Starting phenix.real_space_refine on Fri May 16 05:01:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oii_16892/05_2025/8oii_16892.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oii_16892/05_2025/8oii_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/cci-nas-00/data/ceres_data/8oii_16892/05_2025/8oii_16892.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oii_16892/05_2025/8oii_16892.map" model { file = "/net/cci-nas-00/data/ceres_data/8oii_16892/05_2025/8oii_16892.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oii_16892/05_2025/8oii_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-5687/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: 8.29, per 1000 atoms: 0.59 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: 3.41 Conformation dependent library (CDL) restraints added in 1.8 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: 1.92 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: 4.99 Time building geometry restraints manager: 4.00 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: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 33.830 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.060 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:12.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.950 ------------------------------------------------------------------------------- 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= 0.219 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 Details of bonding type rmsd hydrogen bonds : bond 0.21436 ( 601) hydrogen bonds : angle 8.87307 ( 1695) covalent geometry : bond 0.00487 (14380) covalent geometry : angle 0.52856 (19522) *********************** 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 : 1.477 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 1.3873 time to fit residues: 355.2862 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 : 1.424 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.087186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.068125 restraints weight = 24408.086| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.88 r_work: 0.2821 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 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= 0.161 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 Details of bonding type rmsd hydrogen bonds : bond 0.04485 ( 601) hydrogen bonds : angle 6.23556 ( 1695) covalent geometry : bond 0.00361 (14380) covalent geometry : angle 0.62726 (19522) *********************** 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 : 1.503 Fit side-chains revert: symmetry clash REVERT: A 444 GLN cc_start: 0.7912 (tt0) cc_final: 0.7466 (pt0) REVERT: A 771 GLN cc_start: 0.7846 (tm-30) cc_final: 0.7621 (tm-30) REVERT: A 798 GLN cc_start: 0.8243 (tm-30) cc_final: 0.7980 (tm-30) REVERT: A 876 GLU cc_start: 0.7834 (tt0) cc_final: 0.7250 (mt-10) REVERT: B 147 ASN cc_start: 0.8810 (m-40) cc_final: 0.8577 (m-40) REVERT: B 222 ASP cc_start: 0.8852 (m-30) cc_final: 0.8615 (t0) REVERT: B 616 ARG cc_start: 0.8735 (mmm-85) cc_final: 0.8232 (mmp80) REVERT: B 771 GLN cc_start: 0.7930 (tm-30) cc_final: 0.7713 (tm-30) REVERT: B 877 ARG cc_start: 0.7745 (ttm110) cc_final: 0.7518 (ttm110) outliers start: 25 outliers final: 5 residues processed: 149 average time/residue: 1.1872 time to fit residues: 196.3231 Evaluate side-chains 110 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 105 time to evaluate : 2.710 ------------------------------------------------------------------------------- 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 96 optimal weight: 4.9990 chunk 123 optimal weight: 0.0030 chunk 27 optimal weight: 7.9990 chunk 71 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 95 optimal weight: 0.0370 chunk 93 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 111 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 overall best weight: 0.5670 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN B 248 ASN B 483 GLN B 498 GLN B 843 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.096753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.076336 restraints weight = 