Starting phenix.real_space_refine on Fri Aug 7 14:16:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10dp_75094/08_2026/10dp_75094.cif Found real_map, /net/cci-nas-00/data/ceres_data/10dp_75094/08_2026/10dp_75094.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/10dp_75094/08_2026/10dp_75094.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10dp_75094/08_2026/10dp_75094.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/10dp_75094/08_2026/10dp_75094.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10dp_75094/08_2026/10dp_75094.map" } resolution = 3.25 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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 113 5.16 5 C 14009 2.51 5 N 3760 2.21 5 O 4244 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22126 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 928, 7378 Classifications: {'peptide': 928} Link IDs: {'PCIS': 4, 'PTRANS': 49, 'TRANS': 874} Chain breaks: 1 Chain: "B" Number of atoms: 7378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 928, 7378 Classifications: {'peptide': 928} Link IDs: {'PCIS': 4, 'PTRANS': 48, 'TRANS': 875} Chain breaks: 1 Chain: "C" Number of atoms: 7370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 927, 7370 Classifications: {'peptide': 927} Link IDs: {'PCIS': 4, 'PTRANS': 48, 'TRANS': 874} Chain breaks: 1 Time building chain proxies: 4.62, per 1000 atoms: 0.21 Number of scatterers: 22126 At special positions: 0 Unit cell: (119, 117.6, 141.4, 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 113 16.00 O 4244 8.00 N 3760 7.00 C 14009 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS B 420 " distance=2.89 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: 1.89 Conformation dependent library (CDL) restraints added in 1.0 seconds 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5182 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 48 sheets defined 17.5% alpha, 26.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 9 through 14 Processing helix chain 'A' and resid 19 through 24 removed outlier: 3.500A pdb=" N LEU A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 35 Processing helix chain 'A' and resid 41 through 45 removed outlier: 3.985A pdb=" N LYS A 44 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE A 45 " --> pdb=" O ASN A 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 41 through 45' Processing helix chain 'A' and resid 97 through 99 No H-bonds generated for 'chain 'A' and resid 97 through 99' Processing helix chain 'A' and resid 318 through 323 removed outlier: 3.955A pdb=" N GLN A 323 " --> pdb=" O MET A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 340 Processing helix chain 'A' and resid 372 through 383 Processing helix chain 'A' and resid 401 through 406 removed outlier: 3.520A pdb=" N ARG A 405 " --> pdb=" O ASP A 401 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE A 406 " --> pdb=" O PRO A 402 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 401 through 406' Processing helix chain 'A' and resid 470 through 484 removed outlier: 3.886A pdb=" N ASN A 474 " --> pdb=" O ASN A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 488 removed outlier: 3.829A pdb=" N LEU A 488 " --> pdb=" O ALA A 485 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 485 through 488' Processing helix chain 'A' and resid 489 through 493 removed outlier: 3.818A pdb=" N LYS A 493 " --> pdb=" O ASP A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 514 removed outlier: 3.658A pdb=" N ARG A 514 " --> pdb=" O TYR A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 521 removed outlier: 3.601A pdb=" N LEU A 520 " --> pdb=" O ALA A 517 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A 521 " --> pdb=" O PRO A 518 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 517 through 521' Processing helix chain 'A' and resid 535 through 539 removed outlier: 4.032A pdb=" N ASN A 538 " --> pdb=" O TYR A 535 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL A 539 " --> pdb=" O MET A 536 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 535 through 539' Processing helix chain 'A' and resid 547 through 556 Processing helix chain 'A' and resid 595 through 599 Processing helix chain 'A' and resid 630 through 642 Processing helix chain 'A' and resid 712 through 717 Processing helix chain 'A' and resid 721 through 723 No H-bonds generated for 'chain 'A' and resid 721 through 723' Processing helix chain 'A' and resid 770 through 782 Processing helix chain 'A' and resid 801 through 805 removed outlier: 3.652A pdb=" N PHE A 805 " --> pdb=" O PHE A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 829 removed outlier: 3.695A pdb=" N GLN A 829 " --> pdb=" O ILE A 826 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 13 Processing helix chain 'B' and resid 19 through 24 removed outlier: 3.534A pdb=" N TYR B 23 " --> pdb=" O ASP B 19 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU B 24 " --> pdb=" O ALA B 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 19 through 24' Processing helix chain 'B' and resid 25 through 35 Processing helix chain 'B' and resid 41 through 45 removed outlier: 3.759A pdb=" N LYS B 44 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE B 45 " --> pdb=" O ASN B 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 41 through 45' Processing helix chain 'B' and resid 97 through 99 No H-bonds generated for 'chain 'B' and resid 97 through 99' Processing helix chain 'B' and resid 318 through 323 removed outlier: 4.039A pdb=" N GLN B 323 " --> pdb=" O MET B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 340 Processing helix chain 'B' and resid 372 through 383 Processing helix chain 'B' and resid 401 through 406 removed outlier: 3.673A pdb=" N ILE B 406 " --> pdb=" O PRO B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 484 Processing helix chain 'B' and resid 489 through 493 removed outlier: 3.551A pdb=" N LYS B 493 " --> pdb=" O ASP B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 514 removed outlier: 3.583A pdb=" N ARG B 514 " --> pdb=" O TYR B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 521 removed outlier: 3.595A pdb=" N LEU B 520 " --> pdb=" O ALA B 517 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL B 521 " --> pdb=" O PRO B 518 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 517 through 521' Processing helix chain 'B' and resid 547 through 556 Processing helix chain 'B' and resid 595 through 599 Processing helix chain 'B' and resid 630 through 642 Processing helix chain 'B' and resid 712 through 717 Processing helix chain 'B' and resid 721 through 723 No H-bonds generated for 'chain 'B' and resid 721 through 723' Processing helix chain 'B' and resid 770 through 782 Processing helix chain 'B' and resid 792 through 796 Processing helix chain 'B' and resid 894 through 897 removed outlier: 3.570A pdb=" N GLN B 897 " --> pdb=" O ASP B 894 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 894 through 897' Processing helix chain 'B' and resid 898 through 903 Processing helix chain 'C' and resid 8 through 13 Processing helix chain 'C' and resid 19 through 24 removed outlier: 3.539A pdb=" N LEU C 24 " --> pdb=" O ALA C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 35 Processing helix chain 'C' and resid 41 through 45 removed outlier: 3.798A pdb=" N LYS C 44 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N PHE C 45 " --> pdb=" O ASN C 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 41 through 45' Processing helix chain 'C' and resid 194 through 198 removed outlier: 4.225A pdb=" N GLY C 197 " --> pdb=" O ALA C 194 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASN C 198 " --> pdb=" O THR C 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 194 through 198' Processing helix chain 'C' and resid 277 through 281 removed outlier: 3.986A pdb=" N ASN C 281 " --> pdb=" O ASN C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 323 removed outlier: 3.652A pdb=" N GLN C 323 " --> pdb=" O MET C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 340 Processing helix chain 'C' and resid 372 through 383 Processing helix chain 'C' and resid 401 through 406 removed outlier: 3.606A pdb=" N ILE C 406 " --> pdb=" O PRO C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 484 removed outlier: 3.537A pdb=" N ASN C 474 " --> pdb=" O ASN C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 488 removed outlier: 3.838A pdb=" N LEU C 488 " --> pdb=" O ALA C 485 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 485 through 488' Processing helix chain 'C' and resid 489 through 493 removed outlier: 3.707A pdb=" N LEU C 492 " --> pdb=" O PRO C 489 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LYS C 493 " --> pdb=" O ASP C 490 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 489 through 493' Processing helix chain 'C' and resid 507 through 514 removed outlier: 3.508A pdb=" N ARG C 514 " --> pdb=" O TYR C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 517 through 522 removed outlier: 3.613A pdb=" N VAL C 521 " --> pdb=" O PRO C 518 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP C 522 " --> pdb=" O GLY C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 556 Processing helix chain 'C' and resid 595 through 599 removed outlier: 3.502A pdb=" N VAL C 599 " --> pdb=" O ASP C 595 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 595 through 599' Processing helix chain 'C' and resid 630 through 641 Processing helix chain 'C' and resid 712 through 717 Processing helix chain 'C' and resid 721 through 723 No H-bonds generated for 'chain 'C' and resid 721 through 723' Processing helix chain 'C' and resid 769 through 782 removed outlier: 3.526A pdb=" N PHE C 773 " --> pdb=" O THR C 769 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 803 No H-bonds generated for 'chain 'C' and resid 801 through 803' Processing helix chain 'C' and resid 825 through 829 removed outlier: 3.634A pdb=" N GLN C 829 " --> pdb=" O ILE C 826 " (cutoff:3.500A) Processing helix chain 'C' and resid 898 through 903 removed outlier: 3.560A pdb=" N ASN C 903 " --> pdb=" O LEU C 899 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 68 removed outlier: 6.857A pdb=" N ARG A 104 " --> pdb=" O ASP A 618 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ILE A 620 " --> pdb=" O ASP A 102 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ASP A 102 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N LEU A 622 " --> pdb=" O TYR A 100 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TYR A 100 " --> pdb=" O LEU A 622 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY A 105 " --> pdb=" O PHE A 565 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 75 removed outlier: 3.705A pdb=" N ASP A 72 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TRP A 590 " --> pdb=" O ALA A 82 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR A 588 " --> pdb=" O PHE A 84 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 94 through 95 Processing sheet with id=AA4, first strand: chain 'A' and resid 133 through 137 removed outlier: 3.578A pdb=" N CYS A 133 " --> pdb=" O TYR A 171 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU C 458 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP C 430 " --> pdb=" O ILE C 459 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N PHE A 272 " --> pdb=" O ILE C 435 " (cutoff:3.500A) removed outlier: 9.156A pdb=" N ALA C 437 " --> pdb=" O MET A 270 " (cutoff:3.500A) removed outlier: 12.871A pdb=" N MET A 270 " --> pdb=" O ALA C 437 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 133 through 137 removed outlier: 3.578A pdb=" N CYS A 133 " --> pdb=" O TYR A 171 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU C 458 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP C 430 " --> pdb=" O ILE C 459 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 181 through 182 removed outlier: 7.021A pdb=" N ILE A 201 " --> pdb=" O ILE A 188 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 258 through 260 Processing sheet with id=AA8, first strand: chain 'A' and resid 304 through 308 removed outlier: 6.334A pdb=" N GLN A 324 " --> pdb=" O SER A 307 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 333 through 335 Processing sheet with id=AB1, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AB2, first strand: chain 'A' and resid 467 through 468 removed outlier: 3.605A pdb=" N MET C 467 " --> pdb=" O CYS C 420 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASN C 418 " --> pdb=" O ILE C 469 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASN B 418 " --> pdb=" O ILE B 469 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 447 through 449 removed outlier: 7.114A pdb=" N GLU A 458 " --> pdb=" O ALA B 172 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N ALA B 174 " --> pdb=" O GLU A 458 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLY A 460 " --> pdb=" O ALA B 174 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 447 through 449 removed outlier: 4.415A pdb=" N PHE B 272 " --> pdb=" O ILE A 435 " (cutoff:3.500A) removed outlier: 9.075A pdb=" N ALA A 437 " --> pdb=" O MET B 270 " (cutoff:3.500A) removed outlier: 12.682A pdb=" N MET B 270 " --> pdb=" O ALA A 437 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE B 176 " --> pdb=" O GLY B 227 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 648 through 651 removed outlier: 3.504A pdb=" N GLN A 648 " --> pdb=" O VAL A 935 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU A 948 " --> pdb=" O VAL A 932 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 656 through 663 removed outlier: 3.509A pdb=" N THR A 921 " --> pdb=" O ILE A 663 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLY A 684 " --> pdb=" O GLU A 928 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 670 through 677 removed outlier: 7.403A pdb=" N PHE A 912 " --> pdb=" O PRO A 671 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N SER A 673 " --> pdb=" O MET A 910 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N MET A 910 " --> pdb=" O SER A 673 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N LEU A 908 " --> pdb=" O PRO A 675 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ALA A 907 " --> pdb=" O PHE A 732 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N PHE A 732 " --> pdb=" O ALA A 907 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ASP A 909 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ILE A 730 " --> pdb=" O ASP A 909 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR A 911 " --> pdb=" O VAL A 728 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N VAL A 728 " --> pdb=" O THR A 911 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLU A 913 " --> pdb=" O LYS A 726 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 670 through 677 removed outlier: 7.403A pdb=" N PHE A 912 " --> pdb=" O PRO A 671 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N SER A 673 " --> pdb=" O MET A 910 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N MET A 910 " --> pdb=" O SER A 673 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N LEU A 908 " --> pdb=" O PRO A 675 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ALA A 907 " --> pdb=" O PHE A 732 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N PHE A 732 " --> pdb=" O ALA A 907 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ASP A 909 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ILE A 730 " --> pdb=" O ASP A 909 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR A 911 " --> pdb=" O VAL A 728 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N VAL A 728 " --> pdb=" O THR A 911 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLU A 913 " --> pdb=" O LYS A 726 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 762 through 763 removed outlier: 4.589A pdb=" N MET A 768 " --> pdb=" O VAL A 763 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 806 through 813 Processing sheet with id=AC2, first strand: chain 'B' and resid 65 through 68 removed outlier: 6.849A pdb=" N ARG B 104 " --> pdb=" O ASP B 618 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ILE B 620 " --> pdb=" O ASP B 102 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ASP B 102 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N LEU B 622 " --> pdb=" O TYR B 100 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N TYR B 100 " --> pdb=" O LEU B 622 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY B 105 " --> pdb=" O PHE B 565 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 72 through 73 removed outlier: 3.727A pdb=" N ASP B 72 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA B 82 " --> pdb=" O TRP B 590 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TRP B 590 " --> pdb=" O ALA B 82 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR B 588 " --> pdb=" O PHE B 84 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 94 through 95 Processing sheet with id=AC5, first strand: chain 'B' and resid 181 through 182 removed outlier: 3.504A pdb=" N GLY B 189 " --> pdb=" O ILE B 201 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 258 through 260 removed outlier: 3.514A pdb=" N VAL B 258 " --> pdb=" O GLU B 265 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 304 through 308 removed outlier: 6.534A pdb=" N GLN B 324 " --> pdb=" O SER B 307 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 333 through 335 Processing sheet with id=AC9, first strand: chain 'B' and resid 407 through 408 removed outlier: 3.616A pdb=" N ILE B 407 " --> pdb=" O TRP B 531 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 447 through 449 removed outlier: 3.692A pdb=" N ASP B 430 " --> pdb=" O ILE B 459 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLU B 458 " --> pdb=" O ALA C 172 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N ALA C 174 " --> pdb=" O GLU B 458 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLY B 460 " --> pdb=" O ALA C 174 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 447 through 449 removed outlier: 4.097A pdb=" N PHE C 272 " --> pdb=" O ILE B 435 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N ALA B 437 " --> pdb=" O MET C 270 " (cutoff:3.500A) removed outlier: 12.631A pdb=" N MET C 270 " --> pdb=" O ALA B 437 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE C 273 " --> pdb=" O LEU C 290 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 648 through 651 Processing sheet with id=AD4, first strand: chain 'B' and resid 656 through 663 removed outlier: 4.053A pdb=" N GLY B 684 " --> pdb=" O GLU B 928 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 670 through 677 removed outlier: 4.321A pdb=" N SER B 676 " --> pdb=" O HIS B 906 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N HIS B 906 " --> pdb=" O SER B 676 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 670 through 677 removed outlier: 4.321A pdb=" N SER B 676 " --> pdb=" O HIS B 906 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N HIS B 906 " --> pdb=" O SER B 676 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N THR B 911 " --> pdb=" O VAL B 728 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N VAL B 728 " --> pdb=" O THR B 911 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLU B 913 " --> pdb=" O LYS B 726 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 762 through 763 removed outlier: 4.517A pdb=" N MET B 768 " --> pdb=" O VAL B 763 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 805 through 813 Processing sheet with id=AD9, first strand: chain 'C' and resid 65 through 68 removed outlier: 3.567A pdb=" N LEU C 622 " --> pdb=" O PHE C 68 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ARG C 104 " --> pdb=" O ASP C 618 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ILE C 620 " --> pdb=" O ASP C 102 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ASP C 102 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LEU C 622 " --> pdb=" O TYR C 100 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TYR C 100 " --> pdb=" O LEU C 622 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY C 105 " --> pdb=" O PHE C 565 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 72 through 75 removed outlier: 3.798A pdb=" N ASP C 72 " --> pdb=" O ARG C 83 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA C 82 " --> pdb=" O TRP C 590 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TRP C 590 " --> pdb=" O ALA C 82 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TYR C 588 " --> pdb=" O PHE C 84 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 72 through 75 removed outlier: 3.798A pdb=" N ASP C 72 " --> pdb=" O ARG C 83 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA C 82 " --> pdb=" O TRP C 590 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TRP C 590 " --> pdb=" O ALA C 82 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TYR C 588 " --> pdb=" O PHE C 84 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 94 through 95 Processing sheet with id=AE4, first strand: chain 'C' and resid 181 through 182 Processing sheet with id=AE5, first strand: chain 'C' and resid 258 through 260 removed outlier: 3.516A pdb=" N VAL C 258 " --> pdb=" O GLU C 265 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 304 through 308 removed outlier: 6.411A pdb=" N GLN C 324 " --> pdb=" O SER C 307 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 333 through 335 Processing sheet with id=AE8, first strand: chain 'C' and resid 648 through 651 removed outlier: 3.718A pdb=" N GLN C 648 " --> pdb=" O VAL C 935 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU C 948 " --> pdb=" O VAL C 932 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 656 through 663 removed outlier: 4.288A pdb=" N GLY C 684 " --> pdb=" O GLU C 928 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 669 through 677 removed outlier: 4.377A pdb=" N SER C 676 " --> pdb=" O HIS C 906 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N HIS C 906 " --> pdb=" O SER C 676 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ALA C 907 " --> pdb=" O PHE C 732 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N PHE C 732 " --> pdb=" O ALA C 907 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ASP C 909 " --> pdb=" O ILE C 730 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ILE C 730 " --> pdb=" O ASP C 909 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N THR C 911 " --> pdb=" O VAL C 728 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N VAL C 728 " --> pdb=" O THR C 911 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLU C 913 " --> pdb=" O LYS C 726 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ILE C 730 " --> pdb=" O TRP C 738 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 669 through 677 removed outlier: 4.377A pdb=" N SER C 676 " --> pdb=" O HIS C 906 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N HIS C 906 " --> pdb=" O SER C 676 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ALA C 907 " --> pdb=" O PHE C 732 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N PHE C 732 " --> pdb=" O ALA C 907 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ASP C 909 " --> pdb=" O ILE C 730 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ILE C 730 " --> pdb=" O ASP C 909 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N THR C 911 " --> pdb=" O VAL C 728 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N VAL C 728 " --> pdb=" O THR C 911 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLU C 913 " --> pdb=" O LYS C 726 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 805 through 813 601 hydrogen bonds defined for protein. 