Starting phenix.real_space_refine on Thu Sep 18 04:31:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oii_16892/09_2025/8oii_16892.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oii_16892/09_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_16892/09_2025/8oii_16892.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oii_16892/09_2025/8oii_16892.map" model { file = "/net/cci-nas-00/data/ceres_data/8oii_16892/09_2025/8oii_16892.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oii_16892/09_2025/8oii_16892.cif" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.89, per 1000 atoms: 0.28 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: 1.33 Conformation dependent library (CDL) restraints added in 782.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.58 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: 2.67 Time building geometry restraints manager: 1.83 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: 1.810 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: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.540 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.230 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.009 0.001 ARG B 616 TYR 0.016 0.001 TYR A 260 PHE 0.013 0.002 PHE B 423 TRP 0.006 0.001 TRP A 54 HIS 0.007 0.001 HIS B 491 Details of bonding type rmsd covalent geometry : bond 0.00487 (14380) covalent geometry : angle 0.52856 (19522) hydrogen bonds : bond 0.21436 ( 601) hydrogen bonds : angle 8.87307 ( 1695) *********************** 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 : 0.419 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 0.7557 time to fit residues: 192.3592 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 : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.0770 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 0.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- 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 798 GLN 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.087329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.068269 restraints weight = 24454.701| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.88 r_work: 0.2822 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14380 Z= 0.160 Angle : 0.619 8.104 19522 Z= 0.317 Chirality : 0.043 0.211 2148 Planarity : 0.005 0.063 2558 Dihedral : 4.381 21.835 1970 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.58 % Allowed : 7.59 % Favored : 90.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.20), residues: 1792 helix: 1.34 (0.22), residues: 568 sheet: -0.64 (0.32), residues: 272 loop : -0.25 (0.21), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 877 TYR 0.016 0.001 TYR B 857 PHE 0.021 0.002 PHE A 741 TRP 0.012 0.001 TRP A 54 HIS 0.005 0.001 HIS B 381 Details of bonding type rmsd covalent geometry : bond 0.00358 (14380) covalent geometry : angle 0.61932 (19522) hydrogen bonds : bond 0.04788 ( 601) hydrogen bonds : angle 6.35045 ( 1695) *********************** 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 158 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 0.363 Fit side-chains REVERT: A 444 GLN cc_start: 0.7878 (tt0) cc_final: 0.7436 (pt0) REVERT: A 771 GLN cc_start: 0.7867 (tm-30) cc_final: 0.7643 (tm-30) REVERT: A 798 GLN cc_start: 0.8155 (tm130) cc_final: 0.7885 (tp-100) REVERT: A 876 GLU cc_start: 0.7844 (tt0) cc_final: 0.7254 (mt-10) REVERT: B 147 ASN cc_start: 0.8783 (m-40) cc_final: 0.8556 (m-40) REVERT: B 222 ASP cc_start: 0.8858 (m-30) cc_final: 0.8620 (t0) REVERT: B 464 MET cc_start: 0.8963 (mtp) cc_final: 0.8755 (mtm) REVERT: B 540 GLN cc_start: 0.8403 (mp10) cc_final: 0.8195 (mp10) REVERT: B 616 ARG cc_start: 0.8740 (mmm-85) cc_final: 0.8235 (mmp80) REVERT: B 771 GLN cc_start: 0.7834 (tm-30) cc_final: 0.7614 (tm-30) REVERT: B 877 ARG cc_start: 0.7748 (ttm110) cc_final: 0.7547 (ttm110) outliers start: 24 outliers final: 6 residues processed: 148 average time/residue: 0.5737 time to fit residues: 93.4973 Evaluate side-chains 112 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 106 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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 B residue 40 LEU 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 