25535.577| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.90 r_work: 0.2829 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 14380 Z= 0.127 Angle : 0.544 7.389 19522 Z= 0.276 Chirality : 0.042 0.181 2148 Planarity : 0.004 0.052 2558 Dihedral : 4.202 19.486 1970 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.72 % Allowed : 8.84 % Favored : 89.44 % 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: 0.38 (0.20), residues: 1792 helix: 1.48 (0.22), residues: 568 sheet: -0.41 (0.31), residues: 276 loop : -0.23 (0.21), residues: 948 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 0.021 0.002 PHE B 755 TYR 0.015 0.001 TYR B 857 ARG 0.009 0.001 ARG A 433 Details of bonding type rmsd hydrogen bonds : bond 0.03836 ( 601) hydrogen bonds : angle 5.73663 ( 1695) covalent geometry : bond 0.00295 (14380) covalent geometry : angle 0.54409 (19522) *********************** 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 156 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 1.631 Fit side-chains REVERT: A 222 ASP cc_start: 0.8901 (OUTLIER) cc_final: 0.8574 (m-30) REVERT: A 444 GLN cc_start: 0.8128 (tt0) cc_final: 0.7780 (pt0) REVERT: A 771 GLN cc_start: 0.7981 (tm-30) cc_final: 0.7674 (tm-30) REVERT: A 798 GLN cc_start: 0.8205 (tm-30) cc_final: 0.7942 (tm-30) REVERT: A 876 GLU cc_start: 0.7820 (tt0) cc_final: 0.7266 (mt-10) REVERT: B 147 ASN cc_start: 0.8870 (m-40) cc_final: 0.8608 (m-40) REVERT: B 222 ASP cc_start: 0.8777 (m-30) cc_final: 0.8572 (t0) REVERT: B 280 ARG cc_start: 0.8379 (mtp180) cc_final: 0.8106 (mtp-110) REVERT: B 540 GLN cc_start: 0.8491 (mp10) cc_final: 0.8268 (mp10) REVERT: B 555 GLN cc_start: 0.8814 (mp10) cc_final: 0.8261 (mp10) REVERT: B 594 ASP cc_start: 0.8639 (m-30) cc_final: 0.8188 (m-30) REVERT: B 877 ARG cc_start: 0.7860 (ttm110) cc_final: 0.7448 (mtp85) outliers start: 26 outliers final: 12 residues processed: 147 average time/residue: 1.1531 time to fit residues: 187.7532 Evaluate side-chains 128 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 424 VAL 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 40 LEU Chi-restraints excluded: chain B residue 175 MET 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 651 CYS Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 773 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 116 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 132 optimal weight: 7.9990 chunk 78 optimal weight: 10.0000 chunk 175 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 166 optimal weight: 5.9990 chunk 168 optimal weight: 5.9990 chunk 129 optimal weight: 0.0000 chunk 161 optimal weight: 4.9990 overall best weight: 2.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN B 248 ASN B 414 GLN ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 790 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.082352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.062014 restraints weight = 24561.606| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 2.80 r_work: 0.2746 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2589 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.055 14380 Z= 0.367 Angle : 0.662 9.448 19522 Z= 0.334 Chirality : 0.046 0.218 2148 Planarity : 0.005 0.048 2558 Dihedral : 4.443 20.884 1970 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.57 % Allowed : 9.04 % Favored : 88.38 % 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: 0.26 (0.20), residues: 1792 helix: 1.35 (0.22), residues: 568 sheet: -0.44 (0.29), residues: 304 loop : -0.28 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 54 HIS 0.007 0.001 HIS A 116 PHE 0.025 0.002 PHE B 755 TYR 0.016 0.002 TYR B 715 ARG 0.010 0.001 ARG B 433 Details of bonding type rmsd hydrogen bonds : bond 0.04327 ( 601) hydrogen bonds : angle 5.78528 ( 1695) covalent geometry : bond 0.00848 (14380) covalent geometry : angle 0.66217 (19522) *********************** 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 153 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 114 time to evaluate : 1.461 Fit side-chains REVERT: A 771 GLN cc_start: 0.8042 (tm-30) cc_final: 0.7594 (tm-30) REVERT: A 798 GLN cc_start: 0.8390 (tm-30) cc_final: 0.8096 (tm-30) REVERT: A 876 GLU cc_start: 0.8210 (tt0) cc_final: 0.7721 (mt-10) REVERT: B 147 ASN cc_start: 0.8943 (m-40) cc_final: 0.8691 (m-40) REVERT: B 175 MET cc_start: 0.9207 (OUTLIER) cc_final: 0.8980 (mtm) REVERT: B 346 LYS cc_start: 0.9066 (ttpp) cc_final: 0.8802 (ttmm) REVERT: B 482 ASP cc_start: 0.8708 (p0) cc_final: 0.8434 (p0) REVERT: B 555 GLN cc_start: 0.8913 (mp10) cc_final: 0.8408 (mp10) REVERT: B 877 ARG cc_start: 0.8397 (ttm110) cc_final: 0.8017 (ttm110) outliers start: 39 outliers final: 11 residues processed: 138 average time/residue: 1.2604 time to fit residues: 192.3388 Evaluate side-chains 113 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 879 CYS Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 175 MET 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 773 LEU Chi-restraints excluded: chain B residue 879 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 21 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 chunk 146 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 154 optimal weight: 0.8980 chunk 175 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 136 optimal weight: 0.9990 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 248 ASN B 217 GLN B 248 ASN ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 411 GLN B 790 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.084835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.065135 restraints weight = 24533.369| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 2.77 r_work: 0.2801 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14380 Z= 0.150 Angle : 0.552 9.904 19522 Z= 0.279 Chirality : 0.042 0.216 2148 Planarity : 0.004 0.047 2558 Dihedral : 4.242 18.696 1970 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.85 % Allowed : 10.69 % Favored : 87.46 % 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: 0.40 (0.20), residues: 1792 helix: 1.53 (0.22), residues: 568 sheet: -0.17 (0.30), residues: 286 loop : -0.32 (0.21), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 54 HIS 0.005 0.001 HIS B 381 PHE 0.026 0.002 PHE B 755 TYR 0.023 0.001 TYR A 810 ARG 0.010 0.001 ARG A 433 Details of bonding type rmsd hydrogen bonds : bond 0.03503 ( 601) hydrogen bonds : angle 5.51313 ( 1695) covalent geometry : bond 0.00348 (14380) covalent geometry : angle 0.55173 (19522) *********************** REFINEMENT MACRO_CYCLE 5 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 143 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 115 time to evaluate : 1.588 Fit side-chains REVERT: A 420 ASP cc_start: 0.8812 (t0) cc_final: 0.8522 (t0) REVERT: A 771 GLN cc_start: 0.8175 (tm-30) cc_final: 0.7754 (tm-30) REVERT: A 773 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7554 (mm) REVERT: A 798 GLN cc_start: 0.8394 (tm-30) cc_final: 0.8094 (tm-30) REVERT: A 876 GLU cc_start: 0.8071 (tt0) cc_final: 0.7595 (mt-10) REVERT: B 147 ASN cc_start: 0.8939 (m-40) cc_final: 0.8692 (m-40) REVERT: B 175 MET cc_start: 0.9117 (OUTLIER) cc_final: 0.8875 (mtp) REVERT: B 280 ARG cc_start: 0.8734 (mtp180) cc_final: 0.8471 (mtp-110) REVERT: B 346 LYS cc_start: 0.9086 (ttpp) cc_final: 0.8813 (ttmm) REVERT: B 482 ASP cc_start: 0.8671 (p0) cc_final: 0.8329 (p0) REVERT: B 555 GLN cc_start: 0.8907 (mp10) cc_final: 0.8393 (mp10) REVERT: B 594 ASP cc_start: 0.8795 (m-30) cc_final: 0.8411 (m-30) REVERT: B 792 SER cc_start: 0.8856 (t) cc_final: 0.8637 (p) REVERT: B 877 ARG cc_start: 0.8277 (ttm110) cc_final: 0.7908 (mtp85) outliers start: 28 outliers final: 11 residues processed: 129 average time/residue: 1.2612 time to fit residues: 179.8237 Evaluate side-chains 121 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 616 ARG Chi-restraints excluded: chain A residue 651 CYS Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 879 CYS Chi-restraints excluded: chain B residue 175 MET 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 742 ASP Chi-restraints excluded: chain B residue 773 LEU Chi-restraints excluded: chain B residue 879 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 62 optimal weight: 0.7980 chunk 102 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 