1554 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: 4.47 Time building geometry restraints manager: 2.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6633 1.33 - 1.45: 3904 1.45 - 1.57: 11964 1.57 - 1.69: 0 1.69 - 1.81: 205 Bond restraints: 22706 Sorted by residual: bond pdb=" N PRO A 422 " pdb=" CA PRO A 422 " ideal model delta sigma weight residual 1.465 1.510 -0.044 1.19e-02 7.06e+03 1.39e+01 bond pdb=" CA SER A 5 " pdb=" CB SER A 5 " ideal model delta sigma weight residual 1.529 1.471 0.058 1.63e-02 3.76e+03 1.28e+01 bond pdb=" CA SER A 16 " pdb=" CB SER A 16 " ideal model delta sigma weight residual 1.534 1.474 0.060 1.77e-02 3.19e+03 1.15e+01 bond pdb=" N TYR A 419 " pdb=" CA TYR A 419 " ideal model delta sigma weight residual 1.454 1.495 -0.041 1.23e-02 6.61e+03 1.13e+01 bond pdb=" N ILE A 469 " pdb=" CA ILE A 469 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.19e-02 7.06e+03 9.55e+00 ... (remaining 22701 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 30371 2.52 - 5.03: 459 5.03 - 7.55: 45 7.55 - 10.06: 7 10.06 - 12.58: 1 Bond angle restraints: 30883 Sorted by residual: angle pdb=" N ILE A 15 " pdb=" CA ILE A 15 " pdb=" C ILE A 15 " ideal model delta sigma weight residual 112.35 102.47 9.88 1.41e+00 5.03e-01 4.91e+01 angle pdb=" N PHE C 421 " pdb=" CA PHE C 421 " pdb=" CB PHE C 421 " ideal model delta sigma weight residual 109.49 101.62 7.87 1.13e+00 7.83e-01 4.85e+01 angle pdb=" C TYR B 419 " pdb=" CA TYR B 419 " pdb=" CB TYR B 419 " ideal model delta sigma weight residual 110.67 98.09 12.58 2.23e+00 2.01e-01 3.18e+01 angle pdb=" N TYR B 419 " pdb=" CA TYR B 419 " pdb=" C TYR B 419 " ideal model delta sigma weight residual 109.14 116.59 -7.45 1.49e+00 4.50e-01 2.50e+01 angle pdb=" N ASN A 472 " pdb=" CA ASN A 472 " pdb=" C ASN A 472 " ideal model delta sigma weight residual 112.90 106.56 6.34 1.31e+00 5.83e-01 2.34e+01 ... (remaining 30878 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 12411 17.76 - 35.53: 835 35.53 - 53.29: 164 53.29 - 71.06: 31 71.06 - 88.82: 16 Dihedral angle restraints: 13457 sinusoidal: 5327 harmonic: 8130 Sorted by residual: dihedral pdb=" CB CYS A 420 " pdb=" SG CYS A 420 " pdb=" SG CYS B 420 " pdb=" CB CYS B 420 " ideal model delta sinusoidal sigma weight residual 93.00 16.84 76.16 1 1.00e+01 1.00e-02 7.30e+01 dihedral pdb=" C TYR B 419 " pdb=" N TYR B 419 " pdb=" CA TYR B 419 " pdb=" CB TYR B 419 " ideal model delta harmonic sigma weight residual -122.60 -107.69 -14.91 0 2.50e+00 1.60e-01 3.56e+01 dihedral pdb=" CA ALA C 283 " pdb=" C ALA C 283 " pdb=" N ASN C 284 " pdb=" CA ASN C 284 " ideal model delta harmonic sigma weight residual 180.00 156.30 23.70 0 5.00e+00 4.00e-02 2.25e+01 ... (remaining 13454 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2513 0.061 - 0.122: 664 0.122 - 0.183: 68 0.183 - 0.244: 10 0.244 - 0.305: 2 Chirality restraints: 3257 Sorted by residual: chirality pdb=" CA TYR B 419 " pdb=" N TYR B 419 " pdb=" C TYR B 419 " pdb=" CB TYR B 419 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CA CYS B 420 " pdb=" N CYS B 420 " pdb=" C CYS B 420 " pdb=" CB CYS B 420 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA GLN A 18 " pdb=" N GLN A 18 " pdb=" C GLN A 18 " pdb=" CB GLN A 18 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 3254 not shown) Planarity restraints: 4091 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 11 " 0.018 2.00e-02 2.50e+03 3.41e-02 1.16e+01 pdb=" C SER A 11 " -0.059 2.00e-02 2.50e+03 pdb=" O SER A 11 " 0.021 2.00e-02 2.50e+03 pdb=" N TYR A 12 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 415 " -0.015 2.00e-02 2.50e+03 2.90e-02 8.42e+00 pdb=" C GLU B 415 " 0.050 2.00e-02 2.50e+03 pdb=" O GLU B 415 " -0.019 2.00e-02 2.50e+03 pdb=" N LEU B 416 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 415 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.88e+00 pdb=" C GLU A 415 " -0.042 2.00e-02 2.50e+03 pdb=" O GLU A 415 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU A 416 " 0.014 2.00e-02 2.50e+03 ... (remaining 4088 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1450 2.73 - 3.27: 19365 3.27 - 3.81: 32166 3.81 - 4.36: 42494 4.36 - 4.90: 76506 Nonbonded interactions: 171981 Sorted by model distance: nonbonded pdb=" N ASP C 644 " pdb=" OD1 ASP C 644 " model vdw 2.185 3.120 nonbonded pdb=" O ASN C 470 " pdb=" ND2 ASN C 474 " model vdw 2.213 3.120 nonbonded pdb=" O ASN B 470 " pdb=" ND2 ASN B 474 " model vdw 2.221 3.120 nonbonded pdb=" O HIS A 14 " pdb=" NH1 ARG A 46 " model vdw 2.242 3.120 nonbonded pdb=" OH TYR C 494 " pdb=" O LEU C 839 " model vdw 2.247 3.040 ... (remaining 171976 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 7 through 955) selection = (chain 'B' and resid 7 through 955) selection = (chain 'C' and resid 7 through 955) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.380 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: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 19.840 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 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 : 0.009 0.861 22707 Z= 0.431 Angle : 0.810 34.198 30885 Z= 0.473 Chirality : 0.054 0.305 3257 Planarity : 0.006 0.055 4091 Dihedral : 12.978 88.819 8272 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 3.48 % Allowed : 6.83 % Favored : 89.70 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 7.64 % 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 are not related in a simple way. whole: -1.95 (0.14), residues: 2771 helix: -0.38 (0.30), residues: 311 sheet: -1.16 (0.19), residues: 623 loop : -1.57 (0.13), residues: 1837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 386 TYR 0.018 0.002 TYR C 400 PHE 0.022 0.002 PHE A 882 TRP 0.017 0.002 TRP A 476 HIS 0.009 0.002 HIS A 830 Details of bonding type rmsd/Z covalent geometry : bond 0.00737 / 0.32 (22706) covalent geometry : angle 0.78450 / 0.46 (30883) SS BOND : bond 0.86060 / 45.29 ( 1) SS BOND : angle 24.91147 / 14.48 ( 2) hydrogen bonds : bond 0.25075 / 17.07 ( 564) hydrogen bonds : angle 8.61361 / 6.00 ( 1554) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 348 time to evaluate : 0.538 Fit side-chains REVERT: A 6 MET cc_start: 0.5905 (mtt) cc_final: 0.5672 (mtt) REVERT: A 7 MET cc_start: 0.4174 (OUTLIER) cc_final: 0.3374 (mpt) REVERT: A 13 MET cc_start: 0.8236 (mmm) cc_final: 0.7972 (tpp) REVERT: A 19 ASP cc_start: 0.7343 (OUTLIER) cc_final: 0.7039 (m-30) REVERT: A 44 LYS cc_start: 0.7170 (OUTLIER) cc_final: 0.6773 (mttm) REVERT: A 73 ARG cc_start: 0.7433 (ptt180) cc_final: 0.7208 (ptt-90) REVERT: A 86 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7278 (tp) REVERT: A 137 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7607 (mt-10) REVERT: A 166 LYS cc_start: 0.8098 (mttt) cc_final: 0.7673 (mtpt) REVERT: A 183 LYS cc_start: 0.8489 (pttt) cc_final: 0.8130 (pttp) REVERT: A 200 GLU cc_start: 0.7978 (mp0) cc_final: 0.7679 (mp0) REVERT: A 264 LEU cc_start: 0.7708 (mt) cc_final: 0.7458 (mt) REVERT: A 309 LYS cc_start: 0.7960 (tttt) cc_final: 0.7699 (tttm) REVERT: A 318 LYS cc_start: 0.8108 (tttt) cc_final: 0.7737 (tttm) REVERT: A 368 GLN cc_start: 0.8985 (mt0) cc_final: 0.8743 (mt0) REVERT: A 369 ASP cc_start: 0.7834 (OUTLIER) cc_final: 0.7533 (p0) REVERT: A 458 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8393 (mt-10) REVERT: A 467 MET cc_start: 0.9035 (mtp) cc_final: 0.8817 (mtt) REVERT: A 513 LYS cc_start: 0.7535 (mttt) cc_final: 0.7293 (mttp) REVERT: A 616 LYS cc_start: 0.7836 (tttt) cc_final: 0.7225 (tttm) REVERT: A 620 ILE cc_start: 0.7537 (mt) cc_final: 0.7036 (tt) REVERT: A 629 MET cc_start: 0.8020 (ttm) cc_final: 0.7816 (ttm) REVERT: A 727 LYS cc_start: 0.4006 (pttt) cc_final: 0.3224 (mtmm) REVERT: A 756 VAL cc_start: 0.8788 (t) cc_final: 0.8524 (p) REVERT: A 808 MET cc_start: 0.8633 (mtm) cc_final: 0.8080 (mtp) REVERT: A 811 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.6076 (mp10) REVERT: A 843 MET cc_start: 0.8784 (ttp) cc_final: 0.8515 (ttp) REVERT: B 13 MET cc_start: 0.8259 (mmm) cc_final: 0.8055 (mmm) REVERT: B 60 ARG cc_start: 0.6915 (mtt180) cc_final: 0.6326 (mtp-110) REVERT: B 73 ARG cc_start: 0.7249 (mtt180) cc_final: 0.6426 (mtp180) REVERT: B 81 LYS cc_start: 0.7797 (ttmt) cc_final: 0.7517 (ttmm) REVERT: B 92 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.7161 (mtm180) REVERT: B 96 MET cc_start: 0.8624 (mmm) cc_final: 0.8264 (mmm) REVERT: B 183 LYS cc_start: 0.8152 (pttt) cc_final: 0.7933 (pttp) REVERT: B 200 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.7105 (mm-30) REVERT: B 201 ILE cc_start: 0.8671 (mt) cc_final: 0.8430 (mm) REVERT: B 249 ASN cc_start: 0.7885 (OUTLIER) cc_final: 0.7673 (p0) REVERT: B 296 ASP cc_start: 0.7781 (m-30) cc_final: 0.7394 (m-30) REVERT: B 318 LYS cc_start: 0.8136 (tttt) cc_final: 0.7883 (tttm) REVERT: B 326 MET cc_start: 0.8464 (ttt) cc_final: 0.8222 (ttt) REVERT: B 398 ASP cc_start: 0.8198 (m-30) cc_final: 0.7951 (m-30) REVERT: B 458 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7585 (mt-10) REVERT: B 616 LYS cc_start: 0.7995 (tttt) cc_final: 0.7598 (tttm) REVERT: B 817 LYS cc_start: 0.7734 (mttt) cc_final: 0.7271 (mtpp) REVERT: B 820 ASP cc_start: 0.7860 (m-30) cc_final: 0.7632 (m-30) REVERT: B 860 LYS cc_start: 0.7941 (mttt) cc_final: 0.7706 (mttt) REVERT: B 910 MET cc_start: 0.8256 (mtp) cc_final: 0.7876 (mtm) REVERT: C 9 GLN cc_start: 0.6597 (mt0) cc_final: 0.6321 (mm-40) REVERT: C 46 