54 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 146 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 137 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 118 optimal weight: 7.9990 chunk 110 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 53 optimal weight: 0.2980 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 A 813 HIS B 248 ASN B 483 GLN B 498 GLN ** B 843 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.095281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.074649 restraints weight = 25976.699| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.91 r_work: 0.2780 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 14380 Z= 0.164 Angle : 0.564 8.611 19522 Z= 0.286 Chirality : 0.042 0.186 2148 Planarity : 0.005 0.052 2558 Dihedral : 4.264 20.222 1970 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.72 % Allowed : 8.91 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.20), residues: 1792 helix: 1.41 (0.22), residues: 568 sheet: -0.50 (0.31), residues: 276 loop : -0.26 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 433 TYR 0.016 0.001 TYR B 857 PHE 0.022 0.002 PHE B 755 TRP 0.012 0.001 TRP A 54 HIS 0.005 0.001 HIS B 381 Details of bonding type rmsd covalent geometry : bond 0.00382 (14380) covalent geometry : angle 0.56409 (19522) hydrogen bonds : bond 0.03951 ( 601) hydrogen bonds : angle 5.81639 ( 1695) *********************** 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 149 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 123 time to evaluate : 0.570 Fit side-chains revert: symmetry clash REVERT: A 420 ASP cc_start: 0.8569 (t0) cc_final: 0.8338 (OUTLIER) REVERT: A 444 GLN cc_start: 0.8123 (tt0) cc_final: 0.7681 (pt0) REVERT: A 771 GLN cc_start: 0.7930 (tm-30) cc_final: 0.7634 (tm-30) REVERT: A 798 GLN cc_start: 0.8196 (tm-30) cc_final: 0.7928 (tm-30) REVERT: A 813 HIS cc_start: 0.7899 (t70) cc_final: 0.7695 (t-90) REVERT: A 876 GLU cc_start: 0.7847 (tt0) cc_final: 0.7288 (mt-10) REVERT: B 147 ASN cc_start: 0.8838 (m-40) cc_final: 0.8572 (m-40) REVERT: B 555 GLN cc_start: 0.8829 (mp10) cc_final: 0.8286 (mp10) REVERT: B 594 ASP cc_start: 0.8637 (m-30) cc_final: 0.8197 (m-30) REVERT: B 616 ARG cc_start: 0.8813 (mmm-85) cc_final: 0.8499 (mtp85) REVERT: B 877 ARG cc_start: 0.7881 (ttm110) cc_final: 0.7607 (ttm110) outliers start: 26 outliers final: 13 residues processed: 141 average time/residue: 0.6103 time to fit residues: 94.9620 Evaluate side-chains 123 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.668 ------------------------------------------------------------------------------- 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 651 CYS Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 879 CYS 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 Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 651 CYS 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 174 optimal weight: 0.0980 chunk 176 optimal weight: 6.9990 chunk 17 optimal weight: 0.9990 chunk 132 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 178 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.0188 ------------------------------------------------------------------------------- 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 248 ASN B 790 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 = 0.3347 r_free = 0.3347 target = 0.094489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.073724 restraints weight = 25937.733| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.90 r_work: 0.2782 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14380 Z= 0.157 Angle : 0.545 10.706 19522 Z= 0.275 Chirality : 0.042 0.185 2148 Planarity : 0.004 0.048 2558 Dihedral : 4.160 18.853 1970 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.38 % Allowed : 9.04 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.20), residues: 1792 helix: 1.56 (0.22), residues: 568 sheet: -0.20 (0.30), residues: 296 loop : -0.27 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 433 TYR 0.013 0.001 TYR A 857 PHE 0.022 0.002 PHE A 755 TRP 0.012 0.001 TRP B 54 HIS 0.005 0.001 HIS B 381 Details of bonding type rmsd covalent geometry : bond 0.00361 (14380) covalent geometry : angle 0.54515 (19522) hydrogen bonds : bond 