129 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 108 optimal weight: 0.5980 chunk 151 optimal weight: 3.9990 chunk 29 optimal weight: 0.0370 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN B 248 ASN ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 790 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.085829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.066317 restraints weight = 24689.633| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 2.78 r_work: 0.2846 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14380 Z= 0.125 Angle : 0.542 10.616 19522 Z= 0.272 Chirality : 0.042 0.219 2148 Planarity : 0.004 0.044 2558 Dihedral : 4.120 17.582 1970 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.91 % Allowed : 11.02 % Favored : 87.06 % 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: 0.49 (0.20), residues: 1792 helix: 1.73 (0.22), residues: 556 sheet: -0.36 (0.28), residues: 314 loop : -0.24 (0.21), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 54 HIS 0.004 0.001 HIS A 116 PHE 0.027 0.002 PHE B 755 TYR 0.013 0.001 TYR A 857 ARG 0.010 0.001 ARG A 433 Details of bonding type rmsd hydrogen bonds : bond 0.03316 ( 601) hydrogen bonds : angle 5.38515 ( 1695) covalent geometry : bond 0.00289 (14380) covalent geometry : angle 0.54169 (19522) *********************** REFINEMENT MACRO_CYCLE 6 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 152 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 123 time to evaluate : 1.594 Fit side-chains REVERT: A 420 ASP cc_start: 0.8789 (t0) cc_final: 0.8543 (t0) REVERT: A 771 GLN cc_start: 0.8096 (tm-30) cc_final: 0.7705 (tm-30) REVERT: A 773 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7682 (mm) REVERT: A 798 GLN cc_start: 0.8400 (tm-30) cc_final: 0.8086 (tm-30) REVERT: A 876 GLU cc_start: 0.7972 (tt0) cc_final: 0.7650 (mt-10) REVERT: B 147 ASN cc_start: 0.8903 (m-40) cc_final: 0.8631 (m-40) REVERT: B 175 MET cc_start: 0.9088 (OUTLIER) cc_final: 0.8882 (ttp) REVERT: B 346 LYS cc_start: 0.9091 (ttpp) cc_final: 0.8818 (ttmm) REVERT: B 482 ASP cc_start: 0.8626 (p0) cc_final: 0.8325 (p0) REVERT: B 555 GLN cc_start: 0.8901 (mp10) cc_final: 0.8367 (mp10) REVERT: B 594 ASP cc_start: 0.8789 (m-30) cc_final: 0.8368 (m-30) REVERT: B 790 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.8651 (mt0) REVERT: B 792 SER cc_start: 0.8823 (t) cc_final: 0.8599 (p) REVERT: B 813 HIS cc_start: 0.7880 (t70) cc_final: 0.7491 (t-90) REVERT: B 877 ARG cc_start: 0.8246 (ttm110) cc_final: 0.7898 (ttm110) outliers start: 29 outliers final: 14 residues processed: 141 average time/residue: 1.1999 time to fit residues: 187.6683 Evaluate side-chains 132 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 248 ASN 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 742 ASP Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 879 CYS Chi-restraints excluded: chain A residue 903 SER Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 235 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 742 ASP Chi-restraints excluded: chain B residue 773 LEU Chi-restraints excluded: chain B residue 790 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 10 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 147 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 110 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN B 248 ASN ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.086527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.066416 restraints weight = 24459.202| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.83 r_work: 0.2837 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 14380 Z= 0.148 Angle : 0.557 10.913 19522 Z= 0.279 Chirality : 0.042 0.224 2148 Planarity : 0.004 0.053 2558 Dihedral : 4.097 19.726 1970 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.78 % Allowed : 11.95 % Favored : 86.27 % 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: 1792 helix: 1.72 (0.22), residues: 564 sheet: -0.32 (0.28), residues: 314 loop : -0.22 (0.21), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 54 HIS 0.004 0.001 HIS B 381 PHE 0.028 0.002 PHE B 755 TYR 0.014 0.001 TYR A 857 ARG 