tt0) cc_final: 0.7615 (tm-30) REVERT: F 453 ARG cc_start: 0.7040 (mmt180) cc_final: 0.6084 (mtt180) REVERT: F 458 GLU cc_start: 0.7649 (tt0) cc_final: 0.7076 (tp30) REVERT: F 502 ARG cc_start: 0.8548 (mtp85) cc_final: 0.7929 (ttm170) REVERT: G 483 ARG cc_start: 0.8066 (mtp85) cc_final: 0.6927 (mmm160) REVERT: G 489 MET cc_start: 0.8742 (ttp) cc_final: 0.8468 (ttp) REVERT: G 490 ARG cc_start: 0.8145 (ptp90) cc_final: 0.7899 (ptp-170) REVERT: G 527 ASP cc_start: 0.7917 (OUTLIER) cc_final: 0.7550 (p0) REVERT: G 630 GLU cc_start: 0.6309 (OUTLIER) cc_final: 0.4896 (tm-30) REVERT: G 635 GLU cc_start: 0.5483 (mt-10) cc_final: 0.4345 (pt0) REVERT: H 483 ARG cc_start: 0.8018 (mtp85) cc_final: 0.6873 (mmm160) REVERT: H 490 ARG cc_start: 0.8086 (ptp90) cc_final: 0.7848 (ptp-170) REVERT: H 580 ARG cc_start: 0.8189 (mmm-85) cc_final: 0.7586 (mmt-90) REVERT: H 599 LYS cc_start: 0.5293 (OUTLIER) cc_final: 0.4774 (tmmt) REVERT: H 630 GLU cc_start: 0.6387 (tt0) cc_final: 0.6050 (tt0) REVERT: H 635 GLU cc_start: 0.5682 (mt-10) cc_final: 0.4988 (pt0) REVERT: I 483 ARG cc_start: 0.8000 (mtp85) cc_final: 0.6916 (mmm160) REVERT: I 521 LEU cc_start: 0.8062 (mt) cc_final: 0.7575 (tp) REVERT: I 527 ASP cc_start: 0.8134 (OUTLIER) cc_final: 0.7712 (p0) REVERT: I 630 GLU cc_start: 0.6461 (tt0) cc_final: 0.6173 (tt0) REVERT: J 483 ARG cc_start: 0.8238 (mtt-85) cc_final: 0.7130 (mmm160) REVERT: J 490 ARG cc_start: 0.8069 (ptp90) cc_final: 0.7581 (ptp-170) REVERT: J 534 ARG cc_start: 0.7931 (mtp85) cc_final: 0.7534 (mtt-85) REVERT: J 630 GLU cc_start: 0.6349 (OUTLIER) cc_final: 0.4858 (tm-30) REVERT: K 483 ARG cc_start: 0.8316 (mtt180) cc_final: 0.7171 (mmm160) REVERT: K 490 ARG cc_start: 0.8113 (ptp90) cc_final: 0.7874 (ptp-170) REVERT: K 534 ARG cc_start: 0.7309 (mtt90) cc_final: 0.6462 (mmm160) REVERT: K 630 GLU cc_start: 0.6349 (OUTLIER) cc_final: 0.5176 (tm-30) REVERT: K 635 GLU cc_start: 0.5473 (mt-10) cc_final: 0.4376 (pt0) REVERT: L 483 ARG cc_start: 0.8033 (mtp85) cc_final: 0.6936 (mmm160) REVERT: L 520 ASP cc_start: 0.5472 (m-30) cc_final: 0.5073 (m-30) REVERT: L 534 ARG cc_start: 0.7905 (ttm-80) cc_final: 0.7646 (ttm-80) REVERT: L 635 GLU cc_start: 0.5243 (mt-10) cc_final: 0.4397 (pt0) outliers start: 62 outliers final: 26 residues processed: 514 average time/residue: 1.9493 time to fit residues: 1158.7965 Evaluate side-chains 517 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 471 time to evaluate : 3.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 499 GLU Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 143 HIS Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 497 GLU Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 29 LYS Chi-restraints excluded: chain E residue 143 HIS Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 257 GLU Chi-restraints excluded: chain E residue 268 SER Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 143 HIS Chi-restraints excluded: chain F residue 251 GLU Chi-restraints excluded: chain G residue 527 ASP Chi-restraints excluded: chain G residue 552 SER Chi-restraints excluded: chain G residue 630 GLU Chi-restraints excluded: chain H residue 552 SER Chi-restraints