Starting phenix.real_space_refine on Sat Mar 16 11:32:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y3e_33592/03_2024/7y3e_33592_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y3e_33592/03_2024/7y3e_33592.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y3e_33592/03_2024/7y3e_33592.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y3e_33592/03_2024/7y3e_33592.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y3e_33592/03_2024/7y3e_33592_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y3e_33592/03_2024/7y3e_33592_updated.pdb" } resolution = 2.8 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= -0.003 sd= 0.142 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: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 9522 2.51 5 N 2364 2.21 5 O 2626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 95": "OE1" <-> "OE2" Residue "A GLU 182": "OE1" <-> "OE2" Residue "A PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 387": "OE1" <-> "OE2" Residue "A PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 485": "OD1" <-> "OD2" Residue "A TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 565": "OD1" <-> "OD2" Residue "A ASP 577": "OD1" <-> "OD2" Residue "A PHE 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 610": "OE1" <-> "OE2" Residue "A PHE 622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 693": "OE1" <-> "OE2" Residue "A GLU 705": "OE1" <-> "OE2" Residue "A GLU 759": "OE1" <-> "OE2" Residue "A TYR 769": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 827": "OD1" <-> "OD2" Residue "A PHE 834": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 856": "OE1" <-> "OE2" Residue "A PHE 870": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 95": "OE1" <-> "OE2" Residue "B GLU 182": "OE1" <-> "OE2" Residue "B TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 387": "OE1" <-> "OE2" Residue "B PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 485": "OD1" <-> "OD2" Residue "B TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 565": "OD1" <-> "OD2" Residue "B ASP 577": "OD1" <-> "OD2" Residue "B PHE 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 610": "OE1" <-> "OE2" Residue "B PHE 622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 693": "OE1" <-> "OE2" Residue "B GLU 705": "OE1" <-> "OE2" Residue "B GLU 759": "OE1" <-> "OE2" Residue "B TYR 769": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 827": "OD1" <-> "OD2" Residue "B PHE 834": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 856": "OE1" <-> "OE2" Residue "B PHE 870": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14572 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 928, 7254 Classifications: {'peptide': 928} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 33, 'TRANS': 894} Chain breaks: 4 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 7254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 928, 7254 Classifications: {'peptide': 928} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 33, 'TRANS': 894} Chain breaks: 4 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'R16': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'R16': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.28, per 1000 atoms: 0.57 Number of scatterers: 14572 At special positions: 0 Unit cell: (115.44, 105.04, 127.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 2626 8.00 N 2364 7.00 C 9522 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=0, symmetry=0 Time building additional restraints: 7.26 Conformation dependent library (CDL) restraints added in 3.7 seconds 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3456 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 76 helices and 6 sheets defined 63.1% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.49 Creating SS restraints... Processing helix chain 'A' and resid 33 through 53 removed outlier: 3.524A pdb=" N LEU A 53 " --> pdb=" O SER A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 77 Processing helix chain 'A' and resid 85 through 94 Processing helix chain 'A' and resid 98 through 115 Proline residue: A 107 - end of helix removed outlier: 4.568A pdb=" N GLU A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 126 through 150 Proline residue: A 135 - end of helix Processing helix chain 'A' and resid 158 through 169 removed outlier: 3.582A pdb=" N SER A 169 " --> pdb=" O GLY A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 183 removed outlier: 3.729A pdb=" N GLU A 182 " --> pdb=" O ALA A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 215 removed outlier: 3.672A pdb=" N ASP A 201 " --> pdb=" O SER A 197 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLY A 202 " --> pdb=" O LEU A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 252 removed outlier: 3.955A pdb=" N ALA A 236 " --> pdb=" O VAL A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 277 removed outlier: 3.597A pdb=" N THR A 265 " --> pdb=" O GLU A 261 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR A 274 " --> pdb=" O TYR A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 298 Processing helix chain 'A' and resid 307 through 338 Processing helix chain 'A' and resid 344 through 346 No H-bonds generated for 'chain 'A' and resid 344 through 346' Processing helix chain 'A' and resid 349 through 376 Proline residue: A 374 - end of helix Processing helix chain 'A' and resid 385 through 393 Processing helix chain 'A' and resid 399 through 410 Processing helix chain 'A' and resid 419 through 452 removed outlier: 3.752A pdb=" N SER A 442 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N THR A 443 " --> pdb=" O VAL A 439 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N GLN A 445 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N PHE A 446 " --> pdb=" O SER A 442 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU A 451 " --> pdb=" O VAL A 447 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ARG A 452 " --> pdb=" O LEU A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 481 Processing helix chain 'A' and resid 493 through 500 Processing helix chain 'A' and resid 528 through 549 Processing helix chain 'A' and resid 554 through 569 removed outlier: 3.907A pdb=" N ASP A 569 " --> pdb=" O ASP A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 584 Proline residue: A 583 - end of helix No H-bonds generated for 'chain 'A' and resid 579 through 584' Processing helix chain 'A' and resid 591 through 593 No H-bonds generated for 'chain 'A' and resid 591 through 593' Processing helix chain 'A' and resid 604 through 637 removed outlier: 5.736A pdb=" N SER A 614 " --> pdb=" O GLU A 610 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ALA A 615 " --> pdb=" O ARG A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 667 removed outlier: 4.159A pdb=" N GLU A 655 " --> pdb=" O GLU A 651 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N GLU A 656 " --> pdb=" O LYS A 652 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ALA A 657 " --> pdb=" O GLU A 653 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS A 658 " --> pdb=" O GLY A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 698 Processing helix chain 'A' and resid 705 through 722 Processing helix chain 'A' and resid 732 through 737 Processing helix chain 'A' and resid 740 through 743 removed outlier: 3.815A pdb=" N VAL A 743 " --> pdb=" O PRO A 740 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 740 through 743' Processing helix chain 'A' and resid 747 through 750 No H-bonds generated for 'chain 'A' and resid 747 through 750' Processing helix chain 'A' and resid 811 through 816 Processing helix chain 'A' and resid 837 through 843 Processing helix chain 'A' and resid 847 through 865 removed outlier: 3.654A pdb=" N PHE A 852 " --> pdb=" O THR A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 870 No H-bonds generated for 'chain 'A' and resid 867 through 870' Processing helix chain 'A' and resid 877 through 883 Processing helix chain 'A' and resid 1013 through 1016 No H-bonds generated for 'chain 'A' and resid 1013 through 1016' Processing helix chain 'A' and resid 1034 through 1041 Processing helix chain 'B' and resid 33 through 53 removed outlier: 3.524A pdb=" N LEU B 53 " --> pdb=" O SER B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 77 Processing helix chain 'B' and resid 85 through 94 Processing helix chain 'B' and resid 98 through 115 Proline residue: B 107 - end of helix removed outlier: 4.568A pdb=" N GLU B 112 " --> pdb=" O ALA B 108 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 126 through 150 Proline residue: B 135 - end of helix Processing helix chain 'B' and resid 158 through 169 removed outlier: 3.582A pdb=" N SER B 169 " --> pdb=" O GLY B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 183 removed outlier: 3.729A pdb=" N GLU B 182 " --> pdb=" O ALA B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 215 removed outlier: 3.673A pdb=" N ASP B 201 " --> pdb=" O SER B 197 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLY B 202 " --> pdb=" O LEU B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 252 removed outlier: 3.956A pdb=" N ALA B 236 " --> pdb=" O VAL B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 277 removed outlier: 3.597A pdb=" N THR B 265 " --> pdb=" O GLU B 261 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR B 274 " --> pdb=" O TYR B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 298 Processing helix chain 'B' and resid 307 through 338 Processing helix chain 'B' and resid 344 through 346 No H-bonds generated for 'chain 'B' and resid 344 through 346' Processing helix chain 'B' and resid 349 through 376 Proline residue: B 374 - end of helix Processing helix chain 'B' and resid 385 through 393 Processing helix chain 'B' and resid 399 through 410 Processing helix chain 'B' and resid 419 through 452 removed outlier: 3.752A pdb=" N SER B 442 " --> pdb=" O ILE B 438 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N THR B 443 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N GLN B 445 " --> pdb=" O GLY B 441 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N PHE B 446 " --> pdb=" O SER B 442 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU B 451 " --> pdb=" O VAL B 447 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ARG B 452 " --> pdb=" O LEU B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 481 Processing helix chain 'B' and resid 493 through 500 Processing helix chain 'B' and resid 528 through 549 Processing helix chain 'B' and resid 554 through 569 removed outlier: 3.906A pdb=" N ASP B 569 " --> pdb=" O ASP B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 584 Proline residue: B 583 - end of helix No H-bonds generated for 'chain 'B' and resid 579 through 584' Processing helix chain 'B' and resid 591 through 593 No H-bonds generated for 'chain 'B' and resid 591 through 593' Processing helix chain 'B' and resid 604 through 637 removed outlier: 5.737A pdb=" N SER B 614 " --> pdb=" O GLU B 610 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ALA B 615 " --> pdb=" O ARG B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 667 removed outlier: 4.159A pdb=" N GLU B 655 " --> pdb=" O GLU B 651 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N GLU B 656 " --> pdb=" O LYS B 652 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N ALA B 657 " --> pdb=" O GLU B 653 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS B 658 " --> pdb=" O GLY B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 698 Processing helix chain 'B' and resid 705 through 722 Processing helix chain 'B' and resid 732 through 737 Processing helix chain 'B' and resid 740 through 743 removed outlier: 3.814A pdb=" N VAL B 743 " --> pdb=" O PRO B 740 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 740 through 743' Processing helix chain 'B' and resid 747 through 750 No H-bonds generated for 'chain 'B' and resid 747 through 750' Processing helix chain 'B' and resid 811 through 816 Processing helix chain 'B' and resid 837 through 843 Processing helix chain 'B' and resid 847 through 865 removed outlier: 3.654A pdb=" N PHE B 852 " --> pdb=" O THR B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 867 through 870 No H-bonds generated for 'chain 'B' and resid 867 through 870' Processing helix chain 'B' and resid 877 through 883 Processing helix chain 'B' and resid 1013 through 1016 No H-bonds generated for 'chain 'B' and resid 1013 through 1016' Processing helix chain 'B' and