Starting phenix.real_space_refine on Fri Sep 27 23:04:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p8w_13256/09_2024/7p8w_13256.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p8w_13256/09_2024/7p8w_13256.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p8w_13256/09_2024/7p8w_13256.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p8w_13256/09_2024/7p8w_13256.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p8w_13256/09_2024/7p8w_13256.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p8w_13256/09_2024/7p8w_13256.cif" } resolution = 2.2 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= 0.004 sd= 0.031 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 Fe 4 7.16 5 P 12 5.49 5 S 52 5.16 5 C 10504 2.51 5 N 2920 2.21 5 O 4176 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 17668 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4047 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 502, 4037 Classifications: {'peptide': 502} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 464} Conformer: "B" Number of residues, atoms: 502, 4037 Classifications: {'peptide': 502} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 464} bond proxies already assigned to first conformer: 4145 Chain: "B" Number of atoms: 4047 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 502, 4037 Classifications: {'peptide': 502} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 464} Conformer: "B" Number of residues, atoms: 502, 4037 Classifications: {'peptide': 502} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 464} bond proxies already assigned to first conformer: 4145 Chain: "C" Number of atoms: 4047 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 502, 4037 Classifications: {'peptide': 502} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 464} Conformer: "B" Number of residues, atoms: 502, 4037 Classifications: {'peptide': 502} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 464} bond proxies already assigned to first conformer: 4145 Chain: "D" Number of atoms: 4047 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 502, 4037 Classifications: {'peptide': 502} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 464} Conformer: "B" Number of residues, atoms: 502, 4037 Classifications: {'peptide': 502} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 464} bond proxies already assigned to first conformer: 4145 Chain: "A" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'HEM': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'HEM': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'HEM': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'HEM': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 281 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 279, 279 Classifications: {'water': 279} Link IDs: {None: 278} Conformer: "B" Number of residues, atoms: 279, 279 Classifications: {'water': 279} Link IDs: {None: 278} Chain: "B" Number of atoms: 280 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 278, 278 Classifications: {'water': 278} Link IDs: {None: 277} Conformer: "B" Number of residues, atoms: 278, 278 Classifications: {'water': 278} Link IDs: {None: 277} Chain: "C" Number of atoms: 277 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 276, 276 Classifications: {'water': 276} Link IDs: {None: 275} Conformer: "B" Number of residues, atoms: 276, 276 Classifications: {'water': 276} Link IDs: {None: 275} Chain: "D" Number of atoms: 278 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 277, 277 Classifications: {'water': 277} Link IDs: {None: 276} Conformer: "B" Number of residues, atoms: 277, 277 Classifications: {'water': 277} Link IDs: {None: 276} Residues with excluded nonbonded symmetry interactions: 10 residue: pdb=" N AHIS A 372 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A 372 " occ=0.50 residue: pdb=" N AHIS B 372 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS B 372 " occ=0.50 residue: pdb=" N AHIS C 372 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS C 372 " occ=0.50 residue: pdb=" N AHIS D 372 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS D 372 " occ=0.50 residue: pdb=" O AHOH A 858 " occ=0.50 pdb=" O BHOH A 858 " occ=0.50 residue: pdb=" O AHOH A 965 " occ=0.50 pdb=" O BHOH A 965 " occ=0.50 residue: pdb=" O AHOH B 857 " occ=0.50 pdb=" O BHOH B 857 " occ=0.50 residue: pdb=" O AHOH B 964 " occ=0.50 pdb=" O BHOH B 964 " occ=0.50 residue: pdb=" O AHOH C 853 " occ=0.50 pdb=" O BHOH C 853 " occ=0.50 residue: pdb=" O AHOH D 847 " occ=0.50 pdb=" O BHOH D 847 " occ=0.50 Time building chain proxies: 18.07, per 1000 atoms: 1.02 Number of scatterers: 17668 At special positions: 0 Unit cell: (108.102, 110.242, 84.5547, 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) Fe 4 26.01 S 52 16.00 P 12 15.00 O 4176 8.00 N 2920 7.00 C 10504 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.83 Conformation dependent library (CDL) restraints added in 3.9 seconds 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3760 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 8 sheets defined 41.2% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.88 Creating SS restraints... Processing helix chain 'A' and resid 10 through 20 Processing helix chain 'A' and resid 54 through 65 Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 157 through 159 No H-bonds generated for 'chain 'A' and resid 157 through 159' Processing helix chain 'A' and resid 160 through 169 Processing helix chain 'A' and resid 178 through 189 Processing helix chain 'A' and resid 192 through 201 Processing helix chain 'A' and resid 202 through 205 Processing helix chain 'A' and resid 208 through 212 removed outlier: 3.837A pdb=" N HIS A 211 " --> pdb=" O GLY A 208 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N MET A 212 " --> pdb=" O HIS A 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 208 through 212' Processing helix chain 'A' and resid 246 through 257 removed outlier: 3.503A pdb=" N GLN A 255 " --> pdb=" O ALA A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 271 Processing helix chain 'A' and resid 285 through 292 Processing helix chain 'A' and resid 324 through 329 Processing helix chain 'A' and resid 348 through 366 removed outlier: 3.736A pdb=" N PHE A 356 " --> pdb=" O GLN A 352 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR A 358 " --> pdb=" O ARG A 354 " (cutoff:3.500A) Proline residue: A 359 - end of helix removed outlier: 3.558A pdb=" N HIS A 364 " --> pdb=" O ASP A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 377 Proline residue: A 374 - end of helix Processing helix chain 'A' and resid 415 through 419 Processing helix chain 'A' and resid 440 through 450 Processing helix chain 'A' and resid 452 through 468 Processing helix chain 'A' and resid 471 through 486 removed