Starting phenix.real_space_refine on Sun Jun 29 20:25:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yyo_14385/06_2025/7yyo_14385.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yyo_14385/06_2025/7yyo_14385.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yyo_14385/06_2025/7yyo_14385.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yyo_14385/06_2025/7yyo_14385.map" model { file = "/net/cci-nas-00/data/ceres_data/7yyo_14385/06_2025/7yyo_14385.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yyo_14385/06_2025/7yyo_14385.cif" } resolution = 2.87 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= 0.020 sd= 0.188 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: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 8 5.21 5 S 192 5.16 5 C 22328 2.51 5 N 6040 2.21 5 O 6552 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 448 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 35136 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3494 Classifications: {'peptide': 445} Link IDs: {'CIS': 5, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 419} Chain: "B" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 876 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 6, 'TRANS': 99} Chain: "C" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3494 Classifications: {'peptide': 445} Link IDs: {'CIS': 5, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 419} Chain: "D" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 876 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 6, 'TRANS': 99} Chain: "E" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3494 Classifications: {'peptide': 445} Link IDs: {'CIS': 5, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 419} Chain: "F" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 876 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 6, 'TRANS': 99} Chain: "G" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3494 Classifications: {'peptide': 445} Link IDs: {'CIS': 5, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 419} Chain: "H" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 876 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 6, 'TRANS': 99} Chain: "I" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3494 Classifications: {'peptide': 445} Link IDs: {'CIS': 5, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 419} Chain: "J" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 876 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 6, 'TRANS': 99} Chain: "K" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3494 Classifications: {'peptide': 445} Link IDs: {'CIS': 5, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 419} Chain: "L" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 876 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 6, 'TRANS': 99} Chain: "M" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3494 Classifications: {'peptide': 445} Link IDs: {'CIS': 5, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 419} Chain: "N" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 876 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 6, 'TRANS': 99} Chain: "O" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3494 Classifications: {'peptide': 445} Link IDs: {'CIS': 5, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 419} Chain: "P" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 876 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 6, 'TRANS': 99} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 18.04, per 1000 atoms: 0.51 Number of scatterers: 35136 At special positions: 0 Unit cell: (144.3, 145.41, 129.87, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 192 16.00 P 16 15.00 Mg 8 11.99 O 6552 8.00 N 6040 7.00 C 22328 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=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.96 Conformation dependent library (CDL) restraints added in 4.2 seconds 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8032 Finding SS restraints... Secondary structure from input PDB file: 200 helices and 32 sheets defined 45.2% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.23 Creating SS restraints... Processing helix chain 'A' and resid 41 through 53 removed outlier: 3.540A pdb=" N SER A 53 " --> pdb=" O VAL A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 66 removed outlier: 3.523A pdb=" N LEU A 65 " --> pdb=" O TRP A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 100 removed outlier: 3.746A pdb=" N PHE A 100 " --> pdb=" O LEU A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 113 removed outlier: 3.693A pdb=" N VAL A 108 " --> pdb=" O SER A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 138 Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 173 through 186 removed outlier: 3.541A pdb=" N GLY A 178 " --> pdb=" O GLY A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 225 removed outlier: 3.636A pdb=" N GLU A 211 " --> pdb=" O GLN A 207 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU A 215 " --> pdb=" O GLU A 211 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN A 222 " --> pdb=" O ALA A 218 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 252 Processing helix chain 'A' and resid 261 through 265 Processing helix chain 'A' and resid 265 through 280 removed outlier: 3.793A pdb=" N ARG A 277 " --> pdb=" O SER A 273 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS A 278 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 295 removed outlier: 3.800A pdb=" N ARG A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 314 removed outlier: 3.644A pdb=" N LEU A 306 " --> pdb=" O HIS A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 343 removed outlier: 3.590A pdb=" N PHE A 337 " --> pdb=" O THR A 333 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN A 340 " --> pdb=" O GLY A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 377 No H-bonds generated for 'chain 'A' and resid 375 through 377' Processing helix chain 'A' and resid 378 through 387 removed outlier: 3.510A pdb=" N ALA A 384 " --> pdb=" O PRO A 380 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE A 386 " --> pdb=" O LEU A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 400 removed outlier: 4.383A pdb=" N HIS A 399 " --> pdb=" O GLY A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 425 removed outlier: 3.575A pdb=" N VAL A 414 " --> pdb=" O ALA A 410 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA A 425 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 438 Processing helix chain 'A' and resid 440 through 443 Processing helix chain 'A' and resid 444 through 454 removed outlier: 3.503A pdb=" N ILE A 449 " --> pdb=" O PRO A 445 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU A 452 " --> pdb=" O ALA A 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 40 Processing helix chain 'B' and resid 50 through 54 removed outlier: 3.785A pdb=" N SER B 54 " --> pdb=" O PRO B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 76 removed outlier: 4.251A pdb=" N ILE B 75 " --> pdb=" O ASP B 71 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL B 76 " --> pdb=" O LEU B 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 71 through 76' Processing helix chain 'B' and resid 77 through 86 removed outlier: 3.507A pdb=" N ALA B 81 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N CYS B 82 " --> pdb=" O GLU B 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 53 removed outlier: 3.540A pdb=" N SER C 53 " --> pdb=" O VAL C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 66 removed outlier: 3.523A pdb=" N LEU C 65 " --> pdb=" O TRP C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 100 removed outlier: 3.746A pdb=" N PHE C 100 " --> pdb=" O LEU C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 113 removed outlier: 3.692A pdb=" N VAL C 108 " --> pdb=" O SER C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 138 Processing helix chain 'C' and resid 146 through 155 Processing helix chain 'C' and resid 173 through 186 removed outlier: 3.541A pdb=" N GLY C 178 " --> pdb=" O GLY C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 225 removed outlier: 3.636A pdb=" N GLU C 211 " --> pdb=" O GLN C 207 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU C 215 " --> pdb=" O GLU C 211 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN C 222 " --> pdb=" O ALA C 218 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU C 223 " --> pdb=" O LEU C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 252 Processing helix chain 'C' and resid 261 through 265 Processing helix chain 'C' and resid 265 through 280 removed outlier: 3.793A pdb=" N ARG C 277 " --> pdb=" O SER C 273 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS C 278 " --> pdb=" O LYS C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 295 removed outlier: 3.800A pdb=" N ARG C 295 " --> pdb=" O ALA C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 314 removed outlier: 3.644A pdb=" N LEU C 306 " --> pdb=" O HIS C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 343 removed outlier: 3.591A pdb=" N PHE C 337 " --> pdb=" O THR C 333 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN C 340 " --> pdb=" O GLY C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 377 No H-bonds generated for 'chain 'C' and resid 375 through 377' Processing helix chain 'C' and resid 378 through 387 removed outlier: 3.511A pdb=" N ALA C 384 " --> pdb=" O PRO C 380 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE C 386 " --> pdb=" O LEU C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 400 removed outlier: 4.383A pdb=" N HIS C 399 " --> pdb=" O GLY C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 425 removed outlier: 3.575A pdb=" N VAL C 414 " --> pdb=" O ALA C 410 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA C 425 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 438 Processing helix chain 'C' and resid 440 through 443 Processing helix chain 'C' and resid 444 through 454 removed outlier: 3.504A pdb=" N ILE C 449 " --> pdb=" O PRO C 445 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU C 452 " --> pdb=" O ALA C 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 40 Processing helix chain 'D' and resid 50 through 54 removed outlier: 3.785A pdb=" N SER D 54 " --> pdb=" O PRO D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 76 removed outlier: 4.251A pdb=" N ILE D 75 " --> pdb=" O ASP D 71 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL D 76 " --> pdb=" O LEU D 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 71 through 76' Processing helix chain 'D' and resid 77 through 86 removed outlier: 3.507A pdb=" N ALA D 81 " --> pdb=" O SER D 77 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N CYS D 82 " --> pdb=" O GLU D 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 53 removed outlier: 3.540A pdb=" N SER E 53 " --> pdb=" O VAL E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 66 removed outlier: 3.523A pdb=" N LEU E 65 " --> pdb=" O TRP E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 100 removed outlier: 3.746A pdb=" N PHE E 100 " --> pdb=" O LEU E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 113 removed outlier: 3.693A pdb=" N VAL E 108 " --> pdb=" O SER E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 138 Processing helix chain 'E' and resid 146 through 155 Processing helix chain 'E' and resid 173 through 186 removed outlier: 3.540A pdb=" N GLY E 178 " --> pdb=" O GLY E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 225 removed outlier: 3.636A pdb=" N GLU E 211 " --> pdb=" O GLN E 207 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU E 215 " --> pdb=" O GLU E 211 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN E 222 " --> pdb=" O ALA E 218 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU E 223 " --> pdb=" O LEU E 219 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 252 Processing helix chain 'E' and resid 261 through 265 Processing helix chain 'E' and resid 265 through 280 removed outlier: 3.793A pdb=" N ARG E 277 " --> pdb=" O SER E 273 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS E 278 " --> pdb=" O LYS E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 290 through 295 removed outlier: 3.800A pdb=" N ARG E 295 " --> pdb=" O ALA E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 314 removed outlier: 3.644A pdb=" N LEU E 306 " --> pdb=" O HIS E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 331 through 343 removed outlier: 3.590A pdb=" N PHE E 337 " --> pdb=" O THR E 333 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN E 340 " --> pdb=" O GLY E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 375 through 377 No H-bonds generated for 'chain 'E' and resid 375 through 377' Processing helix chain 'E' and resid 378 through 387 removed outlier: 3.510A pdb=" N ALA E 384 " --> pdb=" O PRO E 380 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE E 386 " --> pdb=" O LEU E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 400 removed outlier: 4.383A pdb=" N HIS E 399 " --> pdb=" O GLY E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 425 removed outlier: 3.575A pdb=" N VAL E 414 " --> pdb=" O ALA E 410 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA E 425 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 438 Processing helix chain 'E' and resid 440 through 443 Processing helix chain 'E' and resid 444 through 454 removed outlier: 3.504A pdb=" N ILE E 449 " --> pdb=" O PRO E 445 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU E 452 " --> pdb=" O ALA E 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 40 Processing helix chain 'F' and resid 50 through 54 removed outlier: 3.786A pdb=" N SER F 54 " --> pdb=" O PRO F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 