Starting phenix.real_space_refine on Sun Nov 17 15:31:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oii_16892/11_2024/8oii_16892.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oii_16892/11_2024/8oii_16892.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oii_16892/11_2024/8oii_16892.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oii_16892/11_2024/8oii_16892.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oii_16892/11_2024/8oii_16892.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oii_16892/11_2024/8oii_16892.cif" } resolution = 2.84 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= -0.001 sd= 0.026 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 62 5.16 5 C 8901 2.51 5 N 2421 2.21 5 O 2680 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 14064 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 900, 7034 Classifications: {'peptide': 900} Link IDs: {'PTRANS': 41, 'TRANS': 858} Chain breaks: 1 Chain: "B" Number of atoms: 7030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 900, 7030 Classifications: {'peptide': 900} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 41, 'TRANS': 858} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 8.43, per 1000 atoms: 0.60 Number of scatterers: 14064 At special positions: 0 Unit cell: (116.725, 116.725, 117.74, 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 62 16.00 O 2680 8.00 N 2421 7.00 C 8901 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.47 Conformation dependent library (CDL) restraints added in 2.2 seconds 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3328 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 9 sheets defined 37.1% alpha, 18.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'A' and resid 49 through 59 Processing helix chain 'A' and resid 73 through 77 Processing helix chain 'A' and resid 110 through 117 Processing helix chain 'A' and resid 118 through 135 Processing helix chain 'A' and resid 138 through 147 Processing helix chain 'A' and resid 161 through 172 removed outlier: 3.957A pdb=" N GLY A 165 " --> pdb=" O TYR A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 193 removed outlier: 3.510A pdb=" N VAL A 188 " --> pdb=" O ILE A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 206 through 221 Processing helix chain 'A' and resid 237 through 247 removed outlier: 4.010A pdb=" N THR A 241 " --> pdb=" O HIS A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 288 Processing helix chain 'A' and resid 313 through 329 Processing helix chain 'A' and resid 331 through 333 No H-bonds generated for 'chain 'A' and resid 331 through 333' Processing helix chain 'A' and resid 347 through 362 removed outlier: 3.606A pdb=" N ILE A 351 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TRP A 362 " --> pdb=" O ASN A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 380 Processing helix chain 'A' and resid 382 through 384 No H-bonds generated for 'chain 'A' and resid 382 through 384' Processing helix chain 'A' and resid 385 through 401 Processing helix chain 'A' and resid 480 through 484 removed outlier: 3.513A pdb=" N LEU A 484 " --> pdb=" O GLU A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 510 removed outlier: 4.268A pdb=" N ALA A 497 " --> pdb=" O LEU A 493 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N GLN A 498 " --> pdb=" O ALA A 494 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER A 509 " --> pdb=" O ASP A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 525 removed outlier: 3.649A pdb=" N LYS A 525 " --> pdb=" O LEU A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 551 Processing helix chain 'A' and resid 582 through 593 removed outlier: 4.173A pdb=" N LEU A 586 " --> pdb=" O PRO A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 603 removed outlier: 3.510A pdb=" N SER A 601 " --> pdb=" O ASP A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 641 Processing helix chain 'A' and resid 665 through 670 removed outlier: 4.056A pdb=" N LEU A 670 " --> pdb=" O ASP A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 698 Proline residue: A 695 - end of helix Processing helix chain 'A' and resid 718 through 720 No H-bonds generated for 'chain 'A' and resid 718 through 720' Processing helix chain 'A' and resid 769 through 786 removed outlier: 4.076A pdb=" N GLN A 783 " --> pdb=" O LEU A 779 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ALA A 784 " --> pdb=" O LEU A 780 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 