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7705 (tpt170) REVERT: C 73 ARG cc_start: 0.7156 (mtt180) cc_final: 0.6940 (mtm180) REVERT: C 81 LYS cc_start: 0.8226 (ttmt) cc_final: 0.8020 (ttmt) REVERT: C 173 GLN cc_start: 0.8611 (tt0) cc_final: 0.8085 (tt0) REVERT: C 183 LYS cc_start: 0.7936 (pttt) cc_final: 0.7628 (ptpt) REVERT: C 200 GLU cc_start: 0.7510 (mp0) cc_final: 0.7113 (mp0) REVERT: C 265 GLU cc_start: 0.7370 (mt-10) cc_final: 0.7097 (mm-30) REVERT: C 342 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7391 (mp) REVERT: C 455 GLU cc_start: 0.7412 (mt-10) cc_final: 0.6944 (mp0) REVERT: C 458 GLU cc_start: 0.7268 (mm-30) cc_final: 0.6993 (mt-10) REVERT: C 467 MET cc_start: 0.9016 (mtp) cc_final: 0.8644 (mtm) REVERT: C 635 SER cc_start: 0.6858 (t) cc_final: 0.6623 (m) REVERT: C 693 LYS cc_start: 0.7639 (tttt) cc_final: 0.7355 (ttpp) REVERT: C 727 LYS cc_start: 0.7439 (pttt) cc_final: 0.7036 (ptpt) REVERT: C 746 THR cc_start: 0.7692 (m) cc_final: 0.7318 (p) REVERT: C 796 ASP cc_start: 0.8130 (OUTLIER) cc_final: 0.7786 (m-30) REVERT: C 843 MET cc_start: 0.8422 (ttp) cc_final: 0.8178 (ttp) REVERT: C 860 LYS cc_start: 0.8089 (mttt) cc_final: 0.7452 (tttm) REVERT: C 918 ASP cc_start: 0.6935 (p0) cc_final: 0.6657 (p0) outliers start: 83 outliers final: 55 residues processed: 417 average time/residue: 0.1517 time to fit residues: 96.4346 Evaluate side-chains 370 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 303 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 7 MET Chi-restraints excluded: chain A residue 19 ASP Chi-restraints excluded: chain A residue 44 LYS Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 551 ARG Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 811 GLN Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 864 ASP Chi-restraints excluded: chain A residue 865 SER Chi-restraints excluded: chain A residue 921 THR Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 249 ASN Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 430 ASP Chi-restraints excluded: chain B residue 433 GLN Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain B residue 737 SER Chi-restraints excluded: chain B residue 796 ASP Chi-restraints excluded: chain B residue 844 ARG Chi-restraints excluded: chain B residue 864 ASP Chi-restraints excluded: chain B residue 876 THR Chi-restraints excluded: chain B residue 950 THR Chi-restraints excluded: chain B residue 953 SER Chi-restraints excluded: chain C residue 46 ARG Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain C residue 280 MET Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 644 ASP Chi-restraints excluded: chain C residue 692 THR Chi-restraints excluded: chain C residue 731 THR Chi-restraints excluded: chain C residue 796 ASP Chi-restraints excluded: chain C residue 812 VAL Chi-restraints excluded: chain C residue 879 ARG Chi-restraints excluded: chain C residue 897 GLN Chi-restraints excluded: chain C residue 904 SER Chi-restraints excluded: chain C residue 932 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 0.0570 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 7.9990 overall best weight: 2.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 271 GLN B 571 GLN C 433 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.091288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2592 r_free = 0.2592 target = 0.077357 restraints weight = 28608.844| |-----------------------------------------------------------------------------| r_work (start): 0.2595 rms_B_bonded: 1.13 r_work: 0.2507 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.2422 rms_B_bonded: 2.12 restraints_weight: 0.2500 r_work (final): 0.2422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9029 moved from start: 0.0971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 22707 Z= 0.147 Angle : 0.563 9.057 30885 Z= 0.307 Chirality : 0.047 0.218 3257 Planarity : 0.005 0.056 4091 Dihedral : 7.634 70.019 3195 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.97 % Allowed : 9.17 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.64 % 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 are not related in a simple way. whole: -1.51 (0.15), residues: 2771 helix: 0.06 (0.31), residues: 318 sheet: -0.76 (0.19), residues: 650 loop : -1.34 (0.13), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 844 TYR 0.022 0.001 TYR A 23 PHE 0.013 0.002 PHE C 565 TRP 0.013 0.002 TRP C 531 HIS 0.005 0.001 HIS A 830 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (22706) covalent geometry : angle 0.56260 / 0.31 (30883) SS BOND : bond 0.02349 / 1.24 ( 1) SS BOND : angle 3.05152 / 1.76 ( 2) hydrogen bonds : bond 0.05013 / 3.36 ( 564) hydrogen bonds : angle 6.06231 / 4.22 ( 1554) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 303 time to evaluate : 0.848 Fit side-chains REVERT: A 6 MET cc_start: 0.7127 (mtt) cc_final: 0.6761 (mtt) REVERT: A 7 MET cc_start: 0.5830 (OUTLIER) cc_final: 0.4748 (mpt) REVERT: A 166 LYS cc_start: 0.8342 (mttt) cc_final: 0.7983 (mtpt) REVERT: A 183 LYS cc_start: 0.8892 (pttt) cc_final: 0.8615 (pttp) REVERT: A 200 GLU cc_start: 0.8848 (mp0) cc_final: 0.8281 (mp0) REVERT: A 369 ASP cc_start: 0.8897 (p0) cc_final: 0.8627 (p0) REVERT: A 433 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.7876 (pt0) REVERT: A 551 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.8519 (mtp85) REVERT: A 616 LYS cc_start: 0.8240 (tttt) cc_final: 0.7839 (tttm) REVERT: A 727 LYS cc_start: 0.6203 (pttt) cc_final: 0.5682 (mtmm) REVERT: A 808 MET cc_start: 0.8996 (mtm) cc_final: 0.8775 (mtp) REVERT: A 811 GLN cc_start: 0.8937 (OUTLIER) cc_final: 0.7300 (mp10) REVERT: A 843 MET cc_start: 0.9268 (ttp) cc_final: 0.8999 (ttp) REVERT: B 60 ARG cc_start: 0.8125 (mtt180) cc_final: 0.7836 (mtp-110) REVERT: B 73 ARG cc_start: 0.8204 (mtt180) cc_final: 0.7623 (mtp180) REVERT: B 92 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.8009 (mtm180) REVERT: B 187 GLN cc_start: 0.9336 (tt0) cc_final: 0.8983 (tt0) REVERT: B 200 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.6917 (mp0) REVERT: B 326 MET cc_start: 0.9167 (ttt) cc_final: 0.8936 (ttt) REVERT: B 458 GLU cc_start: 0.8906 (mm-30) cc_final: 0.8612 (mt-10) REVERT: B 509 ASP cc_start: 0.8211 (OUTLIER) cc_final: 0.7971 (t0) REVERT: B 817 LYS cc_start: 0.8356 (mttt) cc_final: 0.8140 (mtpp) REVERT: B 910 MET cc_start: 0.8909 (mtp) cc_final: 0.8631 (mtm) REVERT: C 9 GLN cc_start: 0.7953 (mt0) cc_final: 0.7499 (mm-40) REVERT: C 183 LYS cc_start: 0.8449 (pttt) cc_final: 0.8105 (ptpt) REVERT: C 200 GLU cc_start: 0.8115 (mp0) cc_final: 0.7582 (mp0) REVERT: C 265 GLU cc_start: 0.8318 (mt-10) cc_final: 0.7664 (mm-30) REVERT: C 342 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8579 (mp) REVERT: C 368 GLN cc_start: 0.8982 (OUTLIER) cc_final: 0.8420 (mm-40) REVERT: C 455 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7635 (mp0) REVERT: C 458 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7646 (mt-10) REVERT: C 860 LYS cc_start: 0.8579 (mttt) cc_final: 0.8094 (tttm) REVERT: C 918 ASP cc_start: 0.7795 (p0) cc_final: 0.7593 (p0) outliers start: 71 outliers final: 48 residues processed: 358 average time/residue: 0.1596 time to fit residues: 88.0327 Evaluate side-chains 340 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 283 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 7 MET Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 551 ARG Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 811 GLN Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 888 SER Chi-restraints excluded: chain A residue 921 THR Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 430 ASP Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 433 GLN Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 793 SER Chi-restraints excluded: chain B residue 844 ARG Chi-restraints excluded: chain B residue 903 ASN Chi-restraints excluded: chain B residue 904 SER Chi-restraints excluded: chain B residue 953 SER Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 233 LYS Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 280 MET Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 368 GLN Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 692 THR Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 897 GLN Chi-restraints excluded: chain C residue 921 THR Chi-restraints excluded: chain C residue 932 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 256 optimal weight: 10.0000 chunk 188 optimal weight: 20.0000 chunk 15 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 110 optimal weight: 9.9990 chunk 145 optimal weight: 0.0270 chunk 30 optimal weight: 0.5980 chunk 135 optimal weight: 1.9990 chunk 180 optimal weight: 7.9990 chunk 177 optimal weight: 9.9990 chunk 82 optimal weight: 0.9980 overall best weight: 0.9240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 433 GLN B 278 ASN B 331 ASN B 449 GLN C 377 GLN C 433 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.094975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.081216 restraints weight = 28344.310| |-----------------------------------------------------------------------------| r_work (start): 0.2648 rms_B_bonded: 1.15 r_work: 0.2563 rms_B_bonded: 1.22 restraints_weight: 0.5000 r_work: 0.2478 rms_B_bonded: 2.13 restraints_weight: 0.2500 r_work (final): 0.2478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8988 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 22707 Z= 0.083 Angle : 0.463 6.508 30885 Z= 0.253 Chirality : 0.043 0.171 3257 Planarity : 0.004 0.043 4091 Dihedral : 6.201 59.754 3136 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.68 % Allowed : 11.14 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.64 % 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 are not related in a simple way. whole: -1.10 (0.15), residues: 2771 helix: 0.51 (0.32), residues: 317 sheet: -0.50 (0.19), residues: 663 loop : -1.08 (0.14), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 109 TYR 0.019 0.001 TYR A 23 PHE 0.011 0.001 PHE B 465 TRP 0.009 0.001 TRP B 878 HIS 0.004 0.001 HIS B 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00181 / 0.08 (22706) covalent geometry : angle 0.46267 / 0.25 (30883) SS BOND : bond 0.01693 / 0.89 ( 1) SS BOND : angle 2.55994 / 1.50 ( 2) hydrogen bonds : bond 0.03348 / 2.25 ( 564) hydrogen bonds : angle 5.46880 / 3.82 ( 1554) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 305 time to evaluate : 0.868 Fit side-chains REVERT: A 7 MET cc_start: 0.5626 (OUTLIER) cc_final: 0.4162 (mpt) REVERT: A 13 MET cc_start: 0.9125 (mmm) cc_final: 0.8824 (mmm) REVERT: A 41 LEU cc_start: 0.8959 (mt) cc_final: 0.8656 (mp) REVERT: A 166 LYS cc_start: 0.8337 (mttt) cc_final: 0.7960 (mtpt) REVERT: A 183 LYS cc_start: 0.8825 (pttt) cc_final: 0.8561 (pttp) REVERT: A 200 GLU cc_start: 0.8864 (mp0) cc_final: 0.8271 (mp0) REVERT: A 616 LYS cc_start: 0.8158 (tttt) cc_final: 0.7814 (tttm) REVERT: A 727 LYS cc_start: 0.6227 (pttt) cc_final: 0.5688 (mtmm) REVERT: A 811 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.6834 (mp10) REVERT: A 843 MET cc_start: 0.9248 (ttp) cc_final: 0.9045 (ttp) REVERT: B 60 ARG cc_start: 0.8086 (mtt180) cc_final: 0.7748 (mtp-110) REVERT: B 73 ARG cc_start: 0.8126 (mtt180) cc_final: 0.7751 (mtp180) REVERT: B 92 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.6079 (mtm180) REVERT: B 187 GLN cc_start: 0.9327 (tt0) cc_final: 0.8960 (tt0) REVERT: B 200 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7388 (mp0) REVERT: B 249 ASN cc_start: 0.8878 (p0) cc_final: 0.8642 (p0) REVERT: B 267 GLN cc_start: 0.8410 (mm-40) cc_final: 0.7759 (mt0) REVERT: B 320 MET cc_start: 0.9368 (mmm) cc_final: 0.9116 (mmm) REVERT: B 326 MET cc_start: 0.9122 (ttt) cc_final: 0.8866 (ttt) REVERT: B 458 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8659 (mt-10) REVERT: B 727 LYS cc_start: 0.9120 (ptpt) cc_final: 0.8636 (ptpp) REVERT: B 817 LYS cc_start: 0.8500 (mttt) cc_final: 0.8266 (mtpp) REVERT: B 910 MET cc_start: 0.9008 (mtp) cc_final: 0.8796 (mtm) REVERT: C 9 GLN cc_start: 0.7847 (mt0) cc_final: 0.7444 (mm-40) REVERT: C 200 GLU cc_start: 0.8093 (mp0) cc_final: 0.7806 (mp0) REVERT: C 265 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7507 (mm-30) REVERT: C 315 ASP cc_start: 0.8423 (m-30) cc_final: 0.8006 (m-30) REVERT: C 342 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8599 (mp) REVERT: C 368 GLN cc_start: 0.9011 (OUTLIER) cc_final: 0.8726 (tt0) REVERT: C 379 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8368 (tp) REVERT: C 455 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7618 (mp0) REVERT: C 458 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7392 (mt-10) REVERT: C 768 MET cc_start: 0.9132 (ttm) cc_final: 0.8895 (ttp) REVERT: C 777 MET cc_start: 0.9231 (mmm) cc_final: 0.8977 (mmm) REVERT: C 860 LYS cc_start: 0.8612 (mttt) cc_final: 0.8072 (tttm) outliers start: 40 outliers final: 21 residues processed: 335 average time/residue: 0.1590 time to fit residues: 82.9785 Evaluate side-chains 315 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 287 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 MET Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 811 GLN Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 819 LYS Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 433 GLN Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 844 ARG Chi-restraints excluded: chain B residue 903 ASN Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 280 MET Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 368 GLN Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 433 GLN Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 932 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 66 optimal weight: 0.7980 chunk 240 optimal weight: 7.9990 chunk 16 optimal weight: 20.0000 chunk 249 optimal weight: 2.9990 chunk 69 optimal weight: 8.9990 chunk 210 optimal weight: 0.9990 chunk 1 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 101 optimal weight: 10.0000 chunk 164 optimal weight: 8.9990 chunk 144 optimal weight: 10.0000 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 433 GLN B 449 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.090870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2576 r_free = 0.2576 target = 0.076491 restraints weight = 28684.025| |-----------------------------------------------------------------------------| r_work (start): 0.2580 rms_B_bonded: 1.12 r_work: 0.2502 rms_B_bonded: 1.20 restraints_weight: 0.5000 r_work: 0.2416 rms_B_bonded: 2.10 restraints_weight: 0.2500 r_work (final): 0.2416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9032 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 22707 Z= 0.185 Angle : 0.577 7.411 30885 Z= 0.309 Chirality : 0.047 0.195 3257 Planarity : 0.005 0.042 4091 Dihedral : 5.995 59.101 3110 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.93 % Allowed : 11.35 % Favored : 85.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.64 % 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 are not related in a simple way. whole: -1.20 (0.15), residues: 2771 helix: 0.41 (0.32), residues: 313 sheet: -0.58 (0.19), residues: 683 loop : -1.13 (0.14), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 844 TYR 0.017 0.002 TYR C 23 PHE 0.017 0.002 PHE C 565 TRP 0.014 0.002 TRP A 531 HIS 0.007 0.001 HIS A 830 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.18 (22706) covalent geometry : angle 0.57643 / 0.31 (30883) SS BOND : bond 0.02068 / 1.09 ( 1) SS BOND : angle 3.07860 / 1.80 ( 2) hydrogen bonds : bond 0.04664 / 3.12 ( 564) hydrogen bonds : angle 5.55892 / 3.86 ( 1554) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 270 time to evaluate : 0.891 Fit side-chains REVERT: A 7 MET cc_start: 0.6256 (OUTLIER) cc_final: 0.4810 (mpt) REVERT: A 13 MET cc_start: 0.9231 (mmm) cc_final: 0.8903 (mmm) REVERT: A 36 GLU cc_start: 0.8720 (tm-30) cc_final: 0.8318 (tm-30) REVERT: A 166 LYS cc_start: 0.8372 (mttt) cc_final: 0.7989 (mtpt) REVERT: A 183 LYS cc_start: 0.8851 (pttt) cc_final: 0.8555 (pttp) REVERT: A 200 GLU cc_start: 0.8874 (mp0) cc_final: 0.8336 (mp0) REVERT: A 616 LYS cc_start: 0.8329 (tttt) cc_final: 0.7920 (tttm) REVERT: A 727 LYS cc_start: 0.6256 (pttt) cc_final: 0.5689 (mtmm) REVERT: A 811 GLN cc_start: 0.8903 (OUTLIER) cc_final: 0.7191 (mp10) REVERT: A 843 MET cc_start: 0.9282 (ttp) cc_final: 0.9031 (ttp) REVERT: B 60 ARG cc_start: 0.8139 (mtt180) cc_final: 0.7770 (mtp-110) REVERT: B 73 ARG cc_start: 0.8183 (mtt180) cc_final: 0.7785 (mtp180) REVERT: B 92 ARG cc_start: 0.8929 (OUTLIER) cc_final: 0.7956 (mtm180) REVERT: B 187 GLN cc_start: 0.9275 (tt0) cc_final: 0.8838 (tt0) REVERT: B 200 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7453 (mp0) REVERT: B 267 GLN cc_start: 0.8655 (mm-40) cc_final: 0.7971 (mt0) REVERT: B 326 MET cc_start: 0.9183 (ttt) cc_final: 0.8968 (ttt) REVERT: B 458 GLU cc_start: 0.8865 (mm-30) cc_final: 0.8647 (mt-10) REVERT: B 817 LYS cc_start: 0.8434 (mttt) cc_final: 0.8180 (mtpp) REVERT: B 910 MET cc_start: 0.8955 (mtp) cc_final: 0.8665 (mtm) REVERT: C 9 GLN cc_start: 0.7926 (mt0) cc_final: 0.7537 (mm-40) REVERT: C 200 GLU cc_start: 0.8090 (mp0) cc_final: 0.7532 (mp0) REVERT: C 265 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7568 (mm-30) REVERT: C 342 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8604 (mp) REVERT: C 368 GLN cc_start: 0.9019 (OUTLIER) cc_final: 0.8468 (mm-40) REVERT: C 379 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8459 (tp) REVERT: C 386 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.7370 (mmm160) REVERT: C 455 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7632 (mp0) REVERT: C 458 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7431 (mt-10) REVERT: C 768 MET cc_start: 0.9121 (ttm) cc_final: 0.8907 (ttp) REVERT: C 860 LYS cc_start: 0.8613 (mttt) cc_final: 0.8087 (tttm) outliers start: 70 outliers final: 48 residues processed: 319 average time/residue: 0.1586 time to fit residues: 78.6547 Evaluate side-chains 327 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 271 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 MET Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 811 GLN Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 827 ILE Chi-restraints excluded: chain A residue 888 SER Chi-restraints excluded: chain A residue 921 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 433 GLN Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 793 SER Chi-restraints excluded: chain B residue 796 ASP Chi-restraints excluded: chain B residue 844 ARG Chi-restraints excluded: chain B residue 876 THR Chi-restraints excluded: chain B residue 903 ASN Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 280 MET Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 368 GLN Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 386 ARG Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 879 ARG Chi-restraints excluded: chain C residue 921 THR Chi-restraints excluded: chain C residue 932 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 72 optimal weight: 2.9990 chunk 123 optimal weight: 7.9990 chunk 225 optimal weight: 7.9990 chunk 203 optimal weight: 5.9990 chunk 181 optimal weight: 3.9990 chunk 135 optimal weight: 0.8980 chunk 188 optimal weight: 7.9990 chunk 140 optimal weight: 6.9990 chunk 254 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 238 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 449 GLN C 184 ASN C 433 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.091318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2589 r_free = 0.2589 target = 0.077288 restraints weight = 28371.690| |-----------------------------------------------------------------------------| r_work (start): 0.2588 rms_B_bonded: 1.14 r_work: 0.2506 rms_B_bonded: 1.19 restraints_weight: 0.5000 r_work: 0.2422 rms_B_bonded: 2.05 restraints_weight: 0.2500 r_work (final): 0.2422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9015 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22707 Z= 0.160 Angle : 0.547 6.913 30885 Z= 0.295 Chirality : 0.046 0.183 3257 Planarity : 0.004 0.042 4091 Dihedral : 5.978 60.350 3110 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.31 % Allowed : 11.39 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.64 % 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 are not related in a simple way. whole: -1.17 (0.15), residues: 2771 helix: 0.38 (0.32), residues: 313 sheet: -0.50 (0.19), residues: 669 loop : -1.13 (0.14), residues: 1789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 844 TYR 0.017 0.001 TYR C 23 PHE 0.014 0.002 PHE C 565 TRP 0.012 0.002 TRP A 531 HIS 0.005 0.001 HIS A 830 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.16 (22706) covalent geometry : angle 0.54614 / 0.29 (30883) SS BOND : bond 0.02108 / 1.11 ( 1) SS BOND : angle 2.97668 / 1.73 ( 2) hydrogen bonds : bond 0.04282 / 2.86 ( 564) hydrogen bonds : angle 5.47668 / 3.81 ( 1554) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 271 time to evaluate : 0.728 Fit side-chains REVERT: A 7 MET cc_start: 0.6388 (OUTLIER) cc_final: 0.4745 (mpt) REVERT: A 36 GLU cc_start: 0.8746 (tm-30) cc_final: 0.8294 (tm-30) REVERT: A 166 LYS cc_start: 0.8414 (mttt) cc_final: 0.8021 (mtpt) REVERT: A 183 LYS cc_start: 0.8843 (pttt) cc_final: 0.8555 (pttp) REVERT: A 200 GLU cc_start: 0.8798 (mp0) cc_final: 0.8204 (mp0) REVERT: A 616 LYS cc_start: 0.8304 (tttt) cc_final: 0.7893 (tttm) REVERT: A 727 LYS cc_start: 0.6222 (pttt) cc_final: 0.5657 (mtmm) REVERT: A 808 MET cc_start: 0.9108 (mtm) cc_final: 0.8580 (ptp) REVERT: A 811 GLN cc_start: 0.8972 (OUTLIER) cc_final: 0.7360 (mp10) REVERT: A 843 MET cc_start: 0.9293 (ttp) cc_final: 0.9036 (ttp) REVERT: B 60 ARG cc_start: 0.8157 (mtt180) cc_final: 0.7793 (mtp-110) REVERT: B 73 ARG cc_start: 0.8164 (mtt180) cc_final: 0.7751 (mtp180) REVERT: B 92 ARG cc_start: 0.8898 (OUTLIER) cc_final: 0.6202 (mtm180) REVERT: B 187 GLN cc_start: 0.9262 (tt0) cc_final: 0.8837 (tt0) REVERT: B 196 GLU cc_start: 0.4878 (OUTLIER) cc_final: 0.4580 (pp20) REVERT: B 200 