76 removed outlier: 4.250A pdb=" N ILE F 75 " --> pdb=" O ASP F 71 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL F 76 " --> pdb=" O LEU F 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 71 through 76' Processing helix chain 'F' and resid 77 through 86 removed outlier: 3.507A pdb=" N ALA F 81 " --> pdb=" O SER F 77 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N CYS F 82 " --> pdb=" O GLU F 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 41 through 53 removed outlier: 3.540A pdb=" N SER G 53 " --> pdb=" O VAL G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 66 removed outlier: 3.523A pdb=" N LEU G 65 " --> pdb=" O TRP G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 100 removed outlier: 3.747A pdb=" N PHE G 100 " --> pdb=" O LEU G 97 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 113 removed outlier: 3.693A pdb=" N VAL G 108 " --> pdb=" O SER G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 138 Processing helix chain 'G' and resid 146 through 155 Processing helix chain 'G' and resid 173 through 186 removed outlier: 3.541A pdb=" N GLY G 178 " --> pdb=" O GLY G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 225 removed outlier: 3.636A pdb=" N GLU G 211 " --> pdb=" O GLN G 207 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU G 215 " --> pdb=" O GLU G 211 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN G 222 " --> pdb=" O ALA G 218 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU G 223 " --> pdb=" O LEU G 219 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 252 Processing helix chain 'G' and resid 261 through 265 Processing helix chain 'G' and resid 265 through 280 removed outlier: 3.793A pdb=" N ARG G 277 " --> pdb=" O SER G 273 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS G 278 " --> pdb=" O LYS G 274 " (cutoff:3.500A) Processing helix chain 'G' and resid 290 through 295 removed outlier: 3.800A pdb=" N ARG G 295 " --> pdb=" O ALA G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 302 through 314 removed outlier: 3.644A pdb=" N LEU G 306 " --> pdb=" O HIS G 302 " (cutoff:3.500A) Processing helix chain 'G' and resid 331 through 343 removed outlier: 3.590A pdb=" N PHE G 337 " --> pdb=" O THR G 333 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN G 340 " --> pdb=" O GLY G 336 " (cutoff:3.500A) Processing helix chain 'G' and resid 375 through 377 No H-bonds generated for 'chain 'G' and resid 375 through 377' Processing helix chain 'G' and resid 378 through 387 removed outlier: 3.510A pdb=" N ALA G 384 " --> pdb=" O PRO G 380 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE G 386 " --> pdb=" O LEU G 382 " (cutoff:3.500A) Processing helix chain 'G' and resid 395 through 400 removed outlier: 4.383A pdb=" N HIS G 399 " --> pdb=" O GLY G 395 " (cutoff:3.500A) Processing helix chain 'G' and resid 405 through 425 removed outlier: 3.576A pdb=" N VAL G 414 " --> pdb=" O ALA G 410 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA G 425 " --> pdb=" O LYS G 421 " (cutoff:3.500A) Processing helix chain 'G' and resid 432 through 438 Processing helix chain 'G' and resid 440 through 443 Processing helix chain 'G' and resid 444 through 454 removed outlier: 3.503A pdb=" N ILE G 449 " --> pdb=" O PRO G 445 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU G 452 " --> pdb=" O ALA G 448 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 40 Processing helix chain 'H' and resid 50 through 54 removed outlier: 3.786A pdb=" N SER H 54 " --> pdb=" O PRO H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 76 removed outlier: 4.251A pdb=" N ILE H 75 " --> pdb=" O ASP H 71 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL H 76 " --> pdb=" O LEU H 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 71 through 76' Processing helix chain 'H' and resid 77 through 86 removed outlier: 3.507A pdb=" N ALA H 81 " --> pdb=" O SER H 77 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N CYS H 82 " --> pdb=" O GLU H 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 41 through 53 removed outlier: 3.540A pdb=" N SER I 53 " --> pdb=" O VAL I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 66 removed outlier: 3.523A pdb=" N LEU I 65 " --> pdb=" O TRP I 62 " (cutoff:3.500A) Processing helix chain 'I' and resid 96 through 100 removed outlier: 3.747A pdb=" N PHE I 100 " --> pdb=" O LEU I 97 " (cutoff:3.500A) Processing helix chain 'I' and resid 104 through 113 removed outlier: 3.692A pdb=" N VAL I 108 " --> pdb=" O SER I 104 " (cutoff:3.500A) Processing helix chain 'I' and resid 133 through 138 Processing helix chain 'I' and resid 146 through 155 Processing helix chain 'I' and resid 173 through 186 removed outlier: 3.541A pdb=" N GLY I 178 " --> pdb=" O GLY I 174 " (cutoff:3.500A) Processing helix chain 'I' and resid 205 through 225 removed outlier: 3.637A pdb=" N GLU I 211 " --> pdb=" O GLN I 207 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU I 215 " --> pdb=" O GLU I 211 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN I 222 " --> pdb=" O ALA I 218 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU I 223 " --> pdb=" O LEU I 219 " (cutoff:3.500A) Processing helix chain 'I' and resid 238 through 252 Processing helix chain 'I' and resid 261 through 265 Processing helix chain 'I' and resid 265 through 280 removed outlier: 3.793A pdb=" N ARG I 277 " --> pdb=" O SER I 273 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS I 278 " --> pdb=" O LYS I 274 " (cutoff:3.500A) Processing helix chain 'I' and resid 290 through 295 removed outlier: 3.800A pdb=" N ARG I 295 " --> pdb=" O ALA I 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 302 through 314 removed outlier: 3.645A pdb=" N LEU I 306 " --> pdb=" O HIS I 302 " (cutoff:3.500A) Processing helix chain 'I' and resid 331 through 343 removed outlier: 3.589A pdb=" N PHE I 337 " --> pdb=" O THR I 333 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN I 340 " --> pdb=" O GLY I 336 " (cutoff:3.500A) Processing helix chain 'I' and resid 375 through 377 No H-bonds generated for 'chain 'I' and resid 375 through 377' Processing helix chain 'I' and resid 378 through 387 removed outlier: 3.511A pdb=" N ALA I 384 " --> pdb=" O PRO I 380 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE I 386 " --> pdb=" O LEU I 382 " (cutoff:3.500A) Processing helix chain 'I' and resid 395 through 400 removed outlier: 4.383A pdb=" N HIS I 399 " --> pdb=" O GLY I 395 " (cutoff:3.500A) Processing helix chain 'I' and resid 405 through 425 removed outlier: 3.575A pdb=" N VAL I 414 " --> pdb=" O ALA I 410 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA I 425 " --> pdb=" O LYS I 421 " (cutoff:3.500A) Processing helix chain 'I' and resid 432 through 438 Processing helix chain 'I' and resid 440 through 443 Processing helix chain 'I' and resid 444 through 454 removed outlier: 3.503A pdb=" N ILE I 449 " --> pdb=" O PRO I 445 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU I 452 " --> pdb=" O ALA I 448 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 40 Processing helix chain 'J' and resid 50 through 54 removed outlier: 3.786A pdb=" N SER J 54 " --> pdb=" O PRO J 51 " (cutoff:3.500A) Processing helix chain 'J' and resid 71 through 76 removed outlier: 4.251A pdb=" N ILE J 75 " --> pdb=" O ASP J 71 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL J 76 " --> pdb=" O LEU J 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 71 through 76' Processing helix chain 'J' and resid 77 through 86 removed outlier: 3.507A pdb=" N ALA J 81 " --> pdb=" O SER J 77 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N CYS J 82 " --> pdb=" O GLU J 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 41 through 53 removed outlier: 3.540A pdb=" N SER K 53 " --> pdb=" O VAL K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 62 through 66 removed outlier: 3.523A pdb=" N LEU K 65 " --> pdb=" O TRP K 62 " (cutoff:3.500A) Processing helix chain 'K' and resid 96 through 100 removed outlier: 3.747A pdb=" N PHE K 100 " --> pdb=" O LEU K 97 " (cutoff:3.500A) Processing helix chain 'K' and resid 104 through 113 removed outlier: 3.692A pdb=" N VAL K 108 " --> pdb=" O SER K 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 133 through 138 Processing helix chain 'K' and resid 146 through 155 Processing helix chain 'K' and resid 173 through 186 removed outlier: 3.541A pdb=" N GLY K 178 " --> pdb=" O GLY K 174 " (cutoff:3.500A) Processing helix chain 'K' and resid 205 through 225 removed outlier: 3.636A pdb=" N GLU K 211 " --> pdb=" O GLN K 207 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU K 215 " --> pdb=" O GLU K 211 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN K 222 " --> pdb=" O ALA K 218 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU K 223 " --> pdb=" O LEU K 219 " (cutoff:3.500A) Processing helix chain 'K' and resid 238 through 252 Processing helix chain 'K' and resid 261 through 265 Processing helix chain 'K' and resid 265 through 280 removed outlier: 3.792A pdb=" N ARG K 277 " --> pdb=" O SER K 273 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS K 278 " --> pdb=" O LYS K 274 " (cutoff:3.500A) Processing helix chain 'K' and resid 290 through 295 removed outlier: 3.800A pdb=" N ARG K 295 " --> pdb=" O ALA K 291 " (cutoff:3.500A) Processing helix chain 'K' and resid 302 through 314 removed outlier: 3.644A pdb=" N LEU K 306 " --> pdb=" O HIS K 302 " (cutoff:3.500A) Processing helix chain 'K' and resid 331 through 343 removed outlier: 3.590A pdb=" N PHE K 337 " --> pdb=" O THR K 333 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN K 340 " --> pdb=" O GLY K 336 " (cutoff:3.500A) Processing helix chain 'K' and resid 375 through 377 No H-bonds generated for 'chain 'K' and resid 375 through 377' Processing helix chain 'K' and resid 378 through 387 removed outlier: 3.510A pdb=" N ALA K 384 " --> pdb=" O PRO K 380 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE K 386 " --> pdb=" O LEU K 382 " (cutoff:3.500A) Processing helix chain 'K' and resid 395 through 400 removed outlier: 4.382A pdb=" N HIS K 399 " --> pdb=" O GLY K 395 " (cutoff:3.500A) Processing helix chain 'K' and resid 405 through 425 removed outlier: 3.576A pdb=" N VAL K 414 " --> pdb=" O ALA K 410 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA K 425 " --> pdb=" O LYS K 421 " (cutoff:3.500A) Processing helix chain 'K' and resid 432 through 438 Processing helix chain 'K' and resid 440 through 443 Processing helix chain 'K' and resid 444 through 454 removed outlier: 3.503A pdb=" N ILE K 449 " --> pdb=" O PRO K 445 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU K 452 " --> pdb=" O ALA K 448 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 40 Processing helix chain 'L' and resid 50 through 54 removed outlier: 3.786A pdb=" N SER L 54 " --> pdb=" O PRO L 51 " (cutoff:3.500A) Processing helix chain 'L' and resid 71 through 76 removed outlier: 4.251A pdb=" N ILE L 75 " --> pdb=" O ASP L 71 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL L 76 " --> pdb=" O LEU L 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 71 through 76' Processing helix chain 'L' and resid 77 through 86 removed outlier: 3.507A pdb=" N ALA L 81 " --> pdb=" O SER L 77 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N CYS L 82 " --> pdb=" O GLU L 78 " (cutoff:3.500A) Processing helix chain 'M' and resid 41 through 53 removed outlier: 3.540A pdb=" N SER M 53 " --> pdb=" O VAL M 49 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 66 removed outlier: 3.524A pdb=" N LEU M 65 " --> pdb=" O TRP M 62 " (cutoff:3.500A) Processing helix chain 'M' and resid 96 through 100 removed outlier: 3.746A pdb=" N PHE M 100 " --> pdb=" O LEU M 97 " (cutoff:3.500A) Processing helix chain 'M' and resid 104 through 113 removed outlier: 3.692A pdb=" N VAL M 108 " --> pdb=" O SER M 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 133 through 138 Processing helix chain 'M' and resid 146 through 155 Processing helix chain 'M' and resid 173 through 186 removed outlier: 3.541A pdb=" N GLY M 178 " --> pdb=" O GLY M 174 " (cutoff:3.500A) Processing helix chain 'M' and resid 205 through 225 removed outlier: 3.636A pdb=" N GLU M 211 " --> pdb=" O GLN M 207 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU M 215 " --> pdb=" O GLU M 211 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN M 222 " --> pdb=" O ALA M 218 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU M 223 " --> pdb=" O LEU M 219 " (cutoff:3.500A) Processing helix chain 'M' and resid 238 through 252 Processing helix chain 'M' and resid 261 through 265 Processing helix chain 'M' and resid 265 through 280 removed outlier: 3.792A pdb=" N ARG M 277 " --> pdb=" O SER M 273 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS M 278 " --> pdb=" O LYS M 274 " (cutoff:3.500A) Processing helix chain 'M' and resid 290 through 295 removed outlier: 3.800A pdb=" N ARG M 295 " --> pdb=" O ALA M 291 " (cutoff:3.500A) Processing helix chain 'M' and resid 302 through 314 removed outlier: 3.644A pdb=" N LEU M 306 " --> pdb=" O HIS M 302 " (cutoff:3.500A) Processing helix chain 'M' and resid 331 through 343 removed outlier: 3.590A pdb=" N PHE M 337 " --> pdb=" O THR M 333 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN M 340 " --> pdb=" O GLY M 336 " (cutoff:3.500A) Processing helix chain 'M' and resid 375 through 377 No H-bonds generated for 'chain 'M' and resid 375 through 377' Processing helix chain 'M' and resid 378 through 387 removed outlier: 3.510A pdb=" N ALA M 384 " --> pdb=" O PRO M 380 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE M 386 " --> pdb=" O LEU M 382 " (cutoff:3.500A) Processing helix chain 'M' and resid 395 through 400 removed outlier: 4.383A pdb=" N HIS M 399 " --> pdb=" O GLY M 395 " (cutoff:3.500A) Processing helix chain 'M' and resid 405 through 425 removed outlier: 3.576A pdb=" N VAL M 414 " --> pdb=" O ALA M 410 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA M 425 " --> pdb=" O LYS M 421 " (cutoff:3.500A) Processing helix chain 'M' and resid 432 through 438 Processing helix chain 'M' and resid 440 through 443 Processing helix chain 'M' and resid 444 through 454 removed outlier: 3.504A pdb=" N ILE M 449 " --> pdb=" O PRO M 445 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU M 452 " --> pdb=" O ALA M 448 " (cutoff:3.500A) Processing helix chain 'N' and resid 26 through 40 Processing helix chain 'N' and resid 50 through 54 removed outlier: 3.786A pdb=" N SER N 54 " --> pdb=" O PRO N 51 " (cutoff:3.500A) Processing helix chain 'N' and resid 71 through 76 removed outlier: 4.251A pdb=" N ILE N 75 " --> pdb=" O ASP N 71 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL N 76 " --> pdb=" O LEU N 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 71 through 76' Processing helix chain 'N' and resid 77 through 86 removed outlier: 3.507A pdb=" N ALA N 81 " --> pdb=" O SER N 77 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N CYS N 82 " --> pdb=" O GLU N 78 " (cutoff:3.500A) Processing helix chain 'O' and resid 41 through 53 removed outlier: 3.541A pdb=" N SER O 53 " --> pdb=" O VAL O 49 " (cutoff:3.500A) Processing helix chain 'O' and resid 62 through 66 removed outlier: 3.523A pdb=" N LEU O 65 " --> pdb=" O TRP O 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 96 through 100 removed outlier: 3.745A pdb=" N PHE O 100 " --> pdb=" O LEU O 97 " (cutoff:3.500A) Processing helix chain 'O' and resid 104 through 113 removed outlier: 3.692A pdb=" N VAL O 108 " --> pdb=" O SER O 104 " (cutoff:3.500A) Processing helix chain 'O' and resid 133 through 138 Processing helix chain 'O' and resid 146 through 155 Processing helix chain 'O' and resid 173 through 186 removed outlier: 3.541A pdb=" N GLY O 178 " --> pdb=" O GLY O 174 " (cutoff:3.500A) Processing helix chain 'O' and resid 205 through 225 removed outlier: 3.637A pdb=" N GLU O 211 " --> pdb=" O GLN O 207 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU O 215 " --> pdb=" O GLU O 211 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN O 222 " --> pdb=" O ALA O 218 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU O 223 " --> pdb=" O LEU O 219 " (cutoff:3.500A) Processing helix chain 'O' and resid 238 through 252 Processing helix chain 'O' and resid 261 through 265 Processing helix chain 'O' and resid 265 through 280 removed outlier: 3.793A pdb=" N ARG O 277 " --> pdb=" O SER O 273 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS O 278 " --> pdb=" O LYS O 274 " (cutoff:3.500A) Processing helix chain 'O' and resid 290 through 295 removed outlier: 3.800A pdb=" N ARG O 295 " --> pdb=" O ALA O 291 " (cutoff:3.500A) Processing helix chain 'O' and resid 302 through 314 removed outlier: 3.643A pdb=" N LEU O 306 " --> pdb=" O HIS O 302 " (cutoff:3.500A) Processing helix chain 'O' and resid 331 through 343 removed outlier: 3.590A pdb=" N PHE O 337 " --> pdb=" O THR O 333 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN O 340 " --> pdb=" O GLY O 336 " (cutoff:3.500A) Processing helix chain 'O' and resid 375 through 377 No H-bonds generated for 'chain 'O' and resid 375 through 377' Processing helix chain 'O' and resid 378 through 387 removed outlier: 3.511A pdb=" N ALA O 384 " --> pdb=" O PRO O 380 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE O 386 " --> pdb=" O LEU O 382 " (cutoff:3.500A) Processing helix chain 'O' and resid 395 through 400 removed outlier: 4.383A pdb=" N HIS O 399 " --> pdb=" O GLY O 395 " (cutoff:3.500A) Processing helix chain 'O' and resid 405 through 425 removed outlier: 3.575A pdb=" N VAL O 414 " --> pdb=" O ALA O 410 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA O 425 " --> pdb=" O LYS O 421 " (cutoff:3.500A) Processing helix chain 'O' and resid 432 through 438 Processing helix chain 'O' and resid 440 through 443 Processing helix chain 'O' and resid 444 through 454 removed outlier: 3.504A pdb=" N ILE O 449 " --> pdb=" O PRO O 445 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU O 452 " --> pdb=" O ALA O 448 " (cutoff:3.500A) Processing helix chain 'P' and resid 26 through 40 Processing helix chain 'P' and resid 50 through 54 removed outlier: 3.785A pdb=" N SER P 54 " --> pdb=" O PRO P 51 " (cutoff:3.500A) Processing helix chain 'P' and resid 71 through 76 removed outlier: 4.250A pdb=" N ILE P 75 " --> pdb=" O ASP P 71 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL P 76 " --> pdb=" O LEU P 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 71 through 76' Processing helix chain 'P' and resid 77 through 86 removed outlier: 3.507A pdb=" N ALA P 81 " --> pdb=" O SER P 77 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N CYS P 82 " --> pdb=" O GLU P 78 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 75 through 81 removed outlier: 5.697A pdb=" N CYS A 76 " --> pdb=" O ALA A 94 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ALA A 94 " --> pdb=" O CYS A 76 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG A 78 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU A 29 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ILE A 130 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N CYS A 31 " --> pdb=" O GLU A 128 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N HIS A 124 " --> pdb=" O THR A 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 161 through 164 removed outlier: 6.546A pdb=" N LEU A 318 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N SER A 371 " --> pdb=" O LEU A 318 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE A 257 " --> pdb=" O HIS A 284 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N HIS A 286 " --> pdb=" O ILE A 257 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N HIS A 259 " --> pdb=" O HIS A 286 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N HIS A 230 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N MET A 258 " --> pdb=" O HIS A 230 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU A 232 " --> pdb=" O MET A 258 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N ASP A 260 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N THR A 192 " --> pdb=" O TYR A 231 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N ASN A 233 " --> pdb=" O THR A 192 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 345 through 346 Processing sheet with id=AA4, first strand: chain 'B' and resid 60 through 62 removed outlier: 3.986A pdb=" N ILE B 46 " --> pdb=" O TRP B 62 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL B 49 " --> pdb=" O HIS B 90 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL B 91 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA B 105 " --> pdb=" O GLY B 95 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ASP B 97 " --> pdb=" O GLN B 103 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N GLN B 103 " --> pdb=" O ASP B 97 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 75 through 81 removed outlier: 5.698A pdb=" N CYS C 76 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ALA C 94 " --> pdb=" O CYS C 76 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG C 78 " --> pdb=" O PHE C 92 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEU C 29 " --> pdb=" O ILE C 130 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ILE C 130 " --> pdb=" O LEU C 29 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N CYS C 31 " --> pdb=" O GLU C 128 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N HIS C 124 " --> pdb=" O THR C 35 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 161 through 164 removed outlier: 6.545A pdb=" N LEU C 318 " --> pdb=" O VAL C 369 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N SER C 371 " --> pdb=" O LEU C 318 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE C 257 " --> pdb=" O HIS C 284 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N HIS C 286 " --> pdb=" O ILE C 257 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N HIS C 259 " --> pdb=" O HIS C 286 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N HIS C 230 " --> pdb=" O ILE C 256 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N MET C 258 " --> pdb=" O HIS C 230 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU C 232 " --> pdb=" O MET C 258 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N ASP C 260 " --> pdb=" O LEU C 232 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N THR C 192 " --> pdb=" O TYR C 231 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N ASN C 233 " --> pdb=" O THR C 192 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 345 through 346 Processing sheet with id=AA8, first strand: chain 'D' and resid 60 through 62 removed outlier: 3.986A pdb=" N ILE D 46 " --> pdb=" O TRP D 62 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL D 49 " --> pdb=" O HIS D 90 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL D 91 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA D 105 " --> pdb=" O GLY D 95 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ASP D 97 " --> pdb=" O GLN D 103 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N GLN D 103 " --> pdb=" O ASP D 97 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 75 through 81 removed outlier: 5.697A pdb=" N CYS E 76 " --> pdb=" O ALA E 94 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ALA E 94 " --> pdb=" O CYS E 76 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG E 78 " --> pdb=" O PHE E 92 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEU E 29 " --> pdb=" O ILE E 130 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ILE E 130 " --> pdb=" O LEU E 29 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N CYS E 31 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N HIS E 124 " --> pdb=" O THR E 35 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 161 through 164 removed outlier: 6.545A pdb=" N LEU E 318 " --> pdb=" O VAL E 369 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N SER E 371 " --> pdb=" O LEU E 318 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE E 257 " --> pdb=" O HIS E 284 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N HIS E 286 " --> pdb=" O ILE E 257 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N HIS E 259 " --> pdb=" O HIS E 286 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N HIS E 230 " --> pdb=" O ILE E 256 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N MET E 258 " --> pdb=" O HIS E 230 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU E 232 " --> pdb=" O MET E 258 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N ASP E 260 " --> pdb=" O LEU E 232 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N THR E 192 " --> pdb=" O TYR E 231 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N ASN E 233 " --> pdb=" O THR E 192 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 345 through 346 Processing sheet with id=AB3, first strand: chain 'F' and resid 60 through 62 removed outlier: 3.986A pdb=" N ILE F 46 " --> pdb=" O TRP F 62 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL F 49 " --> pdb=" O HIS F 90 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL F 91 " --> pdb=" O VAL F 109 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA F 105 " --> pdb=" O GLY F 95 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ASP F 97 " --> pdb=" O GLN F 103 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N GLN F 103 " --> pdb=" O ASP F 97 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 75 through 81 removed outlier: 5.698A pdb=" N CYS G 76 " --> pdb=" O ALA G 94 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ALA G 94 " --> pdb=" O CYS G 76 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG G 78 " --> pdb=" O PHE G 92 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU G 29 " --> pdb=" O ILE G 130 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ILE G 130 " --> pdb=" O LEU G 29 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N CYS G 31 " --> pdb=" O GLU G 128 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N HIS G 124 " --> pdb=" O THR G 35 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 161 through 164 removed outlier: 6.545A pdb=" N LEU G 318 " --> pdb=" O VAL G 369 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N SER G 371 " --> pdb=" O LEU G 318 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE G 257 " --> pdb=" O HIS G 284 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N HIS G 286 " --> pdb=" O ILE G 257 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N HIS G 259 " --> pdb=" O HIS G 286 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N HIS G 230 " --> pdb=" O ILE G 256 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N MET G 258 " --> pdb=" O HIS G 230 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU G 232 " --> pdb=" O MET G 258 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N ASP G 260 " --> pdb=" O LEU G 232 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N THR G 192 " --> pdb=" O TYR G 231 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N ASN G 233 " --> pdb=" O THR G 192 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 345 through 346 Processing sheet with id=AB7, first strand: chain 'H' and resid 60 through 62 removed outlier: 3.986A pdb=" N ILE H 46 " --> pdb=" O TRP H 62 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL H 49 " --> pdb=" O HIS H 90 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL H 91 " --> pdb=" O VAL H 109 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA H 105 " --> pdb=" O GLY H 95 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ASP H 97 " --> pdb=" O GLN H 103 