785 " --> pdb=" O ASN A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 803 removed outlier: 3.586A pdb=" N ALA A 803 " --> pdb=" O ARG A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 864 Processing helix chain 'A' and resid 927 through 932 Processing helix chain 'B' and resid 49 through 60 Processing helix chain 'B' and resid 73 through 78 removed outlier: 3.912A pdb=" N ILE B 77 " --> pdb=" O ASP B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 117 Processing helix chain 'B' and resid 118 through 135 Processing helix chain 'B' and resid 138 through 147 Processing helix chain 'B' and resid 161 through 172 removed outlier: 3.929A pdb=" N GLY B 165 " --> pdb=" O TYR B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 193 removed outlier: 3.587A pdb=" N VAL B 188 " --> pdb=" O ILE B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 205 No H-bonds generated for 'chain 'B' and resid 203 through 205' Processing helix chain 'B' and resid 206 through 221 Processing helix chain 'B' and resid 237 through 247 removed outlier: 4.010A pdb=" N THR B 241 " --> pdb=" O HIS B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 288 Processing helix chain 'B' and resid 313 through 329 Processing helix chain 'B' and resid 331 through 333 No H-bonds generated for 'chain 'B' and resid 331 through 333' Processing helix chain 'B' and resid 347 through 362 removed outlier: 3.501A pdb=" N ILE B 351 " --> pdb=" O LEU B 347 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TRP B 362 " --> pdb=" O ASN B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 380 Processing helix chain 'B' and resid 382 through 384 No H-bonds generated for 'chain 'B' and resid 382 through 384' Processing helix chain 'B' and resid 385 through 401 Processing helix chain 'B' and resid 417 through 421 Processing helix chain 'B' and resid 457 through 459 No H-bonds generated for 'chain 'B' and resid 457 through 459' Processing helix chain 'B' and resid 480 through 483 Processing helix chain 'B' and resid 493 through 510 removed outlier: 4.245A pdb=" N ALA B 497 " --> pdb=" O LEU B 493 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLN B 498 " --> pdb=" O ALA B 494 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER B 509 " --> pdb=" O ASP B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 525 removed outlier: 3.694A pdb=" N LYS B 525 " --> pdb=" O LEU B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 552 Processing helix chain 'B' and resid 582 through 593 removed outlier: 3.887A pdb=" N LEU B 586 " --> pdb=" O PRO B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 603 removed outlier: 3.528A pdb=" N SER B 601 " --> pdb=" O ASP B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 641 Processing helix chain 'B' and resid 665 through 670 removed outlier: 4.015A pdb=" N LEU B 670 " --> pdb=" O ASP B 667 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 698 Proline residue: B 695 - end of helix Processing helix chain 'B' and resid 718 through 720 No H-bonds generated for 'chain 'B' and resid 718 through 720' Processing helix chain 'B' and resid 769 through 786 removed outlier: 3.645A pdb=" N GLN B 783 " --> pdb=" O LEU B 779 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA B 784 " --> pdb=" O LEU B 780 " (cutoff:3.500A) Processing helix chain 'B' and resid 792 through 803 removed outlier: 3.686A pdb=" N ALA B 803 " --> pdb=" O ARG B 799 " (cutoff:3.500A) Processing helix chain 'B' and resid 845 through 864 removed outlier: 3.512A pdb=" N GLU B 862 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing helix chain 'B' and resid 927 through 932 Processing sheet with id=AA1, first strand: chain 'A' and resid 372 through 373 removed outlier: 8.159A pdb=" N GLY A 373 " --> pdb=" O SER A 336 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE A 338 " --> pdb=" O GLY A 373 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ARG A 449 " --> pdb=" O ILE A 335 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR A 337 " --> pdb=" O ARG A 449 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N GLU A 467 " --> pdb=" O ILE A 295 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ILE A 295 " --> pdb=" O GLU A 467 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE A 35 " --> pdb=" O ILE A 295 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU A 277 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LEU A 40 " --> pdb=" O ALA A 275 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ALA A 275 