0.012 0.001 ARG A 433 Details of bonding type rmsd hydrogen bonds : bond 0.03333 ( 601) hydrogen bonds : angle 5.33396 ( 1695) covalent geometry : bond 0.00348 (14380) covalent geometry : angle 0.55663 (19522) *********************** REFINEMENT MACRO_CYCLE 7 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 140 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 1.700 Fit side-chains REVERT: A 420 ASP cc_start: 0.8770 (t0) cc_final: 0.8519 (t0) REVERT: A 637 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8624 (mp) REVERT: A 771 GLN cc_start: 0.8165 (tm-30) cc_final: 0.7809 (tm-30) REVERT: A 773 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7065 (mm) REVERT: A 798 GLN cc_start: 0.8296 (tm-30) cc_final: 0.7976 (tm-30) REVERT: A 876 GLU cc_start: 0.7828 (tt0) cc_final: 0.7423 (mt-10) REVERT: B 147 ASN cc_start: 0.8834 (m-40) cc_final: 0.8560 (m-40) REVERT: B 175 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.8782 (ttp) REVERT: B 346 LYS cc_start: 0.9057 (ttpp) cc_final: 0.8786 (ttmm) REVERT: B 460 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.7704 (mtp) REVERT: B 555 GLN cc_start: 0.8826 (mp10) cc_final: 0.8314 (mp10) REVERT: B 594 ASP cc_start: 0.8716 (m-30) cc_final: 0.8350 (m-30) REVERT: B 792 SER cc_start: 0.8772 (t) cc_final: 0.8553 (p) REVERT: B 813 HIS cc_start: 0.7734 (t70) cc_final: 0.7343 (t-90) REVERT: B 877 ARG cc_start: 0.8020 (ttm110) cc_final: 0.7652 (ttm110) outliers start: 27 outliers final: 14 residues processed: 129 average time/residue: 1.2473 time to fit residues: 178.3788 Evaluate side-chains 129 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 651 CYS Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 879 CYS Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 248 ASN Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 460 MET Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 773 LEU Chi-restraints excluded: chain B residue 879 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 109 optimal weight: 0.0870 chunk 79 optimal weight: 3.9990 chunk 173 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 116 optimal weight: 0.0870 chunk 73 optimal weight: 0.0030 chunk 7 optimal weight: 2.9990 chunk 178 optimal weight: 3.9990 overall best weight: 0.8348 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 248 ASN ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 596 GLN ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.085711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.066273 restraints weight = 24490.807| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.76 r_work: 0.2850 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 14380 Z= 0.144 Angle : 0.563 11.182 19522 Z= 0.281 Chirality : 0.043 0.296 2148 Planarity : 0.004 0.058 2558 Dihedral : 4.087 19.510 1970 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.45 % Allowed : 12.08 % Favored : 86.47 % 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: 0.55 (0.20), residues: 1792 helix: 1.74 (0.22), residues: 564 sheet: -0.26 (0.28), residues: 314 loop : -0.21 (0.21), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 54 HIS 0.004 0.001 HIS B 381 PHE 0.028 0.002 PHE B 755 TYR 0.014 0.001 TYR A 857 ARG 0.013 0.001 ARG B 912 Details of bonding type rmsd hydrogen bonds : bond 0.03305 ( 601) hydrogen bonds : angle 5.30367 ( 1695) covalent geometry : bond 0.00337 (14380) covalent geometry : angle 0.56271 (19522) *********************** REFINEMENT MACRO_CYCLE 8 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 138 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 1.868 Fit side-chains REVERT: A 420 ASP cc_start: 0.8823 (t0) cc_final: 0.8593 (t0) REVERT: A 680 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.6828 (mmp-170) REVERT: A 771 GLN cc_start: 0.8181 (tm-30) cc_final: 0.7923 (tm-30) REVERT: A 773 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7083 (mm) REVERT: A 798 GLN cc_start: 0.8404 (tm-30) cc_final: 0.8080 (tm-30) REVERT: A 876 GLU cc_start: 0.8033 (tt0) cc_final: 0.7611 (mt-10) REVERT: B 147 ASN cc_start: 0.8901 (m-40) cc_final: 0.8636 (m-40) REVERT: B 346 LYS cc_start: 0.9075 (ttpp) cc_final: 0.8790 (ttmm) REVERT: B 555 GLN cc_start: 0.8920 (mp10) cc_final: 0.8395 (mp10) REVERT: B 594 ASP cc_start: 0.8799 (m-30) cc_final: 0.8381 (m-30) REVERT: B 773 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7148 (mm) REVERT: B 792 SER cc_start: 0.8824 (t) cc_final: 0.8596 (p) REVERT: B 813 HIS cc_start: 0.7816 (t70) cc_final: 0.7428 (t-90) REVERT: B 877 ARG cc_start: 0.8214 (ttm110) cc_final: 0.7851 (ttm110) REVERT: B 901 GLU cc_start: 0.7007 (tp30) cc_final: 0.6803 (tp30) outliers start: 22 outliers final: 11 residues processed: 130 average time/residue: 1.2550 time to fit residues: 181.5131 Evaluate side-chains 124 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 MET 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 680 ARG Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 879 CYS Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 773 LEU Chi-restraints excluded: chain B residue 879 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 177 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 37 optimal weight: 0.0970 chunk 157 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 170 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN A 357 ASN ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.085951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.065847 restraints weight = 24452.952| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.83 r_work: 0.2802 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 14380 Z= 0.172 Angle : 0.575 11.412 19522 Z= 0.288 Chirality : 0.043 0.264 2148 Planarity : 0.004 0.061 2558 Dihedral : 4.105 19.433 1970 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.12 % Allowed : 12.67 % Favored : 86.20 % 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: 0.56 (0.20), residues: 1792 helix: 1.69 (0.22), residues: 564 sheet: -0.08 (0.29), residues: 302 loop : -0.23 (0.21), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 54 HIS 0.004 0.001 HIS B 381 PHE 0.029 0.002 PHE B 755 TYR 0.015 0.001 TYR A 857 ARG 0.015 0.001 ARG B 433 Details of bonding type rmsd hydrogen bonds : bond 0.03365 ( 601) hydrogen bonds : angle 5.32240 ( 1695) covalent geometry : bond 0.00404 (14380) covalent geometry : angle 0.57523 (19522) *********************** REFINEMENT MACRO_CYCLE 9 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 130 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 1.488 Fit side-chains REVERT: A 255 GLU cc_start: 0.9059 (mm-30) cc_final: 0.8688 (mm-30) REVERT: A 637 LEU cc_start: 0.8664 (mt) cc_final: 0.8425 (mp) REVERT: A 680 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.6776 (mmp-170) REVERT: A 771 GLN cc_start: 0.8255 (tm-30) cc_final: 0.7998 (tm-30) REVERT: A 773 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.7014 (mm) REVERT: A 798 GLN cc_start: 0.8311 (tm-30) cc_final: 0.7979 (tm-30) REVERT: A 876 GLU cc_start: 0.7863 (tt0) cc_final: 0.7536 (mt-10) REVERT: B 147 ASN cc_start: 0.8848 (m-40) cc_final: 0.8591 (m-40) REVERT: B 346 LYS cc_start: 0.9063 (ttpp) cc_final: 0.8786 (ttmm) REVERT: B 555 GLN cc_start: 0.8806 (mp10) cc_final: 0.8303 (mp10) REVERT: B 594 ASP cc_start: 0.8692 (m-30) cc_final: 0.8296 (m-30) REVERT: B 792 SER cc_start: 0.8824 (t) cc_final: 0.8599 (p) REVERT: B 813 HIS cc_start: 0.7745 (t70) cc_final: 0.7373 (t-90) REVERT: B 877 ARG cc_start: 0.8000 (ttm110) cc_final: 0.7655 (mtp85) outliers start: 17 outliers final: 11 residues processed: 125 average time/residue: 1.1977 time to fit residues: 165.7327 Evaluate side-chains 122 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 651 CYS Chi-restraints excluded: chain A residue 680 ARG Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 879 CYS Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 773 LEU Chi-restraints excluded: chain B residue 879 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 120 optimal weight: 2.9990 chunk 117 optimal weight: 10.0000 chunk 159 optimal weight: 3.9990 chunk 125 optimal weight: 0.9980 chunk 134 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 135 optimal weight: 0.6980 chunk 78 optimal weight: 7.