Starting phenix.real_space_refine on Thu Feb 15 21:52:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnz_33331/02_2024/7xnz_33331_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnz_33331/02_2024/7xnz_33331.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnz_33331/02_2024/7xnz_33331.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnz_33331/02_2024/7xnz_33331.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnz_33331/02_2024/7xnz_33331_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnz_33331/02_2024/7xnz_33331_trim_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 60 5.16 5 C 8484 2.51 5 N 2336 2.21 5 O 2640 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13524 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 3366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3366 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 29, 'TRANS': 428} Chain: "A" Number of atoms: 3366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3366 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 29, 'TRANS': 428} Chain: "C" Number of atoms: 3366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3366 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 29, 'TRANS': 428} Chain: "D" Number of atoms: 3366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3366 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 29, 'TRANS': 428} Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 7.19, per 1000 atoms: 0.53 Number of scatterers: 13524 At special positions: 0 Unit cell: (86.67, 146.59, 84.53, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 60 16.00 P 4 15.00 O 2640 8.00 N 2336 7.00 C 8484 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 - 3.50 Amino acid : False - 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: 5.25 Conformation dependent library (CDL) restraints added in 2.4 seconds 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3208 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 72 helices and 20 sheets defined 35.8% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.69 Creating SS restraints... Processing helix chain 'B' and resid 7 through 9 No H-bonds generated for 'chain 'B' and resid 7 through 9' Processing helix chain 'B' and resid 44 through 57 Processing helix chain 'B' and resid 75 through 86 removed outlier: 3.913A pdb=" N ARG B 85 " --> pdb=" O LEU B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 108 Processing helix chain 'B' and resid 128 through 138 Processing helix chain 'B' and resid 151 through 160 removed outlier: 3.638A pdb=" N HIS B 157 " --> pdb=" O GLY B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 168 Processing helix chain 'B' and resid 185 through 195 removed outlier: 4.086A pdb=" N TYR B 192 " --> pdb=" O GLY B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 261 Processing helix chain 'B' and resid 268 through 283 removed outlier: 4.259A pdb=" N GLU B 282 " --> pdb=" O LEU B 278 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLU B 283 " --> pdb=" O LYS B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 303 removed outlier: 4.434A pdb=" N SER B 303 " --> pdb=" O GLY B 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 300 through 303' Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'B' and resid 330 through 337 removed outlier: 3.800A pdb=" N LEU B 334 " --> pdb=" O VAL B 330 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG B 335 " --> pdb=" O GLY B 331 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ARG B 336 " --> pdb=" O ASP B 332 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LYS B 337 " --> pdb=" O VAL B 333 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 330 through 337' Processing helix chain 'B' and resid 353 through 363 Processing helix chain 'B' and resid 388 through 396 Processing helix chain 'B' and resid 406 through 408 No H-bonds generated for 'chain 'B' and resid 406 through 408' Processing helix chain 'B' and resid 423 through 430 Processing helix chain 'B' and resid 450 through 457 Processing helix chain 'A' and resid 7 through 9 No H-bonds generated for 'chain 'A' and resid 7 through 9' Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 75 through 86 removed outlier: 3.913A pdb=" N ARG A 85 " --> pdb=" O LEU A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 108 Processing helix chain 'A' and resid 128 through 138 Processing helix chain 'A' and resid 151 through 160 removed outlier: 3.638A pdb=" N HIS A 157 " --> pdb=" O GLY A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 168 Processing helix chain 'A' and resid 185 through 195 removed outlier: 4.086A pdb=" N TYR A 192 " --> pdb=" O GLY A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 261 Processing helix chain 'A' and resid 268 through 283 removed outlier: 4.259A pdb=" N GLU A 282 " --> pdb=" O LEU A 278 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLU A 283 " --> pdb=" O LYS A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 303 removed outlier: 4.434A pdb=" N SER A 303 " --> pdb=" O GLY A 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 