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLY A 42 " --> pdb=" O ILE A 273 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE A 273 " --> pdb=" O GLY A 42 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N LEU B 199 " --> pdb=" O VAL B 150 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N VAL B 152 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ILE B 201 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N LEU B 154 " --> pdb=" O ILE B 201 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE B 273 " --> pdb=" O GLY B 42 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLY B 42 " --> pdb=" O ILE B 273 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ALA B 275 " --> pdb=" O LEU B 40 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LEU B 40 " --> pdb=" O ALA B 275 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU B 277 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY B 293 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N ILE B 295 " --> pdb=" O GLU B 467 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N GLU B 467 " --> pdb=" O ILE B 295 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY B 297 " --> pdb=" O ILE B 465 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA B 456 " --> pdb=" O MET B 460 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ARG B 449 " --> pdb=" O ILE B 335 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N GLY B 373 " --> pdb=" O SER B 336 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ILE B 338 " --> pdb=" O GLY B 373 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 402 through 403 Processing sheet with id=AA3, first strand: chain 'A' and resid 486 through 490 removed outlier: 3.557A pdb=" N TYR A 564 " --> pdb=" O GLN A 573 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 658 through 662 removed outlier: 3.624A pdb=" N ILE A 732 " --> pdb=" O GLN A 736 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLN A 736 " --> pdb=" O ILE A 732 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N PHE A 743 " --> pdb=" O HIS A 752 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N HIS A 752 " --> pdb=" O PHE A 743 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N LEU A 706 " --> pdb=" O CYS A 880 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N CYS A 880 " --> pdb=" O LEU A 706 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N CYS A 710 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N GLU A 876 " --> pdb=" O CYS A 710 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N SER A 923 " --> pdb=" O ARG A 873 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ILE A 875 " --> pdb=" O LYS A 921 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LYS A 921 " --> pdb=" O ILE A 875 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ARG A 877 " --> pdb=" O LEU A 919 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU A 919 " --> pdb=" O ARG A 877 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N CYS A 879 " --> pdb=" O VAL A 917 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N VAL A 917 " --> pdb=" O CYS A 879 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N CYS A 916 " --> pdb=" O ASP A 910 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N ASP A 910 " --> pdb=" O CYS A 916 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N LYS A 918 " --> pdb=" O VAL A 908 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL A 908 " --> pdb=" O LYS A 918 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ASP A 920 " --> pdb=" O LEU A 906 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N LEU A 906 " --> pdb=" O ASP A 920 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N SER A 905 " --> pdb=" O GLY A 894 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N GLY A 894 " --> pdb=" O SER A 905 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N LEU A 907 " --> pdb=" O LEU A 892 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N LEU A 892 " --> pdb=" O LEU A 907 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LEU A 909 " --> pdb=" O VAL A 890 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N VAL A 890 " --> pdb=" O LEU A 909 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY A 823 " --> pdb=" O GLY A 820 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 673 through 675 Processing sheet with id=AA6, first strand: chain 'B' and resid 402 through 403 Processing sheet with id=AA7, first strand: chain 'B' and resid 485 through 490 Processing