0.03581 ( 601) hydrogen bonds : angle 5.50157 ( 1695) *********************** 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 163 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 127 time to evaluate : 0.574 Fit side-chains REVERT: A 420 ASP cc_start: 0.8669 (t0) cc_final: 0.8360 (t0) REVERT: A 444 GLN cc_start: 0.8236 (tt0) cc_final: 0.7795 (pt0) REVERT: A 771 GLN cc_start: 0.8071 (tm-30) cc_final: 0.7808 (tm-30) REVERT: A 798 GLN cc_start: 0.8237 (tm-30) cc_final: 0.7954 (tm-30) REVERT: A 813 HIS cc_start: 0.7877 (t70) cc_final: 0.7677 (t-90) REVERT: A 876 GLU cc_start: 0.7754 (tt0) cc_final: 0.7315 (mt-10) REVERT: B 147 ASN cc_start: 0.8888 (m-40) cc_final: 0.8609 (m-40) REVERT: B 280 ARG cc_start: 0.8377 (mtp180) cc_final: 0.8144 (mtp-110) REVERT: B 346 LYS cc_start: 0.9023 (ttpp) cc_final: 0.8749 (ttmm) REVERT: B 460 MET cc_start: 0.7885 (OUTLIER) cc_final: 0.7684 (mmt) REVERT: B 555 GLN cc_start: 0.8832 (mp10) cc_final: 0.8285 (mp10) REVERT: B 594 ASP cc_start: 0.8659 (m-30) cc_final: 0.8206 (m-30) REVERT: B 616 ARG cc_start: 0.8831 (mmm-85) cc_final: 0.8510 (mtp85) REVERT: B 790 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.8628 (mt0) REVERT: B 792 SER cc_start: 0.8708 (t) cc_final: 0.8469 (p) REVERT: B 877 ARG cc_start: 0.7982 (ttm110) cc_final: 0.7591 (mtp85) outliers start: 36 outliers final: 14 residues processed: 147 average time/residue: 0.6410 time to fit residues: 103.6919 Evaluate side-chains 131 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.618 ------------------------------------------------------------------------------- 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 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 A residue 909 LEU 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 651 CYS 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 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 134 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 129 optimal weight: 0.4980 chunk 175 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 118 optimal weight: 0.9990 chunk 111 optimal weight: 0.5980 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 248 ASN ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 ASN ** B 641 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 = 0.3274 r_free = 0.3274 target = 0.088101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.067908 restraints weight = 24310.623| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.83 r_work: 0.2864 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14380 Z= 0.134 Angle : 0.532 9.831 19522 Z= 0.267 Chirality : 0.042 0.222 2148 Planarity : 0.004 0.044 2558 Dihedral : 4.083 17.980 1970 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.98 % Allowed : 10.63 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.20), residues: 1792 helix: 1.70 (0.22), residues: 568 sheet: -0.19 (0.29), residues: 304 loop : -0.25 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 912 TYR 0.025 0.001 TYR A 810 PHE 0.024 0.002 PHE A 755 TRP 0.012 0.001 TRP B 54 HIS 0.004 0.001 HIS A 116 Details of bonding type rmsd covalent geometry : bond 0.00309 (14380) covalent geometry : angle 0.53228 (19522) hydrogen bonds : bond 0.03370 ( 601) hydrogen bonds : angle 5.37863 ( 1695) *********************** 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 152 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 122 time to evaluate : 0.576 Fit side-chains REVERT: A 420 ASP cc_start: 0.8671 (t0) cc_final: 0.8387 (t0) REVERT: A 444 GLN cc_start: 0.8265 (tt0) cc_final: 0.7877 (pt0) REVERT: A 771 GLN cc_start: 0.8086 (tm-30) cc_final: 0.7761 (tm-30) REVERT: A 773 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7782 (mm) REVERT: A 798 GLN cc_start: 0.8266 (tm-30) cc_final: 0.7976 (tm-30) REVERT: A 876 GLU cc_start: 0.7752 (tt0) cc_final: 0.7356 (mt-10) REVERT: B 117 MET cc_start: 0.9002 (ttm) cc_final: 0.8771 (ttm) REVERT: B 147 ASN cc_start: 0.8854 (m-40) cc_final: 0.8593 (m-40) REVERT: B 346 LYS cc_start: 0.9069 (ttpp) cc_final: 0.8812 (ttmm) REVERT: B 555 GLN cc_start: 0.8809 (mp10) cc_final: 0.8295 (mp10) REVERT: B 594 ASP cc_start: 0.8672 (m-30) cc_final: 0.8259 (m-30) REVERT: B 792 SER cc_start: 0.8758 (t) cc_final: 0.8535 (p) REVERT: B 877 ARG