outlier: 3.507A pdb=" N VAL A 485 " --> pdb=" O ASN A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 504 Processing helix chain 'B' and resid 10 through 20 Processing helix chain 'B' and resid 54 through 65 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 157 through 159 No H-bonds generated for 'chain 'B' and resid 157 through 159' Processing helix chain 'B' and resid 160 through 169 Processing helix chain 'B' and resid 178 through 189 Processing helix chain 'B' and resid 192 through 201 Processing helix chain 'B' and resid 202 through 205 Processing helix chain 'B' and resid 208 through 212 removed outlier: 3.837A pdb=" N HIS B 211 " --> pdb=" O GLY B 208 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N MET B 212 " --> pdb=" O HIS B 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 208 through 212' Processing helix chain 'B' and resid 246 through 257 removed outlier: 3.504A pdb=" N GLN B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 271 Processing helix chain 'B' and resid 285 through 292 Processing helix chain 'B' and resid 324 through 329 Processing helix chain 'B' and resid 348 through 366 removed outlier: 3.736A pdb=" N PHE B 356 " --> pdb=" O GLN B 352 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR B 358 " --> pdb=" O ARG B 354 " (cutoff:3.500A) Proline residue: B 359 - end of helix removed outlier: 3.558A pdb=" N HIS B 364 " --> pdb=" O ASP B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 377 Proline residue: B 374 - end of helix Processing helix chain 'B' and resid 415 through 419 Processing helix chain 'B' and resid 440 through 450 Processing helix chain 'B' and resid 452 through 468 Processing helix chain 'B' and resid 471 through 486 removed outlier: 3.507A pdb=" N VAL B 485 " --> pdb=" O ASN B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 504 Processing helix chain 'C' and resid 10 through 20 Processing helix chain 'C' and resid 54 through 65 Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 157 through 159 No H-bonds generated for 'chain 'C' and resid 157 through 159' Processing helix chain 'C' and resid 160 through 169 Processing helix chain 'C' and resid 178 through 189 Processing helix chain 'C' and resid 192 through 201 Processing helix chain 'C' and resid 202 through 205 Processing helix chain 'C' and resid 208 through 212 removed outlier: 3.837A pdb=" N HIS C 211 " --> pdb=" O GLY C 208 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N MET C 212 " --> pdb=" O HIS C 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 208 through 212' Processing helix chain 'C' and resid 246 through 257 removed outlier: 3.504A pdb=" N GLN C 255 " --> pdb=" O ALA C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 271 Processing helix chain 'C' and resid 285 through 292 Processing helix chain 'C' and resid 324 through 329 Processing helix chain 'C' and resid 348 through 366 removed outlier: 3.736A pdb=" N PHE C 356 " --> pdb=" O GLN C 352 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR C 358 " --> pdb=" O ARG C 354 " (cutoff:3.500A) Proline residue: C 359 - end of helix removed outlier: 3.558A pdb=" N HIS C 364 " --> pdb=" O ASP C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 377 Proline residue: C 374 - end of helix Processing helix chain 'C' and resid 415 through 419 Processing helix chain 'C' and resid 440 through 450 Processing helix chain 'C' and resid 452 through 468 Processing helix chain 'C' and resid 471 through 486 removed outlier: 3.507A pdb=" N VAL C 485 " --> pdb=" O ASN C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 504 Processing helix chain 'D' and resid 10 through 20 Processing helix chain 'D' and resid 54 through 65 Processing helix chain 'D' and resid 97 through 101 Processing helix chain 'D' and resid 157 through 159 No H-bonds generated for 'chain 'D' and resid 157 through 159' Processing helix chain 'D' and resid 160 through 169 Processing helix chain 'D' and resid 178 through 189 Processing helix chain 'D' and resid 192 through 201 Processing helix chain 'D' and resid 202 through 205 Processing helix chain 'D' and resid 208 through 212 removed outlier: 3.837A pdb=" N HIS D 211 " --> pdb=" O GLY D 208 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N MET D 212 " --> pdb=" O HIS D 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 208 through 212' Processing helix chain 'D' and resid 246 through 257 removed outlier: 3.504A pdb=" N GLN D 255 " --> pdb=" O ALA D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 271 Processing helix chain 'D' and resid 285 through 292 Processing helix chain 'D' and resid 324 through 329 Processing helix chain 'D' and resid 348 through 366 removed outlier: 3.736A pdb=" N PHE D 356 " --> pdb=" O GLN D 352 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR D 358 " --> pdb=" O ARG D 354 " (cutoff:3.500A) Proline residue: D 359 - end of helix removed outlier: 3.557A pdb=" N HIS D 364 " --> pdb=" O ASP D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 377 Proline residue: D 374 - end of helix Processing helix chain 'D' and resid 415 through 419 Processing helix chain 'D' and resid 440 through 450 Processing helix chain 'D' and resid 452 through 468 Processing helix chain 'D' and resid 471 through 486 removed outlier: 3.508A pdb=" N VAL D 485 " --> pdb=" O ASN D 481 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 504 Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 44 removed outlier: 3.899A pdb=" N ILE B 423 " --> pdb=" O VAL D 429 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 343 through 345 removed outlier: 6.453A pdb=" N TRP A 277 " --> pdb=" O LYS A 315 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LYS A 315 " --> pdb=" O TRP A 277 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N PHE A 279 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N LEU A 316 " --> pdb=" O GLU A 86 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N GLU A 86 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N LEU A 318 " --> pdb=" O TYR A 84 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N TYR A 84 " --> pdb=" O LEU A 318 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 423 through 424 removed outlier: 3.899A pdb=" N ILE A 423 " --> pdb=" O VAL C 429 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 423 through 424 removed outlier: 3.899A pdb=" N ILE C 423 " --> pdb=" O VAL A 429 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 343 through 345 removed outlier: 6.454A pdb=" N TRP B 277 " --> pdb=" O LYS B 315 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LYS B 315 " --> pdb=" O TRP B 277 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N PHE B 279 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N LEU B 316 " --> pdb=" O GLU B 86 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N