sheet with id=AA8, first strand: chain 'B' and resid 658 through 662 removed outlier: 3.656A pdb=" N ILE B 732 " --> pdb=" O GLN B 736 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLN B 736 " --> pdb=" O ILE B 732 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N PHE B 743 " --> pdb=" O HIS B 752 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N HIS B 752 " --> pdb=" O PHE B 743 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N LEU B 706 " --> pdb=" O CYS B 880 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N CYS B 880 " --> pdb=" O LEU B 706 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N CYS B 710 " --> pdb=" O GLU B 876 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N GLU B 876 " --> pdb=" O CYS B 710 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N PHE B 712 " --> pdb=" O ASN B 874 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N ASN B 874 " --> pdb=" O PHE B 712 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N ARG B 873 " --> pdb=" O LEU B 924 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N LEU B 924 " --> pdb=" O ARG B 873 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ILE B 875 " --> pdb=" O VAL B 922 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL B 922 " --> pdb=" O ILE B 875 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N ARG B 877 " --> pdb=" O ASP B 920 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL B 908 " --> pdb=" O CYS B 916 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N LYS B 918 " --> pdb=" O LEU B 906 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LEU B 906 " --> pdb=" O LYS B 918 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ASP B 920 " --> pdb=" O LEU B 904 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N LEU B 904 " --> pdb=" O ASP B 920 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N VAL B 922 " --> pdb=" O LEU B 902 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N LEU B 902 " --> pdb=" O VAL B 922 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N GLU B 901 " --> pdb=" O LEU B 897 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LEU B 897 " --> pdb=" O GLU B 901 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N SER B 903 " --> pdb=" O ILE B 895 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ILE B 895 " --> pdb=" O SER B 903 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY B 823 " --> pdb=" O GLY B 820 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 673 through 675 601 hydrogen bonds defined for protein. 1695 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: 5.29 Time building geometry restraints manager: 4.02 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: 4688 1.34 - 1.45: 2063 1.45 - 1.57: 7533 1.57 - 1.69: 0 1.69 - 1.81: 96 Bond restraints: 14380 Sorted by residual: bond pdb=" N LEU A 811 " pdb=" CA LEU A 811 " ideal model delta sigma weight residual 1.458 1.489 -0.031 9.00e-03 1.23e+04 1.15e+01 bond pdb=" N LEU B 811 " pdb=" CA LEU B 811 " ideal model delta sigma weight residual 1.458 1.489 -0.030 9.00e-03 1.23e+04 1.14e+01 bond pdb=" N ALA A 808 " pdb=" CA ALA A 808 " ideal model delta sigma weight residual 1.461 1.483 -0.022 9.20e-03 1.18e+04 5.83e+00 bond pdb=" N ALA B 808 " pdb=" CA ALA B 808 " ideal model delta sigma weight residual 1.462 1.484 -0.022 9.50e-03 1.11e+04 5.32e+00 bond pdb=" CA ALA B 808 " pdb=" CB ALA B 808 " ideal model delta sigma weight residual 1.534 1.510 0.025 1.18e-02 7.18e+03 4.34e+00 ... (remaining 14375 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 18941 1.28 - 2.57: 456 2.57 - 3.85: 103 3.85 - 5.14: 20 5.14 - 6.42: 2 Bond angle restraints: 19522 Sorted by residual: angle pdb=" N LEU A 232 " pdb=" CA LEU A 232 " pdb=" C LEU A 232 " ideal model delta sigma weight residual 108.55 114.03 -5.48 1.62e+00 3.81e-01 1.14e+01 angle pdb=" CA TYR B 810 " pdb=" C TYR B 810 " pdb=" O TYR B 810 " ideal model delta sigma weight residual 121.54 118.05 3.49 1.16e+00 7.43e-01 9.07e+00 angle pdb=" CA TYR A 810 " pdb=" C TYR A 810 " pdb=" O TYR A 810 " ideal model delta sigma weight residual 121.54 118.18 3.36 1.16e+00 7.43e-01 8.39e+00 angle pdb=" N LEU A 811 " pdb=" CA LEU A 811 " pdb=" C LEU A 811 " ideal model delta sigma weight residual 113.50 109.42 4.08 1.65e+00 3.67e-01 6.13e+00 angle pdb=" N THR B 253 " pdb=" CA THR B 253 " pdb=" C THR B 253 " ideal model delta sigma weight residual 114.56 111.48 3.08 1.27e+00 6.20e-01 5.88e+00 ... (remaining 19517 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 