cc_start: 0.8036 (ttm110) cc_final: 0.7654 (ttm110) outliers start: 30 outliers final: 11 residues processed: 139 average time/residue: 0.6413 time to fit residues: 98.1095 Evaluate side-chains 122 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 424 VAL 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 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 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 150 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 156 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 74 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 A 813 HIS B 248 ASN B 641 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.085331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.064894 restraints weight = 24494.477| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.84 r_work: 0.2784 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 14380 Z= 0.209 Angle : 0.571 9.418 19522 Z= 0.288 Chirality : 0.043 0.191 2148 Planarity : 0.005 0.048 2558 Dihedral : 4.152 18.457 1970 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.85 % Allowed : 11.09 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.20), residues: 1792 helix: 1.62 (0.22), residues: 568 sheet: -0.25 (0.29), residues: 304 loop : -0.22 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 280 TYR 0.012 0.001 TYR B 857 PHE 0.028 0.002 PHE B 755 TRP 0.013 0.001 TRP B 54 HIS 0.005 0.001 HIS A 116 Details of bonding type rmsd covalent geometry : bond 0.00485 (14380) covalent geometry : angle 0.57052 (19522) hydrogen bonds : bond 0.03633 ( 601) hydrogen bonds : angle 5.41043 ( 1695) *********************** 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 142 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 0.501 Fit side-chains REVERT: A 420 ASP cc_start: 0.8758 (t0) cc_final: 0.8473 (t0) REVERT: A 444 GLN cc_start: 0.8249 (tt0) cc_final: 0.7888 (pt0) REVERT: A 771 GLN cc_start: 0.8163 (tm-30) cc_final: 0.7754 (tm-30) REVERT: A 798 GLN cc_start: 0.8301 (tm-30) cc_final: 0.7989 (tm-30) REVERT: A 876 GLU cc_start: 0.7829 (tt0) cc_final: 0.7532 (mt-10) REVERT: B 117 MET cc_start: 0.9082 (ttm) cc_final: 0.8834 (ttm) REVERT: B 147 ASN cc_start: 0.8859 (m-40) cc_final: 0.8594 (m-40) REVERT: B 346 LYS cc_start: 0.9082 (ttpp) cc_final: 0.8824 (ttmm) REVERT: B 482 ASP cc_start: 0.8641 (p0) cc_final: 0.8298 (p0) REVERT: B 555 GLN cc_start: 0.8800 (mp10) cc_final: 0.8302 (mp10) REVERT: B 594 ASP cc_start: 0.8703 (m-30) cc_final: 0.8297 (m-30) REVERT: B 773 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.6910 (mm) REVERT: B 792 SER cc_start: 0.8820 (t) cc_final: 0.8595 (p) REVERT: B 877 ARG cc_start: 0.8124 (ttm110) cc_final: 0.7738 (ttm110) outliers start: 28 outliers final: 12 residues processed: 134 average time/residue: 0.6207 time to fit residues: 91.8179 Evaluate side-chains 123 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 424 VAL 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 235 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 742 ASP Chi-restraints excluded: chain B residue 773 LEU Chi-restraints excluded: chain B residue 879 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 63 optimal weight: 0.7980 chunk 163 optimal weight: 6.9990 chunk 172 optimal weight: 0.9980 chunk 171 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 42 optimal weight: 0.0670 chunk 105 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN ** B 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3253 r_free = 0.3253 target = 0.086622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.067070 restraints weight = 24365.343| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.75 r_work: 0.2864 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14380 Z= 0.122 Angle : 0.534 7.914 19522 Z= 0.269 Chirality : 0.041 0.155 2148 Planarity : 0.004 0.053 2558 Dihedral : 4.057 19.850 1970 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.58 % Allowed : 11.68 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.20), residues: 1792 helix: 1.79 (0.22), residues: 562 sheet: -0.29 (0.29), residues: 314 loop : -0.20 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 912 TYR 0.025 0.001 TYR A 810 PHE 0.027 0.002 PHE B 755 TRP 0.012 0.001 TRP B 54 HIS 0.004 