300 through 303' Processing helix chain 'A' and resid 308 through 313 Processing helix chain 'A' and resid 330 through 337 removed outlier: 3.799A pdb=" N LEU A 334 " --> pdb=" O VAL A 330 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG A 335 " --> pdb=" O GLY A 331 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ARG A 336 " --> pdb=" O ASP A 332 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LYS A 337 " --> pdb=" O VAL A 333 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 330 through 337' Processing helix chain 'A' and resid 353 through 363 Processing helix chain 'A' and resid 388 through 396 Processing helix chain 'A' and resid 406 through 408 No H-bonds generated for 'chain 'A' and resid 406 through 408' Processing helix chain 'A' and resid 423 through 430 Processing helix chain 'A' and resid 450 through 457 Processing helix chain 'C' and resid 7 through 9 No H-bonds generated for 'chain 'C' and resid 7 through 9' Processing helix chain 'C' and resid 44 through 57 Processing helix chain 'C' and resid 75 through 86 removed outlier: 3.913A pdb=" N ARG C 85 " --> pdb=" O LEU C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 108 Processing helix chain 'C' and resid 128 through 138 Processing helix chain 'C' and resid 151 through 160 removed outlier: 3.637A pdb=" N HIS C 157 " --> pdb=" O GLY C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 168 Processing helix chain 'C' and resid 185 through 195 removed outlier: 4.086A pdb=" N TYR C 192 " --> pdb=" O GLY C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 261 Processing helix chain 'C' and resid 268 through 283 removed outlier: 4.259A pdb=" N GLU C 282 " --> pdb=" O LEU C 278 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLU C 283 " --> pdb=" O LYS C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 303 removed outlier: 4.434A pdb=" N SER C 303 " --> pdb=" O GLY C 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 300 through 303' Processing helix chain 'C' and resid 308 through 313 Processing helix chain 'C' and resid 330 through 337 removed outlier: 3.799A pdb=" N LEU C 334 " --> pdb=" O VAL C 330 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG C 335 " --> pdb=" O GLY C 331 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ARG C 336 " --> pdb=" O ASP C 332 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LYS C 337 " --> pdb=" O VAL C 333 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 330 through 337' Processing helix chain 'C' and resid 353 through 363 Processing helix chain 'C' and resid 388 through 396 Processing helix chain 'C' and resid 406 through 408 No H-bonds generated for 'chain 'C' and resid 406 through 408' Processing helix chain 'C' and resid 423 through 430 Processing helix chain 'C' and resid 450 through 457 Processing helix chain 'D' and resid 7 through 9 No H-bonds generated for 'chain 'D' and resid 7 through 9' Processing helix chain 'D' and resid 44 through 57 Processing helix chain 'D' and resid 75 through 86 removed outlier: 3.913A pdb=" N ARG D 85 " --> pdb=" O LEU D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 108 Processing helix chain 'D' and resid 128 through 138 Processing helix chain 'D' and resid 151 through 160 removed outlier: 3.638A pdb=" N HIS D 157 " --> pdb=" O GLY D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 168 Processing helix chain 'D' and resid 185 through 195 removed outlier: 4.086A pdb=" N TYR D 192 " --> pdb=" O GLY D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 261 Processing helix chain 'D' and resid 268 through 283 removed outlier: 4.260A pdb=" N GLU D 282 " --> pdb=" O LEU D 278 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLU D 283 " --> pdb=" O LYS D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 303 removed outlier: 4.434A pdb=" N SER D 303 " --> pdb=" O GLY D 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 300 through 303' Processing helix chain 'D' and resid 308 through 313 Processing helix chain 'D' and resid 331 through 337 removed outlier: 4.222A pdb=" N ARG D 336 " --> pdb=" O VAL D 333 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LYS D 337 " --> pdb=" O LEU D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 363 Processing helix chain 'D' and resid 388 through 396 Processing helix chain 'D' and resid 406 through 408 No H-bonds generated for 'chain 'D' and resid 406 through 408' Processing helix chain 'D' and resid 423 through 430 Processing helix chain 'D' and resid 450 through 457 Processing sheet with id= A, first strand: chain 'B' and resid 17 through 19 removed outlier: 4.781A pdb=" N VAL B 30 " --> pdb=" O LEU B 19 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 67 through 69 Processing sheet with id= C, first strand: chain 'B' and resid 175 through 179 removed outlier: 7.015A pdb=" N ARG B 202 " --> pdb=" O PHE B 176 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N ALA B 178 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL B 204 " --> pdb=" O ALA B 178 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLU B 242 " --> pdb=" O