7892 17.81 - 35.63: 575 35.63 - 53.44: 74 53.44 - 71.25: 16 71.25 - 89.06: 15 Dihedral angle restraints: 8572 sinusoidal: 3368 harmonic: 5204 Sorted by residual: dihedral pdb=" CA LYS A 921 " pdb=" C LYS A 921 " pdb=" N VAL A 922 " pdb=" CA VAL A 922 " ideal model delta harmonic sigma weight residual 180.00 160.02 19.98 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA LYS A 640 " pdb=" C LYS A 640 " pdb=" N ASN A 641 " pdb=" CA ASN A 641 " ideal model delta harmonic sigma weight residual 180.00 160.71 19.29 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA TYR B 564 " pdb=" C TYR B 564 " pdb=" N ARG B 565 " pdb=" CA ARG B 565 " ideal model delta harmonic sigma weight residual 180.00 161.18 18.82 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 8569 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1403 0.034 - 0.067: 517 0.067 - 0.101: 144 0.101 - 0.134: 77 0.134 - 0.168: 7 Chirality restraints: 2148 Sorted by residual: chirality pdb=" CA LEU A 811 " pdb=" N LEU A 811 " pdb=" C LEU A 811 " pdb=" CB LEU A 811 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.01e-01 chirality pdb=" CA LEU B 811 " pdb=" N LEU B 811 " pdb=" C LEU B 811 " pdb=" CB LEU B 811 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.58e-01 chirality pdb=" CA ILE A 875 " pdb=" N ILE A 875 " pdb=" C ILE A 875 " pdb=" CB ILE A 875 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.20e-01 ... (remaining 2145 not shown) Planarity restraints: 2558 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 349 " 0.059 5.00e-02 4.00e+02 8.83e-02 1.25e+01 pdb=" N PRO B 350 " -0.153 5.00e-02 4.00e+02 pdb=" CA PRO B 350 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 350 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 331 " 0.041 5.00e-02 4.00e+02 6.23e-02 6.22e+00 pdb=" N PRO A 332 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 332 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 332 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 349 " -0.040 5.00e-02 4.00e+02 6.11e-02 5.98e+00 pdb=" N PRO A 350 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO A 350 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 350 " -0.034 5.00e-02 4.00e+02 ... (remaining 2555 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2160 2.75 - 3.29: 14386 3.29 - 3.83: 24814 3.83 - 4.36: 32238 4.36 - 4.90: 53440 Nonbonded interactions: 127038 Sorted by model distance: nonbonded pdb=" OE1 GLU B 167 " pdb=" OG SER B 631 " model vdw 2.213 3.040 nonbonded pdb=" O ASP A 115 " pdb=" OH TYR A 161 " model vdw 2.222 3.040 nonbonded pdb=" OH TYR A 337 " pdb=" NZ LYS A 393 " model vdw 2.235 3.120 nonbonded pdb=" O ASP B 115 " pdb=" OH TYR B 161 " model vdw 2.235 3.040 nonbonded pdb=" NZ LYS A 279 " pdb=" OD2 ASP A 287 " model vdw 2.248 3.120 ... (remaining 127033 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 30 through 442 or (resid 443 and (name N or name CA or nam \ e C or name O or name CB )) or resid 444 through 932)) 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: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 33.880 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 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 : 0.005 0.037 14380 Z= 0.319 Angle : 0.529 6.422 19522 Z= 0.289 Chirality : 0.042 0.168 2148 Planarity : 0.005 0.088 2558 Dihedral : 12.888 89.064 5244 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.21), residues: 1792 helix: 1.21 (0.23), residues: 542 sheet: -0.95 (0.30), residues: 310 loop : -0.28 (0.21), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 54 HIS 0.007 0.001 HIS B 491 PHE 0.013 0.002 PHE B 423 TYR 0.016 0.001 TYR A 260 ARG 0.009 0.001 ARG B 616 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 1.719 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 1.3963 time to fit residues: 358.9759 Evaluate side-chains 117 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 2.9990 chunk 136 optimal weight: 0.9980 chunk 75 optimal weight: 0.0980 chunk 46 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 141 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 163 optimal weight: 7.