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N GLN H 103 " --> pdb=" O ASP H 97 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 75 through 81 removed outlier: 5.697A pdb=" N CYS I 76 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ALA I 94 " --> pdb=" O CYS I 76 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG I 78 " --> pdb=" O PHE I 92 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU I 29 " --> pdb=" O ILE I 130 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ILE I 130 " --> pdb=" O LEU I 29 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N CYS I 31 " --> pdb=" O GLU I 128 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N HIS I 124 " --> pdb=" O THR I 35 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 161 through 164 removed outlier: 6.545A pdb=" N LEU I 318 " --> pdb=" O VAL I 369 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N SER I 371 " --> pdb=" O LEU I 318 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE I 257 " --> pdb=" O HIS I 284 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N HIS I 286 " --> pdb=" O ILE I 257 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N HIS I 259 " --> pdb=" O HIS I 286 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N HIS I 230 " --> pdb=" O ILE I 256 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N MET I 258 " --> pdb=" O HIS I 230 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU I 232 " --> pdb=" O MET I 258 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N ASP I 260 " --> pdb=" O LEU I 232 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N THR I 192 " --> pdb=" O TYR I 231 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N ASN I 233 " --> pdb=" O THR I 192 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 345 through 346 Processing sheet with id=AC2, first strand: chain 'J' and resid 60 through 62 removed outlier: 3.986A pdb=" N ILE J 46 " --> pdb=" O TRP J 62 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL J 49 " --> pdb=" O HIS J 90 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL J 91 " --> pdb=" O VAL J 109 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA J 105 " --> pdb=" O GLY J 95 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ASP J 97 " --> pdb=" O GLN J 103 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N GLN J 103 " --> pdb=" O ASP J 97 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 75 through 81 removed outlier: 5.697A pdb=" N CYS K 76 " --> pdb=" O ALA K 94 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ALA K 94 " --> pdb=" O CYS K 76 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG K 78 " --> pdb=" O PHE K 92 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU K 29 " --> pdb=" O ILE K 130 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ILE K 130 " --> pdb=" O LEU K 29 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N CYS K 31 " --> pdb=" O GLU K 128 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N HIS K 124 " --> pdb=" O THR K 35 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 161 through 165 removed outlier: 6.697A pdb=" N LEU K 162 " --> pdb=" O PHE K 191 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N LYS K 193 " --> pdb=" O LEU K 162 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N CYS K 164 " --> pdb=" O LYS K 193 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N THR K 192 " --> pdb=" O TYR K 231 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N ASN K 233 " --> pdb=" O THR K 192 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N HIS K 230 " --> pdb=" O ILE K 256 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N MET K 258 " --> pdb=" O HIS K 230 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU K 232 " --> pdb=" O MET K 258 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N ASP K 260 " --> pdb=" O LEU K 232 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE K 257 " --> pdb=" O HIS K 284 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N HIS K 286 " --> pdb=" O ILE K 257 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N HIS K 259 " --> pdb=" O HIS K 286 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU K 318 " --> pdb=" O VAL K 369 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N SER K 371 " --> pdb=" O LEU K 318 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 345 through 346 Processing sheet with id=AC6, first strand: chain 'L' and resid 60 through 62 removed outlier: 3.986A pdb=" N ILE L 46 " --> pdb=" O TRP L 62 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL L 49 " --> pdb=" O HIS L 90 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL L 91 " --> pdb=" O VAL L 109 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA L 105 " --> pdb=" O GLY L 95 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ASP L 97 " --> pdb=" O GLN L 103 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N GLN L 103 " --> pdb=" O ASP L 97 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 75 through 81 removed outlier: 5.696A pdb=" N CYS M 76 " --> pdb=" O ALA M 94 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ALA M 94 " --> pdb=" O CYS M 76 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG M 78 " --> pdb=" O PHE M 92 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU M 29 " --> pdb=" O ILE M 130 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ILE M 130 " --> pdb=" O LEU M 29 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N CYS M 31 " --> pdb=" O GLU M 128 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N HIS M 124 " --> pdb=" O THR M 35 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 161 through 164 removed outlier: 6.545A pdb=" N LEU M 318 " --> pdb=" O VAL M 369 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N SER M 371 " --> pdb=" O LEU M 318 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE M 257 " --> pdb=" O HIS M 284 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N HIS M 286 " --> pdb=" O ILE M 257 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N HIS M 259 " --> pdb=" O HIS M 286 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N HIS M 230 " --> pdb=" O ILE M 256 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N MET M 258 " --> pdb=" O HIS M 230 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU M 232 " --> pdb=" O MET M 258 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N ASP M 260 " --> pdb=" O LEU M 232 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N THR M 192 " --> pdb=" O TYR M 231 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N ASN M 233 " --> pdb=" O THR M 192 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 345 through 346 Processing sheet with id=AD1, first strand: chain 'N' and resid 60 through 62 removed outlier: 3.987A pdb=" N ILE N 46 " --> pdb=" O TRP N 62 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL N 49 " --> pdb=" O HIS N 90 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL N 91 " --> pdb=" O VAL N 109 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA N 105 " --> pdb=" O GLY N 95 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ASP N 97 " --> pdb=" O GLN N 103 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N GLN N 103 " --> pdb=" O ASP N 97 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'O' and resid 75 through 81 removed outlier: 5.697A pdb=" N CYS O 76 " --> pdb=" O ALA O 94 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ALA O 94 " --> pdb=" O CYS O 76 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG O 78 " --> pdb=" O PHE O 92 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU O 29 " --> pdb=" O ILE O 130 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ILE O 130 " --> pdb=" O LEU O 29 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N CYS O 31 " --> pdb=" O GLU O 128 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N HIS O 124 " --> pdb=" O THR O 35 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'O' and resid 161 through 165 removed outlier: 6.697A pdb=" N LEU O 162 " --> pdb=" O PHE O 191 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N LYS O 193 " --> pdb=" O LEU O 162 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N CYS O 164 " --> pdb=" O LYS O 193 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N THR O 192 " --> pdb=" O TYR O 231 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N ASN O 233 " --> pdb=" O THR O 192 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N HIS O 230 " --> pdb=" O ILE O 256 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N MET O 258 " --> pdb=" O HIS O 230 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU O 232 " --> pdb=" O MET O 258 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N ASP O 260 " --> pdb=" O LEU O 232 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE O 257 " --> pdb=" O HIS O 284 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N HIS O 286 " --> pdb=" O ILE O 257 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N HIS O 259 " --> pdb=" O HIS O 286 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU O 318 " --> pdb=" O VAL O 369 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N SER O 371 " --> pdb=" O LEU O 318 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'O' and resid 345 through 346 Processing sheet with id=AD5, first strand: chain 'P' and resid 60 through 62 removed outlier: 3.986A pdb=" N ILE P 46 " --> pdb=" O TRP P 62 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL P 49 " --> pdb=" O HIS P 90 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL P 91 " --> pdb=" O VAL P 109 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA P 105 " --> pdb=" O GLY P 95 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ASP P 97 " --> pdb=" O GLN P 103 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N GLN P 103 " --> pdb=" O ASP P 97 " (cutoff:3.500A) 1370 hydrogen bonds defined for protein. 3798 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: 12.23 Time building geometry restraints manager: 9.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.57: 35760 1.57 - 1.93: 296 1.93 - 2.28: 0 2.28 - 2.64: 0 2.64 - 3.00: 8 Bond restraints: 36064 Sorted by residual: bond pdb=" C GLU G 328 " pdb=" N ASP G 330 " ideal model delta sigma weight residual 1.329 2.999 -1.670 1.40e-02 5.10e+03 1.42e+04 bond pdb=" C GLU K 328 " pdb=" N ASP K 330 " ideal model delta sigma weight residual 1.329 2.999 -1.670 1.40e-02 5.10e+03 1.42e+04 bond pdb=" C GLU O 328 " pdb=" N ASP O 330 " ideal model delta sigma weight residual 1.329 2.999 -1.670 1.40e-02 5.10e+03 1.42e+04 bond pdb=" C GLU M 328 " pdb=" N ASP M 330 " ideal model delta sigma weight residual 1.329 2.998 -1.669 1.40e-02 5.10e+03 1.42e+04 bond pdb=" C GLU A 328 " pdb=" N ASP A 330 " ideal model delta sigma weight residual 1.329 2.998 -1.669 1.40e-02 5.10e+03 1.42e+04 ... (remaining 36059 not shown) Histogram of bond angle deviations from ideal: 0.00 - 16.12: 48928 16.12 - 32.24: 0 32.24 - 48.37: 0 48.37 - 64.49: 0 64.49 - 80.61: 8 Bond angle restraints: 48936 Sorted by residual: angle pdb=" O GLU G 328 " pdb=" C GLU G 328 " pdb=" N ASP G 330 " ideal model delta sigma weight residual 122.59 41.98 80.61 1.33e+00 5.65e-01 3.67e+03 angle pdb=" O GLU A 328 " pdb=" C GLU A 328 " pdb=" N ASP A 330 " ideal model delta sigma weight residual 122.59 42.00 80.59 1.33e+00 5.65e-01 3.67e+03 angle pdb=" O GLU I 328 " pdb=" C GLU I 328 " pdb=" N ASP I 330 " ideal model delta sigma weight residual 122.59 42.00 80.59 1.33e+00 5.65e-01 3.67e+03 angle pdb=" O GLU E 328 " pdb=" C GLU E 328 " pdb=" N ASP E 330 " ideal model delta sigma weight residual 122.59 42.00 80.59 1.33e+00 5.65e-01 3.67e+03 angle pdb=" O GLU C 328 " pdb=" C GLU C 328 " pdb=" N ASP C 330 " ideal model delta sigma weight residual 122.59 42.01 80.58 1.33e+00 5.65e-01 3.67e+03 ... (remaining 48931 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.74: 19778 34.74 - 69.48: 1122 69.48 - 104.23: 116 104.23 - 138.97: 4 138.97 - 173.71: 12 Dihedral angle restraints: 21032 sinusoidal: 8424 harmonic: 12608 Sorted by residual: dihedral pdb=" C3 CAP C 501 " pdb=" C CAP C 501 " pdb=" C2 CAP C 501 " pdb=" O6 CAP C 501 " ideal model delta sinusoidal sigma weight residual 81.86 -104.43 -173.71 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C3 CAP G 501 " pdb=" C CAP G 501 " pdb=" C2 CAP G 501 " pdb=" O6 CAP G 501 " ideal model delta sinusoidal sigma weight residual 81.86 -104.44 -173.70 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C3 CAP E 501 " pdb=" C CAP E 501 " pdb=" C2 CAP E 501 " pdb=" O6 CAP E 501 " ideal model delta sinusoidal sigma weight residual 81.86 -104.45 -173.69 1 2.00e+01 2.50e-03 4.79e+01 ... (remaining 21029 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 4382 0.073 - 0.146: 728 0.146 - 0.220: 18 0.220 - 0.293: 0 0.293 - 0.366: 8 Chirality restraints: 5136 Sorted by residual: chirality pdb=" CB VAL C 324 " pdb=" CA VAL C 324 " pdb=" CG1 VAL C 324 " pdb=" CG2 VAL C 324 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.35e+00 chirality pdb=" CB VAL A 324 " pdb=" CA VAL A 324 " pdb=" CG1 VAL A 324 " pdb=" CG2 VAL A 324 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.35e+00 chirality pdb=" CB VAL O 324 " pdb=" CA VAL O 324 " pdb=" CG1 VAL O 324 " pdb=" CG2 VAL O 324 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.36 2.00e-01 2.50e+01 3.32e+00 ... (remaining 5133 not shown) Planarity restraints: 6368 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C 328 " 0.132 2.00e-02 2.50e+03 2.45e-01 6.01e+02 pdb=" C GLU C 328 " -0.367 2.00e-02 2.50e+03 pdb=" O GLU C 328 " 0.291 2.00e-02 2.50e+03 pdb=" N ASP C 330 " -0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU I 328 " -0.133 2.00e-02 2.50e+03 2.45e-01 6.00e+02 pdb=" C GLU I 328 " 0.367 2.00e-02 2.50e+03 pdb=" O GLU I 328 " -0.291 2.00e-02 2.50e+03 pdb=" N ASP I 330 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU K 328 " -0.133 2.00e-02 2.50e+03 2.45e-01 6.00e+02 pdb=" C GLU K 328 " 0.367 2.00e-02 2.50e+03 pdb=" O GLU K 328 " -0.291 2.00e-02 2.50e+03 pdb=" N ASP K 330 " 0.057 2.00e-02 2.50e+03 ... (remaining 6365 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 418 2.60 - 3.17: 28373 3.17 - 3.75: 52192 3.75 - 4.32: 81485 4.32 - 4.90: 134697 Nonbonded interactions: 297165 Sorted by model distance: nonbonded pdb=" NH1 ARG M 304 " pdb=" O GLY M 353 " model vdw 2.025 3.120 nonbonded pdb=" NH1 ARG A 304 " pdb=" O GLY A 353 " model vdw 2.025 3.120 nonbonded pdb=" NH1 ARG C 304 " pdb=" O GLY C 353 " model vdw 2.025 3.120 nonbonded pdb=" NH1 ARG O 304 " pdb=" O GLY O 353 " model vdw 2.025 3.120 nonbonded pdb=" NH1 ARG K 304 " pdb=" O GLY K 353 " model vdw 2.025 3.120 ... (remaining 297160 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: 0.29 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' } 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: 0.010 Normalize map: mean=0, sd=1: 0.910 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: 0.020 Extract box with map and model: 1.310 Check model and map are aligned: 0.250 Set scattering table: 0.330 Process input model: 71.650 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 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 : 0.026 1.670 36072 Z= 1.828 Angle : 1.415 80.612 48936 Z= 0.971 Chirality : 0.052 0.366 5136 Planarity : 0.011 0.245 6368 Dihedral : 20.684 173.709 13000 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 12.83 % Allowed : 16.63 % Favored : 70.