GLU B 86 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N LEU B 318 " --> pdb=" O TYR B 84 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N TYR B 84 " --> pdb=" O LEU B 318 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 42 through 44 removed outlier: 3.899A pdb=" N ILE D 423 " --> pdb=" O VAL B 429 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 343 through 345 removed outlier: 6.453A pdb=" N TRP C 277 " --> pdb=" O LYS C 315 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LYS C 315 " --> pdb=" O TRP C 277 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N PHE C 279 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N LEU C 316 " --> pdb=" O GLU C 86 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N GLU C 86 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N LEU C 318 " --> pdb=" O TYR C 84 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N TYR C 84 " --> pdb=" O LEU C 318 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 343 through 345 removed outlier: 6.453A pdb=" N TRP D 277 " --> pdb=" O LYS D 315 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LYS D 315 " --> pdb=" O TRP D 277 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N PHE D 279 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N LEU D 316 " --> pdb=" O GLU D 86 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N GLU D 86 " --> pdb=" O LEU D 316 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N LEU D 318 " --> pdb=" O TYR D 84 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N TYR D 84 " --> pdb=" O LEU D 318 " (cutoff:3.500A) 680 hydrogen bonds defined for protein. 1872 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: 6.55 Time building geometry restraints manager: 5.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.37: 5922 1.37 - 1.55: 11038 1.55 - 1.73: 20 1.73 - 1.91: 92 1.91 - 2.09: 12 Bond restraints: 17084 Sorted by residual: bond pdb=" O2B NDP B 601 " pdb=" P2B NDP B 601 " ideal model delta sigma weight residual 1.833 1.615 0.218 3.80e-02 6.93e+02 3.29e+01 bond pdb=" O2B NDP D 601 " pdb=" P2B NDP D 601 " ideal model delta sigma weight residual 1.833 1.615 0.218 3.80e-02 6.93e+02 3.28e+01 bond pdb=" O2B NDP A 601 " pdb=" P2B NDP A 601 " ideal model delta sigma weight residual 1.833 1.616 0.217 3.80e-02 6.93e+02 3.28e+01 bond pdb=" O2B NDP C 601 " pdb=" P2B NDP C 601 " ideal model delta sigma weight residual 1.833 1.616 0.217 3.80e-02 6.93e+02 3.27e+01 bond pdb=" O5D NDP A 601 " pdb=" PN NDP A 601 " ideal model delta sigma weight residual 1.757 1.589 0.168 3.50e-02 8.16e+02 2.29e+01 ... (remaining 17079 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.27: 23148 5.27 - 10.53: 148 10.53 - 15.80: 4 15.80 - 21.07: 8 21.07 - 26.33: 4 Bond angle restraints: 23312 Sorted by residual: angle pdb=" PA NDP A 601 " pdb=" O3 NDP A 601 " pdb=" PN NDP A 601 " ideal model delta sigma weight residual 107.74 134.07 -26.33 1.95e+00 2.62e-01 1.82e+02 angle pdb=" PA NDP D 601 " pdb=" O3 NDP D 601 " pdb=" PN NDP D 601 " ideal model delta sigma weight residual 107.74 134.07 -26.33 1.95e+00 2.62e-01 1.82e+02 angle pdb=" PA NDP B 601 " pdb=" O3 NDP B 601 " pdb=" PN NDP B 601 " ideal model delta sigma weight residual 107.74 134.06 -26.32 1.95e+00 2.62e-01 1.81e+02 angle pdb=" PA NDP C 601 " pdb=" O3 NDP C 601 " pdb=" PN NDP C 601 " ideal model delta sigma weight residual 107.74 134.06 -26.32 1.95e+00 2.62e-01 1.81e+02 angle pdb=" C5B NDP C 601 " pdb=" O5B NDP C 601 " pdb=" PA NDP C 601 " ideal model delta sigma weight residual 103.84 119.78 -15.94 1.91e+00 2.73e-01 6.93e+01 ... (remaining 23307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.02: 9341 21.02 - 42.04: 491 42.04 - 63.06: 100 63.06 - 84.09: 44 84.09 - 105.11: 12 Dihedral angle restraints: 9988 sinusoidal: 4132 harmonic: 5856 Sorted by residual: dihedral pdb=" CA ILE B 281 " pdb=" C ILE B 281 " pdb=" N GLN B 282 " pdb=" CA GLN B 282 " ideal model delta harmonic sigma weight residual 180.00 155.68 24.32 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA ILE A 281 " pdb=" C ILE A 281 " pdb=" N GLN A 282 " pdb=" CA GLN A 282 " ideal model delta harmonic sigma weight residual 180.00 155.70 24.30 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA ILE C 281 " pdb=" C ILE C 281 " pdb=" N GLN C 282 " pdb=" CA GLN C 282 " ideal model delta harmonic sigma weight residual 180.00 155.72 24.28 0 5.00e+00 4.00e-02 2.36e+01 ... (remaining 9985 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1162 0.064 - 0.128: 819 0.128 - 0.192: 326 0.192 - 0.256: 37 0.256 - 0.320: 8 Chirality restraints: 2352 Sorted by residual: chirality pdb=" CA TYR B 236 " pdb=" N TYR B 236 " pdb=" C TYR B 236 " pdb=" CB TYR B 236 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CA TYR C 236 " pdb=" N TYR C 236 " pdb=" C TYR C 236 " pdb=" CB TYR C 236 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" CA TYR D 236 " pdb=" N TYR D 236 " pdb=" C TYR D 236 " pdb=" CB TYR D 236 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.52e+00 ... (remaining 2349 not shown) Planarity restraints: 3092 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2N NDP C 601 " -0.075 2.00e-02 2.50e+03 5.13e-02 3.29e+01 pdb=" C3N NDP C 601 " -0.031 2.00e-02 2.50e+03 pdb=" C4N NDP C 601 " -0.007 2.00e-02 2.50e+03 pdb=" C7N NDP C 601 " 0.050 2.00e-02 2.50e+03 pdb=" N1N NDP C 601 " 0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2N NDP B 601 " 0.074 2.00e-02 2.50e+03 5.10e-02 3.26e+01 pdb=" C3N NDP B 601 " 0.031 2.00e-02 2.50e+03 pdb=" C4N NDP B 601 " 0.007 2.00e-02 2.50e+03 pdb=" C7N NDP B 601 " -0.049 2.00e-02 2.50e+03 pdb=" N1N NDP B 601 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2N NDP D 601 " -0.075 2.00e-02 2.50e+03 5.10e-02 3.26e+01 pdb=" C3N NDP D 601 " -0.031 2.00e-02 2.50e+03 pdb=" C4N NDP D 601 " -0.007 2.00e-02 2.50e+03 pdb=" C7N NDP D 601 " 0.049 2.00e-02 2.50e+03 pdb=" N1N NDP D 601 " 0.063 2.00e-02 2.50e+03 ... (remaining 3089 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 5749 2.85 - 3.36: 18510 3.36 - 3.88: 37900 3.88 - 4.39: 44424 4.39 - 4.90: 67343 Nonbonded interactions: 173926 Sorted by model distance: nonbonded pdb=" ND1 HIS C 364 " pdb=" O HOH C 701 " model vdw 2.340 3.120 nonbonded pdb=" ND1 HIS B 364 " pdb=" O HOH B 701 " model vdw 2.341 3.120 nonbonded pdb=" ND1 HIS D 364 " pdb=" O HOH D 701 " model vdw 2.342 3.120 nonbonded pdb=" ND1 HIS A 364 " pdb=" O HOH A 701 " model vdw 2.342 3.120 nonbonded pdb=" OE1 GLU A 191 " pdb=" O HOH A 702 " model vdw 2.413 3.040 ... (remaining 173921 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 371 or resid 373 through 505 or resid 601 throug \ h 602)) selection = (chain 'B' and (resid 4 through 371 or resid 373 through 505 or resid 601 throug \ h 602)) selection = (chain 'C' and (resid 4 through 371 or resid 373 through 505 or