GLY B 205 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ASP B 207 " --> pdb=" O GLU B 242 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE B 244 " --> pdb=" O ASP B 207 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 367 through 370 Processing sheet with id= E, first strand: chain 'B' and resid 416 through 418 removed outlier: 8.261A pdb=" N ILE B 417 " --> pdb=" O ALA B 435 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N MET B 437 " --> pdb=" O ILE B 417 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 17 through 19 removed outlier: 4.781A pdb=" N VAL A 30 " --> pdb=" O LEU A 19 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 67 through 69 Processing sheet with id= H, first strand: chain 'A' and resid 175 through 179 removed outlier: 7.016A pdb=" N ARG A 202 " --> pdb=" O PHE A 176 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N ALA A 178 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL A 204 " --> pdb=" O ALA A 178 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N GLU A 242 " --> pdb=" O GLY A 205 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ASP A 207 " --> pdb=" O GLU A 242 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ILE A 244 " --> pdb=" O ASP A 207 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'A' and resid 367 through 370 Processing sheet with id= J, first strand: chain 'A' and resid 416 through 418 removed outlier: 8.260A pdb=" N ILE A 417 " --> pdb=" O ALA A 435 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N MET A 437 " --> pdb=" O ILE A 417 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 17 through 19 removed outlier: 4.781A pdb=" N VAL C 30 " --> pdb=" O LEU C 19 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 67 through 69 Processing sheet with id= M, first strand: chain 'C' and resid 175 through 179 removed outlier: 7.016A pdb=" N ARG C 202 " --> pdb=" O PHE C 176 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N ALA C 178 " --> pdb=" O ARG C 202 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL C 204 " --> pdb=" O ALA C 178 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLU C 242 " --> pdb=" O GLY C 205 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ASP C 207 " --> pdb=" O GLU C 242 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE C 244 " --> pdb=" O ASP C 207 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'C' and resid 367 through 370 Processing sheet with id= O, first strand: chain 'C' and resid 416 through 418 removed outlier: 8.261A pdb=" N ILE C 417 " --> pdb=" O ALA C 435 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N MET C 437 " --> pdb=" O ILE C 417 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 17 through 19 removed outlier: 4.782A pdb=" N VAL D 30 " --> pdb=" O LEU D 19 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 67 through 69 Processing sheet with id= R, first strand: chain 'D' and resid 175 through 179 removed outlier: 7.015A pdb=" N ARG D 202 " --> pdb=" O PHE D 176 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N ALA D 178 " --> pdb=" O ARG D 202 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL D 204 " --> pdb=" O ALA D 178 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N GLU D 242 " --> pdb=" O GLY D 205 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ASP D 207 " --> pdb=" O GLU D 242 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE D 244 " --> pdb=" O ASP D 207 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'D' and resid 367 through 370 Processing sheet with id= T, first strand: chain 'D' and resid 416 through 418 removed outlier: 8.261A pdb=" N ILE D 417 " --> pdb=" O ALA D 435 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N MET D 437 " --> pdb=" O ILE D 417 " (cutoff:3.500A) 422 hydrogen bonds defined for protein. 1236 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: 3.73 Time building geometry restraints manager: 5.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4493 1.34 - 1.45: 1552 1.45 - 1.57: 7643 1.57 - 1.69: 4 1.69 - 1.81: 104 Bond restraints: 13796 Sorted by residual: bond pdb=" N THR D 329 " pdb=" CA THR D 329 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.29e-02 6.01e+03 8.20e+00 bond pdb=" N LEU D 344 " pdb=" CA LEU D 344 " ideal model delta sigma weight residual 1.457 1.492 -0.034 1.29e-02 6.01e+03 7.12e+00 bond pdb=" N VAL C 345 " pdb=" CA VAL C 345 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.25e-02 6.40e+03 6.24e+00 bond pdb=" N HIS C 346 " pdb=" CA HIS C 346 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.26e-02 6.30e+03 6.19e+00 bond pdb=" N ALA B 343 " pdb=" CA ALA B 343 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 6.10e+00 ... (remaining 13791 not shown) Histogram of bond angle deviations from ideal: 100.01 - 106.82: 563 106.82 - 113.63: 7698 113.63 - 120.44: 5203 120.44 - 127.25: 5136 127.25 - 134.06: 168 Bond angle restraints: 18768 Sorted by residual: angle pdb=" C SER B 328 " pdb=" N THR B 329 " pdb=" CA THR B 329 " ideal model delta sigma weight residual 122.92 133.61 -10.69 1.76e+00 