excluded: chain H residue 599 LYS Chi-restraints excluded: chain I residue 482 LYS Chi-restraints excluded: chain I residue 527 ASP Chi-restraints excluded: chain I residue 552 SER Chi-restraints excluded: chain J residue 552 SER Chi-restraints excluded: chain J residue 630 GLU Chi-restraints excluded: chain K residue 552 SER Chi-restraints excluded: chain K residue 591 VAL Chi-restraints excluded: chain K residue 630 GLU Chi-restraints excluded: chain L residue 552 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 130 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 301 optimal weight: 5.9990 chunk 302 optimal weight: 1.9990 chunk 415 optimal weight: 5.9990 chunk 312 optimal weight: 0.8980 chunk 203 optimal weight: 0.5980 chunk 423 optimal weight: 2.9990 chunk 405 optimal weight: 0.0670 chunk 291 optimal weight: 0.6980 chunk 262 optimal weight: 0.9990 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 67 GLN E 67 GLN G 479 ASN H 479 ASN H 556 GLN J 479 ASN J 556 GLN K 479 ASN K 556 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.139221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.085448 restraints weight = 34052.222| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 1.84 r_work: 0.2879 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 34056 Z= 0.104 Angle : 0.475 9.280 46062 Z= 0.252 Chirality : 0.044 0.141 5148 Planarity : 0.003 0.035 6048 Dihedral : 7.221 52.568 5158 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.39 % Allowed : 11.57 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.13), residues: 4290 helix: 1.49 (0.14), residues: 1512 sheet: 1.23 (0.17), residues: 792 loop : 0.10 (0.14), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 544 HIS 0.007 0.001 HIS C 104 PHE 0.011 0.001 PHE C 351 TYR 0.007 0.001 TYR C 173 ARG 0.007 0.000 ARG A 453 Details of bonding type rmsd hydrogen bonds : bond 0.03824 ( 1551) hydrogen bonds : angle 5.01212 ( 4476) covalent geometry : bond 0.00231 (34050) covalent geometry : angle 0.47541 (46062) Misc. bond : bond 0.00007 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 480 time to evaluate : 4.081 Fit side-chains REVERT: A 21 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7048 (mp0) REVERT: A 29 LYS cc_start: 0.8317 (tppt) cc_final: 0.7923 (mmmt) REVERT: A 49 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8431 (tt0) REVERT: A 171 ASP cc_start: 0.8825 (m-30) cc_final: 0.8276 (t0) REVERT: A 257 GLU cc_start: 0.8166 (tt0) cc_final: 0.7642 (tm-30) REVERT: A 317 ARG cc_start: 0.8380 (mtt-85) cc_final: 0.7920 (mtp85) REVERT: B 21 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7012 (mp0) REVERT: B 22 LYS cc_start: 0.7815 (tttt) cc_final: 0.7311 (ttpt) REVERT: B 30 ARG cc_start: 0.7987 (mtt90) cc_final: 0.7713 (mtm-85) REVERT: B 49 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8394 (tt0) REVERT: B 171 ASP cc_start: 0.8804 (m-30) cc_final: 0.8214 (t0) REVERT: B 220 LYS cc_start: 0.8800 (mtpp) cc_final: 0.8528 (mtmm) REVERT: B 257 GLU cc_start: 0.8207 (tt0) cc_final: 0.7659 (tm-30) REVERT: B 266 ASP cc_start: 0.8285 (t70) cc_final: 0.7924 (t0) REVERT: B 317 ARG cc_start: 0.8425 (mtt-85) cc_final: 