resid 601 throug \ h 602)) selection = (chain 'D' and (resid 4 through 371 or resid 373 through 505 or resid 601 throug \ h 602)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.400 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: 0.010 Extract box with map and model: 0.750 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 53.010 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9049 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 : 0.014 0.218 17084 Z= 0.935 Angle : 1.791 26.335 23312 Z= 1.239 Chirality : 0.089 0.320 2352 Planarity : 0.008 0.051 3092 Dihedral : 14.824 105.107 6228 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.80 % Favored : 96.00 % Rotamer: Outliers : 0.75 % Allowed : 3.87 % Favored : 95.38 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.16), residues: 2012 helix: -1.24 (0.15), residues: 692 sheet: 0.15 (0.28), residues: 284 loop : -0.86 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.009 TRP D 15 HIS 0.014 0.005 HIS D 75 PHE 0.051 0.008 PHE D 82 TYR 0.042 0.008 TYR B 236 ARG 0.018 0.003 ARG D 365 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 148 time to evaluate : 2.017 Fit side-chains REVERT: A 18 GLN cc_start: 0.8170 (mt0) cc_final: 0.7910 (mp10) REVERT: A 23 LYS cc_start: 0.8087 (tttt) cc_final: 0.7793 (ptmm) REVERT: A 248 GLU cc_start: 0.8528 (tt0) cc_final: 0.8162 (mp0) REVERT: A 273 LYS cc_start: 0.8810 (mttp) cc_final: 0.8463 (mtpt) REVERT: A 306 LYS cc_start: 0.8915 (mtpt) cc_final: 0.8454 (mppt) REVERT: A 339 MET cc_start: 0.9072 (mtm) cc_final: 0.8517 (mtm) REVERT: A 382 ARG cc_start: 0.8733 (ttm110) cc_final: 0.8444 (ttm-80) REVERT: B 18 GLN cc_start: 0.8168 (mt0) cc_final: 0.7909 (mp10) REVERT: B 23 LYS cc_start: 0.8088 (tttt) cc_final: 0.7793 (ptmm) REVERT: B 248 GLU cc_start: 0.8525 (tt0) cc_final: 0.8162 (mp0) REVERT: B 273 LYS cc_start: 0.8811 (mttp) cc_final: 0.8465 (mtpt) REVERT: B 306 LYS cc_start: 0.8914 (mtpt) cc_final: 0.8453 (mppt) REVERT: B 339 MET cc_start: 0.9078 (mtm) cc_final: 0.8531 (mtm) REVERT: B 382 ARG cc_start: 0.8705 (ttm110) cc_final: 0.8431 (ttm-80) REVERT: C 18 GLN cc_start: 0.8169 (mt0) cc_final: 0.7910 (mp10) REVERT: C 23 LYS cc_start: 0.8087 (tttt) cc_final: 0.7790 (ptmm) REVERT: C 248 GLU cc_start: 0.8527 (tt0) cc_final: 0.8163 (mp0) REVERT: C 273 LYS cc_start: 0.8813 (mttp) cc_final: 0.8467 (mtpt) REVERT: C 306 LYS cc_start: 0.8916 (mtpt) cc_final: 0.8456 (mppt) REVERT: C 339 MET cc_start: 0.9072 (mtm) cc_final: 0.8517 (mtm) REVERT: C 382 ARG cc_start: 0.8703 (ttm110) cc_final: 0.8430 (ttm-80) REVERT: D 18 GLN cc_start: 0.8169 (mt0) cc_final: 0.7910 (mp10) REVERT: D 23 LYS cc_start: 0.8087 (tttt) cc_final: 0.7791 (ptmm) REVERT: D 248 GLU cc_start: 0.8524 (tt0) cc_final: 0.8160 (mp0) REVERT: D 273 LYS cc_start: 0.8809 (mttp) cc_final: 0.8463 (mtpt) REVERT: D 306 LYS cc_start: 0.8915 (mtpt) cc_final: 0.8454 (mppt) REVERT: D 339 MET cc_start: 0.9078 (mtm) cc_final: 0.8533 (mtm) REVERT: D 382 ARG cc_start: 0.8704 (ttm110) cc_final: 0.8431 (ttm-80) outliers start: 13 outliers final: 4 residues processed: 157 average time/residue: 1.7017 time to fit residues: 293.7231 Evaluate side-chains 116 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 112 time to evaluate : 1.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain D residue 138 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 0.9980 chunk 151 optimal weight: 10.0000 chunk 84 optimal weight: 0.8980 chunk 51 optimal weight: 7.9990 chunk 102 optimal weight: 7.9990 chunk 80 optimal weight: 3.9990 chunk 156 optimal weight: 8.9990 chunk 60 optimal weight: 5.9990 chunk 95 optimal weight: 8.9990 chunk 116 optimal weight: 5.9990 chunk 181 optimal weight: 8.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 GLN A 449 ASN A 492 HIS B 168 GLN B 449 ASN B 492 HIS C 168 GLN C 449 ASN C 492 HIS D 168 GLN D 449 ASN D 492 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8978 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17084 Z= 0.239 Angle : 0.642 5.924 23312 Z= 0.333 Chirality : 0.047 0.168 2352 Planarity : 0.004 0.033 3092 Dihedral : 9.109 97.593 2284 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.73 % Allowed : 4.85 % Favored : 93.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.18), residues: 2012 helix: 1.04 (0.19), residues: 700 sheet: 0.52 (0.28), residues: 304 loop : -0.10 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 183 HIS 0.005 0.001 HIS C 235 PHE 0.022 0.003 PHE D 164 TYR 0.027 0.002 TYR C 236 ARG 0.004 0.001 ARG A 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 120 time to evaluate : 2.418 Fit side-chains REVERT: A 18 GLN cc_start: 0.8033 (mt0) cc_final: 0.7772 (mp10) REVERT: A 248 GLU cc_start: 0.8420 (tt0) cc_final: 0.7984 (mp0) REVERT: A 273 LYS cc_start: 0.8755 (mttp) cc_final: 0.8416 (mtpt) REVERT: A 306 LYS cc_start: 0.8797 (mtpt) cc_final: 0.8369 (mppt) REVERT: A 503 GLU cc_start: 0.6683 (mt-10) cc_final: 0.6381 (tm-30) REVERT: B 18 GLN cc_start: 0.8029 (mt0) cc_final: 0.7770 (mp10) REVERT: B 248 GLU cc_start: 0.8421 (tt0) cc_final: 0.7986 (mp0) REVERT: B 273 LYS cc_start: 0.8755 (mttp) cc_final: 0.8417 (mtpt) REVERT: B 306 LYS cc_start: 0.8796 (mtpt) cc_final: 0.8368 (mppt) REVERT: B 503 GLU cc_start: 0.6679 (mt-10) cc_final: 0.6379 (tm-30) REVERT: C 18 GLN cc_start: 0.8030 (mt0) cc_final: 0.7772 (mp10) REVERT: C 248 GLU cc_start: 0.8420 (tt0) cc_final: 0.7985 (mp0) REVERT: C 273 LYS cc_start: 0.8758 (mttp) cc_final: 0.8419 (mtpt) REVERT: C 306 LYS cc_start: 0.8776 (mtpt) cc_final: 0.8358 (mppt) REVERT: C 394 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.7462 (mpt) REVERT: C 503 GLU cc_start: 0.6683 (mt-10) cc_final: 0.6382 (tm-30) REVERT: D 18 GLN cc_start: 0.8031 (mt0) cc_final: 0.7771 (mp10) REVERT: D 248 GLU cc_start: 0.8417 (tt0) cc_final: 0.7984 (mp0) REVERT: D 273 LYS cc_start: 0.8754 (mttp) cc_final: 0.8415 (mtpt) REVERT: D 306 LYS cc_start: 0.8797 (mtpt) cc_final: 0.8369 (mppt) REVERT: D 394 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.7482 (mpt) REVERT: D 503 GLU cc_start: 0.6685 (mt-10) cc_final: 0.6386 (tm-30) outliers start: 30 outliers final: 8 residues processed: 144 average time/residue: 1.6574 time to fit residues: 263.2734 Evaluate side-chains 134 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 124 time to evaluate : 2.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 394 MET Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 394 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 100 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 151 optimal weight: 3.9990 chunk 123 optimal weight: 20.0000 chunk 50 optimal weight: 0.0870 chunk 181 optimal weight: 0.9990 chunk 196 optimal weight: 7.9990 chunk 162 optimal weight: 7.9990 chunk 180 optimal weight: 0.9980 chunk 62 optimal weight: 7.9990 chunk 145 optimal weight: 5.9990 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17084 Z= 0.167 Angle : 0.561 5.529 23312 Z= 0.284 Chirality : 0.044 0.164 2352 Planarity : 0.004 0.032 3092 Dihedral : 8.045 90.906 2284 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.69 % Allowed : 6.58 % Favored : 92.