resid 1034 through 1041 Processing sheet with id= A, first strand: chain 'A' and resid 807 through 809 removed outlier: 6.413A pdb=" N LEU A 831 " --> pdb=" O PHE A 782 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 786 through 789 Processing sheet with id= C, first strand: chain 'A' and resid 888 through 892 removed outlier: 6.521A pdb=" N ILE A 968 " --> pdb=" O LEU A 908 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N LEU A 908 " --> pdb=" O ILE A 968 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N PHE A 970 " --> pdb=" O GLY A 906 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N GLY A 906 " --> pdb=" O PHE A 970 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 807 through 809 removed outlier: 6.413A pdb=" N LEU B 831 " --> pdb=" O PHE B 782 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 786 through 789 Processing sheet with id= F, first strand: chain 'B' and resid 888 through 892 removed outlier: 6.522A pdb=" N ILE B 968 " --> pdb=" O LEU B 908 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N LEU B 908 " --> pdb=" O ILE B 968 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N PHE B 970 " --> pdb=" O GLY B 906 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N GLY B 906 " --> pdb=" O PHE B 970 " (cutoff:3.500A) 846 hydrogen bonds defined for protein. 2412 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: 4.84 Time building geometry restraints manager: 6.38 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: 4413 1.34 - 1.45: 2051 1.45 - 1.57: 8308 1.57 - 1.69: 0 1.69 - 1.81: 102 Bond restraints: 14874 Sorted by residual: bond pdb=" CA SER A 116 " pdb=" C SER A 116 " ideal model delta sigma weight residual 1.523 1.497 0.026 1.41e-02 5.03e+03 3.39e+00 bond pdb=" CA SER B 116 " pdb=" C SER B 116 " ideal model delta sigma weight residual 1.523 1.497 0.026 1.41e-02 5.03e+03 3.35e+00 bond pdb=" C PHE B 152 " pdb=" N PRO B 153 " ideal model delta sigma weight residual 1.331 1.345 -0.014 7.90e-03 1.60e+04 2.98e+00 bond pdb=" C PHE A 152 " pdb=" N PRO A 153 " ideal model delta sigma weight residual 1.331 1.345 -0.013 7.90e-03 1.60e+04 2.87e+00 bond pdb=" CG1 ILE A 361 " pdb=" CD1 ILE A 361 " ideal model delta sigma weight residual 1.513 1.459 0.054 3.90e-02 6.57e+02 1.94e+00 ... (remaining 14869 not shown) Histogram of bond angle deviations from ideal: 98.75 - 105.81: 258 105.81 - 112.87: 8288 112.87 - 119.93: 4923 119.93 - 126.99: 6494 126.99 - 134.05: 183 Bond angle restraints: 20146 Sorted by residual: angle pdb=" N GLN A 876 " pdb=" CA GLN A 876 " pdb=" C GLN A 876 " ideal model delta sigma weight residual 113.55 107.83 5.72 1.26e+00 6.30e-01 2.06e+01 angle pdb=" N GLN B 876 " pdb=" CA GLN B 876 " pdb=" C GLN B 876 " ideal model delta sigma weight residual 113.55 107.83 5.72 1.26e+00 6.30e-01 2.06e+01 angle pdb=" N VAL B 119 " pdb=" CA VAL B 119 " pdb=" C VAL B 119 " ideal model delta sigma weight residual 110.72 114.10 -3.38 1.01e+00 9.80e-01 1.12e+01 angle pdb=" N VAL A 119 " pdb=" CA VAL A 119 " pdb=" C VAL A 119 " ideal model delta sigma weight residual 110.72 114.09 -3.37 1.01e+00 9.80e-01 1.12e+01 angle pdb=" C ILE B1041 " pdb=" N PHE B1042 " pdb=" CA PHE B1042 " ideal model delta sigma weight residual 122.12 127.94 -5.82 1.76e+00 3.23e-01 1.09e+01 ... (remaining 20141 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 8021 17.87 - 35.74: 709 35.74 - 53.62: 88 53.62 - 71.49: 22 71.49 - 89.36: 18 Dihedral angle restraints: 8858 sinusoidal: 3498 harmonic: 5360 Sorted by residual: dihedral pdb=" CA ARG A 449 " pdb=" C ARG A 449 " pdb=" N LEU A 450 " pdb=" CA LEU A 450 " ideal model delta harmonic sigma weight residual 180.00 161.95 18.05 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA ARG B 449 " pdb=" C ARG B 449 " pdb=" N LEU B 450 " pdb=" CA LEU B 450 " ideal model delta harmonic sigma weight residual 180.00 161.97 18.03 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA LEU A 109 " pdb=" C LEU A 109 " pdb=" N LEU A 110 " pdb=" CA LEU A 110 " ideal model delta harmonic sigma weight residual 180.00 -163.60 -16.40 0 5.00e+00 4.00e-02 1.08e+01 ... (remaining 8855 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1456 0.034 - 0.068: 654 0.068 - 0.101: 209 0.101 - 0.135: 47 0.135 - 0.169: 6 Chirality restraints: 2372 Sorted by residual: chirality pdb=" CA SER A 925 " pdb=" N SER A 925 " pdb=" C SER A 925 " pdb=" CB SER A 925 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.12e-01 chirality pdb=" CA SER B 925 " pdb=" N SER B 925 " pdb=" C SER B 925 " pdb=" CB SER B 925 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.08e-01 chirality pdb=" CG LEU A 700 " pdb=" CB LEU A 700 " pdb=" CD1 LEU A 700 " pdb=" CD2 LEU A 700 " both_signs ideal model delta sigma weight residual False -2.59 -2.75 0.16 2.00e-01 2.50e+01 6.57e-01 ... (remaining 2369 not shown) Planarity restraints: 2472 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B1044 " 0.009 2.00e-02 2.50e+03 1.84e-02 3.37e+00 pdb=" C SER B1044 " -0.032 2.00e-02 2.50e+03 pdb=" O SER B1044 " 0.012 2.00e-02 2.50e+03 pdb=" N MET B1045 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A1044 " -0.009 2.00e-02 2.50e+03 1.82e-02 3.29e+00 pdb=" C SER A1044 " 0.031 2.00e-02 2.50e+03 pdb=" O SER A1044 " -0.012 2.00e-02 2.50e+03 pdb=" N MET A1045 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 774 " -0.028 5.00e-02 4.00e+02 4.24e-02 2.88e+00 pdb=" N PRO B 775 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 775 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 775 " -0.024 5.00e-02 4.00e+02 ... (remaining 2469 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1220 2.74 - 3.28: 15401 3.28 - 3.82: 25392 3.82 - 4.36: 31252 4.36 - 4.90: 53566 Nonbonded interactions: 126831 Sorted by model distance: nonbonded pdb=" O VAL B 439 " pdb=" OG1 THR B 443 " model vdw 2.197 2.440 nonbonded pdb=" O VAL A 439 " pdb=" OG1 THR A 443 " model vdw 2.197 2.440 nonbonded pdb=" OE1 GLU A 470 " pdb=" OH TYR B 691 " model vdw 2.198 2.440 nonbonded pdb=" OG SER A 140 " pdb=" OG SER A 169 " model vdw 2.203 2.440 nonbonded pdb=" OG SER B 140 " pdb=" OG SER B 169 " model vdw 2.203 2.440 ... (remaining 126826 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.350 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: 7.490 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 43.010 Find NCS groups from input model: 0.780 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:12.