0.7748 (mtm180) REVERT: C 9 GLU cc_start: 0.7397 (mm-30) cc_final: 0.6904 (mm-30) REVERT: C 22 LYS cc_start: 0.7874 (ttmm) cc_final: 0.7576 (ttpt) REVERT: C 49 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8466 (tt0) REVERT: C 171 ASP cc_start: 0.8597 (m-30) cc_final: 0.8310 (t0) REVERT: C 257 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7899 (tm-30) REVERT: C 266 ASP cc_start: 0.8584 (t0) cc_final: 0.8188 (t0) REVERT: C 449 LYS cc_start: 0.7472 (tptt) cc_final: 0.7138 (tptm) REVERT: C 452 GLU cc_start: 0.7721 (tt0) cc_final: 0.7199 (tt0) REVERT: C 453 ARG cc_start: 0.6305 (mtt-85) cc_final: 0.5768 (mtt90) REVERT: C 455 LYS cc_start: 0.7567 (OUTLIER) cc_final: 0.7348 (tppp) REVERT: C 456 GLU cc_start: 0.7319 (pt0) cc_final: 0.7040 (pt0) REVERT: C 458 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7140 (tp30) REVERT: C 475 GLU cc_start: 0.8387 (tp30) cc_final: 0.7966 (tp30) REVERT: C 497 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7529 (pt0) REVERT: C 502 ARG cc_start: 0.8531 (mtp85) cc_final: 0.7951 (ttm170) REVERT: D 21 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7037 (mp0) REVERT: D 22 LYS cc_start: 0.8145 (tttm) cc_final: 0.7789 (ttpt) REVERT: D 117 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8090 (ttmm) REVERT: D 171 ASP cc_start: 0.8737 (m-30) cc_final: 0.8266 (t0) REVERT: D 453 ARG cc_start: 0.6688 (mtt-85) cc_final: 0.6066 (mtt180) REVERT: D 475 GLU cc_start: 0.8453 (tp30) cc_final: 0.7920 (tp30) REVERT: E 22 LYS cc_start: 0.7994 (tttt) cc_final: 0.7460 (ttpt) REVERT: E 171 ASP cc_start: 0.8810 (OUTLIER) cc_final: 0.8315 (t0) REVERT: E 220 LYS cc_start: 0.8866 (mtpp) cc_final: 0.8578 (mtmm) REVERT: F 9 GLU cc_start: 0.7394 (mm-30) cc_final: 0.6898 (mm-30) REVERT: F 21 GLU cc_start: 0.7639 (mm-30) cc_final: 0.6876 (mp0) REVERT: F 22 LYS cc_start: 0.7805 (ptmt) cc_final: 0.7146 (pptt) REVERT: F 29 LYS cc_start: 0.8284 (mmtp) cc_final: 0.7945 (mmmt) REVERT: F 30 ARG cc_start: 0.7964 (mtt90) cc_final: 0.7738 (mtm-85) REVERT: F 49 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8449 (tt0) REVERT: F 257 GLU cc_start: 0.8085 (tt0) cc_final: 0.7574 (tm-30) REVERT: F 453 ARG cc_start: 0.7010 (mmt180) cc_final: 0.6057 (mtt180) REVERT: F 458 GLU cc_start: 0.7576 (tt0) cc_final: 0.6996 (tp30) REVERT: F 502 ARG cc_start: 0.8534 (mtp85) cc_final: 0.7918 (ttm170) REVERT: G 483 ARG cc_start: 0.8068 (mtp85) cc_final: 0.6951 (mmm160) REVERT: G 489 MET cc_start: 0.8760 (ttp) cc_final: 0.8443 (ttp) REVERT: G 490 ARG cc_start: 0.8147 (ptp90) cc_final: 0.7634 (ptp-170) REVERT: G 527 ASP cc_start: 0.7845 (OUTLIER) cc_final: 0.7505 (p0) REVERT: G 630 GLU cc_start: 0.6289 (OUTLIER) cc_final: 0.4906 (tm-30) REVERT: G 635 GLU cc_start: 0.5445 (mt-10) cc_final: 0.4305 (pt0) REVERT: H 483 ARG cc_start: 0.7976 (mtp85) cc_final: 0.6881 (mmm160) REVERT: H 490 ARG cc_start: 0.8089 (ptp90) cc_final: 0.7732 (ptp-170) REVERT: H 534 ARG cc_start: 0.7974 (ttm110) cc_final: 0.7267 (mtp85) REVERT: H 580 ARG cc_start: 0.8187 (mmm-85) cc_final: 0.7603 (mmt-90) REVERT: H 599 LYS cc_start: 0.5232 (OUTLIER) cc_final: 0.4695 (tmmt) REVERT: H 630 GLU cc_start: 0.6341 (tt0) cc_final: 