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.19), residues: 2012 helix: 1.48 (0.20), residues: 712 sheet: 0.77 (0.29), residues: 308 loop : 0.13 (0.20), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 183 HIS 0.003 0.001 HIS C 218 PHE 0.014 0.002 PHE D 164 TYR 0.022 0.001 TYR C 236 ARG 0.002 0.000 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 144 time to evaluate : 2.051 Fit side-chains REVERT: A 18 GLN cc_start: 0.8028 (mt0) cc_final: 0.7762 (mp10) REVERT: A 23 LYS cc_start: 0.8192 (ttpp) cc_final: 0.7964 (tttm) REVERT: A 248 GLU cc_start: 0.8196 (tt0) cc_final: 0.7914 (mp0) REVERT: A 273 LYS cc_start: 0.8645 (mttp) cc_final: 0.8346 (mtpt) REVERT: A 306 LYS cc_start: 0.8786 (mtpt) cc_final: 0.8486 (tttm) REVERT: A 503 GLU cc_start: 0.6882 (mt-10) cc_final: 0.6558 (tm-30) REVERT: B 18 GLN cc_start: 0.8036 (mt0) cc_final: 0.7772 (mp10) REVERT: B 23 LYS cc_start: 0.8194 (ttpp) cc_final: 0.7966 (tttm) REVERT: B 248 GLU cc_start: 0.8198 (tt0) cc_final: 0.7915 (mp0) REVERT: B 273 LYS cc_start: 0.8644 (mttp) cc_final: 0.8346 (mtpt) REVERT: B 306 LYS cc_start: 0.8788 (mtpt) cc_final: 0.8488 (tttm) REVERT: B 503 GLU cc_start: 0.6882 (mt-10) cc_final: 0.6557 (tm-30) REVERT: C 18 GLN cc_start: 0.8025 (mt0) cc_final: 0.7760 (mp10) REVERT: C 23 LYS cc_start: 0.8194 (ttpp) cc_final: 0.7967 (tttm) REVERT: C 248 GLU cc_start: 0.8198 (tt0) cc_final: 0.7914 (mp0) REVERT: C 273 LYS cc_start: 0.8644 (mttp) cc_final: 0.8345 (mtpt) REVERT: C 306 LYS cc_start: 0.8789 (mtpt) cc_final: 0.8488 (tttm) REVERT: C 394 MET cc_start: 0.8610 (OUTLIER) cc_final: 0.7361 (mpt) REVERT: C 503 GLU cc_start: 0.6885 (mt-10) cc_final: 0.6557 (tm-30) REVERT: D 18 GLN cc_start: 0.8026 (mt0) cc_final: 0.7760 (mp10) REVERT: D 23 LYS cc_start: 0.8193 (ttpp) cc_final: 0.7965 (tttm) REVERT: D 248 GLU cc_start: 0.8190 (tt0) cc_final: 0.7910 (mp0) REVERT: D 273 LYS cc_start: 0.8641 (mttp) cc_final: 0.8343 (mtpt) REVERT: D 306 LYS cc_start: 0.8786 (mtpt) cc_final: 0.8486 (tttm) REVERT: D 394 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.7215 (mpt) REVERT: D 503 GLU cc_start: 0.6883 (mt-10) cc_final: 0.6560 (tm-30) outliers start: 12 outliers final: 4 residues processed: 148 average time/residue: 1.6744 time to fit residues: 273.3413 Evaluate side-chains 126 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 120 time to evaluate : 2.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 394 MET Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 394 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 179 optimal weight: 0.8980 chunk 136 optimal weight: 8.9990 chunk 94 optimal weight: 7.9990 chunk 20 optimal weight: 10.0000 chunk 86 optimal weight: 9.9990 chunk 122 optimal weight: 7.9990 chunk 182 optimal weight: 8.9990 chunk 193 optimal weight: 9.9990 chunk 95 optimal weight: 6.9990 chunk 173 optimal weight: 20.0000 chunk 52 optimal weight: 5.9990 overall best weight: 5.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8977 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 17084 Z= 0.328 Angle : 0.667 8.274 23312 Z= 0.339 Chirality : 0.048 0.166 2352 Planarity : 0.005 0.043 3092 Dihedral : 9.321 105.505 2280 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.46 % Allowed : 8.03 % Favored : 91.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.18), residues: 2012 helix: 1.22 (0.19), residues: 708 sheet: 0.58 (0.30), residues: 308 loop : 0.01 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 183 HIS 0.007 0.002 HIS B 218 PHE 0.022 0.003 PHE D 57 TYR 0.029 0.002 TYR A 236 ARG 0.005 0.001 ARG C 156 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 120 time to evaluate : 2.161 Fit side-chains REVERT: A 18 GLN cc_start: 0.8051 (mt0) cc_final: 0.7752 (mp10) REVERT: A 23 LYS cc_start: 0.8175 (ttpp) cc_final: 0.7924 (tttp) REVERT: A 248 GLU cc_start: 0.8254 (tt0) cc_final: 0.7865 (mp0) REVERT: A 273 LYS cc_start: 0.8748 (mttp) cc_final: 0.8378 (mtpt) REVERT: A 306 LYS cc_start: 0.8846 (mtpt) cc_final: 0.8549 (tttm) REVERT: A 503 GLU cc_start: 0.6717 (mt-10) cc_final: 0.6411 (tm-30) REVERT: B 18 GLN cc_start: 0.8050 (mt0) cc_final: 0.7751 (mp10) REVERT: B 23 LYS cc_start: 0.8176 (ttpp) cc_final: 0.7925 (tttp) REVERT: B 248 GLU cc_start: 0.8255 (tt0) cc_final: 0.7867 (mp0) REVERT: B 273 LYS cc_start: 0.8749 (mttp) cc_final: 0.8380 (mtpt) REVERT: B 306 LYS cc_start: 0.8890 (mtpt) cc_final: 0.8602 (tttm) REVERT: B 503 GLU cc_start: 0.6716 (mt-10) cc_final: 0.6411 (tm-30) REVERT: C 18 GLN cc_start: 0.8052 (mt0) cc_final: 0.7753 (mp10) REVERT: C 23 LYS cc_start: 0.8176 (ttpp) cc_final: 0.7925 (tttp) REVERT: C 248 GLU cc_start: 0.8255 (tt0) cc_final: 0.7867 (mp0) REVERT: C 273 LYS cc_start: 0.8748 (mttp) cc_final: 0.8378 (mtpt) REVERT: C 306 LYS cc_start: 0.8846 (mtpt) cc_final: 0.8548 (tttm) REVERT: C 503 GLU cc_start: 0.6718 (mt-10) cc_final: 0.6410 (tm-30) REVERT: D 18 GLN cc_start: 0.8052 (mt0) cc_final: 0.7752 (mp10) REVERT: D 23 LYS cc_start: 0.8175 (ttpp) cc_final: 0.7924 (tttp) REVERT: D 248 GLU cc_start: 0.8247 (tt0) cc_final: 0.7864 (mp0) REVERT: D 273 LYS cc_start: 0.8753 (mttp) cc_final: 0.8384 (mtpt) REVERT: D 306 LYS cc_start: 0.8847 (mtpt) cc_final: 0.8550 (tttm) REVERT: D 503 GLU cc_start: 0.6723 (mt-10) cc_final: 0.6416 (tm-30) outliers start: 8 outliers final: 4 residues processed: 128 average time/residue: 1.7418 time to fit residues: 246.8727 Evaluate side-chains 128 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 124 time to evaluate : 2.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 236 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 161 optimal weight: 6.9990 chunk 109 optimal weight: 20.0000 chunk 2 optimal weight: 10.0000 chunk 143 optimal weight: 8.9990 chunk 79 optimal weight: 0.7980 chunk 164 optimal weight: 7.9990 chunk 133 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 98 optimal weight: 5.9990 chunk 173 optimal weight: 9.9990 chunk 48 optimal weight: 5.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8968 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17084 Z= 0.277 Angle : 0.627 6.896 23312 Z= 0.320 Chirality : 0.047 0.166 2352 Planarity : 0.005 0.043 3092 Dihedral : 9.080 104.549 2280 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.46 % Allowed : 8.08 % Favored : 91.