3.23e-01 3.69e+01 angle pdb=" C SER C 328 " pdb=" N THR C 329 " pdb=" CA THR C 329 " ideal model delta sigma weight residual 122.92 133.35 -10.43 1.76e+00 3.23e-01 3.51e+01 angle pdb=" CA PRO B 342 " pdb=" C PRO B 342 " pdb=" O PRO B 342 " ideal model delta sigma weight residual 121.31 117.17 4.14 7.40e-01 1.83e+00 3.13e+01 angle pdb=" CA PRO D 342 " pdb=" C PRO D 342 " pdb=" O PRO D 342 " ideal model delta sigma weight residual 121.38 117.24 4.14 7.70e-01 1.69e+00 2.89e+01 angle pdb=" C SER A 328 " pdb=" N THR A 329 " pdb=" CA THR A 329 " ideal model delta sigma weight residual 122.92 130.73 -7.81 1.76e+00 3.23e-01 1.97e+01 ... (remaining 18763 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.07: 8076 33.07 - 66.15: 136 66.15 - 99.22: 6 99.22 - 132.30: 0 132.30 - 165.37: 2 Dihedral angle restraints: 8220 sinusoidal: 3124 harmonic: 5096 Sorted by residual: dihedral pdb=" C5A PLP D 501 " pdb=" O4P PLP D 501 " pdb=" P PLP D 501 " pdb=" O1P PLP D 501 " ideal model delta sinusoidal sigma weight residual 76.43 -118.20 -165.37 1 2.00e+01 2.50e-03 4.72e+01 dihedral pdb=" C5A PLP A 501 " pdb=" O4P PLP A 501 " pdb=" P PLP A 501 " pdb=" O1P PLP A 501 " ideal model delta sinusoidal sigma weight residual 76.43 -118.24 -165.33 1 2.00e+01 2.50e-03 4.72e+01 dihedral pdb=" C5A PLP C 501 " pdb=" O4P PLP C 501 " pdb=" P PLP C 501 " pdb=" O1P PLP C 501 " ideal model delta sinusoidal sigma weight residual 76.43 1.22 75.20 1 2.00e+01 2.50e-03 1.79e+01 ... (remaining 8217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1474 0.041 - 0.083: 433 0.083 - 0.124: 184 0.124 - 0.165: 9 0.165 - 0.207: 4 Chirality restraints: 2104 Sorted by residual: chirality pdb=" CA LEU A 341 " pdb=" N LEU A 341 " pdb=" C LEU A 341 " pdb=" CB LEU A 341 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA VAL C 345 " pdb=" N VAL C 345 " pdb=" C VAL C 345 " pdb=" CB VAL C 345 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.66e-01 chirality pdb=" CA ALA A 343 " pdb=" N ALA A 343 " pdb=" C ALA A 343 " pdb=" CB ALA A 343 " both_signs ideal model delta sigma weight residual False 2.48 2.66 -0.18 2.00e-01 2.50e+01 7.73e-01 ... (remaining 2101 not shown) Planarity restraints: 2472 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN B 327 " -0.010 2.00e-02 2.50e+03 2.01e-02 4.02e+00 pdb=" C GLN B 327 " 0.035 2.00e-02 2.50e+03 pdb=" O GLN B 327 " -0.013 2.00e-02 2.50e+03 pdb=" N SER B 328 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 327 " 0.010 2.00e-02 2.50e+03 1.92e-02 3.67e+00 pdb=" C GLN C 327 " -0.033 2.00e-02 2.50e+03 pdb=" O GLN C 327 " 0.012 2.00e-02 2.50e+03 pdb=" N SER C 328 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 340 " 0.008 2.00e-02 2.50e+03 1.53e-02 2.34e+00 pdb=" C ALA C 340 " -0.026 2.00e-02 2.50e+03 pdb=" O ALA C 340 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU C 341 " 0.009 2.00e-02 2.50e+03 ... (remaining 2469 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 447 2.70 - 3.25: 14923 3.25 - 3.80: 20728 3.80 - 4.35: 27234 4.35 - 4.90: 44982 Nonbonded interactions: 108314 Sorted by model distance: nonbonded pdb=" O PRO A 145 " pdb=" ND2 ASN A 150 " model vdw 2.146 2.520 nonbonded pdb=" O PRO C 145 " pdb=" ND2 ASN C 150 " model vdw 2.146 2.520 nonbonded pdb=" O PRO D 145 " pdb=" ND2 ASN D 150 " model vdw 2.146 2.520 nonbonded pdb=" O PRO B 145 " pdb=" ND2 ASN B 150 " model vdw 2.147 2.520 nonbonded pdb=" O LEU C 265 " pdb=" N GLY C 298 " model vdw 2.152 2.520 ... (remaining 108309 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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 group one per residue 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: 0.560 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: 3.760 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 36.350 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.070 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13796 Z= 0.275 Angle : 0.597 10.692 18768 Z= 0.337 Chirality : 0.044 0.207 2104 Planarity : 0.004 0.034 2472 Dihedral : 13.119 165.370 5012 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 35.80 Ramachandran Plot: Outliers : 0.27 % Allowed : 12.01 % Favored : 87.72 % Rotamer: Outliers : 3.42 % Allowed : 5.56 % Favored : 91.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.94 (0.17), residues: 1824 helix: -1.98 (0.18), residues: 684 sheet: -3.33 (0.28), residues: 180 loop : -3.00 (0.18), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 310 HIS 0.002 0.001 HIS A 175 PHE 0.004 0.001 PHE A 316 TYR 0.014 0.001 TYR B 128 ARG 0.002 0.000 ARG D 399 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 320 time to evaluate : 1.791 Fit side-chains REVERT: B 278 LEU cc_start: 0.9272 (mt) cc_final: 0.9002 (mp) REVERT: B 311 MET cc_start: 0.9084 (tpp) cc_final: 0.8045 (tpt) REVERT: B 437 MET cc_start: 0.8404 (ptp) cc_final: 0.8140 (ptt) REVERT: A 172 LYS cc_start: 0.7631 (ttpp) cc_final: 0.7333 (tptt) REVERT: C 311 MET cc_start: 0.9077 (tpp) cc_final: 0.8017 (tpt) REVERT: C 437 MET cc_start: 0.8393 (ptp) cc_final: 0.8145 (ptt) REVERT: D 172 LYS cc_start: 0.7663 (ttpp) cc_final: 