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 1.15 % 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: -4.07 (0.10), residues: 4376 helix: -3.75 (0.08), residues: 1680 sheet: -1.23 (0.19), residues: 696 loop : -2.14 (0.11), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 206 HIS 0.020 0.004 HIS E 259 PHE 0.035 0.004 PHE A 92 TYR 0.034 0.003 TYR E 157 ARG 0.020 0.002 ARG E 209 Details of bonding type rmsd hydrogen bonds : bond 0.28890 ( 1370) hydrogen bonds : angle 9.74448 ( 3798) covalent geometry : bond 0.02602 (36064) covalent geometry : angle 1.41531 (48936) Misc. bond : bond 0.18316 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8752 Ramachandran restraints generated. 4376 Oldfield, 0 Emsley, 4376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 920 residues out of total 3632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 466 poor density : 454 time to evaluate : 3.817 Fit side-chains REVERT: A 434 ARG cc_start: 0.7370 (OUTLIER) cc_final: 0.7129 (ttm-80) REVERT: B 63 LYS cc_start: 0.7754 (OUTLIER) cc_final: 0.7498 (mttp) REVERT: E 44 GLU cc_start: 0.5349 (OUTLIER) cc_final: 0.4811 (tp30) REVERT: E 134 MET cc_start: 0.7454 (mmm) cc_final: 0.7007 (tpp) REVERT: G 434 ARG cc_start: 0.7405 (OUTLIER) cc_final: 0.6867 (ttm-80) REVERT: H 63 LYS cc_start: 0.7749 (OUTLIER) cc_final: 0.7479 (mttp) REVERT: I 134 MET cc_start: 0.7816 (mmm) cc_final: 0.7377 (tpp) REVERT: K 35 THR cc_start: 0.8977 (OUTLIER) cc_final: 0.8138 (p) REVERT: K 87 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7799 (tm-30) REVERT: K 322 THR cc_start: 0.6989 (t) cc_final: 0.6663 (m) REVERT: K 434 ARG cc_start: 0.7445 (OUTLIER) cc_final: 0.7002 (ttm-80) REVERT: L 63 LYS cc_start: 0.7749 (OUTLIER) cc_final: 0.7439 (mmtp) REVERT: M 423 ARG cc_start: 0.7790 (OUTLIER) cc_final: 0.7459 (tmm160) REVERT: M 434 ARG cc_start: 0.7491 (OUTLIER) cc_final: 0.7171 (ttm110) REVERT: N 63 LYS cc_start: 0.7322 (OUTLIER) cc_final: 0.7010 (mttp) REVERT: O 231 TYR cc_start: 0.9003 (OUTLIER) cc_final: 0.8526 (m-80) REVERT: O 294 ASP cc_start: 0.7144 (m-30) cc_final: 0.6899 (t0) outliers start: 466 outliers final: 55 residues processed: 814 average time/residue: 1.7036 time to fit residues: 1643.3957 Evaluate side-chains 412 residues out of total 3632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 344 time to evaluate : 4.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 434 ARG Chi-restraints excluded: chain B residue 63 LYS Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 281 MET Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 385 ILE Chi-restraints excluded: chain C residue 394 PHE Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 44 GLU Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 231 TYR Chi-restraints excluded: chain E residue 281 MET Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain F residue 63 LYS Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 281 MET Chi-restraints excluded: chain G residue 324 VAL Chi-restraints excluded: chain G residue 434 ARG Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 173 SER Chi-restraints excluded: chain I residue 213 VAL Chi-restraints excluded: chain J residue 63 LYS Chi-restraints excluded: chain J residue 102 SER Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 53 SER Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain K residue 238 THR Chi-restraints excluded: chain K residue 281 MET Chi-restraints excluded: chain K residue 324 VAL Chi-restraints excluded: chain K residue 434 ARG Chi-restraints excluded: chain L residue 63 LYS Chi-restraints excluded: chain L residue 102 SER Chi-restraints excluded: chain M residue 15 THR Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain M residue 324 VAL Chi-restraints excluded: chain M residue 385 ILE Chi-restraints excluded: chain M residue 394 PHE Chi-restraints excluded: chain M residue 423 ARG Chi-restraints excluded: chain M residue 434 ARG Chi-restraints excluded: chain N residue 63 LYS Chi-restraints excluded: chain N residue 102 SER Chi-restraints excluded: chain O residue 15 THR Chi-restraints excluded: chain O residue 213 VAL Chi-restraints excluded: chain O residue 231 TYR Chi-restraints excluded: chain O residue 324 VAL Chi-restraints excluded: chain O residue 394 PHE Chi-restraints excluded: chain P residue 63 LYS Chi-restraints excluded: chain P residue 102 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 364 optimal weight: 0.8980 chunk 327 optimal weight: 1.9990 chunk 181 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 220 optimal weight: 6.9990 chunk 174 optimal weight: 2.9990 chunk 338 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 chunk 205 optimal weight: 2.9990 chunk 252 optimal weight: 8.9990 chunk 392 optimal weight: 0.6980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN A 155 ASN ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 HIS A 401 HIS A 412 ASN B 48 HIS B 101 GLN C 37 GLN C 145 ASN C 155 ASN ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 401 HIS C 412 ASN D 33 GLN D 48 HIS D 101 GLN E 37 GLN E 107 ASN E 155 ASN ** E 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 375 HIS E 378 HIS E 401 HIS E 412 ASN F 101 GLN G 37 GLN G 145 ASN ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 378 HIS G 401 HIS G 412 ASN H 48 HIS H 101 GLN I 107 ASN I 155 ASN ** I 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 401 HIS I 412 ASN J 48 HIS J 101 GLN K 145 ASN K 155 ASN ** K 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 286 HIS ** K 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 401 HIS K 412 ASN L 48 HIS L 101 GLN M 145 ASN ** M 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 401 HIS M 412 ASN N 101 GLN O 145 ASN ** O 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 399 HIS O 401 HIS O 412 ASN P 33 GLN P 48 HIS P 101 GLN Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.146255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.123031 restraints weight = 44669.829| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.60 r_work: 0.3466 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 36072 Z= 0.136 Angle : 0.640 7.406 48936 Z= 0.334 Chirality : 0.045 0.310 5136 Planarity : 0.006 0.077 6368 Dihedral : 10.817 170.779 5032 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.94 % Favored : 96.88 % Rotamer: Outliers : 3.74 % Allowed : 22.71 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 1.33 % 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: -2.16 (0.11), residues: 4392 helix: -1.44 (0.12), residues: 1680 sheet: -0.81 (0.20), residues: 600 loop : -1.53 (0.12), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 206 HIS 0.012 0.001 HIS E 401 PHE 0.017 0.002 PHE O 119 TYR 0.018 0.001 TYR M 157 ARG 0.011 0.001 ARG I 304 Details of bonding type rmsd hydrogen bonds : bond 0.03975 ( 1370) hydrogen bonds : angle 5.18320 ( 3798) covalent geometry : bond 0.00313 (36064) covalent geometry : angle 0.63953 (48936) Misc. bond : bond 0.00339 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 3632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 414 time to evaluate : 4.354 Fit side-chains REVERT: A 83 PRO cc_start: 0.8091 (Cg_endo) cc_final: 0.7833 (Cg_exo) REVERT: A 134 MET cc_start: 0.8391 (mmm) cc_final: 0.8170 (tpp) REVERT: A 151 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.8299 (mmt180) REVERT: A 431 LYS cc_start: 0.8111 (tptp) cc_final: 0.7872 (ttpp) REVERT: A 438 MET cc_start: 0.7872 (OUTLIER) cc_final: 0.7599 (mpt) REVERT: C 151 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.8344 (mmt180) REVERT: D 86 TYR cc_start: 0.8409 (m-80) cc_final: 0.8146 (m-80) REVERT: E 108 VAL cc_start: 0.8025 (OUTLIER) cc_final: 0.7797 (p) REVERT: E 134 MET cc_start: 0.7923 (mmm) cc_final: 0.7514 (tpp) REVERT: E 201 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.8130 (mp-120) REVERT: G 434 ARG cc_start: 0.7782 (ttm170) cc_final: 0.7502 (ttm-80) REVERT: G 438 MET cc_start: 0.7977 (OUTLIER) cc_final: 0.7570 (mpt) REVERT: I 108 VAL cc_start: 0.8171 (OUTLIER) cc_final: 0.7957 (p) REVERT: I 134 MET cc_start: 0.7982 (mmm) cc_final: 0.7608 (tpp) REVERT: I 201 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.7952 (mp-120) REVERT: I 211 GLU cc_start: 0.8320 (tm-30) cc_final: 0.7970 (tm-30) REVERT: I 379 MET cc_start: 0.8787 (mmt) cc_final: 0.8120 (mmt) REVERT: K 294 ASP cc_start: 0.6737 (t70) cc_final: 0.6524 (t0) REVERT: K 438 MET cc_start: 0.7595 (OUTLIER) cc_final: 0.7299 (mpt) REVERT: M 87 GLU cc_start: 0.7169 (tm-30) cc_final: 0.6519 (tm-30) REVERT: M 438 MET cc_start: 0.7663 (OUTLIER) cc_final: 0.7419 (mpt) REVERT: O 151 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.8417 (mtt90) REVERT: P 78 GLU cc_start: 0.8067 (tp30) cc_final: 0.7835 (tp30) outliers start: 136 outliers final: 27 residues processed: 524 average time/residue: 1.6278 time to fit residues: 1010.2898 Evaluate side-chains 364 residues out of total 3632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 326 time to evaluate : 4.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 394 PHE Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 201 GLN Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 196 GLU Chi-restraints excluded: chain G residue 344 SER Chi-restraints excluded: chain G residue 438 MET Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 201 GLN Chi-restraints excluded: chain I residue 231 TYR Chi-restraints excluded: chain I residue 324 VAL Chi-restraints excluded: chain I residue 344 SER Chi-restraints excluded: chain I residue 428 GLU Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain K residue 196 GLU Chi-restraints excluded: chain K residue 374 ILE Chi-restraints excluded: chain K residue 438 MET Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 374 ILE Chi-restraints excluded: chain M residue 438 MET Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain O residue 151 ARG Chi-restraints excluded: chain O residue 351 SER Chi-restraints excluded: chain P residue 45 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 165 optimal weight: 6.9990 chunk 272 optimal weight: 0.5980 chunk 141 optimal weight: 0.6980 chunk 419 optimal weight: 7.9990 chunk 297 optimal weight: 10.0000 chunk 375 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 chunk 160 optimal weight: 4.9990 chunk 370 optimal weight: 5.9990 chunk 192 optimal weight: 10.0000 chunk 378 optimal weight: 10.0000 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 HIS ** A 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 HIS C 37 GLN ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 286 HIS ** C 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 GLN D 89 HIS E 145 ASN E 286 HIS ** E 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 354 ASN F 11 GLN F 48 HIS G 37 GLN ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 286 HIS ** G 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 354 ASN ** G 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 89 HIS I 286 HIS ** I 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 354 ASN I 375 HIS I 378 HIS ** K 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 354 ASN ** K 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 HIS M 155 ASN M 286 HIS M 354 ASN ** M 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 11 GLN N 48 HIS ** O 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 286 HIS ** O 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 33 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.139418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.115962 restraints weight = 45557.728| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.60 r_work: 0.3253 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 36072 Z= 0.211 Angle : 0.681 7.544 48936 Z= 0.354 Chirality : 0.048 0.250 5136 Planarity : 0.006 0.077 6368 Dihedral : 10.357 172.616 4911 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.83 % Favored : 94.99 % Rotamer: Outliers : 4.02 % Allowed : 21.70 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 1.33 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.46 (0.12), residues: 4392 helix: -0.60 (0.12), residues: 1696 