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 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 0.054 14874 Z= 0.283 Angle : 0.709 6.858 20146 Z= 0.392 Chirality : 0.042 0.169 2372 Planarity : 0.004 0.042 2472 Dihedral : 14.073 89.359 5402 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % 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: 0.52 (0.20), residues: 1836 helix: 1.04 (0.15), residues: 1210 sheet: 1.67 (0.62), residues: 76 loop : -1.36 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 493 HIS 0.006 0.001 HIS A 120 PHE 0.026 0.002 PHE A 834 TYR 0.012 0.002 TYR A 590 ARG 0.008 0.001 ARG A 966 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 275 time to evaluate : 1.661 Fit side-chains REVERT: A 99 GLU cc_start: 0.7119 (tt0) cc_final: 0.6888 (mm-30) REVERT: A 234 LEU cc_start: 0.8220 (mp) cc_final: 0.7905 (mp) REVERT: A 375 LEU cc_start: 0.8641 (mp) cc_final: 0.8416 (mp) REVERT: A 445 GLN cc_start: 0.7672 (tp-100) cc_final: 0.7176 (mp-120) REVERT: A 449 ARG cc_start: 0.6648 (mtm110) cc_final: 0.6353 (ttp-110) REVERT: A 562 GLN cc_start: 0.7540 (tt0) cc_final: 0.7336 (tt0) REVERT: A 579 ARG cc_start: 0.7380 (ttm170) cc_final: 0.7161 (ttp80) REVERT: A 652 LYS cc_start: 0.7869 (mmtm) cc_final: 0.7613 (pttm) REVERT: A 771 GLU cc_start: 0.7561 (tt0) cc_final: 0.6874 (tt0) REVERT: B 234 LEU cc_start: 0.8243 (mp) cc_final: 0.7963 (mp) REVERT: B 375 LEU cc_start: 0.8553 (mp) cc_final: 0.8320 (mp) REVERT: B 445 GLN cc_start: 0.7682 (tp-100) cc_final: 0.7171 (mp-120) REVERT: B 449 ARG cc_start: 0.6622 (mtm110) cc_final: 0.6334 (ttp-110) REVERT: B 562 GLN cc_start: 0.7548 (tt0) cc_final: 0.7345 (tt0) REVERT: B 579 ARG cc_start: 0.7401 (ttm170) cc_final: 0.7172 (ttp80) REVERT: B 652 LYS cc_start: 0.7906 (mmtm) cc_final: 0.7605 (pttm) REVERT: B 771 GLU cc_start: 0.7605 (tt0) cc_final: 0.7078 (tt0) REVERT: B 822 CYS cc_start: 0.8250 (p) cc_final: 0.7925 (p) outliers start: 0 outliers final: 0 residues processed: 275 average time/residue: 1.2297 time to fit residues: 372.5743 Evaluate side-chains 196 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.9990 chunk 139 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 94 optimal weight: 0.0470 chunk 74 optimal weight: 4.9990 chunk 144 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 107 optimal weight: 0.4980 chunk 167 optimal weight: 3.9990 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 219 ASN A 277 GLN A 347 GLN A 855 GLN B 94 ASN B 219 ASN B 277 GLN B 347 GLN B 679 GLN B 855 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14874 Z= 0.227 Angle : 0.587 6.206 20146 Z= 0.298 Chirality : 0.040 0.148 2372 Planarity : 0.005 0.040 2472 Dihedral : 5.258 46.642 2020 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.00 % Allowed : 11.00 % Favored : 86.00 % 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: 0.70 (0.20), residues: 1836 helix: 1.18 (0.15), residues: 1204 sheet: 1.86 (0.60), residues: 72 loop : -1.28 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 854 HIS 0.005 0.001 HIS A 120 PHE 0.016 0.002 PHE A 353 TYR 0.016 0.002 TYR A 769 ARG 0.004 0.000 ARG B 58 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 214 time to evaluate : 1.612 Fit side-chains REVERT: A 234 LEU cc_start: 0.8294 (mp) cc_final: 0.8039 (mp) REVERT: A 445 GLN cc_start: 0.7611 (tp-100) cc_final: 0.7390 (mm110) REVERT: A 449 ARG cc_start: 0.6845 (mtm110) cc_final: 0.6439 (ttp-110) REVERT: A 579 ARG cc_start: 0.7310 (ttm170) cc_final: 0.7082 (ttp80) REVERT: A 652 LYS cc_start: 0.7809 (mmtm) cc_final: 0.7571 (pttm) REVERT: A 763 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8202 (mt) REVERT: A 866 ARG cc_start: 0.7183 (OUTLIER) cc_final: 0.6783 (tpt-90) REVERT: A 875 MET cc_start: 0.8192 (OUTLIER) cc_final: 0.7918 (ttp) REVERT: B 234 LEU cc_start: 0.8309 (mp) cc_final: 0.8059 (mp) REVERT: B 449 ARG cc_start: 0.6821 (mtm110) cc_final: 0.6416 (ttp-110) REVERT: B 579 ARG cc_start: 0.7324 (ttm170) cc_final: 0.7084 (ttp80) REVERT: B 652 LYS cc_start: 0.7822 (mmtm) cc_final: 0.7571 (pttm) outliers start: 48 outliers final: 20 residues processed: 233 average time/residue: 1.2062 time to fit residues: 309.9832 Evaluate side-chains 226 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 203 time to evaluate : 1.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain A residue 875 MET Chi-restraints excluded: chain A residue 876 GLN Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 876 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 139 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 46 optimal weight: 0.0470 chunk 167 optimal weight: 3.9990 chunk 180 optimal weight: 10.0000 chunk 149 optimal weight: 0.8980 chunk 165 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 134 optimal weight: 0.9980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 347 GLN A 480 GLN B 347 GLN B 480 GLN ** B 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14874 Z= 0.209 Angle : 0.544 6.251 20146 Z= 0.277 Chirality : 0.039 0.142 2372 Planarity : 0.004 0.037 2472 Dihedral : 5.047 44.622 2020 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.06 % Allowed : 13.69 % Favored : 83.25 % 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: 0.80 (0.20), residues: 1836 helix: 1.21 (0.15), residues: 1212 sheet: 1.77 (0.61), residues: 72 loop : -1.10 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 493 HIS 0.005 0.001 HIS B 626 PHE 0.016 0.001 PHE B 314 TYR 0.013 0.001 TYR A 769 ARG 0.002 0.000 ARG A 58 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 220 time to evaluate : 1.754 Fit side-chains REVERT: A 123 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7964 (pttt) REVERT: A 419 LYS cc_start: 0.8322 (tttm) cc_final: 0.8107 (tttp) REVERT: A 445 GLN cc_start: 0.7781 (tp-100) cc_final: 0.7576 (mm110) REVERT: A 449 ARG cc_start: 0.6900 (mtm110) cc_final: 0.6379 (ttp-110) REVERT: A 579 ARG cc_start: 0.7366 (ttm170) cc_final: 0.7105 (ttp80) REVERT: A 652 LYS cc_start: 0.7821 (mmtm) cc_final: 0.7597 (pttm) REVERT: A 697 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7571 (mtmt) REVERT: A 771 GLU cc_start: 0.7509 (tt0) cc_final: 0.6559 (tt0) REVERT: A 866 ARG cc_start: 0.7205 (OUTLIER) cc_final: 0.6793 (tpt-90) REVERT: B 123 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7953 (pttt) REVERT: B 199 MET cc_start: 0.8101 (OUTLIER) cc_final: 0.7643 (mtt) REVERT: B 342 ASP cc_start: 0.7758 (t0) cc_final: 0.7553 (t0) REVERT: B 419 LYS cc_start: 0.8317 (tttm) cc_final: 0.8106 (tttp) REVERT: B 449 ARG cc_start: 0.6901 (mtm110) cc_final: 0.6359 (ttp-110) REVERT: B 579 ARG cc_start: 0.7374 (ttm170) cc_final: 0.7106 (ttp80) REVERT: B 652 LYS cc_start: 0.7820 (mmtm) cc_final: 0.7609 (pttm) REVERT: B 697 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7593 (mtmt) REVERT: B 771 GLU cc_start: 0.7520 (tt0) cc_final: 0.6656 (tt0) outliers start: 49 outliers final: 17 residues processed: 241 average time/residue: 1.2925 time to fit residues: 345.7385 Evaluate side-chains 229 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 206 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 656 GLU Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 835 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 86 optimal weight: 8.9990 chunk 18 optimal weight: 2.9990 chunk 79 optimal weight: 9.9990 chunk 112 optimal weight: 0.9980 chunk 167 optimal weight: 0.9980 chunk 177 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 159 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 347 GLN A 480 GLN ** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 GLN B 480 GLN B 679 GLN ** B 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14874 Z= 0.241 Angle : 0.552 7.222 20146 Z= 0.279 Chirality : 0.040 0.139 2372 Planarity : 0.004 0.037 2472 Dihedral : 5.050 44.793 2020 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.69 % Allowed : 14.69 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.20), residues: 1836 helix: 1.17 (0.15), residues: 1212 sheet: 1.72 (0.62), residues: 72 loop : -1.01 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 493 HIS 0.005 0.001 HIS A 120 PHE 0.015 0.002 PHE B 314 TYR 0.012 0.001 TYR A 769 ARG 0.003 0.000 ARG B 452 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 215 time to evaluate : 1.596 Fit side-chains REVERT: A 123 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.7921 (pttt) REVERT: A 449 ARG cc_start: 0.6989 (mtm110) cc_final: 0.6400 (ttp-110) REVERT: A 555 VAL cc_start: 0.8626 (OUTLIER) cc_final: 0.8344 (m) REVERT: A 652 LYS cc_start: 0.7808 (mmtm) cc_final: 0.7601 (pttm) REVERT: A 697 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.7634 (mtmt) REVERT: A 703 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.7018 (mt-10) REVERT: A 771 GLU cc_start: 0.7525 (tt0) cc_final: 0.6592 (tt0) REVERT: A 866 ARG cc_start: 0.7201 (OUTLIER) cc_final: 0.6788 (tpt-90) REVERT: A 1045 MET cc_start: 0.5882 (tpp) cc_final: 0.5679 (tpp) REVERT: B 123 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7912 (pttt) REVERT: B 199 MET cc_start: 0.8119 (OUTLIER) cc_final: 0.7622 (mtt) REVERT: B 342 ASP cc_start: 0.7708 (t0) cc_final: 0.7487 (t0) REVERT: B 449 ARG cc_start: 0.6978 (mtm110) cc_final: 0.6373 (ttp-110) REVERT: B 555 VAL cc_start: 0.8572 (OUTLIER) cc_final: 0.8294 (m) REVERT: B 579 ARG cc_start: 0.7366 (ttm170) cc_final: 0.7106 (ttp80) REVERT: B 697 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.7680 (mtmt) REVERT: B 703 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.6982 (mt-10) REVERT: B 771 GLU cc_start: 0.7561 (tt0) cc_final: 0.6675 (tt0) outliers start: 59 outliers final: 28 residues processed: 246 average time/residue: 1.2286 time to fit residues: 333.5461 Evaluate side-chains 236 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 198 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain A residue 876 GLN Chi-restraints excluded: chain A residue 890 THR Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 656 GLU Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 703 GLU Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 835 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 132 optimal weight: 0.5980 chunk 73 optimal weight: 4.9990 chunk 151 optimal weight: 0.9980 chunk 122 optimal weight: 0.0980 chunk 0 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 159 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 480 GLN ** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 GLN B 480 GLN ** B 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14874 Z= 0.197 Angle : 0.530 7.191 20146 Z= 0.267 Chirality : 0.038 0.141 2372 Planarity : 0.004 0.036 2472 Dihedral : 4.930 42.298 2020 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.75 % Allowed : 16.44 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.20), residues: 1836 helix: 1.24 (0.15), residues: 1218 sheet: 1.76 (0.61), residues: 76 loop : -0.89 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 493 HIS 0.004 0.001 HIS A 120 PHE 0.016 0.001 PHE A 636 TYR 0.011 0.001 TYR B 634 ARG 0.004 0.000 ARG B 452 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 214 time to evaluate : 1.339 Fit side-chains REVERT: A 129 MET cc_start: 0.7209 (mmp) cc_final: 0.6879 (mmp) REVERT: A 449 ARG cc_start: 0.6943 (mtm110) cc_final: 0.6524 (ttp-110) REVERT: A 611 ARG cc_start: 0.6884 (ttp-170) cc_final: 0.6681 (ttm170) REVERT: A 652 LYS cc_start: 0.7796 (mmtm) cc_final: 0.7591 (pttm) REVERT: A 697 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7607 (mtmt) REVERT: A 703 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.6981 (mt-10) REVERT: A 771 GLU cc_start: 0.7549 (tt0) cc_final: 0.6612 (tt0) REVERT: A 866 ARG cc_start: 0.7172 (OUTLIER) cc_final: 0.6757 (tpt-90) REVERT: B 199 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7658 (mtt) REVERT: B 342 ASP cc_start: 0.7807 (t0) cc_final: 0.7563 (t0) REVERT: B 449 ARG cc_start: 0.6913 (mtm110) cc_final: 0.6495 (ttp-110) REVERT: B 611 ARG cc_start: 0.6936 (ttp-170) cc_final: 0.5963 (mtp180) REVERT: B 697 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.7628 (mtmt) REVERT: B 703 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.6959 (mt-10) REVERT: B 771 GLU cc_start: 0.7608 (tt0) cc_final: 0.6721 (tt0) REVERT: B 875 MET cc_start: 0.7955 (tpp) cc_final: 0.7667 (tpp) outliers start: 60 outliers final: 28 residues processed: 