0.6008 (tt0) REVERT: H 635 GLU cc_start: 0.5753 (mt-10) cc_final: 0.5016 (pt0) REVERT: I 483 ARG cc_start: 0.7972 (mtp85) cc_final: 0.6904 (mmm160) REVERT: I 521 LEU cc_start: 0.8039 (mt) cc_final: 0.7580 (tp) REVERT: I 527 ASP cc_start: 0.8123 (OUTLIER) cc_final: 0.7694 (p0) REVERT: I 630 GLU cc_start: 0.6513 (tt0) cc_final: 0.6172 (tt0) REVERT: J 483 ARG cc_start: 0.8177 (mtt-85) cc_final: 0.7108 (mmm160) REVERT: J 490 ARG cc_start: 0.8064 (ptp90) cc_final: 0.7587 (ptp-170) REVERT: J 534 ARG cc_start: 0.7880 (mtp85) cc_final: 0.7499 (mtt-85) REVERT: J 630 GLU cc_start: 0.6342 (OUTLIER) cc_final: 0.4862 (tm-30) REVERT: K 483 ARG cc_start: 0.8278 (mtt180) cc_final: 0.7166 (mmm160) REVERT: K 490 ARG cc_start: 0.8133 (ptp90) cc_final: 0.7895 (ptp-170) REVERT: K 534 ARG cc_start: 0.7190 (mtt90) cc_final: 0.6375 (mmm160) REVERT: K 630 GLU cc_start: 0.6410 (OUTLIER) cc_final: 0.5240 (tm-30) REVERT: K 635 GLU cc_start: 0.5452 (mt-10) cc_final: 0.4367 (pt0) REVERT: L 483 ARG cc_start: 0.7998 (mtp85) cc_final: 0.6931 (mmm160) REVERT: L 534 ARG cc_start: 0.7844 (ttm-80) cc_final: 0.7456 (ttm-80) REVERT: L 635 GLU cc_start: 0.5229 (mt-10) cc_final: 0.4345 (pt0) outliers start: 48 outliers final: 25 residues processed: 505 average time/residue: 1.9307 time to fit residues: 1123.6895 Evaluate side-chains 516 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 476 time to evaluate : 3.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 143 HIS Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain C residue 497 GLU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 29 LYS Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 268 SER Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 143 HIS Chi-restraints excluded: chain F residue 251 GLU Chi-restraints excluded: chain G residue 527 ASP Chi-restraints excluded: chain G residue 630 GLU Chi-restraints excluded: chain H residue 552 SER Chi-restraints excluded: chain H residue 599 LYS Chi-restraints excluded: chain I residue 527 ASP Chi-restraints excluded: chain I residue 552 SER Chi-restraints excluded: chain J residue 552 SER Chi-restraints excluded: chain J residue 630 GLU Chi-restraints excluded: chain K residue 552 SER Chi-restraints excluded: chain K residue 591 VAL Chi-restraints excluded: chain K residue 630 GLU Chi-restraints excluded: chain L residue 552 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 160 optimal weight: 4.9990 chunk 176 optimal weight: 0.8980 chunk 126 optimal weight: 0.8980 chunk 109 optimal weight: 0.9980 chunk 353 optimal weight: 7.9990 chunk 372 optimal weight: 5.9990 chunk 348 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 297 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 67 GLN E 67 GLN G 479 ASN H 479 ASN H 556 GLN J 479 ASN ** J 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 479 ASN K 556 GLN L 556 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.138287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.084338 restraints weight = 33883.207| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 1.84 r_work: 0.2861 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 34056 Z= 0.123 