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.18), residues: 2012 helix: 1.24 (0.20), residues: 708 sheet: 0.71 (0.31), residues: 288 loop : -0.03 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 183 HIS 0.007 0.001 HIS D 218 PHE 0.018 0.003 PHE B 136 TYR 0.027 0.002 TYR A 236 ARG 0.003 0.000 ARG D 156 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 132 time to evaluate : 2.059 Fit side-chains REVERT: A 18 GLN cc_start: 0.8065 (mt0) cc_final: 0.7760 (mp10) REVERT: A 23 LYS cc_start: 0.8169 (ttpp) cc_final: 0.7925 (tttp) REVERT: A 248 GLU cc_start: 0.8236 (tt0) cc_final: 0.7849 (mp0) REVERT: A 273 LYS cc_start: 0.8708 (mttp) cc_final: 0.8342 (mtpt) REVERT: A 306 LYS cc_start: 0.8879 (mtpt) cc_final: 0.8594 (tttm) REVERT: A 503 GLU cc_start: 0.6713 (mt-10) cc_final: 0.6393 (tm-30) REVERT: B 18 GLN cc_start: 0.8042 (mt0) cc_final: 0.7741 (mp10) REVERT: B 23 LYS cc_start: 0.8169 (ttpp) cc_final: 0.7924 (tttp) REVERT: B 248 GLU cc_start: 0.8239 (tt0) cc_final: 0.7851 (mp0) REVERT: B 273 LYS cc_start: 0.8708 (mttp) cc_final: 0.8344 (mtpt) REVERT: B 306 LYS cc_start: 0.8877 (mtpt) cc_final: 0.8592 (tttm) REVERT: B 503 GLU cc_start: 0.6714 (mt-10) cc_final: 0.6394 (tm-30) REVERT: C 18 GLN cc_start: 0.8044 (mt0) cc_final: 0.7744 (mp10) REVERT: C 23 LYS cc_start: 0.8169 (ttpp) cc_final: 0.7925 (tttp) REVERT: C 248 GLU cc_start: 0.8238 (tt0) cc_final: 0.7850 (mp0) REVERT: C 273 LYS cc_start: 0.8706 (mttp) cc_final: 0.8340 (mtpt) REVERT: C 306 LYS cc_start: 0.8880 (mtpt) cc_final: 0.8594 (tttm) REVERT: C 503 GLU cc_start: 0.6717 (mt-10) cc_final: 0.6395 (tm-30) REVERT: D 18 GLN cc_start: 0.8066 (mt0) cc_final: 0.7759 (mp10) REVERT: D 23 LYS cc_start: 0.8168 (ttpp) cc_final: 0.7923 (tttp) REVERT: D 128 ASP cc_start: 0.9136 (OUTLIER) cc_final: 0.8933 (m-30) REVERT: D 248 GLU cc_start: 0.8248 (tt0) cc_final: 0.7863 (mp0) REVERT: D 273 LYS cc_start: 0.8728 (mttp) cc_final: 0.8359 (mtpt) REVERT: D 306 LYS cc_start: 0.8880 (mtpt) cc_final: 0.8596 (tttm) REVERT: D 503 GLU cc_start: 0.6714 (mt-10) cc_final: 0.6395 (tm-30) outliers start: 8 outliers final: 4 residues processed: 136 average time/residue: 1.6830 time to fit residues: 252.1535 Evaluate side-chains 130 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 125 time to evaluate : 2.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 236 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 65 optimal weight: 0.9990 chunk 174 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 47 optimal weight: 20.0000 chunk 193 optimal weight: 7.9990 chunk 160 optimal weight: 6.9990 chunk 89 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 101 optimal weight: 10.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 HIS B 211 HIS C 211 HIS D 211 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8930 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17084 Z= 0.178 Angle : 0.551 5.468 23312 Z= 0.280 Chirality : 0.044 0.166 2352 Planarity : 0.004 0.038 3092 Dihedral : 8.186 96.244 2280 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.29 % Allowed : 8.49 % Favored : 91.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.19), residues: 2012 helix: 1.46 (0.20), residues: 712 sheet: 0.87 (0.31), residues: 308 loop : 0.11 (0.20), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 183 HIS 0.004 0.001 HIS A 218 PHE 0.013 0.002 PHE A 136 TYR 0.022 0.002 TYR A 236 ARG 0.002 0.000 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 122 time to evaluate : 2.065 Fit side-chains REVERT: A 18 GLN cc_start: 0.8058 (mt0) cc_final: 0.7766 (mp10) REVERT: A 23 LYS cc_start: 0.8179 (ttpp) cc_final: 0.7944 (tttp) REVERT: A 248 GLU cc_start: 0.8212 (tt0) cc_final: 0.7903 (mp0) REVERT: A 273 LYS cc_start: 0.8625 (mttp) cc_final: 0.8271 (mtpt) REVERT: A 306 LYS cc_start: 0.8763 (mtpt) cc_final: 0.8484 (tttm) REVERT: A 454 GLU cc_start: 0.8297 (mp0) cc_final: 0.7777 (mm-30) REVERT: A 503 GLU cc_start: 0.6787 (mt-10) cc_final: 0.6425 (tm-30) REVERT: B 18 GLN cc_start: 0.8055 (mt0) cc_final: 0.7765 (mp10) REVERT: B 23 LYS cc_start: 0.8177 (ttpp) cc_final: 0.7943 (tttp) REVERT: B 248 GLU cc_start: 0.8214 (tt0) cc_final: 0.7905 (mp0) REVERT: B 273 LYS cc_start: 0.8624 (mttp) cc_final: 0.8270 (mtpt) REVERT: B 306 LYS cc_start: 0.8762 (mtpt) cc_final: 0.8483 (tttm) REVERT: B 454 GLU cc_start: 0.8291 (mp0) cc_final: 0.7774 (mm-30) REVERT: B 503 GLU cc_start: 0.6787 (mt-10) cc_final: 0.6427 (tm-30) REVERT: C 18 GLN cc_start: 0.8057 (mt0) cc_final: 0.7765 (mp10) REVERT: C 23 LYS cc_start: 0.8179 (ttpp) cc_final: 0.7944 (tttp) REVERT: C 248 GLU cc_start: 0.8214 (tt0) cc_final: 0.7906 (mp0) REVERT: C 273 LYS cc_start: 0.8642 (mttp) cc_final: 0.8286 (mtpt) REVERT: C 306 LYS cc_start: 0.8763 (mtpt) cc_final: 0.8483 (tttm) REVERT: C 454 GLU cc_start: 0.8293 (mp0) cc_final: 0.7776 (mm-30) REVERT: C 503 GLU cc_start: 0.6787 (mt-10) cc_final: 0.6426 (tm-30) REVERT: D 18 GLN cc_start: 0.8057 (mt0) cc_final: 0.7766 (mp10) REVERT: D 23 LYS cc_start: 0.8177 (ttpp) cc_final: 0.7942 (tttp) REVERT: D 128 ASP cc_start: 0.9053 (OUTLIER) cc_final: 0.8826 (m-30) REVERT: D 248 GLU cc_start: 0.8207 (tt0) cc_final: 0.7900 (mp0) REVERT: D 273 LYS cc_start: 0.8627 (mttp) cc_final: 0.8268 (mtpt) REVERT: D 306 LYS cc_start: 0.8764 (mtpt) cc_final: 0.8485 (tttm) REVERT: D 454 GLU cc_start: 0.8292 (mp0) cc_final: 0.7776 (mm-30) REVERT: D 503 GLU cc_start: 0.6786 (mt-10) cc_final: 0.6427 (tm-30) outliers start: 5 outliers final: 4 residues processed: 126 average time/residue: 1.6721 time to fit residues: 232.5264 Evaluate side-chains 126 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 121 time to evaluate : 1.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 236 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 186 optimal weight: 9.9990 chunk 21 optimal weight: 20.0000 chunk 110 optimal weight: 3.9990 chunk 141 optimal weight: 7.9990 chunk 109 optimal weight: 20.0000 chunk 162 optimal weight: 0.5980 chunk 108 optimal weight: 5.9990 chunk 192 optimal weight: 10.0000 chunk 120 optimal weight: 0.2980 chunk 117 optimal weight: 8.9990 chunk 88 optimal weight: 1.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17084 Z= 0.199 Angle : 0.565 5.496 23312 Z= 0.286 Chirality : 0.044 0.167 2352 Planarity : 0.004 0.041 3092 Dihedral : 8.386 98.833 2280 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.69 % Allowed : 7.97 % Favored : 91.