244 average time/residue: 1.2021 time to fit residues: 324.0801 Evaluate side-chains 235 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 201 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 656 GLU Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain A residue 876 GLN Chi-restraints excluded: chain A residue 890 THR Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 703 GLU Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 890 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 0.9980 chunk 160 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 178 optimal weight: 2.9990 chunk 147 optimal weight: 0.9980 chunk 82 optimal weight: 7.9990 chunk 14 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 347 GLN A 480 GLN ** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 GLN B 480 GLN ** B 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14874 Z= 0.241 Angle : 0.546 7.206 20146 Z= 0.274 Chirality : 0.039 0.143 2372 Planarity : 0.004 0.037 2472 Dihedral : 4.969 43.948 2020 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.94 % Allowed : 16.81 % Favored : 79.25 % 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: 0.91 (0.20), residues: 1836 helix: 1.20 (0.15), residues: 1214 sheet: 1.82 (0.65), residues: 72 loop : -0.84 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 493 HIS 0.006 0.001 HIS A 120 PHE 0.015 0.002 PHE B 636 TYR 0.011 0.001 TYR A 769 ARG 0.002 0.000 ARG B 452 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 211 time to evaluate : 1.690 Fit side-chains REVERT: A 199 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7700 (mtt) REVERT: A 449 ARG cc_start: 0.7002 (mtm110) cc_final: 0.6526 (ttp-110) REVERT: A 503 LEU cc_start: 0.8275 (mp) cc_final: 0.8032 (mt) REVERT: A 555 VAL cc_start: 0.8557 (OUTLIER) cc_final: 0.8292 (m) REVERT: A 611 ARG cc_start: 0.6945 (ttp-170) cc_final: 0.5962 (mtp180) REVERT: A 697 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.7640 (mtmt) REVERT: A 703 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.6967 (mt-10) REVERT: A 771 GLU cc_start: 0.7561 (tt0) cc_final: 0.6603 (tt0) REVERT: A 866 ARG cc_start: 0.7171 (OUTLIER) cc_final: 0.6763 (tpt-90) REVERT: B 129 MET cc_start: 0.7247 (mmp) cc_final: 0.6939 (mmp) REVERT: B 199 MET cc_start: 0.8154 (OUTLIER) cc_final: 0.7659 (mtt) REVERT: B 449 ARG cc_start: 0.7010 (mtm110) cc_final: 0.6447 (ttp-110) REVERT: B 555 VAL cc_start: 0.8565 (OUTLIER) cc_final: 0.8293 (m) REVERT: B 611 ARG cc_start: 0.7014 (ttp-170) cc_final: 0.6030 (mtp180) REVERT: B 697 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.7644 (mtmt) REVERT: B 703 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.6978 (mt-10) REVERT: B 771 GLU cc_start: 0.7616 (tt0) cc_final: 0.6720 (tt0) REVERT: B 875 MET cc_start: 0.7788 (tpp) cc_final: 0.7503 (tpp) outliers start: 63 outliers final: 33 residues processed: 244 average time/residue: 1.1781 time to fit residues: 319.4879 Evaluate side-chains 246 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 204 time to evaluate : 1.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 656 GLU Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain A residue 876 GLN Chi-restraints excluded: chain A residue 890 THR Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 577 ASP Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 703 GLU Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 890 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 101 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 149 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 chunk 177 optimal weight: 5.9990 chunk 110 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 347 GLN A 480 GLN ** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 GLN B 480 GLN ** B 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14874 Z= 0.222 Angle : 0.539 7.486 20146 Z= 0.271 Chirality : 0.039 0.141 2372 Planarity : 0.004 0.037 2472 Dihedral : 4.939 44.347 2020 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.81 % Allowed : 18.06 % Favored : 78.12 % 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: 0.92 (0.20), residues: 1836 helix: 1.19 (0.15), residues: 1218 sheet: 1.88 (0.66), residues: 72 loop : -0.81 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 493 HIS 0.005 0.001 HIS A 120 PHE 0.016 0.002 PHE B 636 TYR 0.011 0.001 TYR A 634 ARG 0.002 0.000 ARG B 452 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 213 time to evaluate : 1.798 Fit side-chains REVERT: A 123 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7976 (pttt) REVERT: A 129 MET cc_start: 0.7235 (mmp) cc_final: 0.6867 (mmp) REVERT: A 199 MET cc_start: 0.8154 (OUTLIER) cc_final: 0.7692 (mtt) REVERT: A 449 ARG cc_start: 0.7042 (mtm110) cc_final: 0.6396 (ttp-110) REVERT: A 461 LYS cc_start: 0.7833 (tptp) cc_final: 0.7319 (mttp) REVERT: A 555 VAL cc_start: 0.8546 (OUTLIER) cc_final: 0.8292 (m) REVERT: A 611 ARG cc_start: 0.6923 (ttp-170) cc_final: 0.5972 (mtp180) REVERT: A 697 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.7690 (mtmt) REVERT: A 703 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.6969 (mt-10) REVERT: A 771 GLU cc_start: 0.7558 (tt0) cc_final: 0.6593 (tt0) REVERT: A 866 ARG cc_start: 0.7136 (OUTLIER) cc_final: 0.6732 (tpt-90) REVERT: A 875 MET cc_start: 0.7584 (tpp) cc_final: 0.7210 (tpt) REVERT: B 199 MET cc_start: 0.8171 (OUTLIER) cc_final: 0.7721 (mtt) REVERT: B 342 ASP cc_start: 0.7544 (t70) cc_final: 0.7138 (t0) REVERT: B 449 ARG cc_start: 0.7046 (mtm110) cc_final: 0.6442 (ttp-110) REVERT: B 461 LYS cc_start: 0.7824 (tptp) cc_final: 0.7325 (mttp) REVERT: B 555 VAL cc_start: 0.8558 (OUTLIER) cc_final: 0.8291 (m) REVERT: B 611 ARG cc_start: 0.7006 (ttp-170) cc_final: 0.5976 (mtp180) REVERT: B 697 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.7676 (mtmt) REVERT: B 703 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.6982 (mt-10) REVERT: B 771 GLU cc_start: 0.7608 (tt0) cc_final: 0.6714 (tt0) REVERT: B 875 MET cc_start: 0.7754 (tpp) cc_final: 0.7488 (tpt) outliers start: 61 outliers final: 34 residues processed: 244 average time/residue: 1.1501 time to fit residues: 311.1474 Evaluate side-chains 248 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 204 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 656 GLU Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain A residue 876 GLN Chi-restraints excluded: chain A residue 890 THR Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 656 GLU Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 703 GLU Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 890 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 chunk 87 optimal weight: 8.9990 chunk 16 optimal weight: 0.9980 chunk 139 optimal weight: 3.9990 chunk 161 optimal weight: 4.