0.7346 (tptt) outliers start: 48 outliers final: 17 residues processed: 349 average time/residue: 0.2708 time to fit residues: 133.1861 Evaluate side-chains 216 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 199 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 436 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 141 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 85 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 chunk 163 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 GLN ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 ASN ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 GLN ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13796 Z= 0.279 Angle : 0.628 7.959 18768 Z= 0.317 Chirality : 0.047 0.179 2104 Planarity : 0.005 0.057 2472 Dihedral : 8.645 171.945 2028 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.02 % Favored : 92.93 % Rotamer: Outliers : 4.34 % Allowed : 13.11 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.19), residues: 1824 helix: -1.09 (0.19), residues: 692 sheet: -2.33 (0.32), residues: 176 loop : -2.26 (0.20), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 310 HIS 0.006 0.001 HIS D 409 PHE 0.007 0.001 PHE D 92 TYR 0.018 0.001 TYR D 129 ARG 0.004 0.000 ARG B 431 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 223 time to evaluate : 1.730 Fit side-chains REVERT: B 278 LEU cc_start: 0.9211 (mt) cc_final: 0.8971 (mp) REVERT: B 279 LYS cc_start: 0.8673 (tptm) cc_final: 0.8024 (mttt) REVERT: A 146 ASP cc_start: 0.8201 (t0) cc_final: 0.7711 (t70) REVERT: A 172 LYS cc_start: 0.7497 (ttpp) cc_final: 0.7165 (tptt) REVERT: D 172 LYS cc_start: 0.7498 (ttpp) cc_final: 0.7130 (tptt) outliers start: 61 outliers final: 36 residues processed: 264 average time/residue: 0.2083 time to fit residues: 85.0357 Evaluate side-chains 236 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 200 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 436 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 0.9990 chunk 50 optimal weight: 0.2980 chunk 136 optimal weight: 0.6980 chunk 111 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 163 optimal weight: 0.0970 chunk 176 optimal weight: 6.9990 chunk 145 optimal weight: 3.9990 chunk 162 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 131 optimal weight: 20.0000 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 ASN ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13796 Z= 0.164 Angle : 0.555 8.240 18768 Z= 0.276 Chirality : 0.045 0.192 2104 Planarity : 0.005 0.048 2472 Dihedral : 8.060 171.864 2020 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.43 % Favored : 94.52 % Rotamer: Outliers : 4.77 % Allowed : 17.09 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.19), residues: 1824 helix: -0.31 (0.20), residues: 668 sheet: -1.73 (0.33), residues: 172 loop : -1.92 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 310 HIS 0.006 0.001 HIS D 409 PHE 0.005 0.001 PHE A 316 TYR 0.017 0.001 TYR A 451 ARG 0.003 0.000 ARG C 336 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 221 time to evaluate : 1.480 Fit side-chains REVERT: B 103 ARG cc_start: 0.7811 (ptt180) cc_final: 0.7457 (ptm-80) REVERT: A 146 ASP cc_start: 0.8115 (t0) cc_final: 0.7608 (t70) REVERT: A 172 LYS cc_start: 0.7511 (ttpp) cc_final: 0.7094 (tptt) REVERT: A 221 TYR cc_start: 0.8441 (m-80) cc_final: 0.8195 (m-80) REVERT: C 103 ARG cc_start: 0.7797 (ptt180) cc_final: 0.7477 (ptm-80) REVERT: D 172 LYS cc_start: 0.7405 (ttpp) cc_final: 0.7027 (tptt) outliers start: 67 outliers final: 41 residues processed: 272 average time/residue: 0.2138 time to fit residues: 88.8209 Evaluate side-chains 226 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 185 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 104 ASN Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 436 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 3.9990 chunk 123 optimal weight: 0.1980 chunk 84 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 109 optimal weight: 6.9990 chunk 164 optimal weight: 3.9990 chunk 173 optimal weight: 5.9990 chunk 85 optimal weight: 0.7980 chunk 155 optimal weight: 0.3980 chunk 46 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13796 Z= 0.214 Angle : 0.568 7.117 18768 Z= 0.285 Chirality : 0.045 0.212 2104 Planarity : 0.005 0.050 2472 Dihedral : 7.879 170.993 2020 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.65 % Favored : 94.30 % Rotamer: Outliers : 5.06 % Allowed : 18.73 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.19), residues: 1824 helix: -0.08 (0.20), residues: 684 sheet: -1.73 (0.31), residues: 196 loop : -1.72 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 310 HIS 0.006 0.001 HIS D 409 PHE 0.004 0.001 PHE B 316 TYR 0.019 0.001 TYR D 129 ARG 0.002 0.000 ARG C 256 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 199 time to evaluate : 1.491 Fit side-chains REVERT: B 9 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7567 (mm-30) REVERT: B 103 ARG cc_start: 0.7750 (ptt180) cc_final: 0.7533 (ptm-80) REVERT: A 146 ASP cc_start: 0.8084 (t0) cc_final: 0.7558 (t70) REVERT: A 172 LYS cc_start: 0.7525 (ttpp) cc_final: 0.7089 (tptt) REVERT: C 9 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7574 (mm-30) REVERT: C 279 LYS cc_start: 0.8594 (tptm) cc_final: 0.7887 (mttt) REVERT: D 172 LYS cc_start: 0.7489 (ttpp) cc_final: 0.7035 (tptt) REVERT: D 441 GLU cc_start: 0.8144 (mp0) cc_final: 0.7176 (pt0) outliers start: 71 outliers final: 51 residues processed: 247 average time/residue: 0.2378 time to fit residues: 87.9549 Evaluate side-chains 239 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 188 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 436 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 0.0980 chunk 98 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 129 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 148 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 88 optimal weight: 0.6980 chunk 156 optimal weight: 0.0570 chunk 43 optimal weight: 7.9990 overall best weight: 0.9500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 ASN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13796 Z= 0.191 Angle : 0.547 6.648 18768 Z= 0.274 Chirality : 0.045 0.189 2104 Planarity : 0.004 0.049 2472 Dihedral : 7.481 165.026 2018 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.99 % Favored : 94.96 % Rotamer: Outliers : 5.13 % Allowed : 20.23 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.19), residues: 1824 helix: 0.17 (0.20), residues: 684 sheet: -1.44 (0.32), residues: 196 loop : -1.60 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 310 HIS 0.005 0.001 HIS A 409 PHE 0.005 0.001 PHE A 316 TYR 0.014 0.001 TYR D 451 ARG 0.003 0.000 ARG C 256 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 197 time to evaluate : 1.563 Fit side-chains REVERT: B 9 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7540 (mm-30) REVERT: B 279 LYS cc_start: 0.8608 (tptm) cc_final: 0.7764 (mttt) REVERT: A 146 ASP cc_start: 0.8046 (t0) cc_final: 0.7500 (t70) REVERT: A 172 LYS cc_start: 0.7547 (ttpp) cc_final: 0.7125 (tptt) REVERT: C 9 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7556 (mm-30) REVERT: C 279 LYS cc_start: 0.8470 (tptm) cc_final: 0.7693 (mttt) REVERT: D 172 LYS cc_start: 0.7497 (ttpp) cc_final: 0.7058 (tptt) REVERT: D 264 MET cc_start: 0.9170 (mtt) cc_final: 0.8774 (mtt) REVERT: D 441 GLU cc_start: 0.8002 (mp0) cc_final: 0.7006 (pt0) outliers start: 72 outliers final: 57 residues processed: 249 average time/residue: 0.2245 time to fit residues: 84.9385 Evaluate side-chains 247 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 190 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 436 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 8.9990 chunk 156 optimal weight: 3.9990 chunk 34 optimal weight: 0.1980 chunk 102 optimal weight: 9.9990 chunk 42 optimal weight: 7.9990 chunk 174 optimal weight: 1.9990 chunk 144 optimal weight: 0.6980 chunk 80 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 57 optimal weight: 0.0070 chunk 91 optimal weight: 0.9980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 38 ASN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 13796 Z= 0.147 Angle : 0.527 6.233 18768 Z= 0.262 Chirality : 0.044 0.155 2104 Planarity : 0.004 0.049 2472 Dihedral : 7.294 162.978 2018 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.22 % Favored : 95.72 % Rotamer: Outliers : 4.70 % Allowed : 20.73 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.19), residues: 1824 helix: 0.42 (0.20), residues: 684 sheet: -1.20 (0.33), residues: 196 loop : -1.44 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 310 HIS 0.004 0.001 HIS A 409 PHE 0.006 0.001 PHE A 316 TYR 0.017 0.001 TYR A 451 ARG 0.002 0.000 ARG C 256 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 215 time to evaluate : 1.559 Fit side-chains REVERT: B 86 ARG cc_start: 0.5982 (OUTLIER) cc_final: 0.5763 (mmm160) REVERT: B 279 LYS cc_start: 0.8554 (tptm) cc_final: 0.7534 (mttt) REVERT: B 410 MET cc_start: 0.8591 (ptt) cc_final: 0.8376 (ptp) REVERT: A 146 ASP cc_start: 0.8028 (t0) cc_final: 0.7492 (t70) REVERT: A 172 LYS cc_start: 0.7470 (ttpp) cc_final: 0.7052 (tptt) REVERT: A 221 TYR cc_start: 0.8516 (m-80) cc_final: 0.8132 (m-80) REVERT: A 441 GLU cc_start: 0.8152 (mp0) cc_final: 0.7150 (pt0) REVERT: C 279 LYS cc_start: 0.8423 (tptm) cc_final: 0.7403 (mttt) REVERT: C 410 MET cc_start: 0.8577 (ptt) cc_final: 0.8376 (ptp) REVERT: D 172 LYS cc_start: 0.7375 (ttpp) cc_final: 0.7003 (tptt) REVERT: D 221 TYR cc_start: 0.8468 (m-80) cc_final: 0.8073 (m-80) REVERT: D 264 MET cc_start: 0.9222 (mtt) cc_final: 0.8835 (mtt) REVERT: D 441 GLU cc_start: 0.8044 (mp0) cc_final: 0.6959 (pt0) outliers start: 66 outliers final: 43 residues processed: 263 average time/residue: 0.2301 time to fit residues: 91.9727 Evaluate side-chains 238 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 194 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 436 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 8.9990 chunk 19 optimal weight: 0.0070 chunk 99 optimal weight: 1.9990 chunk 127 optimal weight: 0.3980 