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7213 (mp0) REVERT: B 267 GLN cc_start: 0.8651 (mm-40) cc_final: 0.7982 (mt0) REVERT: B 326 MET cc_start: 0.9169 (ttt) cc_final: 0.8936 (ttt) REVERT: B 458 GLU cc_start: 0.8956 (mm-30) cc_final: 0.8647 (mt-10) REVERT: B 817 LYS cc_start: 0.8430 (mttt) cc_final: 0.8158 (mtpp) REVERT: B 910 MET cc_start: 0.8974 (mtp) cc_final: 0.8698 (mtm) REVERT: C 9 GLN cc_start: 0.7912 (mt0) cc_final: 0.7522 (mm-40) REVERT: C 200 GLU cc_start: 0.8135 (mp0) cc_final: 0.7549 (mp0) REVERT: C 215 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7547 (mt-10) REVERT: C 265 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7518 (mm-30) REVERT: C 342 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8601 (mp) REVERT: C 368 GLN cc_start: 0.9013 (OUTLIER) cc_final: 0.8459 (mm-40) REVERT: C 379 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8455 (tp) REVERT: C 386 ARG cc_start: 0.8839 (OUTLIER) cc_final: 0.7362 (mmm160) REVERT: C 455 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7599 (mp0) REVERT: C 458 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7370 (mt-10) REVERT: C 768 MET cc_start: 0.9124 (ttm) cc_final: 0.8905 (ttp) REVERT: C 860 LYS cc_start: 0.8606 (mttt) cc_final: 0.8062 (tttm) outliers start: 79 outliers final: 51 residues processed: 327 average time/residue: 0.1551 time to fit residues: 79.3649 Evaluate side-chains 328 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 268 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 MET Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 811 GLN Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 827 ILE Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 888 SER Chi-restraints excluded: chain A residue 904 SER Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 433 GLN Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 616 LYS Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 793 SER Chi-restraints excluded: chain B residue 844 ARG Chi-restraints excluded: chain B residue 876 THR Chi-restraints excluded: chain B residue 903 ASN Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 280 MET Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 368 GLN Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 386 ARG Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 861 THR Chi-restraints excluded: chain C residue 879 ARG Chi-restraints excluded: chain C residue 921 THR Chi-restraints excluded: chain C residue 932 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 42 optimal weight: 9.9990 chunk 263 optimal weight: 5.9990 chunk 188 optimal weight: 7.9990 chunk 275 optimal weight: 5.9990 chunk 190 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 122 optimal weight: 0.9980 chunk 110 optimal weight: 7.9990 chunk 87 optimal weight: 0.0670 chunk 170 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 overall best weight: 3.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 184 ASN C 433 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.091486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2590 r_free = 0.2590 target = 0.077302 restraints weight = 28676.112| |-----------------------------------------------------------------------------| r_work (start): 0.2592 rms_B_bonded: 1.08 r_work: 0.2508 rms_B_bonded: 1.22 restraints_weight: 0.5000 r_work: 0.2423 rms_B_bonded: 2.11 restraints_weight: 0.2500 r_work (final): 0.2423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9022 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22707 Z= 0.153 Angle : 0.543 7.239 30885 Z= 0.293 Chirality : 0.046 0.182 3257 Planarity : 0.004 0.044 4091 Dihedral : 5.936 60.405 3110 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 1.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.56 % Allowed : 11.68 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.64 % 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 are not related in a simple way. whole: -1.16 (0.15), residues: 2771 helix: 0.43 (0.32), residues: 313 sheet: -0.51 (0.19), residues: 674 loop : -1.11 (0.14), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 844 TYR 0.017 0.001 TYR C 23 PHE 0.014 0.002 PHE C 565 TRP 0.013 0.002 TRP A 531 HIS 0.005 0.001 HIS A 830 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.15 (22706) covalent geometry : angle 0.54297 / 0.29 (30883) SS BOND : bond 0.01995 / 1.05 ( 1) SS BOND : angle 2.63460 / 1.54 ( 2) hydrogen bonds : bond 0.04197 / 2.80 ( 564) hydrogen bonds : angle 5.43877 / 3.79 ( 1554) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 270 time to evaluate : 0.847 Fit side-chains REVERT: A 7 MET cc_start: 0.6368 (OUTLIER) cc_final: 0.4693 (mpt) REVERT: A 166 LYS cc_start: 0.8421 (mttt) cc_final: 0.8020 (mtpt) REVERT: A 183 LYS cc_start: 0.8816 (pttt) cc_final: 0.8534 (pttp) REVERT: A 200 GLU cc_start: 0.8825 (mp0) cc_final: 0.8250 (mp0) REVERT: A 287 GLN cc_start: 0.8618 (mm-40) cc_final: 0.8196 (mm110) REVERT: A 616 LYS cc_start: 0.8304 (tttt) cc_final: 0.7896 (tttm) REVERT: A 629 MET cc_start: 0.8705 (ttm) cc_final: 0.8319 (ttm) REVERT: A 727 LYS cc_start: 0.6250 (pttt) cc_final: 0.5677 (mtmm) REVERT: A 811 GLN cc_start: 0.8887 (OUTLIER) cc_final: 0.7124 (mp10) REVERT: A 843 MET cc_start: 0.9299 (ttp) cc_final: 0.9053 (ttp) REVERT: B 60 ARG cc_start: 0.8180 (mtt180) cc_final: 0.7812 (mtp-110) REVERT: B 73 ARG cc_start: 0.8190 (mtt180) cc_final: 0.7792 (mtp180) REVERT: B 92 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.6199 (mtm180) REVERT: B 187 GLN cc_start: 0.9270 (tt0) cc_final: 0.8860 (tt0) REVERT: B 196 GLU cc_start: 0.4890 (OUTLIER) cc_final: 0.4587 (pp20) REVERT: B 200 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7257 (mp0) REVERT: B 267 GLN cc_start: 0.8656 (mm-40) cc_final: 0.8007 (mt0) REVERT: B 326 MET cc_start: 0.9170 (ttt) cc_final: 0.8933 (ttt) REVERT: B 458 GLU cc_start: 0.8964 (mm-30) cc_final: 0.8656 (mt-10) REVERT: B 817 LYS cc_start: 0.8427 (mttt) cc_final: 0.8167 (mtpp) REVERT: B 910 MET cc_start: 0.8980 (mtp) cc_final: 0.8700 (mtm) REVERT: C 9 GLN cc_start: 0.7932 (mt0) cc_final: 0.7544 (mm-40) REVERT: C 200 GLU cc_start: 0.8135 (mp0) cc_final: 0.7544 (mp0) REVERT: C 215 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7529 (mt-10) REVERT: C 265 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7526 (mm-30) REVERT: C 342 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8614 (mp) REVERT: C 361 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7899 (tp) REVERT: C 368 GLN cc_start: 0.9021 (OUTLIER) cc_final: 0.8468 (mm-40) REVERT: C 379 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8455 (tp) REVERT: C 386 ARG cc_start: 0.8840 (OUTLIER) cc_final: 0.7382 (mmm160) REVERT: C 433 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7748 (pt0) REVERT: C 455 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7605 (mp0) REVERT: C 458 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7342 (mt-10) REVERT: C 768 MET cc_start: 0.9133 (ttm) cc_final: 0.8917 (ttp) REVERT: C 860 LYS cc_start: 0.8608 (mttt) cc_final: 0.8062 (tttm) outliers start: 85 outliers final: 62 residues processed: 333 average time/residue: 0.1526 time to fit residues: 79.6551 Evaluate side-chains 343 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 270 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 MET Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 811 GLN Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 827 ILE Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 879 ARG Chi-restraints excluded: chain A residue 888 SER Chi-restraints excluded: chain A residue 904 SER Chi-restraints excluded: chain A residue 921 THR Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 433 GLN Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 616 LYS Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 793 SER Chi-restraints excluded: chain B residue 844 ARG Chi-restraints excluded: chain B residue 876 THR Chi-restraints excluded: chain B residue 903 ASN Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 280 MET Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 368 GLN Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 386 ARG Chi-restraints excluded: chain C residue 433 GLN Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 861 THR Chi-restraints excluded: chain C residue 879 ARG Chi-restraints excluded: chain C residue 897 GLN Chi-restraints excluded: chain C residue 921 THR Chi-restraints excluded: chain C residue 932 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 13 optimal weight: 2.9990 chunk 178 optimal weight: 9.9990 chunk 146 optimal weight: 1.9990 chunk 228 optimal weight: 7.9990 chunk 222 optimal weight: 0.7980 chunk 43 optimal weight: 9.9990 chunk 129 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 chunk 42 optimal weight: 9.9990 chunk 70 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 512 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.093112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.079300 restraints weight = 28227.183| |-----------------------------------------------------------------------------| r_work (start): 0.2618 rms_B_bonded: 1.11 r_work: 0.2535 rms_B_bonded: 1.20 restraints_weight: 0.5000 r_work: 0.2450 rms_B_bonded: 2.09 restraints_weight: 0.2500 r_work (final): 0.2450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9009 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22707 Z= 0.106 Angle : 0.490 8.001 30885 Z= 0.265 Chirality : 0.044 0.170 3257 Planarity : 0.004 0.040 4091 Dihedral : 5.679 61.043 3110 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.68 % Allowed : 12.56 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.64 % 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 are not related in a simple way. whole: -1.03 (0.15), residues: 2771 helix: 0.62 (0.32), residues: 312 sheet: -0.50 (0.19), residues: 676 loop : -1.01 (0.14), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 456 TYR 0.017 0.001 TYR A 23 PHE 0.010 0.001 PHE A 687 TRP 0.011 0.001 TRP B 878 HIS 0.004 0.001 HIS B 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (22706) covalent geometry : angle 0.48944 / 0.26 (30883) SS BOND : bond 0.01863 / 0.98 ( 1) SS BOND : angle 2.29760 / 1.35 ( 2) hydrogen bonds : bond 0.03544 / 2.37 ( 564) hydrogen bonds : angle 5.29628 / 3.69 ( 1554) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 277 time to evaluate : 0.790 Fit side-chains REVERT: A 7 MET cc_start: 0.6371 (OUTLIER) cc_final: 0.4826 (mpt) REVERT: A 36 GLU cc_start: 0.8650 (tm-30) cc_final: 0.8337 (tm-30) REVERT: A 41 LEU cc_start: 0.8960 (mt) cc_final: 0.8561 (mp) REVERT: A 166 LYS cc_start: 0.8370 (mttt) cc_final: 0.7980 (mtpt) REVERT: A 183 LYS cc_start: 0.8785 (pttt) cc_final: 0.8513 (pttp) REVERT: A 281 ASN cc_start: 0.4382 (OUTLIER) cc_final: 0.4043 (p0) REVERT: A 287 GLN cc_start: 0.8592 (mm-40) cc_final: 0.8172 (mm110) REVERT: A 616 LYS cc_start: 0.8275 (tttt) cc_final: 0.7893 (tttm) REVERT: A 727 LYS cc_start: 0.6244 (pttt) cc_final: 0.5728 (mtmm) REVERT: A 811 GLN cc_start: 0.8856 (OUTLIER) cc_final: 0.7013 (mp10) REVERT: A 843 MET cc_start: 0.9289 (ttp) cc_final: 0.9071 (ttp) REVERT: B 60 ARG cc_start: 0.8130 (mtt180) cc_final: 0.7844 (mtp-110) REVERT: B 73 ARG cc_start: 0.8150 (mtt180) cc_final: 0.7777 (mtp180) REVERT: B 92 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.6469 (mtm180) REVERT: B 184 ASN cc_start: 0.8826 (m-40) cc_final: 0.8391 (m-40) REVERT: B 187 GLN cc_start: 0.9260 (tt0) cc_final: 0.8853 (tt0) REVERT: B 200 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7659 (mp0) REVERT: B 267 GLN cc_start: 0.8655 (mm-40) cc_final: 0.8035 (mt0) REVERT: B 326 MET cc_start: 0.9131 (ttt) cc_final: 0.8871 (ttt) REVERT: B 458 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8658 (mt-10) REVERT: B 817 LYS cc_start: 0.8435 (mttt) cc_final: 0.8174 (mtpp) REVERT: B 910 MET cc_start: 0.9003 (mtp) cc_final: 0.8728 (mtm) REVERT: C 9 GLN cc_start: 0.7887 (mt0) cc_final: 0.7537 (mm-40) REVERT: C 200 GLU cc_start: 0.8123 (mp0) cc_final: 0.7599 (mp0) REVERT: C 265 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7504 (mm-30) REVERT: C 315 ASP cc_start: 0.8427 (m-30) cc_final: 0.7938 (m-30) REVERT: C 342 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8587 (mp) REVERT: C 368 GLN cc_start: 0.9019 (OUTLIER) cc_final: 0.8470 (mm-40) REVERT: C 379 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8404 (tp) REVERT: C 386 ARG cc_start: 0.8818 (OUTLIER) cc_final: 0.7420 (mmm160) REVERT: C 455 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7584 (mp0) REVERT: C 768 MET cc_start: 0.9112 (ttm) cc_final: 0.8870 (ttp) REVERT: C 860 LYS cc_start: 0.8617 (mttt) cc_final: 0.8061 (tttm) outliers start: 64 outliers final: 47 residues processed: 325 average time/residue: 0.1417 time to fit residues: 72.2414 Evaluate side-chains 332 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 276 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 MET Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 811 GLN Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 879 ARG Chi-restraints excluded: chain A residue 888 SER Chi-restraints excluded: chain A residue 921 THR Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 616 LYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain B residue 844 ARG Chi-restraints excluded: chain B residue 903 ASN Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 280 MET Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 368 GLN Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 386 ARG Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 649 SER Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 861 THR Chi-restraints excluded: chain C residue 889 MET Chi-restraints excluded: chain C residue 921 THR Chi-restraints excluded: chain C residue 932 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 185 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 68 optimal weight: 0.7980 chunk 247 optimal weight: 0.2980 chunk 174 optimal weight: 3.9990 chunk 100 optimal weight: 10.0000 chunk 152 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 120 optimal weight: 7.9990 chunk 219 optimal weight: 9.9990 chunk 112 optimal weight: 6.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 903 ASN C 433 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.093803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.080102 restraints weight = 28245.579| |-----------------------------------------------------------------------------| r_work (start): 0.2649 rms_B_bonded: 1.12 r_work: 0.2559 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.2474 rms_B_bonded: 2.16 restraints_weight: 0.2500 r_work (final): 0.2474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9005 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 22707 Z= 0.100 Angle : 0.482 8.172 30885 Z= 0.260 Chirality : 0.044 0.165 3257 Planarity : 0.004 0.039 4091 Dihedral : 5.461 59.592 3107 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.72 % Allowed : 12.60 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.64 % 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 are not related in a simple way. whole: -0.95 (0.15), residues: 2771 helix: 0.65 (0.32), residues: 318 sheet: -0.41 (0.19), residues: 673 loop : -0.98 (0.14), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 456 TYR 0.017 0.001 TYR A 23 PHE 0.010 0.001 PHE C 687 TRP 0.011 0.001 TRP B 878 HIS 0.004 0.001 HIS B 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.10 (22706) covalent geometry : angle 0.48139 / 0.26 (30883) SS BOND : bond 0.01640 / 0.86 ( 1) SS BOND : angle 2.26667 / 1.33 ( 2) hydrogen bonds : bond 0.03409 / 2.28 ( 564) hydrogen bonds : angle 5.19476 / 3.62 ( 1554) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 280 time to evaluate : 0.603 Fit side-chains REVERT: A 4 PRO cc_start: 0.7615 (Cg_endo) cc_final: 0.7372 (Cg_exo) REVERT: A 7 MET cc_start: 0.6320 (OUTLIER) cc_final: 0.4779 (mpt) REVERT: A 36 GLU cc_start: 0.8696 (tm-30) cc_final: 0.8345 (tm-30) REVERT: A 41 LEU cc_start: 0.8976 (mt) cc_final: 0.8572 (mp) REVERT: A 166 LYS cc_start: 0.8422 (mttt) cc_final: 0.8012 (mtpt) REVERT: A 183 LYS cc_start: 0.8824 (pttt) cc_final: 0.8552 (pttp) REVERT: A 281 ASN cc_start: 0.4248 (OUTLIER) cc_final: 0.3910 (p0) REVERT: A 287 GLN cc_start: 0.8546 (mm-40) cc_final: 0.8135 (mm110) REVERT: A 509 ASP cc_start: 0.8867 (t70) cc_final: 0.8444 (t0) REVERT: A 616 LYS cc_start: 0.8288 (tttt) cc_final: 0.7881 (tttm) REVERT: A 620 ILE cc_start: 0.8298 (mt) cc_final: 0.7906 (tt) REVERT: A 727 LYS cc_start: 0.6255 (pttt) cc_final: 0.5730 (mtmm) REVERT: A 811 GLN cc_start: 0.8868 (OUTLIER) cc_final: 0.7117 (mp10) REVERT: A 843 MET cc_start: 0.9277 (ttp) cc_final: 0.9070 (ttp) REVERT: B 60 ARG cc_start: 0.8133 (mtt180) cc_final: 0.7792 (mtp-110) REVERT: B 73 ARG cc_start: 0.8144 (mtt180) cc_final: 0.7756 (mtp180) REVERT: B 184 ASN cc_start: 0.8801 (m-40) cc_final: 0.8350 (m-40) REVERT: B 187 GLN cc_start: 0.9259 (tt0) cc_final: 0.8869 (tt0) REVERT: B 200 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7680 (mp0) REVERT: B 267 GLN cc_start: 0.8646 (mm-40) cc_final: 0.8050 (mt0) REVERT: B 326 MET cc_start: 0.9137 (ttt) cc_final: 0.8906 (ttt) REVERT: B 458 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8659 (mt-10) REVERT: B 817 LYS cc_start: 0.8446 (mttt) cc_final: 0.8193 (mtpp) REVERT: B 910 MET cc_start: 0.9026 (mtp) cc_final: 0.8784 (mtm) REVERT: C 9 GLN cc_start: 0.7858 (mt0) cc_final: 0.7504 (mm-40) REVERT: C 200 GLU cc_start: 0.8179 (mp0) cc_final: 0.7623 (mp0) REVERT: C 265 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7471 (mm-30) REVERT: C 315 ASP cc_start: 0.8440 (m-30) cc_final: 0.7943 (m-30) REVERT: C 342 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8578 (mp) REVERT: C 368 GLN cc_start: 0.9019 (OUTLIER) cc_final: 0.8458 (mm-40) REVERT: C 379 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8409 (tp) REVERT: C 386 ARG cc_start: 0.8812 (OUTLIER) cc_final: 0.7487 (mmm160) REVERT: C 433 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.7605 (pt0) REVERT: C 455 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7575 (mp0) REVERT: C 768 MET cc_start: 0.9102 (ttm) cc_final: 0.8844 (ttp) REVERT: C 860 LYS cc_start: 0.8633 (mttt) cc_final: 0.8056 (tttm) outliers start: 65 outliers final: 50 residues processed: 330 average time/residue: 0.1437 time to fit residues: 73.9996 Evaluate side-chains 330 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 271 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 MET Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 811 GLN Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 879 ARG Chi-restraints excluded: chain A residue 888 SER Chi-restraints excluded: chain A residue 921 THR Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 616 LYS Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain B residue 793 SER Chi-restraints excluded: chain B residue 844 ARG Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 280 MET Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 368 GLN Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 386 ARG Chi-restraints excluded: chain C residue 433 GLN Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 649 SER Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 861 THR Chi-restraints excluded: chain C residue 897 GLN Chi-restraints excluded: chain C residue 921 THR Chi-restraints excluded: chain C residue 932 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 233 optimal weight: 0.0270 chunk 58 optimal weight: 9.9990 chunk 214 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 138 optimal weight: 2.9990 chunk 15 optimal weight: 9.9990 chunk 189 optimal weight: 10.0000 chunk 219 optimal weight: 9.9990 chunk 264 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 152 optimal weight: 5.9990 overall best weight: 2.5444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 449 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.092502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.078696 restraints weight = 28372.667| |-----------------------------------------------------------------------------| r_work (start): 0.2610 rms_B_bonded: 1.13 r_work: 0.2525 rms_B_bonded: 1.20 restraints_weight: 0.5000 r_work: 0.2440 rms_B_bonded: 2.10 restraints_weight: 0.2500 r_work (final): 0.2440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9017 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22707 Z= 0.134 Angle : 0.521 8.210 30885 Z= 0.280 Chirality : 0.045 0.173 3257 Planarity : 0.004 0.039 4091 Dihedral : 5.475 60.040 3102 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 1.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.89 % Allowed : 12.52 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.64 % 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 are not related in a simple way. whole: -1.00 (0.15), residues: 2771 helix: 0.67 (0.32), residues: 312 sheet: -0.45 (0.19), residues: 680 loop : -1.01 (0.14), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 844 TYR 0.016 0.001 TYR C 23 PHE 0.013 0.001 PHE C 565 TRP 0.011 0.001 TRP A 531 HIS 0.005 0.001 HIS A 830 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.13 (22706) covalent geometry : angle 0.52096 / 0.28 (30883) SS BOND : bond 0.01785 / 0.94 ( 1) SS BOND : angle 2.43819 / 1.43 ( 2) hydrogen bonds : bond 0.03890 / 2.60 ( 564) hydrogen bonds : angle 5.26435 / 3.66 ( 1554) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 269 time to evaluate : 0.703 Fit side-chains REVERT: A 7 MET cc_start: 0.6370 (OUTLIER) cc_final: 0.4756 (mpt) REVERT: A 36 GLU cc_start: 0.8728 (tm-30) cc_final: 0.8338 (tm-30) REVERT: A 166 LYS cc_start: 0.8428 (mttt) cc_final: 0.8027 (mtpt) REVERT: A 183 LYS cc_start: 0.8823 (pttt) cc_final: 0.8594 (pttp) REVERT: A 281 ASN cc_start: 0.4195 (OUTLIER) cc_final: 0.3866 (p0) REVERT: A 287 GLN cc_start: 0.8623 (mm-40) cc_final: 0.8202 (mm110) REVERT: A 551 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.8026 (mtp85) REVERT: A 616 LYS cc_start: 0.8305 (tttt) cc_final: 0.7905 (tttm) REVERT: A 727 LYS cc_start: 0.6255 (pttt) cc_final: 0.5739 (mtmm) REVERT: A 811 GLN cc_start: 0.8875 (OUTLIER) cc_final: 0.7121 (mp10) REVERT: A 843 MET cc_start: 0.9286 (ttp) cc_final: 0.9070 (ttp) REVERT: B 60 ARG cc_start: 0.8149 (mtt180) cc_final: 0.7857 (mtp-110) REVERT: B 73 ARG cc_start: 0.8164 (mtt180) cc_final: 0.7797 (mtp180) REVERT: B 184 ASN cc_start: 0.8824 (m-40) cc_final: 0.8360 (m-40) REVERT: B 187 GLN cc_start: 0.9231 (tt0) cc_final: 0.8880 (tt0) REVERT: B 196 GLU cc_start: 0.4835 (OUTLIER) cc_final: 0.4565 (pp20) REVERT: B 200 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7716 (mp0) REVERT: B 267 GLN cc_start: 0.8686 (mm-40) cc_final: 0.8071 (mt0) REVERT: B 326 MET cc_start: 0.9133 (ttt) cc_final: 0.8878 (ttt) REVERT: B 458 GLU cc_start: 0.8934 (mm-30) cc_final: 0.8670 (mt-10) REVERT: B 817 LYS cc_start: 0.8440 (mttt) cc_final: 0.8175 (mtpp) REVERT: B 910 MET cc_start: 0.8965 (mtp) cc_final: 0.8690 (mtm) REVERT: C 9 GLN cc_start: 0.7872 (mt0) cc_final: 0.7521 (mm-40) REVERT: C 200 GLU cc_start: 0.8166 (mp0) cc_final: 0.7584 (mp0) REVERT: C 265 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7495 (mm-30) REVERT: C 315 ASP cc_start: 0.8420 (m-30) cc_final: 0.7912 (m-30) REVERT: C 342 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8567 (mp) REVERT: C 368 GLN cc_start: 0.9011 (OUTLIER) cc_final: 0.8464 (mm-40) REVERT: C 379 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8437 (tp) REVERT: C 386 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.7438 (mmm160) REVERT: C 455 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7586 (mp0) REVERT: C 768 MET cc_start: 0.9124 (ttm) cc_final: 0.8886 (ttp) REVERT: C 860 LYS cc_start: 0.8617 (mttt) cc_final: 0.8062 (tttm) outliers start: 69 outliers final: 57 residues processed: 321 average time/residue: 0.1473 time to fit residues: 73.7114 Evaluate side-chains 337 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 270 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 MET Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 551 ARG Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 811 GLN Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 879 ARG Chi-restraints excluded: chain A residue 888 SER Chi-restraints excluded: chain A residue 904 SER Chi-restraints excluded: chain A residue 921 THR Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 616 LYS Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 793 SER Chi-restraints excluded: chain B residue 844 ARG Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 280 MET Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 368 GLN Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 386 ARG Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 649 SER Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 861 THR Chi-restraints excluded: chain C residue 889 MET Chi-restraints excluded: chain C residue 897 GLN Chi-restraints excluded: chain C residue 921 THR Chi-restraints excluded: chain C residue 932 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 199 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 chunk 123 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 149 optimal weight: 10.0000 chunk 207 optimal weight: 10.0000 chunk 171 optimal weight: 0.8980 chunk 117 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 217 optimal weight: 0.0020 chunk 36 optimal weight: 0.0670 overall best weight: 1.7930 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 449 GLN C 433 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.093760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.079800 restraints weight = 28203.098| |-----------------------------------------------------------------------------| r_work (start): 0.2643 rms_B_bonded: 1.15 r_work: 0.2553 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.2467 rms_B_bonded: 2.20 restraints_weight: 0.2500 r_work (final): 0.2467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9004 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22707 Z= 0.106 Angle : 0.488 8.256 30885 Z= 0.263 Chirality : 0.044 0.169 3257 Planarity : 0.004 0.039 4091 Dihedral : 5.365 59.662 3102 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 1.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.76 % Allowed : 12.69 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.64 % 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 are not related in a simple way. whole: -0.90 (0.15), residues: 2771 helix: 0.76 (0.32), residues: 312 sheet: -0.39 (0.19), residues: 673 loop : -0.94 (0.14), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 456 TYR 0.017 0.001 TYR A 23 PHE 0.010 0.001 PHE C 565 TRP 0.011 0.001 TRP B 878 HIS 0.004 0.001 HIS B 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (22706) covalent geometry : angle 0.48786 / 0.26 (30883) SS BOND : bond 0.01713 / 0.90 ( 1) SS BOND : angle 2.33035 / 1.37 ( 2) hydrogen bonds : bond 0.03458 / 2.32 ( 564) hydrogen bonds : angle 5.19353 / 3.61 ( 1554) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 272 time to evaluate : 0.718 Fit side-chains REVERT: A 7 MET cc_start: 0.6338 (OUTLIER) cc_final: 0.4789 (mpt) REVERT: A 36 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8346 (tm-30) REVERT: A 41 LEU cc_start: 0.8965 (mt) cc_final: 0.8557 (mp) REVERT: A 166 LYS cc_start: 0.8426 (mttt) cc_final: 0.8016 (mtpt) REVERT: A 183 LYS cc_start: 0.8734 (pttt) cc_final: 0.8489 (pttp) REVERT: A 281 ASN cc_start: 0.4165 (OUTLIER) cc_final: 0.3867 (p0) REVERT: A 287 GLN cc_start: 0.8544 (mm-40) cc_final: 0.8138 (mm110) REVERT: A 509 ASP cc_start: 0.8855 (t70) cc_final: 0.8428 (t0) REVERT: A 551 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.8588 (mtp85) REVERT: A 616 LYS cc_start: 0.8302 (tttt) cc_final: 0.7903 (tttm) REVERT: A 727 LYS cc_start: 0.6257 (pttt) cc_final: 0.5719 (mtmm) REVERT: A 811 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.7093 (mp10) REVERT: A 843 MET cc_start: 0.9314 (ttp) cc_final: 0.9109 (ttp) REVERT: B 60 ARG cc_start: 0.8144 (mtt180) cc_final: 0.7790 (mtp-110) REVERT: B 73 ARG cc_start: 0.8144 (mtt180) cc_final: 0.7774 (mtp180) REVERT: B 184 ASN cc_start: 0.8803 (m-40) cc_final: 0.8342 (m-40) REVERT: B 187 GLN cc_start: 0.9257 (tt0) cc_final: 0.8849 (tt0) REVERT: B 200 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7713 (mp0) REVERT: B 267 GLN cc_start: 0.8665 (mm-40) cc_final: 0.8063 (mt0) REVERT: B 326 MET cc_start: 0.9126 (ttt) cc_final: 0.8865 (ttt) REVERT: B 449 GLN cc_start: 0.8454 (tt0) cc_final: 0.8195 (tt0) REVERT: B 458 GLU cc_start: 0.8925 (mm-30) cc_final: 0.8665 (mt-10) REVERT: B 817 LYS cc_start: 0.8447 (mttt) cc_final: 0.8175 (mtpp) REVERT: B 910 MET cc_start: 0.8974 (mtp) cc_final: 0.8692 (mtm) REVERT: C 9 GLN cc_start: 0.7858 (mt0) cc_final: 0.7501 (mm-40) REVERT: C 200 GLU cc_start: 0.8161 (mp0) cc_final: 0.7575 (mp0) REVERT: C 265 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7470 (mm-30) REVERT: C 291 LEU cc_start: 0.8751 (tp) cc_final: 0.8505 (tp) REVERT: C 315 ASP cc_start: 0.8434 (m-30) cc_final: 0.7926 (m-30) REVERT: C 342 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8556 (mp) REVERT: C 368 GLN cc_start: 0.9012 (OUTLIER) cc_final: 0.8454 (mm-40) REVERT: C 379 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8403 (tp) REVERT: C 386 ARG cc_start: 0.8819 (OUTLIER) cc_final: 0.7507 (mmm160) REVERT: C 433 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7688 (pt0) REVERT: C 455 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7593 (mp0) REVERT: C 768 MET cc_start: 0.9112 (ttm) cc_final: 0.8854 (ttp) REVERT: C 860 LYS cc_start: 0.8626 (mttt) cc_final: 0.8047 (tttm) outliers start: 66 outliers final: 56 residues processed: 322 average time/residue: 0.1456 time to fit residues: 72.7725 Evaluate side-chains 338 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 272 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 MET Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 551 ARG Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 811 GLN Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 879 ARG Chi-restraints excluded: chain A residue 888 SER Chi-restraints excluded: chain A residue 904 SER Chi-restraints excluded: chain A residue 921 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 616 LYS Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 793 SER Chi-restraints excluded: chain B residue 844 ARG Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 280 MET Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 368 GLN Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 386 ARG Chi-restraints excluded: chain C residue 433 GLN Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 649 SER Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 861 THR Chi-restraints excluded: chain C residue 879 ARG Chi-restraints excluded: chain C residue 889 MET Chi-restraints excluded: chain C residue 897 GLN Chi-restraints excluded: chain C residue 921 THR Chi-restraints excluded: chain C residue 932 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 32 optimal weight: 0.9990 chunk 14 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 193 optimal weight: 9.9990 chunk 58 optimal weight: 0.9990 chunk 235 optimal weight: 6.9990 chunk 264 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 220 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 185 optimal weight: 0.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 433 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.094567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.080471 restraints weight = 28156.608| |-----------------------------------------------------------------------------| r_work (start): 0.2661 rms_B_bonded: 1.13 r_work: 0.2577 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.2488 rms_B_bonded: 2.19 restraints_weight: 0.2500 r_work (final): 0.2488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8981 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 22707 Z= 0.086 Angle : 0.464 8.133 30885 Z= 0.250 Chirality : 0.043 0.161 3257 Planarity : 0.004 0.039 4091 Dihedral : 5.217 58.610 3102 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.51 % Allowed : 12.90 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.64 % 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 are not related in a simple way. whole: -0.77 (0.15), residues: 2771 helix: 1.00 (0.33), residues: 306 sheet: -0.33 (0.19), residues: 688 loop : -0.86 (0.14), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 456 TYR 0.017 0.001 TYR A 23 PHE 0.010 0.001 PHE C 687 TRP 0.012 0.001 TRP B 878 HIS 0.004 0.001 HIS B 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00198 / 0.09 (22706) covalent geometry : angle 0.46385 / 0.25 (30883) SS BOND : bond 0.01622 / 0.85 ( 1) SS BOND : angle 2.23587 / 1.31 ( 2) hydrogen bonds : bond 0.03123 / 2.09 ( 564) hydrogen bonds : angle 5.10298 / 3.55 ( 1554) =============================================================================== Job complete usr+sys time: 4273.66 seconds wall clock time: 74 minutes 5.83 seconds (4445.83 seconds total)