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 480 GLN ** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 GLN B 480 GLN ** B 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14874 Z= 0.290 Angle : 0.575 7.624 20146 Z= 0.287 Chirality : 0.041 0.136 2372 Planarity : 0.004 0.039 2472 Dihedral : 5.084 46.466 2020 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.94 % Allowed : 18.06 % Favored : 78.00 % 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: 0.80 (0.20), residues: 1836 helix: 1.07 (0.15), residues: 1216 sheet: 1.94 (0.65), residues: 72 loop : -0.80 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 493 HIS 0.007 0.001 HIS B 120 PHE 0.018 0.002 PHE B 636 TYR 0.012 0.002 TYR B 769 ARG 0.002 0.000 ARG B 452 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 201 time to evaluate : 1.698 Fit side-chains REVERT: A 123 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.8002 (pttt) REVERT: A 129 MET cc_start: 0.7270 (mmp) cc_final: 0.6932 (mmp) REVERT: A 168 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7920 (pp) REVERT: A 199 MET cc_start: 0.8164 (OUTLIER) cc_final: 0.7723 (mtt) REVERT: A 449 ARG cc_start: 0.7029 (mtm110) cc_final: 0.6804 (mtm-85) REVERT: A 555 VAL cc_start: 0.8559 (OUTLIER) cc_final: 0.8295 (m) REVERT: A 610 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7658 (mp0) REVERT: A 611 ARG cc_start: 0.7003 (ttp-170) cc_final: 0.5941 (mtp180) REVERT: A 697 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.7734 (mtmt) REVERT: A 703 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.6951 (mt-10) REVERT: A 771 GLU cc_start: 0.7559 (tt0) cc_final: 0.6771 (tt0) REVERT: A 866 ARG cc_start: 0.7170 (OUTLIER) cc_final: 0.6760 (tpt-90) REVERT: A 875 MET cc_start: 0.7607 (tpp) cc_final: 0.7200 (tpt) REVERT: B 121 GLN cc_start: 0.8293 (mt0) cc_final: 0.7989 (mp10) REVERT: B 123 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7984 (pttt) REVERT: B 129 MET cc_start: 0.7241 (mmp) cc_final: 0.6849 (mmp) REVERT: B 168 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7916 (pp) REVERT: B 199 MET cc_start: 0.8152 (OUTLIER) cc_final: 0.7658 (mtt) REVERT: B 342 ASP cc_start: 0.7510 (t70) cc_final: 0.7074 (t0) REVERT: B 449 ARG cc_start: 0.7045 (mtm110) cc_final: 0.6429 (ttp-110) REVERT: B 503 LEU cc_start: 0.8314 (mp) cc_final: 0.8112 (tp) REVERT: B 555 VAL cc_start: 0.8568 (OUTLIER) cc_final: 0.8290 (m) REVERT: B 611 ARG cc_start: 0.7070 (ttp-170) cc_final: 0.5942 (mtm180) REVERT: B 697 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7744 (mtmt) REVERT: B 703 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.6954 (mt-10) REVERT: B 875 MET cc_start: 0.7633 (tpp) cc_final: 0.7176 (tpt) outliers start: 63 outliers final: 39 residues processed: 231 average time/residue: 1.1872 time to fit residues: 303.2563 Evaluate side-chains 250 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 198 time to evaluate : 1.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 656 GLU Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain A residue 876 GLN Chi-restraints excluded: chain A residue 890 THR Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 453 MET Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 577 ASP Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 652 LYS Chi-restraints excluded: chain B residue 656 GLU Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 703 GLU Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 876 GLN Chi-restraints excluded: chain B residue 890 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 0.7980 chunk 155 optimal weight: 0.6980 chunk 165 optimal weight: 0.9980 chunk 99 optimal weight: 0.5980 chunk 71 optimal weight: 3.9990 chunk 129 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 149 optimal weight: 0.6980 chunk 156 optimal weight: 0.6980 chunk 164 optimal weight: 0.7980 chunk 108 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 347 GLN A 480 GLN ** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 GLN B 480 GLN ** B 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14874 Z= 0.214 Angle : 0.543 7.345 20146 Z= 0.272 Chirality : 0.039 0.140 2372 Planarity : 0.004 0.039 2472 Dihedral : 4.980 45.844 2020 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.69 % Allowed : 18.25 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.20), residues: 1836 helix: 1.13 (0.15), residues: 1220 sheet: 1.95 (0.65), residues: 72 loop : -0.79 (0.28), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 493 HIS 0.005 0.001 HIS A 120 PHE 0.019 0.001 PHE A 636 TYR 0.011 0.001 TYR A 634 ARG 0.002 0.000 ARG B 58 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 206 time to evaluate : 1.605 Fit side-chains REVERT: A 123 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.8002 (pttt) REVERT: A 129 MET cc_start: 0.7241 (mmp) cc_final: 0.6913 (mmp) REVERT: A 199 MET cc_start: 0.8150 (OUTLIER) cc_final: 0.7688 (mtt) REVERT: A 555 VAL cc_start: 0.8518 (OUTLIER) cc_final: 0.8254 (m) REVERT: A 611 ARG cc_start: 0.7011 (ttp-170) cc_final: 0.5985 (mtp180) REVERT: A 697 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.7757 (mtmt) REVERT: A 703 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.6971 (mt-10) REVERT: A 866 ARG cc_start: 0.7195 (OUTLIER) cc_final: 0.6787 (tpt-90) REVERT: A 875 MET cc_start: 0.7481 (tpp) cc_final: 0.7083 (tpt) REVERT: B 121 GLN cc_start: 0.8221 (mt0) cc_final: 0.7933 (mp10) REVERT: B 123 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7984 (pttt) REVERT: B 129 MET cc_start: 0.7238 (mmp) cc_final: 0.6920 (mmp) REVERT: B 199 MET cc_start: 0.8127 (OUTLIER) cc_final: 0.7607 (mtt) REVERT: B 342 ASP cc_start: 0.7532 (t70) cc_final: 0.7101 (t0) REVERT: B 449 ARG cc_start: 0.7028 (mtm110) cc_final: 0.6471 (ttp-110) REVERT: B 503 LEU cc_start: 0.8376 (mp) cc_final: 0.8103 (tp) REVERT: B 555 VAL cc_start: 0.8526 (OUTLIER) cc_final: 0.8248 (m) REVERT: B 610 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7698 (mp0) REVERT: B 611 ARG cc_start: 0.7101 (ttp-170) cc_final: 0.5977 (mtm110) REVERT: B 697 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.7731 (mtmt) REVERT: B 703 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.6968 (mt-10) REVERT: B 771 GLU cc_start: 0.7471 (tt0) cc_final: 0.6522 (tt0) REVERT: B 875 MET cc_start: 0.7563 (tpp) cc_final: 0.7130 (tpt) outliers start: 59 outliers final: 37 residues processed: 231 average time/residue: 1.2392 time to fit residues: 319.5998 Evaluate side-chains 249 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 201 time to evaluate : 1.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 656 GLU Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain A residue 876 GLN Chi-restraints excluded: chain A residue 890 THR Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 577 ASP Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 652 LYS Chi-restraints excluded: chain B residue 656 GLU Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 703 GLU Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 876 GLN Chi-restraints excluded: chain B residue 890 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 121 optimal weight: 0.9990 chunk 183 optimal weight: 0.9990 chunk 168 optimal weight: 0.2980 chunk 145 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 112 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 chunk 115 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN ** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 GLN ** B 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14874 Z= 0.218 Angle : 0.545 7.616 20146 Z= 0.273 Chirality : 0.039 0.137 2372 Planarity : 0.004 0.040 2472 Dihedral : 4.924 45.614 2020 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.62 % Allowed : 18.69 % Favored : 77.69 % 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: 0.93 (0.20), residues: 1836 helix: 1.18 (0.15), residues: 1220 sheet: 1.99 (0.65), residues: 72 loop : -0.78 (0.28), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 493 HIS 0.005 0.001 HIS A 120 PHE 0.018 0.002 PHE B 636 TYR 0.011 0.001 TYR A 634 ARG 0.003 0.000 ARG B 452 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 203 time to evaluate : 1.502 Fit side-chains REVERT: A 123 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7997 (pttt) REVERT: A 129 MET cc_start: 0.7296 (mmp) cc_final: 0.6986 (mmp) REVERT: A 199 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7692 (mtt) REVERT: A 449 ARG cc_start: 0.6986 (mtm-85) cc_final: 0.6715 (mtm-85) REVERT: A 461 LYS cc_start: 0.7660 (tmtt) cc_final: 0.7253 (mttp) REVERT: A 480 GLN cc_start: 0.7472 (OUTLIER) cc_final: 0.7264 (mt0) REVERT: A 555 VAL cc_start: 0.8515 (OUTLIER) cc_final: 0.8256 (m) REVERT: A 611 ARG cc_start: 0.7086 (ttp-170) cc_final: 0.5955 (mtp180) REVERT: A 697 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.7768 (mtmt) REVERT: A 703 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.6947 (mt-10) REVERT: A 866 ARG cc_start: 0.7214 (OUTLIER) cc_final: 0.6798 (tpt-90) REVERT: B 121 GLN cc_start: 0.8188 (mt0) cc_final: 0.7927 (mp10) REVERT: B 123 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7977 (pttt) REVERT: B 199 MET cc_start: 0.8111 (OUTLIER) cc_final: 0.7558 (mtt) REVERT: B 342 ASP cc_start: 0.7444 (t70) cc_final: 0.7109 (t0) REVERT: B 461 LYS cc_start: 0.7652 (tmtt) cc_final: 0.7252 (mttp) REVERT: B 555 VAL cc_start: 0.8522 (OUTLIER) cc_final: 0.8247 (m) REVERT: B 611 ARG cc_start: 0.7040 (ttp-170) cc_final: 0.5795 (mtm180) REVERT: B 697 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.7781 (mtmt) REVERT: B 703 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.6965 (mt-10) REVERT: B 875 MET cc_start: 0.7484 (tpp) cc_final: 0.7070 (tpt) outliers start: 58 outliers final: 39 residues processed: 230 average time/residue: 1.1846 time to fit residues: 301.0544 Evaluate side-chains 251 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 200 time to evaluate : 1.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 656 GLU Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 866 ARG Chi-restraints excluded: chain A residue 876 GLN Chi-restraints excluded: chain A residue 890 THR Chi-restraints excluded: chain A residue 1011 MET Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 577 ASP Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 652 LYS Chi-restraints excluded: chain B residue 656 GLU Chi-restraints excluded: chain B residue 671 VAL Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 703 GLU Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 846 ASP Chi-restraints excluded: chain B residue 890 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 134 optimal weight: 0.0370 chunk 21 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 146 optimal weight: 0.0030 chunk 61 optimal weight: 0.7980 chunk 150 optimal weight: 0.1980 chunk 18 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 128 optimal weight: 4.9990 overall best weight: 0.3068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 480 GLN ** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 GLN ** B 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.191352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.149153 restraints weight = 14573.473| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 1.60 r_work: 0.3506 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14874 Z= 0.161 Angle : 0.513 9.378 20146 Z= 0.256 Chirality : 0.038 0.138 2372 Planarity : 0.004 0.040 2472 Dihedral : 4.651 40.012 2020 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.81 % Allowed : 19.88 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.20), residues: 1836 helix: 1.36 (0.15), residues: 1220 sheet: 1.90 (0.64), residues: 72 loop : -0.79 (0.28), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 493 HIS 0.007 0.001 HIS A 120 PHE 0.016 0.001 PHE B 353 TYR 0.012 0.001 TYR A 634 ARG 0.003 0.000 ARG B1035 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5627.66 seconds wall clock time: 100 minutes 7.11 seconds (6007.11 seconds total)