chunk 98 optimal weight: 4.9990 chunk 146 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 105 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 overall best weight: 1.0602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13796 Z= 0.206 Angle : 0.562 11.481 18768 Z= 0.275 Chirality : 0.045 0.149 2104 Planarity : 0.004 0.049 2472 Dihedral : 7.120 158.677 2012 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.66 % Favored : 95.29 % Rotamer: Outliers : 4.99 % Allowed : 19.66 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.19), residues: 1824 helix: 0.50 (0.20), residues: 680 sheet: -1.10 (0.33), residues: 196 loop : -1.30 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 310 HIS 0.005 0.001 HIS D 409 PHE 0.016 0.001 PHE D 230 TYR 0.016 0.001 TYR A 451 ARG 0.003 0.000 ARG C 256 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 189 time to evaluate : 1.463 Fit side-chains REVERT: B 279 LYS cc_start: 0.8489 (tptm) cc_final: 0.7446 (mttt) REVERT: A 146 ASP cc_start: 0.8050 (t0) cc_final: 0.7486 (t70) REVERT: A 172 LYS cc_start: 0.7705 (ttpp) cc_final: 0.7358 (tptt) REVERT: A 441 GLU cc_start: 0.8179 (mp0) cc_final: 0.7145 (pt0) REVERT: C 86 ARG cc_start: 0.6061 (OUTLIER) cc_final: 0.5561 (mmm-85) REVERT: C 279 LYS cc_start: 0.8464 (tptm) cc_final: 0.7421 (mttt) REVERT: D 172 LYS cc_start: 0.7440 (ttpp) cc_final: 0.7045 (tptt) REVERT: D 264 MET cc_start: 0.9219 (mtt) cc_final: 0.8841 (mtt) REVERT: D 441 GLU cc_start: 0.8028 (mp0) cc_final: 0.7058 (pt0) outliers start: 70 outliers final: 56 residues processed: 240 average time/residue: 0.2457 time to fit residues: 88.4318 Evaluate side-chains 241 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 184 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 436 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 0.4980 chunk 69 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 chunk 110 optimal weight: 0.6980 chunk 118 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 16 optimal weight: 0.0470 chunk 136 optimal weight: 0.9980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13796 Z= 0.158 Angle : 0.542 10.841 18768 Z= 0.265 Chirality : 0.044 0.158 2104 Planarity : 0.004 0.048 2472 Dihedral : 6.995 155.021 2012 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.28 % Favored : 95.67 % Rotamer: Outliers : 4.34 % Allowed : 20.51 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.20), residues: 1824 helix: 0.68 (0.21), residues: 676 sheet: -0.98 (0.34), residues: 196 loop : -1.26 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 310 HIS 0.004 0.001 HIS A 409 PHE 0.006 0.001 PHE D 316 TYR 0.015 0.001 TYR D 129 ARG 0.003 0.000 ARG C 256 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 190 time to evaluate : 1.577 Fit side-chains REVERT: B 86 ARG cc_start: 0.5945 (OUTLIER) cc_final: 0.5714 (mmm160) REVERT: B 279 LYS cc_start: 0.8437 (tptm) cc_final: 0.7418 (mttt) REVERT: B 410 MET cc_start: 0.8581 (ptt) cc_final: 0.8367 (ptp) REVERT: A 35 GLU cc_start: 0.7447 (tt0) cc_final: 0.7218 (tt0) REVERT: A 86 ARG cc_start: 0.6596 (OUTLIER) cc_final: 0.6275 (tpt170) REVERT: A 146 ASP cc_start: 0.8074 (t0) cc_final: 0.7536 (t70) REVERT: A 172 LYS cc_start: 0.7720 (ttpp) cc_final: 0.7409 (tptt) REVERT: A 441 GLU cc_start: 0.8133 (mp0) cc_final: 0.7105 (pt0) REVERT: C 86 ARG cc_start: 0.5923 (OUTLIER) cc_final: 0.5426 (mmm-85) REVERT: C 279 LYS cc_start: 0.8381 (tptm) cc_final: 0.7371 (mttt) REVERT: C 410 MET cc_start: 0.8562 (ptt) cc_final: 0.8347 (ptp) REVERT: D 86 ARG cc_start: 0.6744 (OUTLIER) cc_final: 0.6439 (tpt170) REVERT: D 172 LYS cc_start: 0.7407 (ttpp) cc_final: 0.7040 (tptt) REVERT: D 264 MET cc_start: 0.9258 (mtt) cc_final: 0.8854 (mtt) REVERT: D 441 GLU cc_start: 0.7912 (mp0) cc_final: 0.7062 (pt0) outliers start: 61 outliers final: 51 residues processed: 237 average time/residue: 0.2583 time to fit residues: 90.8710 Evaluate side-chains 239 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 184 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 436 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 3.9990 chunk 166 optimal weight: 0.1980 chunk 151 optimal weight: 0.9980 chunk 161 optimal weight: 4.9990 chunk 97 optimal weight: 0.4980 chunk 70 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 chunk 106 optimal weight: 0.0670 overall best weight: 0.9520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13796 Z= 0.193 Angle : 0.555 10.644 18768 Z= 0.272 Chirality : 0.044 0.161 2104 Planarity : 0.004 0.047 2472 Dihedral : 6.919 151.775 2012 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.39 % Favored : 95.56 % Rotamer: Outliers : 4.63 % Allowed : 20.51 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.20), residues: 1824 helix: 0.70 (0.21), residues: 676 sheet: -0.94 (0.34), residues: 196 loop : -1.16 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 310 HIS 0.005 0.001 HIS A 409 PHE 0.009 0.001 PHE A 230 TYR 0.015 0.001 TYR A 451 ARG 0.003 0.000 ARG C 256 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 186 time to evaluate : 1.330 Fit side-chains REVERT: B 