0.001 HIS A 116 Details of bonding type rmsd covalent geometry : bond 0.00284 (14380) covalent geometry : angle 0.53391 (19522) hydrogen bonds : bond 0.03225 ( 601) hydrogen bonds : angle 5.29251 ( 1695) *********************** 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: 24 poor density : 116 time to evaluate : 0.571 Fit side-chains REVERT: A 420 ASP cc_start: 0.8798 (t0) cc_final: 0.8562 (t0) REVERT: A 444 GLN cc_start: 0.8322 (tt0) cc_final: 0.7897 (pt0) REVERT: A 680 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.6822 (mmp-170) REVERT: A 771 GLN cc_start: 0.8119 (tm-30) cc_final: 0.7785 (tm-30) REVERT: A 773 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7041 (mm) REVERT: A 798 GLN cc_start: 0.8406 (tm-30) cc_final: 0.8081 (tm-30) REVERT: A 876 GLU cc_start: 0.7968 (tt0) cc_final: 0.7597 (mt-10) REVERT: B 147 ASN cc_start: 0.8892 (m-40) cc_final: 0.8614 (m-40) REVERT: B 346 LYS cc_start: 0.9081 (ttpp) cc_final: 0.8812 (ttmm) REVERT: B 482 ASP cc_start: 0.8713 (p0) cc_final: 0.8380 (p0) REVERT: B 555 GLN cc_start: 0.8873 (mp10) cc_final: 0.8332 (mp10) REVERT: B 594 ASP cc_start: 0.8780 (m-30) cc_final: 0.8403 (m-30) REVERT: B 732 ILE cc_start: 0.8797 (mm) cc_final: 0.8551 (mp) REVERT: B 773 LEU cc_start: 0.7514 (OUTLIER) cc_final: 0.6877 (mm) REVERT: B 792 SER cc_start: 0.8824 (t) cc_final: 0.8593 (p) REVERT: B 877 ARG cc_start: 0.8220 (ttm110) cc_final: 0.7855 (ttm110) outliers start: 24 outliers final: 10 residues processed: 133 average time/residue: 0.6372 time to fit residues: 93.4844 Evaluate side-chains 126 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 0.573 ------------------------------------------------------------------------------- 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 B residue 424 VAL Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 651 CYS Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 755 PHE Chi-restraints excluded: chain B residue 773 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 165 optimal weight: 4.9990 chunk 111 optimal weight: 0.9990 chunk 109 optimal weight: 0.7980 chunk 131 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 114 optimal weight: 0.9980 chunk 179 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 chunk 91 optimal weight: 0.0570 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN ** B 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 ASN ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 596 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.086447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.066924 restraints weight = 24452.961| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 2.76 r_work: 0.2863 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14380 Z= 0.132 Angle : 0.537 10.791 19522 Z= 0.269 Chirality : 0.042 0.158 2148 Planarity : 0.004 0.057 2558 Dihedral : 4.028 19.432 1970 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.52 % Allowed : 12.21 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.20), residues: 1792 helix: 1.80 (0.22), residues: 562 sheet: -0.20 (0.29), residues: 312 loop : -0.19 (0.21), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 912 TYR 0.011 0.001 TYR B 857 PHE 0.027 0.002 PHE B 755 TRP 0.012 0.001 TRP B 54 HIS 0.004 0.001 HIS B 381 Details of bonding type rmsd covalent geometry : bond 0.00308 (14380) covalent geometry : angle 0.53714 (19522) hydrogen bonds : bond 0.03248 ( 601) hydrogen bonds : angle 5.24246 ( 1695) *********************** 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 140 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 0.595 Fit side-chains REVERT: A 186 MET cc_start: 0.9215 (mtm) cc_final: 0.8961 (mtm) REVERT: A 420 ASP cc_start: 0.8833 (t0) cc_final: 0.8593 (t0) REVERT: A 444 GLN cc_start: 0.8339 (tt0) cc_final: 0.7924 (pt0) REVERT: A 680 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.6848 (mmp-170) REVERT: A 771 GLN cc_start: 0.8170 (tm-30) cc_final: 0.7912 (tm-30) REVERT: A 798 GLN cc_start: 0.8409 (tm-30) cc_final: 0.8080 (tm-30) REVERT: A 876 GLU cc_start: 0.7971 (tt0) cc_final: 0.7599 (mt-10) REVERT: B 147 ASN cc_start: 0.8920 (m-40) cc_final: 0.8659 (m-40) REVERT: B 346 LYS cc_start: 0.9071 (ttpp) cc_final: 0.8793 (ttmm) REVERT: B 482 ASP cc_start: 