Angle : 0.493 9.581 46062 Z= 0.262 Chirality : 0.045 0.144 5148 Planarity : 0.004 0.036 6048 Dihedral : 7.190 51.582 5158 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.33 % Allowed : 11.74 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.13), residues: 4290 helix: 1.48 (0.14), residues: 1512 sheet: 1.23 (0.17), residues: 792 loop : 0.09 (0.14), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 544 HIS 0.008 0.001 HIS E 104 PHE 0.012 0.001 PHE F 351 TYR 0.009 0.001 TYR F 173 ARG 0.008 0.000 ARG A 453 Details of bonding type rmsd hydrogen bonds : bond 0.04156 ( 1551) hydrogen bonds : angle 5.03051 ( 4476) covalent geometry : bond 0.00281 (34050) covalent geometry : angle 0.49298 (46062) Misc. bond : bond 0.00005 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 475 time to evaluate : 3.914 Fit side-chains REVERT: A 21 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7044 (mp0) REVERT: A 29 LYS cc_start: 0.8319 (tppt) cc_final: 0.7926 (mmmt) REVERT: A 49 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8424 (tt0) REVERT: A 171 ASP cc_start: 0.8834 (m-30) cc_final: 0.8302 (t0) REVERT: A 257 GLU cc_start: 0.8161 (tt0) cc_final: 0.7725 (tm-30) REVERT: A 317 ARG cc_start: 0.8385 (mtt-85) cc_final: 0.7917 (mtp85) REVERT: B 21 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7010 (mp0) REVERT: B 22 LYS cc_start: 0.7813 (tttt) cc_final: 0.7309 (ttpt) REVERT: B 30 ARG cc_start: 0.7998 (mtt90) cc_final: 0.7719 (mtm-85) REVERT: B 49 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8387 (tt0) REVERT: B 171 ASP cc_start: 0.8806 (m-30) cc_final: 0.8233 (t0) REVERT: B 220 LYS cc_start: 0.8802 (mtpp) cc_final: 0.8495 (mtmm) REVERT: B 257 GLU cc_start: 0.8197 (tt0) cc_final: 0.7677 (tm-30) REVERT: B 266 ASP cc_start: 0.8268 (t70) cc_final: 0.8007 (t0) REVERT: B 317 ARG cc_start: 0.8421 (mtt-85) cc_final: 0.7728 (mtm180) REVERT: C 9 GLU cc_start: 0.7414 (mm-30) cc_final: 0.6925 (mm-30) REVERT: C 21 GLU cc_start: 0.7781 (tp30) cc_final: 0.7067 (mp0) REVERT: C 22 LYS cc_start: 0.7871 (ttmm) cc_final: 0.7510 (ttpt) REVERT: C 49 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8441 (tt0) REVERT: C 171 ASP cc_start: 0.8588 (m-30) cc_final: 0.8329 (t0) REVERT: C 257 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7887 (tm-30) REVERT: C 266 ASP cc_start: 0.8598 (t0) cc_final: 0.8204 (t0) REVERT: C 449 LYS cc_start: 0.7501 (tptt) cc_final: 0.7160 (tptm) REVERT: C 452 GLU cc_start: 0.7732 (tt0) cc_final: 0.7261 (tt0) REVERT: C 453 ARG cc_start: 0.6302 (mtt-85) cc_final: 0.5765 (mtt90) REVERT: C 455 LYS cc_start: 0.7590 (OUTLIER) cc_final: 0.7372 (tppp) REVERT: C 456 GLU cc_start: 0.7336 (pt0) cc_final: 0.7034 (pt0) REVERT: C 458 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7128 (tp30) REVERT: C 475 GLU cc_start: 0.8379 (tp30) cc_final: 0.7967 (tp30) REVERT: C 497 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7516 (pt0) REVERT: C 502 ARG cc_start: 0.8538 (mtp85) cc_final: 0.7960 (ttm170) REVERT: D 21 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7046 (mp0) REVERT: D 22 LYS cc_start: 0.8144 (tttm) cc_final: 0.7787 (ttpt) REVERT: D 117 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8144 (ttmm) REVERT: D 171 ASP cc_start: 0.8726 (m-30) cc_final: 0.8294 (t0) REVERT: D 215 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8109 (ttmm) REVERT: D 453 ARG cc_start: 0.6707 (mtt-85) cc_final: 0.6082 (mtt180) REVERT: D 475 GLU cc_start: 0.8447 (tp30) cc_final: 0.7904 (tp30) REVERT: E 22 LYS cc_start: 0.7993 (tttt) cc_final: 0.7453 (ttpt) REVERT: E 29 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8165 (mtmt) REVERT: E 171 ASP cc_start: 0.8811 (OUTLIER) cc_final: 0.8332 (t0) REVERT: E 220 LYS cc_start: 0.8871 (mtpp) cc_final: 0.8575 (mtmm) REVERT: F 9 GLU cc_start: 0.7392 (mm-30) cc_final: 0.6901 (mm-30) REVERT: F 21 GLU cc_start: 0.7630 (mm-30) cc_final: 0.6882 (mp0) REVERT: F 22 LYS cc_start: 0.7805 (ptmt) cc_final: 0.7145 (pptt) REVERT: F 29 LYS cc_start: 0.8291 (mmtp) cc_final: 0.7957 (mmmt) REVERT: F 30 ARG cc_start: 0.7965 (mtt90) cc_final: 0.7739 (mtm-85) REVERT: F 49 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8444 (tt0) REVERT: F 257 GLU cc_start: 0.8058 (tt0) cc_final: 0.7546 (tm-30) REVERT: F 453 ARG cc_start: 0.7016 (mmt180) cc_final: 0.6072 (mtt180) REVERT: F 458 GLU cc_start: 0.7615 (tt0) cc_final: 0.7034 (tp30) REVERT: F 502 ARG cc_start: 0.8547 (mtp85) cc_final: 0.7930 (ttm170) REVERT: G 483 ARG cc_start: 0.8066 (mtp85) cc_final: 0.6940 (mmm160) REVERT: G 489 MET cc_start: 0.8750 (ttp) cc_final: 0.8431 (ttp) REVERT: G 490 ARG cc_start: 0.8131 (ptp90) cc_final: 0.7634 (ptp-170) REVERT: G 527 ASP cc_start: 0.7856 (OUTLIER) cc_final: 0.7495 (p0) REVERT: G 630 GLU cc_start: 0.6300 (OUTLIER) cc_final: 0.4934 (tm-30) REVERT: G 635 GLU cc_start: 0.5303 (mt-10) cc_final: 0.4299 (pt0) REVERT: H 483 ARG cc_start: 0.7991 (mtp85) cc_final: 0.6871 (mmm160) REVERT: H 490 ARG cc_start: 0.8096 (ptp90) cc_final: 0.7739 (ptp-170) REVERT: H 534 ARG cc_start: 0.7984 (ttm110) cc_final: 0.7294 (mtp85) REVERT: H 580 ARG cc_start: 0.8232 (mmm-85) cc_final: 0.7630 (mmt-90) REVERT: H 599 LYS cc_start: 0.5260 (OUTLIER) cc_final: 0.4729 (tmmt) REVERT: H 630 GLU cc_start: 0.6350 (tt0) cc_final: 0.6017 (tt0) REVERT: H 635 GLU cc_start: 0.5771 (mt-10) cc_final: 0.5050 (pt0) REVERT: I 483 ARG cc_start: 0.7981 (mtp85) cc_final: 0.6905 (mmm160) REVERT: I 527 ASP cc_start: 0.8133 (OUTLIER) cc_final: 0.7715 (p0) REVERT: I 534 ARG cc_start: 0.7707 (ttm-80) cc_final: 0.7275 (ttm170) REVERT: I 630 GLU cc_start: 0.6526 (tt0) cc_final: 0.6189 (tt0) REVERT: J 483 ARG cc_start: 0.8174 (mtt-85) cc_final: 0.7090 (mmm160) REVERT: J 490 ARG cc_start: 0.8051 (ptp90) cc_final: 0.7580 (ptp-170) REVERT: J 534 ARG cc_start: 0.7887 (mtp85) cc_final: 0.7507 (mtt-85) REVERT: J 630 GLU cc_start: 0.6366 (OUTLIER) cc_final: 0.4894 (tm-30) REVERT: K 483 ARG cc_start: 0.8288 (mtt180) cc_final: 0.7158 (mmm160) REVERT: K 490 ARG cc_start: 0.8128 (ptp90) cc_final: 0.7893 (ptp-170) REVERT: K 534 ARG cc_start: 0.7174 (mtt90) cc_final: 0.6363 (mmm160) REVERT: K 630 GLU cc_start: 0.6398 (OUTLIER) cc_final: 0.5234 (tm-30) REVERT: K 635 GLU cc_start: 0.5449 (mt-10) cc_final: 0.4361 (pt0) REVERT: L 483 ARG cc_start: 0.8019 (mtp85) cc_final: 0.6929 (mmm160) REVERT: L 520 ASP cc_start: 0.5463 (m-30) cc_final: 0.5101 (m-30) REVERT: L 534 ARG cc_start: 0.7845 (ttm-80) cc_final: 0.7614 (ttm-80) REVERT: L 635 GLU cc_start: 0.5286 (mt-10) cc_final: 0.4377 (pt0) outliers start: 46 outliers final: 24 residues processed: 500 average time/residue: 1.9103 time to fit residues: 1103.9743 Evaluate side-chains 516 residues out of total 3450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 475 time to evaluate : 3.