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.19), residues: 2012 helix: 1.46 (0.20), residues: 712 sheet: 0.79 (0.31), residues: 308 loop : 0.11 (0.20), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 183 HIS 0.005 0.001 HIS D 218 PHE 0.015 0.002 PHE A 136 TYR 0.024 0.002 TYR D 236 ARG 0.002 0.000 ARG B 156 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 121 time to evaluate : 2.040 Fit side-chains REVERT: A 18 GLN cc_start: 0.8071 (mt0) cc_final: 0.7755 (mp10) REVERT: A 23 LYS cc_start: 0.8164 (ttpp) cc_final: 0.7929 (tttp) REVERT: A 248 GLU cc_start: 0.8216 (tt0) cc_final: 0.7914 (mp0) REVERT: A 273 LYS cc_start: 0.8654 (mttp) cc_final: 0.8303 (mtpt) REVERT: A 306 LYS cc_start: 0.8776 (mtpt) cc_final: 0.8493 (tttm) REVERT: A 454 GLU cc_start: 0.8299 (mp0) cc_final: 0.7778 (mm-30) REVERT: A 503 GLU cc_start: 0.6900 (mt-10) cc_final: 0.6463 (tm-30) REVERT: B 18 GLN cc_start: 0.8069 (mt0) cc_final: 0.7755 (mp10) REVERT: B 23 LYS cc_start: 0.8162 (ttpp) cc_final: 0.7927 (tttp) REVERT: B 248 GLU cc_start: 0.8219 (tt0) cc_final: 0.7917 (mp0) REVERT: B 273 LYS cc_start: 0.8654 (mttp) cc_final: 0.8303 (mtpt) REVERT: B 306 LYS cc_start: 0.8779 (mtpt) cc_final: 0.8496 (tttm) REVERT: B 454 GLU cc_start: 0.8296 (mp0) cc_final: 0.7776 (mm-30) REVERT: B 503 GLU cc_start: 0.6901 (mt-10) cc_final: 0.6466 (tm-30) REVERT: C 18 GLN cc_start: 0.8069 (mt0) cc_final: 0.7755 (mp10) REVERT: C 23 LYS cc_start: 0.8164 (ttpp) cc_final: 0.7929 (tttp) REVERT: C 248 GLU cc_start: 0.8220 (tt0) cc_final: 0.7917 (mp0) REVERT: C 273 LYS cc_start: 0.8656 (mttp) cc_final: 0.8303 (mtpt) REVERT: C 306 LYS cc_start: 0.8773 (mtpt) cc_final: 0.8468 (tttm) REVERT: C 454 GLU cc_start: 0.8298 (mp0) cc_final: 0.7779 (mm-30) REVERT: C 503 GLU cc_start: 0.6901 (mt-10) cc_final: 0.6463 (tm-30) REVERT: D 18 GLN cc_start: 0.8071 (mt0) cc_final: 0.7756 (mp10) REVERT: D 23 LYS cc_start: 0.8162 (ttpp) cc_final: 0.7928 (tttp) REVERT: D 128 ASP cc_start: 0.9061 (OUTLIER) cc_final: 0.8832 (m-30) REVERT: D 248 GLU cc_start: 0.8213 (tt0) cc_final: 0.7913 (mp0) REVERT: D 273 LYS cc_start: 0.8650 (mttp) cc_final: 0.8299 (mtpt) REVERT: D 306 LYS cc_start: 0.8777 (mtpt) cc_final: 0.8493 (tttm) REVERT: D 454 GLU cc_start: 0.8295 (mp0) cc_final: 0.7777 (mm-30) REVERT: D 503 GLU cc_start: 0.6901 (mt-10) cc_final: 0.6466 (tm-30) outliers start: 12 outliers final: 4 residues processed: 132 average time/residue: 1.7216 time to fit residues: 249.8729 Evaluate side-chains 124 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 119 time to evaluate : 2.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 236 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 119 optimal weight: 5.9990 chunk 76 optimal weight: 9.9990 chunk 115 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 122 optimal weight: 9.9990 chunk 131 optimal weight: 8.9990 chunk 95 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 chunk 151 optimal weight: 6.9990 chunk 175 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8972 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 17084 Z= 0.336 Angle : 0.662 8.576 23312 Z= 0.335 Chirality : 0.048 0.170 2352 Planarity : 0.005 0.046 3092 Dihedral : 9.436 112.513 2280 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.29 % Allowed : 8.60 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.18), residues: 2012 helix: 1.22 (0.20), residues: 712 sheet: 0.66 (0.32), residues: 284 loop : 0.03 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 183 HIS 0.008 0.002 HIS D 218 PHE 0.020 0.003 PHE B 136 TYR 0.029 0.003 TYR A 236 ARG 0.005 0.001 ARG D 156 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 120 time to evaluate : 2.098 Fit side-chains REVERT: A 18 GLN cc_start: 0.8082 (mt0) cc_final: 0.7780 (mp10) REVERT: A 23 LYS cc_start: 0.8195 (ttpp) cc_final: 0.7984 (tttm) REVERT: A 128 ASP cc_start: 0.9145 (t0) cc_final: 0.8937 (m-30) REVERT: A 248 GLU cc_start: 0.8232 (tt0) cc_final: 0.7855 (mp0) REVERT: A 273 LYS cc_start: 0.8725 (mttp) cc_final: 0.8376 (mtpt) REVERT: A 306 LYS cc_start: 0.8881 (mtpt) cc_final: 0.8591 (tttm) REVERT: A 454 GLU cc_start: 0.8319 (mp0) cc_final: 0.8086 (mp0) REVERT: A 503 GLU cc_start: 0.6825 (mt-10) cc_final: 0.6368 (tm-30) REVERT: B 18 GLN cc_start: 0.8082 (mt0) cc_final: 0.7779 (mp10) REVERT: B 23 LYS cc_start: 0.8195 (ttpp) cc_final: 0.7984 (tttm) REVERT: B 248 GLU cc_start: 0.8236 (tt0) cc_final: 0.7857 (mp0) REVERT: B 273 LYS cc_start: 0.8726 (mttp) cc_final: 0.8379 (mtpt) REVERT: B 306 LYS cc_start: 0.8880 (mtpt) cc_final: 0.8591 (tttm) REVERT: B 454 GLU cc_start: 0.8316 (mp0) cc_final: 0.8084 (mp0) REVERT: B 503 GLU cc_start: 0.6824 (mt-10) cc_final: 0.6369 (tm-30) REVERT: C 18 GLN cc_start: 0.8082 (mt0) cc_final: 0.7780 (mp10) REVERT: C 23 LYS cc_start: 0.8195 (ttpp) cc_final: 0.7985 (tttm) REVERT: C 128 ASP cc_start: 0.9146 (t0) cc_final: 0.8937 (m-30) REVERT: C 248 GLU cc_start: 0.8236 (tt0) cc_final: 0.7858 (mp0) REVERT: C 273 LYS cc_start: 0.8726 (mttp) cc_final: 0.8377 (mtpt) REVERT: C 306 LYS cc_start: 0.8882 (mtpt) cc_final: 0.8592 (tttm) REVERT: C 454 GLU cc_start: 0.8317 (mp0) cc_final: 0.8085 (mp0) REVERT: C 503 GLU cc_start: 0.6824 (mt-10) cc_final: 0.6367 (tm-30) REVERT: D 18 GLN cc_start: 0.8083 (mt0) cc_final: 0.7780 (mp10) REVERT: D 23 LYS cc_start: 0.8192 (ttpp) cc_final: 0.7981 (tttm) REVERT: D 248 GLU cc_start: 0.8233 (tt0) cc_final: 0.7855 (mp0) REVERT: D 273 LYS cc_start: 0.8722 (mttp) cc_final: 0.8374 (mtpt) REVERT: D 306 LYS cc_start: 0.8883 (mtpt) cc_final: 0.8593 (tttm) REVERT: D 454 GLU cc_start: 0.8316 (mp0) cc_final: 0.8084 (mp0) REVERT: D 503 GLU cc_start: 0.6824 (mt-10) cc_final: 0.6368 (tm-30) outliers start: 5 outliers final: 4 residues processed: 124 average time/residue: 1.6612 time to fit residues: 228.0703 Evaluate side-chains 122 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 118 time to evaluate : 2.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 236 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 184 optimal weight: 5.9990 chunk 168 optimal weight: 0.9990 chunk 179 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 141 optimal weight: 0.8980 chunk 55 optimal weight: 10.0000 chunk 162 optimal weight: 7.9990 chunk 169 optimal weight: 10.0000 chunk 117 optimal weight: 7.9990 chunk 189 optimal weight: 6.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17084 Z= 0.192 Angle : 0.561 5.484 23312 Z= 0.285 Chirality : 0.044 0.166 2352 Planarity : 0.004 0.041 3092 Dihedral : 8.440 101.387 2280 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.29 % Allowed : 8.60 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.19), residues: 2012 helix: 1.45 (0.20), residues: 712 sheet: 0.85 (0.31), residues: 304 loop : 0.12 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 183 HIS 0.005 0.001 HIS A 218 PHE 0.014 0.002 PHE A 136 TYR 0.023 0.002 TYR C 236 ARG 0.002 0.000 ARG C 263 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 118 time to evaluate : 1.910 Fit side-chains REVERT: A 18 GLN cc_start: 0.8059 (mt0) cc_final: 0.7765 (mp10) REVERT: A 23 LYS cc_start: 0.8185 (ttpp) cc_final: 0.7950 (tttp) REVERT: A 128 ASP cc_start: 0.9093 (t0) cc_final: 0.8878 (m-30) REVERT: A 248 GLU cc_start: 0.8219 (tt0) cc_final: 0.7903 (mp0) REVERT: A 273 LYS cc_start: 0.8615 (mttp) cc_final: 0.8281 (mtpt) REVERT: A 306 LYS cc_start: 0.8771 (mtpt) cc_final: 0.8497 (tttm) REVERT: A 454 GLU cc_start: 0.8288 (mp0) cc_final: 0.7760 (mm-30) REVERT: A 503 GLU cc_start: 0.6881 (mt-10) cc_final: 0.6453 (tm-30) REVERT: B 18 GLN cc_start: 