0.8649 (p0) cc_final: 0.8342 (p0) REVERT: B 555 GLN cc_start: 0.8878 (mp10) cc_final: 0.8351 (mp10) REVERT: B 594 ASP cc_start: 0.8824 (m-30) cc_final: 0.8430 (m-30) REVERT: B 773 LEU cc_start: 0.7487 (OUTLIER) cc_final: 0.6863 (mm) REVERT: B 792 SER cc_start: 0.8830 (t) cc_final: 0.8599 (p) REVERT: B 813 HIS cc_start: 0.7809 (t70) cc_final: 0.7439 (t-90) REVERT: B 877 ARG cc_start: 0.8223 (ttm110) cc_final: 0.7855 (ttm110) outliers start: 23 outliers final: 12 residues processed: 132 average time/residue: 0.6609 time to fit residues: 95.7583 Evaluate side-chains 126 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.570 ------------------------------------------------------------------------------- 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 879 CYS 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 557 SER Chi-restraints excluded: chain B residue 651 CYS 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 133 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 175 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 128 optimal weight: 0.1980 chunk 52 optimal weight: 6.9990 chunk 135 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN ** B 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 ASN ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 641 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.086818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.067274 restraints weight = 24505.913| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.78 r_work: 0.2869 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14380 Z= 0.130 Angle : 0.541 10.308 19522 Z= 0.272 Chirality : 0.042 0.171 2148 Planarity : 0.004 0.062 2558 Dihedral : 4.008 19.128 1970 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.32 % Allowed : 12.74 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.20), residues: 1792 helix: 1.80 (0.22), residues: 562 sheet: -0.14 (0.29), residues: 312 loop : -0.20 (0.21), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 912 TYR 0.011 0.001 TYR B 857 PHE 0.028 0.001 PHE B 755 TRP 0.012 0.001 TRP B 54 HIS 0.004 0.001 HIS B 381 Details of bonding type rmsd covalent geometry : bond 0.00303 (14380) covalent geometry : angle 0.54086 (19522) hydrogen bonds : bond 0.03222 ( 601) hydrogen bonds : angle 5.22523 ( 1695) *********************** 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 136 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 0.583 Fit side-chains REVERT: A 255 GLU cc_start: 0.9172 (mm-30) cc_final: 0.8827 (mm-30) REVERT: A 444 GLN cc_start: 0.8342 (tt0) cc_final: 0.7929 (pt0) REVERT: A 680 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.6849 (mmp-170) REVERT: A 771 GLN cc_start: 0.8172 (tm-30) cc_final: 0.7914 (tm-30) REVERT: A 798 GLN cc_start: 0.8406 (tm-30) cc_final: 0.8075 (tm-30) REVERT: A 876 GLU cc_start: 0.7967 (tt0) cc_final: 0.7631 (mt-10) REVERT: B 147 ASN cc_start: 0.8909 (m-40) cc_final: 0.8638 (m-40) REVERT: B 346 LYS cc_start: 0.9070 (ttpp) cc_final: 0.8785 (ttmm) REVERT: B 482 ASP cc_start: 0.8642 (p0) cc_final: 0.8408 (p0) REVERT: B 555 GLN cc_start: 0.8876 (mp10) cc_final: 0.8344 (mp10) REVERT: B 594 ASP cc_start: 0.8791 (m-30) cc_final: 0.8419 (m-30) REVERT: B 773 LEU cc_start: 0.7537 (OUTLIER) cc_final: 0.6896 (mm) REVERT: B 792 SER cc_start: 0.8827 (t) cc_final: 0.8589 (p) REVERT: B 813 HIS cc_start: 0.7818 (t70) cc_final: 0.7456 (t-90) REVERT: B 877 ARG cc_start: 0.8177 (ttm110) cc_final: 0.7828 (mtp85) outliers start: 20 outliers final: 12 residues processed: 130 average time/residue: 0.6706 time to fit residues: 95.4685 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 : 0.462 ------------------------------------------------------------------------------- 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 616 ARG 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 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 651 CYS 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 119 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 176 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 105 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 132 optimal weight: 0.7980 chunk 178 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.087807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.067632 