86 ARG cc_start: 0.5995 (OUTLIER) cc_final: 0.5745 (mmm160) REVERT: B 279 LYS cc_start: 0.8458 (tptm) cc_final: 0.7456 (mttt) REVERT: A 35 GLU cc_start: 0.7615 (tt0) cc_final: 0.7405 (tt0) REVERT: A 86 ARG cc_start: 0.6574 (OUTLIER) cc_final: 0.6251 (tpt170) REVERT: A 146 ASP cc_start: 0.8106 (t0) cc_final: 0.7556 (t70) REVERT: A 172 LYS cc_start: 0.7718 (ttpp) cc_final: 0.7333 (tptt) REVERT: A 441 GLU cc_start: 0.8123 (mp0) cc_final: 0.7042 (pt0) REVERT: C 74 ASN cc_start: 0.8497 (t0) cc_final: 0.8246 (t0) REVERT: C 86 ARG cc_start: 0.5955 (OUTLIER) cc_final: 0.5483 (mmm-85) REVERT: C 279 LYS cc_start: 0.8381 (tptm) cc_final: 0.7361 (mttt) REVERT: D 86 ARG cc_start: 0.6810 (OUTLIER) cc_final: 0.6485 (tpt170) REVERT: D 172 LYS cc_start: 0.7511 (ttpp) cc_final: 0.7091 (tptt) REVERT: D 264 MET cc_start: 0.9237 (mtt) cc_final: 0.8835 (mtt) REVERT: D 441 GLU cc_start: 0.7879 (mp0) cc_final: 0.7064 (pt0) outliers start: 65 outliers final: 56 residues processed: 237 average time/residue: 0.2428 time to fit residues: 85.5530 Evaluate side-chains 238 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 178 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 436 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 81 optimal weight: 0.4980 chunk 118 optimal weight: 0.8980 chunk 179 optimal weight: 0.4980 chunk 165 optimal weight: 0.0980 chunk 142 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 110 optimal weight: 0.9980 chunk 87 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13796 Z= 0.151 Angle : 0.535 10.480 18768 Z= 0.262 Chirality : 0.043 0.146 2104 Planarity : 0.004 0.048 2472 Dihedral : 6.707 144.423 2012 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.11 % Favored : 95.83 % Rotamer: Outliers : 3.92 % Allowed : 21.51 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.20), residues: 1824 helix: 0.80 (0.21), residues: 684 sheet: -0.77 (0.35), residues: 196 loop : -0.97 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 310 HIS 0.004 0.001 HIS A 409 PHE 0.012 0.001 PHE D 230 TYR 0.015 0.001 TYR A 451 ARG 0.003 0.000 ARG B 260 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 185 time to evaluate : 1.675 Fit side-chains REVERT: B 86 ARG cc_start: 0.5874 (OUTLIER) cc_final: 0.5653 (mmm160) REVERT: B 279 LYS cc_start: 0.8405 (tptm) cc_final: 0.7465 (mttt) REVERT: B 336 ARG cc_start: 0.6529 (mmp80) cc_final: 0.5490 (tmm-80) REVERT: B 410 MET cc_start: 0.8567 (ptt) cc_final: 0.8345 (ptp) REVERT: A 86 ARG cc_start: 0.6596 (OUTLIER) cc_final: 0.6282 (tpt170) REVERT: A 146 ASP cc_start: 0.8049 (t0) cc_final: 0.7487 (t70) REVERT: A 172 LYS cc_start: 0.7748 (ttpp) cc_final: 0.7348 (tptt) REVERT: A 441 GLU cc_start: 0.8096 (mp0) cc_final: 0.7040 (pt0) REVERT: C 74 ASN cc_start: 0.8538 (t0) cc_final: 0.8288 (t0) REVERT: C 86 ARG cc_start: 0.5837 (OUTLIER) cc_final: 0.5629 (mmm160) REVERT: C 279 LYS cc_start: 0.8343 (tptm) cc_final: 0.7357 (mttt) REVERT: C 378 MET cc_start: 0.7512 (tpp) cc_final: 0.7037 (ttm) REVERT: C 410 MET cc_start: 0.8537 (ptt) cc_final: 0.8334 (ptp) REVERT: D 86 ARG cc_start: 0.6603 (OUTLIER) cc_final: 0.6289 (tpt170) REVERT: D 172 LYS cc_start: 0.7511 (ttpp) cc_final: 0.7067 (tptt) REVERT: D 264 MET cc_start: 0.9264 (mtt) cc_final: 0.8864 (mtt) REVERT: D 441 GLU cc_start: 0.7835 (mp0) cc_final: 0.7076 (pt0) outliers start: 55 outliers final: 47 residues processed: 229 average time/residue: 0.2593 time to fit residues: 85.9357 Evaluate side-chains 229 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 178 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 436 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 131 optimal weight: 8.9990 chunk 21 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 chunk 143 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 146 optimal weight: 0.0870 chunk 18 optimal weight: 0.0770 chunk 26 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 overall best weight: 0.5316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.132093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.107820 restraints weight = 17320.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.110544 restraints weight = 11759.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.112408 restraints weight = 9048.445| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.4244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13796 Z= 0.153 Angle : 0.542 10.435 18768 Z= 0.264 Chirality : 0.043 0.145 2104 Planarity : 0.004 0.047 2472 Dihedral : 6.517 137.987 2012 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.56 % Favored : 96.38 % Rotamer: Outliers : 3.99 % Allowed : 20.80 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.20), residues: 1824 helix: 0.86 (0.20), residues: 688 sheet: -0.70 (0.35), residues: 196 loop : -0.99 (0.20), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 310 HIS 0.004 0.001 HIS D 409 PHE 0.008 0.001 PHE A 230 TYR 0.018 0.001 TYR A 451 ARG 0.007 0.000 ARG A 103 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2661.15 seconds wall clock time: 49 minutes 17.07 seconds (2957.07 seconds total)