sheet: -0.51 (0.20), residues: 648 loop : -1.35 (0.12), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 206 HIS 0.007 0.002 HIS E 284 PHE 0.018 0.002 PHE H 110 TYR 0.018 0.002 TYR E 21 ARG 0.011 0.001 ARG I 331 Details of bonding type rmsd hydrogen bonds : bond 0.05278 ( 1370) hydrogen bonds : angle 4.98831 ( 3798) covalent geometry : bond 0.00517 (36064) covalent geometry : angle 0.68092 (48936) Misc. bond : bond 0.00235 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 3632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 353 time to evaluate : 4.131 Fit side-chains REVERT: A 87 GLU cc_start: 0.7176 (tm-30) cc_final: 0.6733 (tm-30) REVERT: A 295 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.8022 (ttp-170) REVERT: A 438 MET cc_start: 0.7917 (OUTLIER) cc_final: 0.7706 (mpt) REVERT: B 30 ILE cc_start: 0.8503 (mm) cc_final: 0.8265 (mt) REVERT: D 30 ILE cc_start: 0.8580 (mm) cc_final: 0.8371 (mt) REVERT: E 35 THR cc_start: 0.8548 (OUTLIER) cc_final: 0.8249 (t) REVERT: E 37 GLN cc_start: 0.7509 (mm-40) cc_final: 0.7135 (mm110) REVERT: E 134 MET cc_start: 0.8487 (mmm) cc_final: 0.8117 (tpp) REVERT: E 151 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.8361 (mtt180) REVERT: F 30 ILE cc_start: 0.8584 (mm) cc_final: 0.8360 (mt) REVERT: G 151 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.8477 (mtt90) REVERT: G 431 LYS cc_start: 0.8036 (tptp) cc_final: 0.7742 (tttp) REVERT: H 30 ILE cc_start: 0.8531 (mm) cc_final: 0.8316 (mt) REVERT: I 134 MET cc_start: 0.8538 (mmm) cc_final: 0.8230 (tpp) REVERT: I 151 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.8427 (mtt180) REVERT: I 379 MET cc_start: 0.8976 (mmt) cc_final: 0.7870 (mmt) REVERT: I 434 ARG cc_start: 0.7492 (OUTLIER) cc_final: 0.7243 (ttm110) REVERT: J 30 ILE cc_start: 0.8580 (mm) cc_final: 0.8355 (mt) REVERT: K 151 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.8499 (mtt90) REVERT: L 30 ILE cc_start: 0.8544 (mm) cc_final: 0.8319 (mt) REVERT: M 151 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.8495 (mtt90) REVERT: N 30 ILE cc_start: 0.8520 (mm) cc_final: 0.8277 (mt) REVERT: O 87 GLU cc_start: 0.7087 (tm-30) cc_final: 0.6722 (tm-30) REVERT: O 294 ASP cc_start: 0.7773 (m-30) cc_final: 0.7421 (t70) REVERT: O 295 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.7467 (ttp-110) REVERT: O 431 LYS cc_start: 0.8303 (ttpp) cc_final: 0.8067 (tptt) REVERT: P 30 ILE cc_start: 0.8596 (mm) cc_final: 0.8372 (mt) outliers start: 146 outliers final: 51 residues processed: 457 average time/residue: 1.6648 time to fit residues: 901.1327 Evaluate side-chains 387 residues out of total 3632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 326 time to evaluate : 4.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 295 ARG Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 231 TYR Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 151 ARG Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 151 ARG Chi-restraints excluded: chain G residue 310 LEU Chi-restraints excluded: chain G residue 344 SER Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 231 TYR Chi-restraints excluded: chain I residue 310 LEU Chi-restraints excluded: chain I residue 324 VAL Chi-restraints excluded: chain I residue 344 SER Chi-restraints excluded: chain I residue 428 GLU Chi-restraints excluded: chain I residue 434 ARG Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain K residue 109 LEU Chi-restraints excluded: chain K residue 151 ARG Chi-restraints excluded: chain K residue 310 LEU Chi-restraints excluded: chain K residue 344 SER Chi-restraints excluded: chain K residue 374 ILE Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 106 THR Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain M residue 151 ARG Chi-restraints excluded: chain M residue 310 LEU Chi-restraints excluded: chain M residue 344 SER Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain O residue 40 VAL Chi-restraints excluded: chain O residue 106 THR Chi-restraints excluded: chain O residue 295 ARG Chi-restraints excluded: chain O residue 310 LEU Chi-restraints excluded: chain O residue 344 SER Chi-restraints excluded: chain P residue 6 THR Chi-restraints excluded: chain P residue 45 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 130 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 195 optimal weight: 2.9990 chunk 284 optimal weight: 5.9990 chunk 261 optimal weight: 2.9990 chunk 265 optimal weight: 7.9990 chunk 364 optimal weight: 5.9990 chunk 153 optimal weight: 2.9990 chunk 400 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 GLN ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 ASN ** E 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 155 ASN ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 145 ASN ** I 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.138680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.115283 restraints weight = 45333.174| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.59 r_work: 0.3229 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 36072 Z= 0.215 Angle : 0.672 7.192 48936 Z= 0.347 Chirality : 0.047 0.202 5136 Planarity : 0.006 0.068 6368 Dihedral : 10.218 172.706 4905 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.05 % Favored : 95.77 % Rotamer: Outliers : 4.65 % Allowed : 22.19 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 1.33 % 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: -1.05 (0.12), residues: 4392 helix: -0.16 (0.12), residues: 1688 sheet: -0.31 (0.20), residues: 656 loop : -1.22 (0.12), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 206 HIS 0.007 0.002 HIS C 296 PHE 0.020 0.002 PHE D 110 TYR 0.017 0.002 TYR G 231 ARG 0.010 0.001 ARG G 331 Details of bonding type rmsd hydrogen bonds : bond 0.05141 ( 1370) hydrogen bonds : angle 4.85113 ( 3798) covalent geometry : bond 0.00529 (36064) covalent geometry : angle 0.67216 (48936) Misc. bond : bond 0.00200 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 3632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 349 time to evaluate : 4.289 Fit side-chains REVERT: A 87 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.7087 (tm-30) REVERT: A 151 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.8435 (mtt90) REVERT: A 295 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7989 (ttp-170) REVERT: A 438 MET cc_start: 0.7843 (OUTLIER) cc_final: 0.7589 (mpt) REVERT: B 30 ILE cc_start: 0.8537 (mm) cc_final: 0.8308 (mt) REVERT: C 87 GLU cc_start: 0.7181 (OUTLIER) cc_final: 0.6751 (tm-30) REVERT: C 151 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.7752 (mtt180) REVERT: D 30 ILE cc_start: 0.8555 (mm) cc_final: 0.8347 (mt) REVERT: E 35 THR cc_start: 0.8920 (OUTLIER) cc_final: 0.8616 (t) REVERT: E 37 GLN cc_start: 0.7827 (mm-40) cc_final: 0.7353 (mm110) REVERT: E 134 MET cc_start: 0.8532 (mmm) cc_final: 0.8295 (tpp) REVERT: E 151 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.8310 (mtt180) REVERT: E 438 MET cc_start: 0.8359 (mtp) cc_final: 0.8090 (mpt) REVERT: F 30 ILE cc_start: 0.8580 (mm) cc_final: 0.8310 (mt) REVERT: G 151 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.8460 (mtt90) REVERT: G 211 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8107 (pp20) REVERT: G 294 ASP cc_start: 0.6813 (OUTLIER) cc_final: 0.6465 (t0) REVERT: H 30 ILE cc_start: 0.8592 (mm) cc_final: 0.8368 (mt) REVERT: I 134 MET cc_start: 0.8482 (mmm) cc_final: 0.8200 (tpp) REVERT: I 151 ARG cc_start: 0.8660 (OUTLIER) cc_final: 0.8281 (mtt180) REVERT: I 428 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7291 (pm20) REVERT: I 434 ARG cc_start: 0.7573 (OUTLIER) cc_final: 0.7348 (ttm110) REVERT: J 30 ILE cc_start: 0.8581 (mm) cc_final: 0.8355 (mt) REVERT: K 151 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.8448 (mtt90) REVERT: K 211 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8125 (pp20) REVERT: K 294 ASP cc_start: 0.6759 (OUTLIER) cc_final: 0.6407 (t0) REVERT: K 431 LYS cc_start: 0.7980 (tptt) cc_final: 0.7770 (ttpp) REVERT: L 30 ILE cc_start: 0.8591 (mm) cc_final: 0.8359 (mt) REVERT: M 151 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.8439 (mtt90) REVERT: M 294 ASP cc_start: 0.6768 (OUTLIER) cc_final: 0.6468 (t0) REVERT: N 30 ILE cc_start: 0.8588 (mm) cc_final: 0.8335 (mt) REVERT: O 57 THR cc_start: 0.5332 (OUTLIER) cc_final: 0.4995 (p) REVERT: O 87 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.7001 (tm-30) REVERT: O 151 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.8390 (mtt90) REVERT: O 294 ASP cc_start: 0.7761 (m-30) cc_final: 0.7474 (t70) REVERT: O 295 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.7551 (ttp-110) REVERT: P 30 ILE cc_start: 0.8591 (mm) cc_final: 0.8334 (mt) outliers start: 169 outliers final: 56 residues processed: 466 average time/residue: 1.6688 time to fit residues: 919.4783 Evaluate side-chains 405 residues out of total 3632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 326 time to evaluate : 4.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 295 ARG Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 231 TYR Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 151 ARG Chi-restraints excluded: chain E residue 251 GLU Chi-restraints excluded: chain E residue 281 MET Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 151 ARG Chi-restraints excluded: chain G residue 211 GLU Chi-restraints excluded: chain G residue 294 ASP Chi-restraints excluded: chain G residue 310 LEU Chi-restraints excluded: chain G residue 344 SER Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 231 TYR Chi-restraints excluded: chain I residue 310 LEU Chi-restraints excluded: chain I residue 324 VAL Chi-restraints excluded: chain I residue 344 SER Chi-restraints excluded: chain I residue 428 GLU Chi-restraints excluded: chain I residue 434 ARG Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 57 THR Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain K residue 151 ARG Chi-restraints excluded: chain K residue 211 GLU Chi-restraints excluded: chain K residue 294 ASP Chi-restraints excluded: chain K residue 310 LEU Chi-restraints excluded: chain K residue 344 SER Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 106 THR Chi-restraints excluded: chain M residue 151 ARG Chi-restraints excluded: chain M residue 294 ASP Chi-restraints excluded: chain M residue 310 LEU Chi-restraints excluded: chain M residue 344 SER Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 81 ASP Chi-restraints excluded: chain O residue 87 GLU Chi-restraints excluded: chain O residue 106 THR Chi-restraints excluded: chain O residue 151 ARG Chi-restraints excluded: chain O residue 295 ARG Chi-restraints excluded: chain O residue 310 LEU Chi-restraints excluded: chain O residue 344 SER Chi-restraints excluded: chain O residue 428 GLU Chi-restraints excluded: chain P residue 6 THR Chi-restraints excluded: chain P residue 45 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 102 optimal weight: 5.9990 chunk 383 optimal weight: 2.9990 chunk 60 optimal weight: 0.0050 chunk 240 optimal weight: 0.9990 chunk 403 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 253 optimal weight: 0.9990 chunk 158 optimal weight: 5.9990 chunk 138 optimal weight: 10.0000 chunk 230 optimal weight: 0.8980 chunk 364 optimal weight: 1.9990 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN A 375 HIS C 37 GLN C 115 ASN K 115 ASN ** K 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 115 ASN ** M 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 37 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.142923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.120047 restraints weight = 45122.525| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.58 r_work: 0.3400 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 36072 Z= 0.104 Angle : 0.541 7.343 48936 Z= 0.280 Chirality : 0.041 0.136 5136 Planarity : 0.005 0.047 6368 Dihedral : 9.675 165.790 4905 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.16 % Favored : 96.65 % Rotamer: Outliers : 3.19 % Allowed : 23.46 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 1.33 % 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: -0.37 (0.12), residues: 4392 helix: 0.44 (0.13), residues: 1712 sheet: 0.10 (0.21), residues: 608 loop : -0.87 (0.12), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 206 HIS 0.004 0.001 HIS E 375 PHE 0.018 0.001 PHE G 337 TYR 0.012 0.001 TYR I 231 ARG 0.011 0.001 ARG G 331 Details of bonding type rmsd hydrogen bonds : bond 0.03284 ( 1370) hydrogen bonds : angle 4.42872 ( 3798) covalent geometry : bond 0.00242 (36064) covalent geometry : angle 0.54093 (48936) Misc. bond : bond 0.00172 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 3632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 352 time to evaluate : 4.174 Fit side-chains REVERT: A 281 MET cc_start: 0.8842 (OUTLIER) cc_final: 0.8508 (ttp) REVERT: A 438 MET cc_start: 0.7853 (OUTLIER) cc_final: 0.7519 (mpt) REVERT: B 29 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7424 (mt-10) REVERT: E 35 THR cc_start: 0.8827 (OUTLIER) cc_final: 0.8559 (t) REVERT: E 37 GLN cc_start: 0.7729 (mm-40) cc_final: 0.7286 (mm110) REVERT: E 134 MET cc_start: 0.8369 (mmm) cc_final: 0.8069 (tpp) REVERT: E 151 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.8283 (mtt180) REVERT: E 438 MET cc_start: 0.8198 (mtp) cc_final: 0.7967 (mpt) REVERT: F 30 ILE cc_start: 0.8561 (mm) cc_final: 0.8348 (mt) REVERT: G 81 ASP cc_start: 0.7982 (p0) cc_final: 0.7551 (p0) REVERT: G 128 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.8116 (mt-10) REVERT: G 151 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.8317 (mmt180) REVERT: G 431 LYS cc_start: 0.7962 (tptp) cc_final: 0.7607 (ttpp) REVERT: I 134 MET cc_start: 0.8414 (mmm) cc_final: 0.8126 (tpp) REVERT: I 281 MET cc_start: 0.8832 (OUTLIER) cc_final: 0.8583 (ttp) REVERT: I 428 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7156 (pm20) REVERT: K 83 PRO cc_start: 0.8318 (Cg_endo) cc_final: 0.8103 (Cg_exo) REVERT: K 128 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8148 (mt-10) REVERT: K 294 ASP cc_start: 0.6687 (t70) cc_final: 0.6453 (t0) REVERT: M 87 GLU cc_start: 0.8341 (mp0) cc_final: 0.7774 (tm-30) REVERT: M 151 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.8292 (mmt180) REVERT: M 281 MET cc_start: 0.8863 (OUTLIER) cc_final: 0.8607 (ttp) REVERT: M 294 ASP cc_start: 0.6775 (t70) cc_final: 0.6562 (t0) REVERT: M 423 ARG cc_start: 0.8006 (tmm-80) cc_final: 0.7719 (tmm-80) REVERT: N 30 ILE cc_start: 0.8507 (mm) cc_final: 0.8299 (mt) REVERT: O 128 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8170 (mt-10) REVERT: O 294 ASP cc_start: 0.7810 (m-30) cc_final: 0.7562 (t70) outliers start: 116 outliers final: 34 residues processed: 431 average time/residue: 1.7992 time to fit residues: 913.5911 Evaluate side-chains 364 residues out of total 3632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 317 time to evaluate : 4.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain C residue 438 MET Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 151 ARG Chi-restraints excluded: chain E residue 289 MET Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 128 GLU Chi-restraints excluded: chain G residue 151 ARG Chi-restraints excluded: chain G residue 344 SER Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 281 MET Chi-restraints excluded: chain I residue 289 MET Chi-restraints excluded: chain I residue 324 VAL Chi-restraints excluded: chain I residue 344 SER Chi-restraints excluded: chain I residue 428 GLU Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain K residue 57 THR Chi-restraints excluded: chain K residue 128 GLU Chi-restraints excluded: chain K residue 344 SER Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 151 ARG Chi-restraints excluded: chain M residue 281 MET Chi-restraints excluded: chain M residue 344 SER Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 81 ASP Chi-restraints excluded: chain O residue 128 GLU Chi-restraints excluded: chain O residue 344 SER Chi-restraints excluded: chain P residue 45 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 325 optimal weight: 6.9990 chunk 269 optimal weight: 10.0000 chunk 423 optimal weight: 1.9990 chunk 228 optimal weight: 6.9990 chunk 386 optimal weight: 4.9990 chunk 136 optimal weight: 8.9990 chunk 429 optimal weight: 3.9990 chunk 404 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 155 optimal weight: 7.9990 chunk 45 optimal weight: 0.6980 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 115 ASN ** I 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 399 HIS ** M 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 37 GLN ** O 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.138694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.115630 restraints weight = 45224.891| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.56 r_work: 0.3237 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 36072 Z= 0.221 Angle : 0.656 7.316 48936 Z= 0.338 Chirality : 0.047 0.196 5136 Planarity : 0.006 0.056 6368 Dihedral : 9.830 164.774 4905 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.69 % Favored : 95.13 % Rotamer: Outliers : 3.22 % Allowed : 23.24 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 1.33 % 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: -0.52 (0.12), residues: 4392 helix: 0.34 (0.13), residues: 1696 sheet: 0.04 (0.21), residues: 656 loop : -1.00 (0.12), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP I 206 HIS 0.007 0.002 HIS A 296 PHE 0.020 0.002 PHE D 110 TYR 0.016 0.002 TYR I 231 ARG 0.010 0.001 ARG I 331 Details of bonding type rmsd hydrogen bonds : bond 0.05032 ( 1370) hydrogen bonds : angle 4.71911 ( 3798) covalent geometry : bond 0.00547 (36064) covalent geometry : angle 0.65558 (48936) Misc. bond : bond 0.00149 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 3632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 318 time to evaluate : 3.970 Fit side-chains REVERT: A 128 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.8059 (mt-10) REVERT: A 431 LYS cc_start: 0.8241 (tttm) cc_final: 0.8016 (tptt) REVERT: C 151 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.7736 (mtt180) REVERT: E 35 THR cc_start: 0.8953 (OUTLIER) cc_final: 0.8663 (t) REVERT: E 37 GLN cc_start: 0.7857 (mm-40) cc_final: 0.7407 (mm110) REVERT: E 134 MET cc_start: 0.8507 (mmm) cc_final: 0.8266 (tpp) REVERT: E 151 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.8276 (mtt180) REVERT: E 431 LYS cc_start: 0.8162 (tptt) cc_final: 0.7826 (tttp) REVERT: E 438 MET cc_start: 0.8329 (mtp) cc_final: 0.8077 (mpt) REVERT: F 30 ILE cc_start: 0.8581 (mm) cc_final: 0.8322 (mt) REVERT: G 81 ASP cc_start: 0.8076 (p0) cc_final: 0.7605 (p0) REVERT: G 151 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.8464 (mtt90) REVERT: G 431 LYS cc_start: 0.8072 (tptp) cc_final: 0.7766 (ttpp) REVERT: I 134 MET cc_start: 0.8509 (mmm) cc_final: 0.8220 (tpp) REVERT: I 151 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.8288 (mtt180) REVERT: I 428 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7257 (pm20) REVERT: I 431 LYS cc_start: 0.7999 (tptp) cc_final: 0.7484 (ttpp) REVERT: M 151 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.8446 (mtt90) REVERT: N 30 ILE cc_start: 0.8625 (mm) cc_final: 0.8374 (mt) REVERT: O 294 ASP cc_start: 0.7899 (m-30) cc_final: 0.7614 (t70) REVERT: O 431 LYS cc_start: 0.8324 (ttpp) cc_final: 0.8048 (tptt) outliers start: 117 outliers final: 46 residues processed: 408 average time/residue: 1.6539 time to fit residues: 796.6363 Evaluate side-chains 366 residues out of total 3632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 312 time to evaluate : 4.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 151 ARG Chi-restraints excluded: chain E residue 289 MET Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 151 ARG Chi-restraints excluded: chain G residue 324 VAL Chi-restraints excluded: chain G residue 344 SER Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 231 TYR Chi-restraints excluded: chain I residue 289 MET Chi-restraints excluded: chain I residue 324 VAL Chi-restraints excluded: chain I residue 344 SER Chi-restraints excluded: chain I residue 428 GLU Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain K residue 57 THR Chi-restraints excluded: chain K residue 324 VAL Chi-restraints excluded: chain K residue 344 SER Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 106 THR Chi-restraints excluded: chain M residue 151 ARG Chi-restraints excluded: chain M residue 344 SER Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 81 ASP Chi-restraints excluded: chain O residue 106 THR Chi-restraints excluded: chain O residue 324 VAL Chi-restraints excluded: chain O residue 344 SER Chi-restraints excluded: chain P residue 6 THR Chi-restraints excluded: chain P residue 45 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 364 optimal weight: 3.9990 chunk 311 optimal weight: 4.9990 chunk 284 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 98 optimal weight: 10.0000 chunk 190 optimal weight: 2.9990 chunk 199 optimal weight: 2.9990 chunk 334 optimal weight: 7.9990 chunk 52 optimal weight: 7.9990 chunk 85 optimal weight: 10.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN ** C 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 37 GLN ** O 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.139917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.117134 restraints weight = 45190.437| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.54 r_work: 0.3330 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.4027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 36072 Z= 0.161 Angle : 0.596 6.450 48936 Z= 0.308 Chirality : 0.044 0.169 5136 Planarity : 0.005 0.048 6368 Dihedral : 9.532 157.641 4905 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.73 % Favored : 96.08 % Rotamer: Outliers : 2.70 % Allowed : 23.54 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 1.33 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.29 (0.12), residues: 4392 helix: 0.54 (0.13), residues: 1688 sheet: 0.21 (0.21), residues: 648 loop : -0.89 (0.13), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 206 HIS 0.005 0.001 HIS A 296 PHE 0.018 0.002 PHE G 337 TYR 0.017 0.001 TYR A 231 ARG 0.012 0.001 ARG G 331 Details of bonding type rmsd hydrogen bonds : bond 0.04272 ( 1370) hydrogen bonds : angle 4.57557 ( 3798) covalent geometry : bond 0.00396 (36064) covalent geometry : angle 0.59614 (48936) Misc. bond : bond 0.00142 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 3632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 313 time to evaluate : 4.086 Fit side-chains REVERT: A 128 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.8080 (mt-10) REVERT: A 431 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.8048 (tptt) REVERT: E 35 THR cc_start: 0.8971 (OUTLIER) cc_final: 0.8696 (t) REVERT: E 37 GLN cc_start: 0.7988 (mm-40) cc_final: 0.7554 (mm110) REVERT: E 134 MET cc_start: 0.8461 (mmm) cc_final: 0.8229 (tpp) REVERT: E 151 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.8266 (mtt180) REVERT: E 431 LYS cc_start: 0.8069 (tptt) cc_final: 0.7787 (tttm) REVERT: E 438 MET cc_start: 0.8290 (mtp) cc_final: 0.8067 (mpt) REVERT: F 30 ILE cc_start: 0.8581 (mm) cc_final: 0.8343 (mt) REVERT: G 81 ASP cc_start: 0.8038 (p0) cc_final: 0.7433 (p0) REVERT: G 151 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.8467 (mtt90) REVERT: G 431 LYS cc_start: 0.8009 (tptp) cc_final: 0.7732 (ttpp) REVERT: I 128 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.8114 (mt-10) REVERT: I 134 MET cc_start: 0.8457 (mmm) cc_final: 0.8218 (tpp) REVERT: I 151 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.8177 (mtt180) REVERT: I 428 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.7241 (pm20) REVERT: I 431 LYS cc_start: 0.8051 (tptp) cc_final: 0.7608 (ttpp) REVERT: K 431 LYS cc_start: 0.8024 (tptp) cc_final: 0.7666 (ttpp) REVERT: M 151 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.8439 (mtt90) REVERT: N 30 ILE cc_start: 0.8613 (mm) cc_final: 0.8380 (mt) REVERT: O 294 ASP cc_start: 0.7898 (m-30) cc_final: 0.7653 (t70) REVERT: O 431 LYS cc_start: 0.8279 (ttpp) cc_final: 0.8035 (tptt) outliers start: 98 outliers final: 44 residues processed: 390 average time/residue: 1.6905 time to fit residues: 779.9658 Evaluate side-chains 354 residues out of total 3632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 301 time to evaluate : 3.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 151 ARG Chi-restraints excluded: chain E residue 289 MET Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 151 ARG Chi-restraints excluded: chain G residue 344 SER Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 128 GLU Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 231 TYR Chi-restraints excluded: chain I residue 289 MET Chi-restraints excluded: chain I residue 324 VAL Chi-restraints excluded: chain I residue 344 SER Chi-restraints excluded: chain I residue 428 GLU Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain K residue 57 THR Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain K residue 344 SER Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 151 ARG Chi-restraints excluded: chain M residue 344 SER Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 81 ASP Chi-restraints excluded: chain O residue 344 SER Chi-restraints excluded: chain O residue 438 MET Chi-restraints excluded: chain P residue 6 THR Chi-restraints excluded: chain P residue 45 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 86 optimal weight: 0.0770 chunk 174 optimal weight: 3.9990 chunk 396 optimal weight: 5.9990 chunk 119 optimal weight: 10.0000 chunk 317 optimal weight: 6.9990 chunk 219 optimal weight: 5.9990 chunk 397 optimal weight: 0.9980 chunk 388 optimal weight: 0.4980 chunk 29 optimal weight: 7.9990 chunk 421 optimal weight: 0.9980 chunk 292 optimal weight: 7.9990 overall best weight: 1.3140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 155 ASN ** K 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 37 GLN O 115 ASN ** O 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.142364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.119451 restraints weight = 45022.215| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.56 r_work: 0.3390 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.4184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 36072 Z= 0.114 Angle : 0.543 9.215 48936 Z= 0.282 Chirality : 0.042 0.137 5136 Planarity : 0.005 0.048 6368 Dihedral : 8.925 146.705 4905 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.42 % Favored : 96.40 % Rotamer: Outliers : 2.15 % Allowed : 24.12 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 1.33 % 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: 0.15 (0.12), residues: 4392 helix: 0.89 (0.13), residues: 1704 sheet: 0.52 (0.21), residues: 640 loop : -0.66 (0.13), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP M 206 HIS 0.004 0.001 HIS E 296 PHE 0.017 0.001 PHE G 337 TYR 0.014 0.001 TYR I 231 ARG 0.011 0.001 ARG E 331 Details of bonding type rmsd hydrogen bonds : bond 0.03422 ( 1370) hydrogen bonds : angle 4.35035 ( 3798) covalent geometry : bond 0.00269 (36064) covalent geometry : angle 0.54285 (48936) Misc. bond : bond 0.00130 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 345 time to evaluate : 4.423 Fit side-chains REVERT: C 83 PRO cc_start: 0.8410 (Cg_endo) cc_final: 0.8167 (Cg_exo) REVERT: C 151 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.8301 (mmt180) REVERT: E 35 THR cc_start: 0.8928 (OUTLIER) cc_final: 0.8659 (t) REVERT: E 37 GLN cc_start: 0.7942 (mm-40) cc_final: 0.7515 (mm110) REVERT: E 134 MET cc_start: 0.8446 (mmm) cc_final: 0.8113 (tpp) REVERT: E 151 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.8298 (mtt180) REVERT: E 281 MET cc_start: 0.8826 (OUTLIER) cc_final: 0.8399 (ttp) REVERT: E 431 LYS cc_start: 0.7996 (tptt) cc_final: 0.7741 (tttm) REVERT: E 438 MET cc_start: 0.8294 (mtp) cc_final: 0.8082 (mpt) REVERT: F 30 ILE cc_start: 0.8586 (mm) cc_final: 0.8370 (mt) REVERT: G 81 ASP cc_start: 0.7955 (p0) cc_final: 0.7343 (p0) REVERT: G 281 MET cc_start: 0.8824 (OUTLIER) cc_final: 0.8511 (ttp) REVERT: I 134 MET cc_start: 0.8438 (mmm) cc_final: 0.8144 (tpp) REVERT: I 151 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.8115 (mtt180) REVERT: I 428 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.7279 (pm20) REVERT: I 431 LYS cc_start: 0.8019 (tptp) cc_final: 0.7644 (ttpp) REVERT: K 294 ASP cc_start: 0.6710 (t70) cc_final: 0.6498 (t0) REVERT: K 331 ARG cc_start: 0.8014 (mtp-110) cc_final: 0.7775 (ptm160) REVERT: K 431 LYS cc_start: 0.8063 (tptp) cc_final: 0.7721 (ttpp) REVERT: M 83 PRO cc_start: 0.8417 (Cg_endo) cc_final: 0.8170 (Cg_exo) REVERT: M 423 ARG cc_start: 0.8071 (tmm-80) cc_final: 0.7757 (tmm-80) REVERT: N 30 ILE cc_start: 0.8596 (mm) cc_final: 0.8392 (mt) REVERT: O 294 ASP cc_start: 0.7876 (m-30) cc_final: 0.7558 (t70) outliers start: 78 outliers final: 43 residues processed: 401 average time/residue: 1.6181 time to fit residues: 769.0378 Evaluate side-chains 380 residues out of total 3632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 330 time to evaluate : 4.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 151 ARG Chi-restraints excluded: chain E residue 169 LYS Chi-restraints excluded: chain E residue 281 MET Chi-restraints excluded: chain E residue 289 MET Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 281 MET Chi-restraints excluded: chain G residue 344 SER Chi-restraints excluded: chain G residue 438 MET Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 428 GLU Chi-restraints excluded: chain I residue 438 MET Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain K residue 57 THR Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain K residue 344 SER Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 106 THR Chi-restraints excluded: chain M residue 344 SER Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 81 ASP Chi-restraints excluded: chain O residue 106 THR Chi-restraints excluded: chain O residue 344 SER Chi-restraints excluded: chain O residue 438 MET Chi-restraints excluded: chain P residue 6 THR Chi-restraints excluded: chain P residue 45 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 72 optimal weight: 6.9990 chunk 22 optimal weight: 8.9990 chunk 288 optimal weight: 7.9990 chunk 359 optimal weight: 7.9990 chunk 46 optimal weight: 7.9990 chunk 367 optimal weight: 7.9990 chunk 69 optimal weight: 4.9990 chunk 420 optimal weight: 2.9990 chunk 149 optimal weight: 7.9990 chunk 293 optimal weight: 5.9990 chunk 357 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 89 HIS ** G 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 399 HIS J 89 HIS ** K 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 89 HIS O 37 GLN ** O 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 412 ASN P 89 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.136529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.113316 restraints weight = 45482.740| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.57 r_work: 0.3187 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.059 36072 Z= 0.340 Angle : 0.772 9.826 48936 Z= 0.397 Chirality : 0.053 0.237 5136 Planarity : 0.007 0.055 6368 Dihedral : 9.359 151.472 4905 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.05 % Favored : 94.76 % Rotamer: Outliers : 2.26 % Allowed : 24.09 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 1.33 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.59 (0.12), residues: 4392 helix: 0.30 (0.12), residues: 1688 sheet: 0.11 (0.21), residues: 648 loop : -1.09 (0.12), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP I 206 HIS 0.009 0.002 HIS I 296 PHE 0.030 0.003 PHE F 110 TYR 0.019 0.003 TYR I 231 ARG 0.017 0.001 ARG E 331 Details of bonding type rmsd hydrogen bonds : bond 0.06253 ( 1370) hydrogen bonds : angle 4.96630 ( 3798) covalent geometry : bond 0.00846 (36064) covalent geometry : angle 0.77167 (48936) Misc. bond : bond 0.00118 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 3632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 312 time to evaluate : 3.946 Fit side-chains REVERT: A 115 ASN cc_start: 0.8645 (t0) cc_final: 0.8407 (t160) REVERT: A 431 LYS cc_start: 0.8028 (tptt) cc_final: 0.7760 (ttpp) REVERT: C 151 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.7755 (mtt180) REVERT: E 35 THR cc_start: 0.9106 (OUTLIER) cc_final: 0.8821 (t) REVERT: E 37 GLN cc_start: 0.8072 (mm-40) cc_final: 0.7621 (mm110) REVERT: E 134 MET cc_start: 0.8510 (mmm) cc_final: 0.8218 (tpp) REVERT: E 151 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.8268 (mtt180) REVERT: E 438 MET cc_start: 0.8283 (mtp) cc_final: 0.7980 (mpt) REVERT: G 115 ASN cc_start: 0.8635 (t0) cc_final: 0.8419 (t160) REVERT: G 431 LYS cc_start: 0.7945 (tptt) cc_final: 0.7603 (ttpp) REVERT: I 115 ASN cc_start: 0.8667 (t0) cc_final: 0.8443 (t160) REVERT: I 151 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.8277 (mtt180) REVERT: I 428 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7362 (pm20) REVERT: K 194 ASP cc_start: 0.8657 (OUTLIER) cc_final: 0.8391 (m-30) REVERT: K 431 LYS cc_start: 0.8051 (tptp) cc_final: 0.7781 (ttpp) REVERT: N 30 ILE cc_start: 0.8621 (mm) cc_final: 0.8328 (mt) REVERT: O 294 ASP cc_start: 0.7930 (m-30) cc_final: 0.7717 (t70) REVERT: O 428 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7248 (pm20) REVERT: O 431 LYS cc_start: 0.8333 (ttpp) cc_final: 0.7972 (tptt) REVERT: P 30 ILE cc_start: 0.8535 (mm) cc_final: 0.8328 (mt) outliers start: 82 outliers final: 45 residues processed: 381 average time/residue: 1.7047 time to fit residues: 770.6755 Evaluate side-chains 360 residues out of total 3632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 308 time to evaluate : 4.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 151 ARG Chi-restraints excluded: chain E residue 169 LYS Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 344 SER Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 169 LYS Chi-restraints excluded: chain I residue 344 SER Chi-restraints excluded: chain I residue 428 GLU Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain K residue 57 THR Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain K residue 194 ASP Chi-restraints excluded: chain K residue 344 SER Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 106 THR Chi-restraints excluded: chain M residue 289 MET Chi-restraints excluded: chain M residue 344 SER Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 81 ASP Chi-restraints excluded: chain O residue 106 THR Chi-restraints excluded: chain O residue 344 SER Chi-restraints excluded: chain O residue 428 GLU Chi-restraints excluded: chain P residue 6 THR Chi-restraints excluded: chain P residue 45 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 350 optimal weight: 0.7980 chunk 188 optimal weight: 0.9990 chunk 335 optimal weight: 1.9990 chunk 187 optimal weight: 3.9990 chunk 378 optimal weight: 10.0000 chunk 296 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 312 optimal weight: 0.7980 chunk 278 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 403 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 375 HIS C 378 HIS K 375 HIS K 378 HIS ** M 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 37 GLN O 375 HIS O 378 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.143390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.119759 restraints weight = 44039.726| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.61 r_work: 0.3379 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.4302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 36072 Z= 0.105 Angle : 0.554 9.736 48936 Z= 0.287 Chirality : 0.041 0.138 5136 Planarity : 0.005 0.051 6368 Dihedral : 8.622 154.077 4905 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.87 % Favored : 96.95 % Rotamer: Outliers : 1.38 % Allowed : 25.03 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 1.33 % 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: 0.17 (0.12), residues: 4392 helix: 1.02 (0.13), residues: 1704 sheet: 0.24 (0.20), residues: 680 loop : -0.68 (0.13), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 206 HIS 0.005 0.001 HIS E 375 PHE 0.019 0.001 PHE E 337 TYR 0.013 0.001 TYR A 231 ARG 0.014 0.001 ARG A 331 Details of bonding type rmsd hydrogen bonds : bond 0.03265 ( 1370) hydrogen bonds : angle 4.37014 ( 3798) covalent geometry : bond 0.00241 (36064) covalent geometry : angle 0.55397 (48936) Misc. bond : bond 0.00126 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 319 time to evaluate : 4.710 Fit side-chains REVERT: A 115 ASN cc_start: 0.8613 (t0) cc_final: 0.8402 (t160) REVERT: C 83 PRO cc_start: 0.8403 (Cg_endo) cc_final: 0.8157 (Cg_exo) REVERT: C 151 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.8281 (mmt180) REVERT: C 431 LYS cc_start: 0.7796 (tptt) cc_final: 0.7505 (ttpp) REVERT: E 35 THR cc_start: 0.9007 (OUTLIER) cc_final: 0.8748 (t) REVERT: E 37 GLN cc_start: 0.7939 (mm-40) cc_final: 0.7523 (mm110) REVERT: E 134 MET cc_start: 0.8473 (mmm) cc_final: 0.8144 (tpp) REVERT: E 151 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.8146 (mmt180) REVERT: E 331 ARG cc_start: 0.8055 (mtp-110) cc_final: 0.7846 (ttm110) REVERT: E 431 LYS cc_start: 0.7929 (tptt) cc_final: 0.7717 (mtpp) REVERT: E 438 MET cc_start: 0.8277 (mtp) cc_final: 0.8068 (mpt) REVERT: G 81 ASP cc_start: 0.7989 (p0) cc_final: 0.7506 (p0) REVERT: G 115 ASN cc_start: 0.8600 (t0) cc_final: 0.8390 (t0) REVERT: I 115 ASN cc_start: 0.8608 (t0) cc_final: 0.8395 (t160) REVERT: I 151 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.8264 (mmt180) REVERT: I 379 MET cc_start: 0.8900 (mmt) cc_final: 0.8477 (tpp) REVERT: I 428 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7317 (pm20) REVERT: I 431 LYS cc_start: 0.7837 (tptt) cc_final: 0.7572 (ttpp) REVERT: K 331 ARG cc_start: 0.8069 (mtp-110) cc_final: 0.7812 (ptm160) REVERT: K 431 LYS cc_start: 0.8087 (tptp) cc_final: 0.7807 (ttpp) REVERT: M 423 ARG cc_start: 0.8054 (tmm-80) cc_final: 0.7746 (tmm-80) REVERT: M 431 LYS cc_start: 0.7781 (tptt) cc_final: 0.7501 (ttpp) REVERT: N 30 ILE cc_start: 0.8569 (mm) cc_final: 0.8366 (mt) REVERT: O 294 ASP cc_start: 0.7893 (m-30) cc_final: 0.7595 (t70) REVERT: O 428 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7321 (pm20) REVERT: O 431 LYS cc_start: 0.8227 (ttpp) cc_final: 0.7947 (tptt) outliers start: 50 outliers final: 37 residues processed: 358 average time/residue: 1.8502 time to fit residues: 786.6673 Evaluate side-chains 357 residues out of total 3632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 314 time to evaluate : 4.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 151 ARG Chi-restraints excluded: chain E residue 344 SER Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 344 SER Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 344 SER Chi-restraints excluded: chain I residue 428 GLU Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain K residue 57 THR Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain K residue 344 SER Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 106 THR Chi-restraints excluded: chain M residue 344 SER Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 81 ASP Chi-restraints excluded: chain O residue 106 THR Chi-restraints excluded: chain O residue 344 SER Chi-restraints excluded: chain O residue 428 GLU Chi-restraints excluded: chain P residue 6 THR Chi-restraints excluded: chain P residue 45 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 44 optimal weight: 6.9990 chunk 233 optimal weight: 3.9990 chunk 214 optimal weight: 5.9990 chunk 246 optimal weight: 9.9990 chunk 360 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 128 optimal weight: 6.9990 chunk 323 optimal weight: 8.9990 chunk 51 optimal weight: 9.9990 chunk 77 optimal weight: 4.9990 chunk 427 optimal weight: 7.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.138488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.115519 restraints weight = 45395.948| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.55 r_work: 0.3236 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.4170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 36072 Z= 0.226 Angle : 0.668 9.119 48936 Z= 0.343 Chirality : 0.047 0.196 5136 Planarity : 0.006 0.058 6368 Dihedral : 8.843 154.246 4905 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.62 % Favored : 95.22 % Rotamer: Outliers : 1.60 % Allowed : 24.97 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 1.33 % 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: -0.19 (0.12), residues: 4392 helix: 0.73 (0.13), residues: 1688 sheet: 0.23 (0.21), residues: 648 loop : -0.93 (0.13), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 206 HIS 0.007 0.002 HIS G 296 PHE 0.020 0.002 PHE N 110 TYR 0.015 0.002 TYR A 231 ARG 0.013 0.001 ARG A 331 Details of bonding type rmsd hydrogen bonds : bond 0.05051 ( 1370) hydrogen bonds : angle 4.69143 ( 3798) covalent geometry : bond 0.00559 (36064) covalent geometry : angle 0.66764 (48936) Misc. bond : bond 0.00120 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24253.06 seconds wall clock time: 418 minutes 33.12 seconds (25113.12 seconds total)