restraints weight = 24482.926| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.85 r_work: 0.2834 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14380 Z= 0.139 Angle : 0.551 10.175 19522 Z= 0.278 Chirality : 0.042 0.164 2148 Planarity : 0.004 0.064 2558 Dihedral : 3.998 19.005 1970 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.06 % Allowed : 13.20 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.20), residues: 1792 helix: 1.81 (0.22), residues: 568 sheet: -0.11 (0.29), residues: 312 loop : -0.19 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 433 TYR 0.011 0.001 TYR B 857 PHE 0.027 0.002 PHE B 755 TRP 0.013 0.001 TRP B 54 HIS 0.004 0.001 HIS B 381 Details of bonding type rmsd covalent geometry : bond 0.00326 (14380) covalent geometry : angle 0.55148 (19522) hydrogen bonds : bond 0.03236 ( 601) hydrogen bonds : angle 5.22727 ( 1695) ********************** 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 133 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.601 Fit side-chains REVERT: A 109 MET cc_start: 0.8956 (mtp) cc_final: 0.8721 (mtm) REVERT: A 255 GLU cc_start: 0.9045 (mm-30) cc_final: 0.8718 (mm-30) REVERT: A 680 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.6758 (mmp-170) REVERT: A 771 GLN cc_start: 0.8236 (tm-30) cc_final: 0.7921 (tm-30) REVERT: A 773 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.7107 (mm) REVERT: A 798 GLN cc_start: 0.8304 (tm-30) cc_final: 0.7979 (tm-30) REVERT: A 876 GLU cc_start: 0.7766 (tt0) cc_final: 0.7459 (mt-10) REVERT: B 117 MET cc_start: 0.9016 (ttm) cc_final: 0.8800 (ttm) REVERT: B 147 ASN cc_start: 0.8808 (m-40) cc_final: 0.8543 (m-40) REVERT: B 346 LYS cc_start: 0.9083 (ttpp) cc_final: 0.8812 (ttmm) REVERT: B 482 ASP cc_start: 0.8521 (p0) cc_final: 0.8318 (p0) REVERT: B 555 GLN cc_start: 0.8800 (mp10) cc_final: 0.8334 (mp10) REVERT: B 594 ASP cc_start: 0.8703 (m-30) cc_final: 0.8315 (m-30) REVERT: B 637 LEU cc_start: 0.8422 (mt) cc_final: 0.8055 (mp) REVERT: B 773 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.6966 (mm) REVERT: B 792 SER cc_start: 0.8818 (t) cc_final: 0.8590 (p) REVERT: B 813 HIS cc_start: 0.7752 (t70) cc_final: 0.7402 (t-90) REVERT: B 877 ARG cc_start: 0.8029 (ttm110) cc_final: 0.7696 (mtp85) outliers start: 16 outliers final: 10 residues processed: 129 average time/residue: 0.6436 time to fit residues: 91.3413 Evaluate side-chains 125 residues out of total 1516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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 53 optimal weight: 5.9990 chunk 176 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 61 optimal weight: 0.0470 chunk 33 optimal weight: 6.9990 chunk 155 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 150 optimal weight: 0.7980 chunk 154 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 167 optimal weight: 0.7980 overall best weight: 0.6678 ------------------------------------------------------------------------------- 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 217 GLN ** 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 = 0.3282 r_free = 0.3282 target = 0.088450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.068430 restraints weight = 24420.327| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.84 r_work: 0.2854 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14380 Z= 0.127 Angle : 0.547 9.531 19522 Z= 0.276 Chirality : 0.042 0.159 2148 Planarity : 0.004 0.064 2558 Dihedral : 3.983 18.761 1970 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.86 % Allowed : 13.33 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.20), residues: 1792 helix: 1.88 (0.22), residues: 566 sheet: -0.07 (0.29), residues: 312 loop : -0.19 (0.21), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 912 TYR 0.010 0.001 TYR B 857 PHE 0.026 0.001 PHE B 755 TRP 0.012 0.001 TRP B 54 HIS 0.004 0.001 HIS B 381 Details of bonding type rmsd covalent geometry : bond 0.00298 (14380) covalent geometry : angle 0.54697 (19522) hydrogen bonds : bond 0.03184 ( 601) hydrogen bonds : angle 5.20693 ( 1695) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3938.71 seconds wall clock time: 68 minutes 30.24 seconds (4110.24 seconds total)