0.8057 (mt0) cc_final: 0.7764 (mp10) REVERT: B 23 LYS cc_start: 0.8187 (ttpp) cc_final: 0.7953 (tttp) REVERT: B 248 GLU cc_start: 0.8221 (tt0) cc_final: 0.7905 (mp0) REVERT: B 273 LYS cc_start: 0.8605 (mttp) cc_final: 0.8273 (mtpt) REVERT: B 306 LYS cc_start: 0.8771 (mtpt) cc_final: 0.8497 (tttm) REVERT: B 454 GLU cc_start: 0.8285 (mp0) cc_final: 0.7758 (mm-30) REVERT: B 503 GLU cc_start: 0.6881 (mt-10) cc_final: 0.6453 (tm-30) REVERT: C 18 GLN cc_start: 0.8059 (mt0) cc_final: 0.7766 (mp10) REVERT: C 23 LYS cc_start: 0.8188 (ttpp) cc_final: 0.7953 (tttp) REVERT: C 128 ASP cc_start: 0.9092 (t0) cc_final: 0.8878 (m-30) REVERT: C 248 GLU cc_start: 0.8221 (tt0) cc_final: 0.7905 (mp0) REVERT: C 273 LYS cc_start: 0.8616 (mttp) cc_final: 0.8281 (mtpt) REVERT: C 306 LYS cc_start: 0.8772 (mtpt) cc_final: 0.8497 (tttm) REVERT: C 454 GLU cc_start: 0.8288 (mp0) cc_final: 0.7761 (mm-30) REVERT: C 503 GLU cc_start: 0.6883 (mt-10) cc_final: 0.6452 (tm-30) REVERT: D 18 GLN cc_start: 0.8060 (mt0) cc_final: 0.7750 (mp10) REVERT: D 23 LYS cc_start: 0.8186 (ttpp) cc_final: 0.7951 (tttp) REVERT: D 248 GLU cc_start: 0.8216 (tt0) cc_final: 0.7901 (mp0) REVERT: D 273 LYS cc_start: 0.8610 (mttp) cc_final: 0.8276 (mtpt) REVERT: D 306 LYS cc_start: 0.8773 (mtpt) cc_final: 0.8498 (tttm) REVERT: D 454 GLU cc_start: 0.8286 (mp0) cc_final: 0.7760 (mm-30) REVERT: D 503 GLU cc_start: 0.6880 (mt-10) cc_final: 0.6454 (tm-30) outliers start: 5 outliers final: 4 residues processed: 123 average time/residue: 1.6257 time to fit residues: 220.8441 Evaluate side-chains 123 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 119 time to evaluate : 1.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 236 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 115 optimal weight: 5.9990 chunk 90 optimal weight: 7.9990 chunk 132 optimal weight: 4.9990 chunk 199 optimal weight: 5.9990 chunk 183 optimal weight: 7.9990 chunk 158 optimal weight: 0.4980 chunk 16 optimal weight: 2.9990 chunk 122 optimal weight: 9.9990 chunk 97 optimal weight: 6.9990 chunk 126 optimal weight: 7.9990 chunk 169 optimal weight: 5.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 17084 Z= 0.256 Angle : 0.606 5.551 23312 Z= 0.307 Chirality : 0.046 0.166 2352 Planarity : 0.004 0.044 3092 Dihedral : 8.932 106.980 2280 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.40 % Allowed : 8.49 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.19), residues: 2012 helix: 1.35 (0.20), residues: 712 sheet: 0.77 (0.32), residues: 284 loop : 0.07 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 183 HIS 0.007 0.001 HIS D 218 PHE 0.017 0.002 PHE B 136 TYR 0.026 0.002 TYR C 236 ARG 0.003 0.000 ARG D 156 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 119 time to evaluate : 2.113 Fit side-chains REVERT: A 18 GLN cc_start: 0.8068 (mt0) cc_final: 0.7757 (mp10) REVERT: A 23 LYS cc_start: 0.8186 (ttpp) cc_final: 0.7951 (tttp) REVERT: A 128 ASP cc_start: 0.9146 (t0) cc_final: 0.8937 (m-30) REVERT: A 248 GLU cc_start: 0.8213 (tt0) cc_final: 0.7876 (mp0) REVERT: A 273 LYS cc_start: 0.8695 (mttp) cc_final: 0.8350 (mtpt) REVERT: A 306 LYS cc_start: 0.8820 (mtpt) cc_final: 0.8521 (tttm) REVERT: A 454 GLU cc_start: 0.8298 (mp0) cc_final: 0.8053 (mp0) REVERT: A 503 GLU cc_start: 0.6898 (mt-10) cc_final: 0.6458 (tm-30) REVERT: B 18 GLN cc_start: 0.8067 (mt0) cc_final: 0.7756 (mp10) REVERT: B 23 LYS cc_start: 0.8187 (ttpp) cc_final: 0.7951 (tttp) REVERT: B 128 ASP cc_start: 0.9116 (t0) cc_final: 0.8911 (m-30) REVERT: B 248 GLU cc_start: 0.8214 (tt0) cc_final: 0.7877 (mp0) REVERT: B 273 LYS cc_start: 0.8694 (mttp) cc_final: 0.8350 (mtpt) REVERT: B 306 LYS cc_start: 0.8819 (mtpt) cc_final: 0.8520 (tttm) REVERT: B 454 GLU cc_start: 0.8294 (mp0) cc_final: 0.8050 (mp0) REVERT: B 503 GLU cc_start: 0.6896 (mt-10) cc_final: 0.6458 (tm-30) REVERT: C 18 GLN cc_start: 0.8068 (mt0) cc_final: 0.7757 (mp10) REVERT: C 23 LYS cc_start: 0.8188 (ttpp) cc_final: 0.7953 (tttp) REVERT: C 128 ASP cc_start: 0.9147 (t0) cc_final: 0.8939 (m-30) REVERT: C 248 GLU cc_start: 0.8214 (tt0) cc_final: 0.7879 (mp0) REVERT: C 273 LYS cc_start: 0.8697 (mttp) cc_final: 0.8351 (mtpt) REVERT: C 306 LYS cc_start: 0.8815 (mtpt) cc_final: 0.8514 (tttm) REVERT: C 454 GLU cc_start: 0.8296 (mp0) cc_final: 0.8052 (mp0) REVERT: C 503 GLU cc_start: 0.6896 (mt-10) cc_final: 0.6457 (tm-30) REVERT: D 18 GLN cc_start: 0.8069 (mt0) cc_final: 0.7758 (mp10) REVERT: D 23 LYS cc_start: 0.8186 (ttpp) cc_final: 0.7950 (tttp) REVERT: D 248 GLU cc_start: 0.8210 (tt0) cc_final: 0.7874 (mp0) REVERT: D 273 LYS cc_start: 0.8691 (mttp) cc_final: 0.8347 (mtpt) REVERT: D 306 LYS cc_start: 0.8816 (mtpt) cc_final: 0.8515 (tttm) REVERT: D 454 GLU cc_start: 0.8293 (mp0) cc_final: 0.8050 (mp0) REVERT: D 503 GLU cc_start: 0.6895 (mt-10) cc_final: 0.6457 (tm-30) outliers start: 7 outliers final: 4 residues processed: 126 average time/residue: 1.7004 time to fit residues: 237.6228 Evaluate side-chains 123 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 119 time to evaluate : 1.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 236 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 48 optimal weight: 5.9990 chunk 146 optimal weight: 10.0000 chunk 23 optimal weight: 20.0000 chunk 44 optimal weight: 0.9980 chunk 158 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 163 optimal weight: 9.9990 chunk 20 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 139 optimal weight: 20.0000 chunk 9 optimal weight: 8.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.097853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.077777 restraints weight = 31235.093| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 1.46 r_work: 0.2711 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2597 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2597 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2597 r_free = 0.2597 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2596 r_free = 0.2596 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2596 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8965 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17084 Z= 0.219 Angle : 0.580 5.524 23312 Z= 0.293 Chirality : 0.045 0.166 2352 Planarity : 0.004 0.042 3092 Dihedral : 8.686 105.472 2280 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.46 % Allowed : 8.89 % Favored : 90.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.19), residues: 2012 helix: 1.39 (0.20), residues: 712 sheet: 0.78 (0.32), residues: 288 loop : 0.04 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 183 HIS 0.006 0.001 HIS D 218 PHE 0.015 0.002 PHE A 136 TYR 0.024 0.002 TYR D 236 ARG 0.002 0.000 ARG A 156 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5418.07 seconds wall clock time: 96 minutes 15.15 seconds (5775.15 seconds total)