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 143 HIS Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain C residue 497 GLU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 29 LYS Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 268 SER Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 143 HIS Chi-restraints excluded: chain F residue 251 GLU Chi-restraints excluded: chain G residue 527 ASP Chi-restraints excluded: chain G residue 552 SER Chi-restraints excluded: chain G residue 630 GLU Chi-restraints excluded: chain H residue 552 SER Chi-restraints excluded: chain H residue 599 LYS Chi-restraints excluded: chain I residue 527 ASP Chi-restraints excluded: chain I residue 552 SER Chi-restraints excluded: chain J residue 552 SER Chi-restraints excluded: chain J residue 630 GLU Chi-restraints excluded: chain K residue 552 SER Chi-restraints excluded: chain K residue 591 VAL Chi-restraints excluded: chain K residue 630 GLU Chi-restraints excluded: chain L residue 552 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 302 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 165 optimal weight: 0.7980 chunk 380 optimal weight: 7.9990 chunk 122 optimal weight: 0.7980 chunk 144 optimal weight: 1.9990 chunk 145 optimal weight: 0.8980 chunk 356 optimal weight: 20.0000 chunk 35 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 335 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 67 GLN E 67 GLN G 479 ASN H 479 ASN H 556 GLN J 479 ASN ** J 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 479 ASN K 556 GLN L 556 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.137852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.083712 restraints weight = 33997.296| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 1.84 r_work: 0.2850 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 34056 Z= 0.137 Angle : 0.506 9.680 46062 Z= 0.268 Chirality : 0.045 0.144 5148 Planarity : 0.004 0.035 6048 Dihedral : 7.220 51.252 5158 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.25 % Allowed : 11.88 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.13), residues: 4290 helix: 1.44 (0.14), residues: 1512 sheet: 1.23 (0.17), residues: 792 loop : 0.08 (0.14), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 544 HIS 0.009 0.001 HIS E 104 PHE 0.012 0.001 PHE C 351 TYR 0.010 0.001 TYR F 173 ARG 0.008 0.000 ARG A 453 Details of bonding type rmsd hydrogen bonds : bond 0.04333 ( 1551) hydrogen bonds : angle 5.06714 ( 4476) covalent geometry : bond 0.00317 (34050) covalent geometry : angle 0.50556 (46062) Misc. bond : bond 0.00006 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 36723.79 seconds wall clock time: 631 minutes 12.59 seconds (37872.59 seconds total)