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.086735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.066570 restraints weight = 24510.563| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.84 r_work: 0.2838 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 14380 Z= 0.152 Angle : 0.575 8.879 19522 Z= 0.288 Chirality : 0.043 0.244 2148 Planarity : 0.005 0.094 2558 Dihedral : 4.096 19.119 1970 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.06 % Allowed : 12.81 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.20), residues: 1792 helix: 1.71 (0.22), residues: 562 sheet: -0.18 (0.29), residues: 312 loop : -0.19 (0.21), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 54 HIS 0.004 0.001 HIS B 381 PHE 0.028 0.002 PHE A 755 TYR 0.013 0.001 TYR A 857 ARG 0.019 0.001 ARG B 912 Details of bonding type rmsd hydrogen bonds : bond 0.03263 ( 601) hydrogen bonds : angle 5.30752 ( 1695) covalent geometry : bond 0.00357 (14380) covalent geometry : angle 0.57469 (19522) ********************** REFINEMENT MACRO_CYCLE 10 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 130 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 1.498 Fit side-chains REVERT: A 255 GLU cc_start: 0.9055 (mm-30) cc_final: 0.8731 (mm-30) REVERT: A 637 LEU cc_start: 0.8624 (mt) cc_final: 0.8377 (mp) REVERT: A 680 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.6668 (mmp-170) REVERT: A 771 GLN cc_start: 0.8243 (tm-30) cc_final: 0.7938 (tm-30) REVERT: A 773 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.6993 (mm) REVERT: A 798 GLN cc_start: 0.8310 (tm-30) cc_final: 0.7973 (tm-30) REVERT: A 876 GLU cc_start: 0.7804 (tt0) cc_final: 0.7445 (mt-10) REVERT: B 147 ASN cc_start: 0.8842 (m-40) cc_final: 0.8565 (m-40) REVERT: B 346 LYS cc_start: 0.9034 (ttpp) cc_final: 0.8746 (ttmm) REVERT: B 555 GLN cc_start: 0.8808 (mp10) cc_final: 0.8297 (mp10) REVERT: B 594 ASP cc_start: 0.8673 (m-30) cc_final: 0.8284 (m-30) REVERT: B 773 LEU cc_start: 0.7413 (OUTLIER) cc_final: 0.6882 (mm) REVERT: B 792 SER cc_start: 0.8797 (t) cc_final: 0.8561 (p) REVERT: B 813 HIS cc_start: 0.7732 (t70) cc_final: 0.7390 (t-90) REVERT: B 816 GLU cc_start: 0.8288 (mp0) cc_final: 0.8060 (mp0) REVERT: B 877 ARG cc_start: 0.7988 (ttm110) cc_final: 0.7646 (mtp85) REVERT: B 914 GLN cc_start: 0.8436 (mt0) cc_final: 0.8153 (mt0) outliers start: 16 outliers final: 11 residues processed: 126 average time/residue: 1.1953 time to fit residues: 167.1118 Evaluate side-chains 125 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 651 CYS Chi-restraints excluded: chain A residue 680 ARG Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 879 CYS Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 773 LEU Chi-restraints excluded: chain B residue 879 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 149 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 35 optimal weight: 0.2980 chunk 44 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 74 optimal weight: 7.9990 chunk 73 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 63 optimal weight: 0.0870 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.086413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.067042 restraints weight = 24667.596| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 2.77 r_work: 0.2861 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 14380 Z= 0.127 Angle : 0.566 11.989 19522 Z= 0.283 Chirality : 0.042 0.236 2148 Planarity : 0.005 0.070 2558 Dihedral : 4.073 18.850 1970 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.79 % Allowed : 13.27 % Favored : 85.94 % 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: 0.60 (0.20), residues: 1792 helix: 1.74 (0.22), residues: 562 sheet: -0.16 (0.29), residues: 312 loop : -0.18 (0.21), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 54 HIS 0.004 0.001 HIS B 381 PHE 0.026 0.001 PHE A 755 TYR 0.010 0.001 TYR B 810 ARG 0.015 0.001 ARG B 912 Details of bonding type rmsd hydrogen bonds : bond 0.03165 ( 601) hydrogen bonds : angle 5.28451 ( 1695) covalent geometry : bond 0.00296 (14380) covalent geometry : angle 0.56644 (19522) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7457.49 seconds wall clock time: 130 minutes 8.85 seconds (7808.85 seconds total)