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 HIS A 248 ASN A 290 GLN A 357 ASN A 427 GLN A 498 GLN A 526 ASN A 837 HIS B 248 ASN B 290 GLN B 837 HIS ** B 843 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 914 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14380 Z= 0.237 Angle : 0.627 9.046 19522 Z= 0.319 Chirality : 0.043 0.217 2148 Planarity : 0.005 0.062 2558 Dihedral : 4.400 21.886 1970 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.65 % Allowed : 7.39 % Favored : 90.96 % 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: 0.25 (0.20), residues: 1792 helix: 1.36 (0.22), residues: 568 sheet: -0.61 (0.32), residues: 272 loop : -0.25 (0.21), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 54 HIS 0.005 0.001 HIS B 381 PHE 0.022 0.002 PHE B 755 TYR 0.016 0.001 TYR A 260 ARG 0.008 0.001 ARG A 677 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 1.337 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 5 residues processed: 149 average time/residue: 1.2849 time to fit residues: 213.2687 Evaluate side-chains 102 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 97 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 145 ARG Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 478 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 136 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 163 optimal weight: 20.0000 chunk 176 optimal weight: 4.9990 chunk 145 optimal weight: 1.9990 chunk 162 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 131 optimal weight: 7.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN A 798 GLN B 248 ASN B 483 GLN ** B 843 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 14380 Z= 0.421 Angle : 0.617 7.375 19522 Z= 0.314 Chirality : 0.045 0.195 2148 Planarity : 0.005 0.052 2558 Dihedral : 4.389 21.157 1970 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.98 % Allowed : 9.04 % Favored : 88.98 % 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: 0.25 (0.20), residues: 1792 helix: 1.33 (0.22), residues: 568 sheet: -0.46 (0.29), residues: 300 loop : -0.28 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 54 HIS 0.006 0.001 HIS B 381 PHE 0.020 0.002 PHE B 755 TYR 0.018 0.002 TYR B 857 ARG 0.008 0.001 ARG B 433 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 118 time to evaluate : 1.709 Fit side-chains outliers start: 30 outliers final: 12 residues processed: 137 average time/residue: 1.2717 time to fit residues: 195.3123 Evaluate side-chains 112 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 651 CYS Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 879 CYS Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 478 GLN Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 773 LEU Chi-restraints excluded: chain B residue 879 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 4.9990 chunk 123 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 78 optimal weight: 7.9990 chunk 109 optimal weight: 0.8980 chunk 164 optimal weight: 8.9990 chunk 173 optimal weight: 7.9990 chunk 85 optimal weight: 0.7980 chunk 155 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN A 313 ASN B 217 GLN B 248 ASN B 790 GLN B 843 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 14380 Z= 0.216 Angle : 0.556 9.747 19522 Z= 0.281 Chirality : 0.042 0.201 2148 Planarity : 0.004 0.048 2558 Dihedral : 4.214 18.704 1970 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.98 % Allowed : 9.77 % Favored : 88.25 % 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: 0.43 (0.20), residues: 1792 helix: 1.55 (0.22), residues: 568 sheet: -0.13 (0.30), residues: 286 loop : -0.31 (0.21), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 54 HIS 0.005 0.001 HIS B 381 PHE 0.023 0.002 PHE A 755 TYR 0.016 0.001 TYR B 857 ARG 0.009 0.001 ARG A 433 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 1.692 Fit side-chains REVERT: A 773 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7741 (mm) outliers start: 30 outliers final: 10 residues processed: 139 average time/residue: 1.2607 time to fit residues: 195.9150 Evaluate side-chains 115 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain A residue 651 CYS Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 879 CYS Chi-restraints excluded: chain B residue 181 MET Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 773 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 129 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 148 optimal weight: 0.7980 chunk 120 optimal weight: 0.0670 chunk 0 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 156 optimal weight: 0.2980 chunk 43 optimal weight: 3.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 GLN B 248 ASN ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 790 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2965 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: