Starting phenix.real_space_refine on Mon Sep 14 08:29:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11sq_76016/09_2026/11sq_76016.cif Found real_map, /net/cci-nas-00/data/ceres_data/11sq_76016/09_2026/11sq_76016.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/11sq_76016/09_2026/11sq_76016.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11sq_76016/09_2026/11sq_76016.map" model { file = "/net/cci-nas-00/data/ceres_data/11sq_76016/09_2026/11sq_76016.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11sq_76016/09_2026/11sq_76016.cif" } resolution = 3.2 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= 0.007 sd= 0.017 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 63 5.16 5 C 17934 2.51 5 N 5201 2.21 5 O 5194 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28392 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 624, 4056 Classifications: {'peptide': 624} Incomplete info: {'truncation_to_alanine': 245} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 598} Chain breaks: 1 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 902 Unresolved non-hydrogen angles: 1174 Unresolved non-hydrogen dihedrals: 766 Unresolved non-hydrogen chiralities: 106 Planarities with less than four sites: {'TRP:plan': 9, 'GLU:plan': 10, 'GLN:plan1': 6, 'ASP:plan': 9, 'ARG:plan': 16, 'PHE:plan': 14, 'TYR:plan': 8, 'HIS:plan': 4, 'ASN:plan1': 7} Unresolved non-hydrogen planarities: 433 Restraints were copied for chains: B, C, D, E, F, G Time building chain proxies: 4.92, per 1000 atoms: 0.17 Number of scatterers: 28392 At special positions: 0 Unit cell: (204.974, 203.28, 120.274, 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 63 16.00 O 5194 8.00 N 5201 7.00 C 17934 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.80 Conformation dependent library (CDL) restraints added in 1.4 seconds 8680 Ramachandran restraints generated. 4340 Oldfield, 0 Emsley, 4340 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8162 Finding SS restraints... Secondary structure from input PDB file: 161 helices and 23 sheets defined 69.2% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 441 through 456 removed outlier: 4.246A pdb=" N GLU A 445 " --> pdb=" O ALA A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 472 Processing helix chain 'A' and resid 475 through 507 removed outlier: 3.515A pdb=" N GLY A 481 " --> pdb=" O LEU A 477 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N ARG A 494 " --> pdb=" O ILE A 490 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N TYR A 495 " --> pdb=" O TYR A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 529 removed outlier: 3.888A pdb=" N THR A 518 " --> pdb=" O HIS A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 545 Processing helix chain 'A' and resid 549 through 576 removed outlier: 3.533A pdb=" N VAL A 553 " --> pdb=" O TYR A 549 " (cutoff:3.500A) Proline residue: A 564 - end of helix Processing helix chain 'A' and resid 590 through 604 Processing helix chain 'A' and resid 606 through 620 Processing helix chain 'A' and resid 621 through 623 No H-bonds generated for 'chain 'A' and resid 621 through 623' Processing helix chain 'A' and resid 624 through 627 removed outlier: 3.554A pdb=" N GLY A 627 " --> pdb=" O GLU A 624 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 624 through 627' Processing helix chain 'A' and resid 628 through 652 removed outlier: 3.936A pdb=" N GLY A 652 " --> pdb=" O LEU A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 689 Proline residue: A 679 - end of helix Processing helix chain 'A' and resid 691 through 743 removed outlier: 3.669A pdb=" N GLN A 695 " --> pdb=" O LEU A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 797 Processing helix chain 'A' and resid 801 through 806 Processing helix chain 'A' and resid 807 through 810 Processing helix chain 'A' and resid 831 through 859 removed outlier: 3.976A pdb=" N ILE A 836 " --> pdb=" O GLY A 832 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ALA A 837 " --> pdb=" O ALA A 833 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE A 838 " --> pdb=" O VAL A 834 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU A 839 " --> pdb=" O LEU A 835 " (cutoff:3.500A) Proline residue: A 852 - end of helix Processing helix chain 'A' and resid 868 through 894 Processing helix chain 'A' and resid 900 through 932 removed outlier: 3.514A pdb=" N ILE A 918 " --> pdb=" O GLY A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 977 Processing helix chain 'A' and resid 1002 through 1017 removed outlier: 3.660A pdb=" N CYS A1017 " --> pdb=" O ALA A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1048 through 1050 No H-bonds generated for 'chain 'A' and resid 1048 through 1050' Processing helix chain 'A' and resid 1051 through 1071 Processing helix chain 'B' and resid 441 through 456 removed outlier: 4.247A pdb=" N GLU B 445 " --> pdb=" O ALA B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 472 Processing helix chain 'B' and resid 475 through 507 removed outlier: 3.516A pdb=" N GLY B 481 " --> pdb=" O LEU B 477 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ARG B 494 " --> pdb=" O ILE B 490 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N TYR B 495 " --> pdb=" O TYR B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 529 removed outlier: 3.888A pdb=" N THR B 518 " --> pdb=" O HIS B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 545 Processing helix chain 'B' and resid 549 through 576 removed outlier: 3.533A pdb=" N VAL B 553 " --> pdb=" O TYR B 549 " (cutoff:3.500A) Proline residue: B 564 - end of helix Processing helix chain 'B' and resid 590 through 604 Processing helix chain 'B' and resid 606 through 620 Processing helix chain 'B' and resid 621 through 623 No H-bonds generated for 'chain 'B' and resid 621 through 623' Processing helix chain 'B' and resid 624 through 627 removed outlier: 3.554A pdb=" N GLY B 627 " --> pdb=" O GLU B 624 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 624 through 627' Processing helix chain 'B' and resid 628 through 652 removed outlier: 3.936A pdb=" N GLY B 652 " --> pdb=" O LEU B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 689 Proline residue: B 679 - end of helix Processing helix chain 'B' and resid 691 through 743 removed outlier: 3.670A pdb=" N GLN B 695 " --> pdb=" O LEU B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 774 through 797 Processing helix chain 'B' and resid 801 through 806 Processing helix chain 'B' and resid 807 through 810 Processing helix chain 'B' and resid 831 through 859 removed outlier: 3.975A pdb=" N ILE B 836 " --> pdb=" O GLY B 832 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ALA B 837 " --> pdb=" O ALA B 833 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ILE B 838 " --> pdb=" O VAL B 834 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU B 839 " --> pdb=" O LEU B 835 " (cutoff:3.500A) Proline residue: B 852 - end of helix Processing helix chain 'B' and resid 868 through 894 Processing helix chain 'B' and resid 900 through 932 removed outlier: 3.515A pdb=" N ILE B 918 " --> pdb=" O GLY B 914 " (cutoff:3.500A) Processing helix chain 'B' and resid 972 through 977 Processing helix chain 'B' and resid 1002 through 1017 removed outlier: 3.658A pdb=" N CYS B1017 " --> pdb=" O ALA B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1048 through 1050 No H-bonds generated for 'chain 'B' and resid 1048 through 1050' Processing helix chain 'B' and resid 1051 through 1071 Processing helix chain 'C' and resid 441 through 456 removed outlier: 4.246A pdb=" N GLU C 445 " --> pdb=" O ALA C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 472 Processing helix chain 'C' and resid 475 through 507 removed outlier: 3.516A pdb=" N GLY C 481 " --> pdb=" O LEU C 477 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ARG C 494 " --> pdb=" O ILE C 490 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N TYR C 495 " --> pdb=" O TYR C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 514 through 529 removed outlier: 3.888A pdb=" N THR C 518 " --> pdb=" O HIS C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 531 through 545 Processing helix chain 'C' and resid 549 through 576 removed outlier: 3.533A pdb=" N VAL C 553 " --> pdb=" O TYR C 549 " (cutoff:3.500A) Proline residue: C 564 - end of helix Processing helix chain 'C' and resid 590 through 604 Processing helix chain 'C' and resid 606 through 620 Processing helix chain 'C' and resid 621 through 623 No H-bonds generated for 'chain 'C' and resid 621 through 623' Processing helix chain 'C' and resid 624 through 627 removed outlier: 3.553A pdb=" N GLY C 627 " --> pdb=" O GLU C 624 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 624 through 627' Processing helix chain 'C' and resid 628 through 652 removed outlier: 3.936A pdb=" N GLY C 652 " --> pdb=" O LEU C 648 " (cutoff:3.500A) Processing helix chain 'C' and resid 666 through 689 Proline residue: C 679 - end of helix Processing helix chain 'C' and resid 691 through 743 removed outlier: 3.669A pdb=" N GLN C 695 " --> pdb=" O LEU C 691 " (cutoff:3.500A) Processing helix chain 'C' and resid 774 through 797 Processing helix chain 'C' and resid 801 through 806 Processing helix chain 'C' and resid 807 through 810 Processing helix chain 'C' and resid 831 through 859 removed outlier: 3.975A pdb=" N ILE C 836 " --> pdb=" O GLY C 832 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ALA C 837 " --> pdb=" O ALA C 833 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ILE C 838 " --> pdb=" O VAL C 834 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU C 839 " --> pdb=" O LEU C 835 " (cutoff:3.500A) Proline residue: C 852 - end of helix Processing helix chain 'C' and resid 868 through 894 Processing helix chain 'C' and resid 900 through 932 removed outlier: 3.513A pdb=" N ILE C 918 " --> pdb=" O GLY C 914 " (cutoff:3.500A) Processing helix chain 'C' and resid 972 through 977 Processing helix chain 'C' and resid 1002 through 1017 removed outlier: 3.659A pdb=" N CYS C1017 " --> pdb=" O ALA C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1048 through 1050 No H-bonds generated for 'chain 'C' and resid 1048 through 1050' Processing helix chain 'C' and resid 1051 through 1071 Processing helix chain 'D' and resid 441 through 456 removed outlier: 4.247A pdb=" N GLU D 445 " --> pdb=" O ALA D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 457 through 472 Processing helix chain 'D' and resid 475 through 507 removed outlier: 3.516A pdb=" N GLY D 481 " --> pdb=" O LEU D 477 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ARG D 494 " --> pdb=" O ILE D 490 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N TYR D 495 " --> pdb=" O TYR D 491 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 529 removed outlier: 3.888A pdb=" N THR D 518 " --> pdb=" O HIS D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 545 Processing helix chain 'D' and resid 549 through 576 removed outlier: 3.533A pdb=" N VAL D 553 " --> pdb=" O TYR D 549 " (cutoff:3.500A) Proline residue: D 564 - end of helix Processing helix chain 'D' and resid 590 through 604 Processing helix chain 'D' and resid 606 through 620 Processing helix chain 'D' and resid 621 through 623 No H-bonds generated for 'chain 'D' and resid 621 through 623' Processing helix chain 'D' and resid 624 through 627 removed outlier: 3.553A pdb=" N GLY D 627 " --> pdb=" O GLU D 624 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 624 through 627' Processing helix chain 'D' and resid 628 through 652 removed outlier: 3.936A pdb=" N GLY D 652 " --> pdb=" O LEU D 648 " (cutoff:3.500A) Processing helix chain 'D' and resid 666 through 689 Proline residue: D 679 - end of helix Processing helix chain 'D' and resid 691 through 743 removed outlier: 3.669A pdb=" N GLN D 695 " --> pdb=" O LEU D 691 " (cutoff:3.500A) Processing helix chain 'D' and resid 774 through 797 Processing helix chain 'D' and resid 801 through 806 Processing helix chain 'D' and resid 807 through 810 Processing helix chain 'D' and resid 831 through 859 removed outlier: 3.975A pdb=" N ILE D 836 " --> pdb=" O GLY D 832 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ALA D 837 " --> pdb=" O ALA D 833 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ILE D 838 " --> pdb=" O VAL D 834 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU D 839 " --> pdb=" O LEU D 835 " (cutoff:3.500A) Proline residue: D 852 - end of helix Processing helix chain 'D' and resid 868 through 894 Processing helix chain 'D' and resid 900 through 932 removed outlier: 3.514A pdb=" N ILE D 918 " --> pdb=" O GLY D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 972 through 977 Processing helix chain 'D' and resid 1002 through 1017 removed outlier: 3.659A pdb=" N CYS D1017 " --> pdb=" O ALA D1013 " (cutoff:3.500A) Processing helix chain 'D' and resid 1048 through 1050 No H-bonds generated for 'chain 'D' and resid 1048 through 1050' Processing helix chain 'D' and resid 1051 through 1071 Processing helix chain 'E' and resid 441 through 456 removed outlier: 4.247A pdb=" N GLU E 445 " --> pdb=" O ALA E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 457 through 472 Processing helix chain 'E' and resid 475 through 507 removed outlier: 3.515A pdb=" N GLY E 481 " --> pdb=" O LEU E 477 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N ARG E 494 " --> pdb=" O ILE E 490 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N TYR E 495 " --> pdb=" O TYR E 491 " (cutoff:3.500A) Processing helix chain 'E' and resid 514 through 529 removed outlier: 3.887A pdb=" N THR E 518 " --> pdb=" O HIS E 514 " (cutoff:3.500A) Processing helix chain 'E' and resid 531 through 545 Processing helix chain 'E' and resid 549 through 576 removed outlier: 3.533A pdb=" N VAL E 553 " --> pdb=" O TYR E 549 " (cutoff:3.500A) Proline residue: E 564 - end of helix Processing helix chain 'E' and resid 590 through 604 Processing helix chain 'E' and resid 606 through 620 Processing helix chain 'E' and resid 621 through 623 No H-bonds generated for 'chain 'E' and resid 621 through 623' Processing helix chain 'E' and resid 624 through 627 removed outlier: 3.553A pdb=" N GLY E 627 " --> pdb=" O GLU E 624 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 624 through 627' Processing helix chain 'E' and resid 628 through 652 removed outlier: 3.936A pdb=" N GLY E 652 " --> pdb=" O LEU E 648 " (cutoff:3.500A) Processing helix chain 'E' and resid 666 through 689 Proline residue: E 679 - end of helix Processing helix chain 'E' and resid 691 through 743 removed outlier: 3.669A pdb=" N GLN E 695 " --> pdb=" O LEU E 691 " (cutoff:3.500A) Processing helix chain 'E' and resid 774 through 797 Processing helix chain 'E' and resid 801 through 806 Processing helix chain 'E' and resid 807 through 810 Processing helix chain 'E' and resid 831 through 859 removed outlier: 3.975A pdb=" N ILE E 836 " --> pdb=" O GLY E 832 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ALA E 837 " --> pdb=" O ALA E 833 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ILE E 838 " --> pdb=" O VAL E 834 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU E 839 " --> pdb=" O LEU E 835 " (cutoff:3.500A) Proline residue: E 852 - end of helix Processing helix chain 'E' and resid 868 through 894 Processing helix chain 'E' and resid 900 through 932 removed outlier: 3.514A pdb=" N ILE E 918 " --> pdb=" O GLY E 914 " (cutoff:3.500A) Processing helix chain 'E' and resid 972 through 977 Processing helix chain 'E' and resid 1002 through 1017 removed outlier: 3.658A pdb=" N CYS E1017 " --> pdb=" O ALA E1013 " (cutoff:3.500A) Processing helix chain 'E' and resid 1048 through 1050 No H-bonds generated for 'chain 'E' and resid 1048 through 1050' Processing helix chain 'E' and resid 1051 through 1071 Processing helix chain 'F' and resid 441 through 456 removed outlier: 4.247A pdb=" N GLU F 445 " --> pdb=" O ALA F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 457 through 472 Processing helix chain 'F' and resid 475 through 507 removed outlier: 3.516A pdb=" N GLY F 481 " --> pdb=" O LEU F 477 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ARG F 494 " --> pdb=" O ILE F 490 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N TYR F 495 " --> pdb=" O TYR F 491 " (cutoff:3.500A) Processing helix chain 'F' and resid 514 through 529 removed outlier: 3.888A pdb=" N THR F 518 " --> pdb=" O HIS F 514 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 545 Processing helix chain 'F' and resid 549 through 576 removed outlier: 3.533A pdb=" N VAL F 553 " --> pdb=" O TYR F 549 " (cutoff:3.500A) Proline residue: F 564 - end of helix Processing helix chain 'F' and resid 590 through 604 Processing helix chain 'F' and resid 606 through 620 Processing helix chain 'F' and resid 621 through 623 No H-bonds generated for 'chain 'F' and resid 621 through 623' Processing helix chain 'F' and resid 624 through 627 removed outlier: 3.553A pdb=" N GLY F 627 " --> pdb=" O GLU F 624 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 624 through 627' Processing helix chain 'F' and resid 628 through 652 removed outlier: 3.937A pdb=" N GLY F 652 " --> pdb=" O LEU F 648 " (cutoff:3.500A) Processing helix chain 'F' and resid 666 through 689 Proline residue: F 679 - end of helix Processing helix chain 'F' and resid 691 through 743 removed outlier: 3.670A pdb=" N GLN F 695 " --> pdb=" O LEU F 691 " (cutoff:3.500A) Processing helix chain 'F' and resid 774 through 797 Processing helix chain 'F' and resid 801 through 806 Processing helix chain 'F' and resid 807 through 810 Processing helix chain 'F' and resid 831 through 859 removed outlier: 3.975A pdb=" N ILE F 836 " --> pdb=" O GLY F 832 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ALA F 837 " --> pdb=" O ALA F 833 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ILE F 838 " --> pdb=" O VAL F 834 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU F 839 " --> pdb=" O LEU F 835 " (cutoff:3.500A) Proline residue: F 852 - end of helix Processing helix chain 'F' and resid 868 through 894 Processing helix chain 'F' and resid 900 through 932 removed outlier: 3.514A pdb=" N ILE F 918 " --> pdb=" O GLY F 914 " (cutoff:3.500A) Processing helix chain 'F' and resid 972 through 977 Processing helix chain 'F' and resid 1002 through 1017 removed outlier: 3.659A pdb=" N CYS F1017 " --> pdb=" O ALA F1013 " (cutoff:3.500A) Processing helix chain 'F' and resid 1048 through 1050 No H-bonds generated for 'chain 'F' and resid 1048 through 1050' Processing helix chain 'F' and resid 1051 through 1071 Processing helix chain 'G' and resid 441 through 456 removed outlier: 4.246A pdb=" N GLU G 445 " --> pdb=" O ALA G 441 " (cutoff:3.500A) Processing helix chain 'G' and resid 457 through 472 Processing helix chain 'G' and resid 475 through 507 removed outlier: 3.515A pdb=" N GLY G 481 " --> pdb=" O LEU G 477 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N ARG G 494 " --> pdb=" O ILE G 490 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N TYR G 495 " --> pdb=" O TYR G 491 " (cutoff:3.500A) Processing helix chain 'G' and resid 514 through 529 removed outlier: 3.888A pdb=" N THR G 518 " --> pdb=" O HIS G 514 " (cutoff:3.500A) Processing helix chain 'G' and resid 531 through 545 Processing helix chain 'G' and resid 549 through 576 removed outlier: 3.533A pdb=" N VAL G 553 " --> pdb=" O TYR G 549 " (cutoff:3.500A) Proline residue: G 564 - end of helix Processing helix chain 'G' and resid 590 through 604 Processing helix chain 'G' and resid 606 through 620 Processing helix chain 'G' and resid 621 through 623 No H-bonds generated for 'chain 'G' and resid 621 through 623' Processing helix chain 'G' and resid 624 through 627 removed outlier: 3.553A pdb=" N GLY G 627 " --> pdb=" O GLU G 624 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 624 through 627' Processing helix chain 'G' and resid 628 through 652 removed outlier: 3.936A pdb=" N GLY G 652 " --> pdb=" O LEU G 648 " (cutoff:3.500A) Processing helix chain 'G' and resid 666 through 689 Proline residue: G 679 - end of helix Processing helix chain 'G' and resid 691 through 743 removed outlier: 3.669A pdb=" N GLN G 695 " --> pdb=" O LEU G 691 " (cutoff:3.500A) Processing helix chain 'G' and resid 774 through 797 Processing helix chain 'G' and resid 801 through 806 Processing helix chain 'G' and resid 807 through 810 Processing helix chain 'G' and resid 831 through 859 removed outlier: 3.975A pdb=" N ILE G 836 " --> pdb=" O GLY G 832 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ALA G 837 " --> pdb=" O ALA G 833 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ILE G 838 " --> pdb=" O VAL G 834 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU G 839 " --> pdb=" O LEU G 835 " (cutoff:3.500A) Proline residue: G 852 - end of helix Processing helix chain 'G' and resid 868 through 894 Processing helix chain 'G' and resid 900 through 932 removed outlier: 3.515A pdb=" N ILE G 918 " --> pdb=" O GLY G 914 " (cutoff:3.500A) Processing helix chain 'G' and resid 972 through 977 Processing helix chain 'G' and resid 1002 through 1017 removed outlier: 3.659A pdb=" N CYS G1017 " --> pdb=" O ALA G1013 " (cutoff:3.500A) Processing helix chain 'G' and resid 1048 through 1050 No H-bonds generated for 'chain 'G' and resid 1048 through 1050' Processing helix chain 'G' and resid 1051 through 1071 Processing sheet with id=AA1, first strand: chain 'A' and resid 812 through 820 removed outlier: 3.900A pdb=" N TRP A 814 " --> pdb=" O ILE A 829 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 939 through 941 removed outlier: 6.964A pdb=" N THR A 958 " --> pdb=" O THR A 950 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ILE A 952 " --> pdb=" O ALA A 956 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ALA A 956 " --> pdb=" O ILE A 952 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE B 979 " --> pdb=" O ILE A 968 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N THR B 958 " --> pdb=" O THR B 950 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ILE B 952 " --> pdb=" O ALA B 956 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ALA B 956 " --> pdb=" O ILE B 952 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE C 979 " --> pdb=" O ILE B 968 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N THR C 958 " --> pdb=" O THR C 950 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ILE C 952 " --> pdb=" O ALA C 956 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ALA C 956 " --> pdb=" O ILE C 952 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE D 979 " --> pdb=" O ILE C 968 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N THR D 958 " --> pdb=" O THR D 950 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ILE D 952 " --> pdb=" O ALA D 956 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ALA D 956 " --> pdb=" O ILE D 952 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE E 979 " --> pdb=" O ILE D 968 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N THR E 958 " --> pdb=" O THR E 950 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ILE E 952 " --> pdb=" O ALA E 956 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ALA E 956 " --> pdb=" O ILE E 952 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE F 979 " --> pdb=" O ILE E 968 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N THR F 958 " --> pdb=" O THR F 950 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ILE F 952 " --> pdb=" O ALA F 956 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ALA F 956 " --> pdb=" O ILE F 952 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE G 979 " --> pdb=" O ILE F 968 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N THR G 958 " --> pdb=" O THR G 950 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ILE G 952 " --> pdb=" O ALA G 956 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ALA G 956 " --> pdb=" O ILE G 952 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE A 979 " --> pdb=" O ILE G 968 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 989 through 990 Processing sheet with id=AA4, first strand: chain 'A' and resid 993 through 997 removed outlier: 7.165A pdb=" N ILE A1039 " --> pdb=" O VAL A1031 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1078 through 1084 removed outlier: 3.600A pdb=" N GLU B1084 " --> pdb=" O MET A1081 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU A1083 " --> pdb=" O GLU B1084 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU C1084 " --> pdb=" O MET B1081 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LEU B1083 " --> pdb=" O GLU C1084 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU D1084 " --> pdb=" O MET C1081 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LEU C1083 " --> pdb=" O GLU D1084 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU E1084 " --> pdb=" O MET D1081 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU D1083 " --> pdb=" O GLU E1084 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU F1084 " --> pdb=" O MET E1081 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LEU E1083 " --> pdb=" O GLU F1084 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU G1084 " --> pdb=" O MET F1081 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU F1083 " --> pdb=" O GLU G1084 " (cutoff:3.500A) removed outlier: 8.710A pdb=" N PHE G1079 " --> pdb=" O PRO A1078 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N GLN A1080 " --> pdb=" O PHE G1079 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N MET G1081 " --> pdb=" O GLN A1080 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ARG A1082 " --> pdb=" O MET G1081 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N LEU G1083 " --> pdb=" O ARG A1082 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N GLU A1084 " --> pdb=" O LEU G1083 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 812 through 820 removed outlier: 3.900A pdb=" N TRP B 814 " --> pdb=" O ILE B 829 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 989 through 990 Processing sheet with id=AA8, first strand: chain 'B' and resid 993 through 997 removed outlier: 7.165A pdb=" N ILE B1039 " --> pdb=" O VAL B1031 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 812 through 820 removed outlier: 3.900A pdb=" N TRP C 814 " --> pdb=" O ILE C 829 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 989 through 990 Processing sheet with id=AB2, first strand: chain 'C' and resid 993 through 997 removed outlier: 7.165A pdb=" N ILE C1039 " --> pdb=" O VAL C1031 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 812 through 820 removed outlier: 3.899A pdb=" N TRP D 814 " --> pdb=" O ILE D 829 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 989 through 990 Processing sheet with id=AB5, first strand: chain 'D' and resid 993 through 997 removed outlier: 7.165A pdb=" N ILE D1039 " --> pdb=" O VAL D1031 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 812 through 820 removed outlier: 3.899A pdb=" N TRP E 814 " --> pdb=" O ILE E 829 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 989 through 990 Processing sheet with id=AB8, first strand: chain 'E' and resid 993 through 997 removed outlier: 7.165A pdb=" N ILE E1039 " --> pdb=" O VAL E1031 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 812 through 820 removed outlier: 3.899A pdb=" N TRP F 814 " --> pdb=" O ILE F 829 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 989 through 990 Processing sheet with id=AC2, first strand: chain 'F' and resid 993 through 997 removed outlier: 7.166A pdb=" N ILE F1039 " --> pdb=" O VAL F1031 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 812 through 820 removed outlier: 3.900A pdb=" N TRP G 814 " --> pdb=" O ILE G 829 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 989 through 990 Processing sheet with id=AC5, first strand: chain 'G' and resid 993 through 997 removed outlier: 7.165A pdb=" N ILE G1039 " --> pdb=" O VAL G1031 " (cutoff:3.500A) 2482 hydrogen bonds defined for protein. 7320 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.84 Time building geometry restraints manager: 3.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9954 1.34 - 1.46: 5979 1.46 - 1.58: 12697 1.58 - 1.70: 0 1.70 - 1.82: 119 Bond restraints: 28749 Sorted by residual: bond pdb=" CB LYS A 899 " pdb=" CG LYS A 899 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.55e+00 bond pdb=" CB LYS D 899 " pdb=" CG LYS D 899 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.50e+00 bond pdb=" CB LYS F 899 " pdb=" CG LYS F 899 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.50e+00 bond pdb=" CB LYS E 899 " pdb=" CG LYS E 899 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.49e+00 bond pdb=" CB LYS G 899 " pdb=" CG LYS G 899 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.46e+00 ... (remaining 28744 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 38969 2.78 - 5.55: 329 5.55 - 8.33: 70 8.33 - 11.10: 14 11.10 - 13.88: 21 Bond angle restraints: 39403 Sorted by residual: angle pdb=" CA LEU D 779 " pdb=" CB LEU D 779 " pdb=" CG LEU D 779 " ideal model delta sigma weight residual 116.30 130.18 -13.88 3.50e+00 8.16e-02 1.57e+01 angle pdb=" CA LEU C 779 " pdb=" CB LEU C 779 " pdb=" CG LEU C 779 " ideal model delta sigma weight residual 116.30 130.17 -13.87 3.50e+00 8.16e-02 1.57e+01 angle pdb=" CA LEU B 779 " pdb=" CB LEU B 779 " pdb=" CG LEU B 779 " ideal model delta sigma weight residual 116.30 130.17 -13.87 3.50e+00 8.16e-02 1.57e+01 angle pdb=" CA LEU A 779 " pdb=" CB LEU A 779 " pdb=" CG LEU A 779 " ideal model delta sigma weight residual 116.30 130.15 -13.85 3.50e+00 8.16e-02 1.57e+01 angle pdb=" CA LEU F 779 " pdb=" CB LEU F 779 " pdb=" CG LEU F 779 " ideal model delta sigma weight residual 116.30 130.15 -13.85 3.50e+00 8.16e-02 1.57e+01 ... (remaining 39398 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.60: 15046 15.60 - 31.19: 1361 31.19 - 46.79: 442 46.79 - 62.38: 91 62.38 - 77.98: 42 Dihedral angle restraints: 16982 sinusoidal: 4438 harmonic: 12544 Sorted by residual: dihedral pdb=" CA ILE C 604 " pdb=" C ILE C 604 " pdb=" N GLY C 605 " pdb=" CA GLY C 605 " ideal model delta harmonic sigma weight residual 180.00 143.82 36.18 0 5.00e+00 4.00e-02 5.24e+01 dihedral pdb=" CA ILE B 604 " pdb=" C ILE B 604 " pdb=" N GLY B 605 " pdb=" CA GLY B 605 " ideal model delta harmonic sigma weight residual 180.00 143.87 36.13 0 5.00e+00 4.00e-02 5.22e+01 dihedral pdb=" CA ILE F 604 " pdb=" C ILE F 604 " pdb=" N GLY F 605 " pdb=" CA GLY F 605 " ideal model delta harmonic sigma weight residual 180.00 143.89 36.11 0 5.00e+00 4.00e-02 5.22e+01 ... (remaining 16979 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 3317 0.038 - 0.075: 1200 0.075 - 0.113: 384 0.113 - 0.151: 76 0.151 - 0.188: 21 Chirality restraints: 4998 Sorted by residual: chirality pdb=" CB VAL C 794 " pdb=" CA VAL C 794 " pdb=" CG1 VAL C 794 " pdb=" CG2 VAL C 794 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.86e-01 chirality pdb=" CB VAL F 794 " pdb=" CA VAL F 794 " pdb=" CG1 VAL F 794 " pdb=" CG2 VAL F 794 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.78e-01 chirality pdb=" CB VAL B 794 " pdb=" CA VAL B 794 " pdb=" CG1 VAL B 794 " pdb=" CG2 VAL B 794 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.69e-01 ... (remaining 4995 not shown) Planarity restraints: 5173 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 798 " -0.029 2.00e-02 2.50e+03 2.31e-02 1.33e+01 pdb=" CG TRP F 798 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP F 798 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP F 798 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP F 798 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP F 798 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP F 798 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 798 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 798 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP F 798 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 798 " 0.029 2.00e-02 2.50e+03 2.30e-02 1.33e+01 pdb=" CG TRP D 798 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP D 798 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP D 798 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP D 798 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP D 798 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP D 798 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 798 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 798 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 798 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 798 " -0.029 2.00e-02 2.50e+03 2.30e-02 1.32e+01 pdb=" CG TRP G 798 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 TRP G 798 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP G 798 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP G 798 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP G 798 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP G 798 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 798 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 798 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP G 798 " -0.004 2.00e-02 2.50e+03 ... (remaining 5170 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 990 2.71 - 3.26: 31523 3.26 - 3.81: 47387 3.81 - 4.35: 51024 4.35 - 4.90: 85131 Nonbonded interactions: 216055 Sorted by model distance: nonbonded pdb=" O LEU C 712 " pdb=" ND1 HIS C 716 " model vdw 2.165 3.120 nonbonded pdb=" O LEU E 712 " pdb=" ND1 HIS E 716 " model vdw 2.166 3.120 nonbonded pdb=" O LEU A 712 " pdb=" ND1 HIS A 716 " model vdw 2.166 3.120 nonbonded pdb=" O LEU F 712 " pdb=" ND1 HIS F 716 " model vdw 2.166 3.120 nonbonded pdb=" O LEU D 712 " pdb=" ND1 HIS D 716 " model vdw 2.166 3.120 ... (remaining 216050 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: 0.12 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 6.200 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: 0.580 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 25.750 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 28749 Z= 0.167 Angle : 0.742 13.879 39403 Z= 0.367 Chirality : 0.045 0.188 4998 Planarity : 0.005 0.051 5173 Dihedral : 14.950 77.981 8820 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 1.61 % Allowed : 0.65 % Favored : 97.74 % Rotamer: Outliers : 0.00 % Allowed : 28.88 % Favored : 71.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 0.83 (0.13), residues: 4340 helix: 1.87 (0.10), residues: 2912 sheet: -1.54 (0.24), residues: 406 loop : -2.55 (0.17), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 720 TYR 0.005 0.001 TYR B1045 PHE 0.015 0.002 PHE F1076 TRP 0.064 0.003 TRP F 798 HIS 0.004 0.001 HIS C1057 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 (28749) covalent geometry : angle 0.74216 / 0.37 (39403) hydrogen bonds : bond 0.14896 / 10.79 ( 2482) hydrogen bonds : angle 5.73271 / 4.35 ( 7320) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8680 Ramachandran restraints generated. 4340 Oldfield, 0 Emsley, 4340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8680 Ramachandran restraints generated. 4340 Oldfield, 0 Emsley, 4340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 1.139 Fit side-chains REVERT: B 787 MET cc_start: 0.8607 (mmm) cc_final: 0.8300 (mmm) REVERT: B 1081 MET cc_start: 0.7543 (mmp) cc_final: 0.7219 (mmp) REVERT: C 787 MET cc_start: 0.8656 (mmm) cc_final: 0.8048 (mmm) REVERT: D 1081 MET cc_start: 0.7601 (mmp) cc_final: 0.7126 (tpp) REVERT: E 1081 MET cc_start: 0.7621 (mmp) cc_final: 0.7210 (tpp) REVERT: F 1081 MET cc_start: 0.7494 (mmp) cc_final: 0.7197 (tpp) outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 0.1731 time to fit residues: 75.5324 Evaluate side-chains 226 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 432 optimal weight: 2.9990 chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 30.0000 chunk 132 optimal weight: 40.0000 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 80.0000 chunk 207 optimal weight: 0.0570 chunk 401 optimal weight: 8.9990 chunk 424 optimal weight: 0.0470 overall best weight: 2.0202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 971 ASN C 971 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.082354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.053457 restraints weight = 125231.322| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 3.23 r_work: 0.2880 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.1054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 28749 Z= 0.153 Angle : 0.655 11.216 39403 Z= 0.323 Chirality : 0.042 0.157 4998 Planarity : 0.004 0.050 5173 Dihedral : 4.188 16.903 4543 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 1.45 % Allowed : 4.72 % Favored : 93.82 % Rotamer: Outliers : 4.00 % Allowed : 23.66 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.13), residues: 4340 helix: 2.64 (0.10), residues: 2898 sheet: -1.16 (0.23), residues: 392 loop : -2.01 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 720 TYR 0.010 0.001 TYR G 715 PHE 0.025 0.001 PHE B1079 TRP 0.023 0.001 TRP A 798 HIS 0.006 0.001 HIS D1057 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (28749) covalent geometry : angle 0.65466 / 0.32 (39403) hydrogen bonds : bond 0.04039 / 2.96 ( 2482) hydrogen bonds : angle 4.07467 / 3.04 ( 7320) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8680 Ramachandran restraints generated. 4340 Oldfield, 0 Emsley, 4340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8680 Ramachandran restraints generated. 4340 Oldfield, 0 Emsley, 4340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 254 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 731 PHE cc_start: 0.8585 (OUTLIER) cc_final: 0.7750 (p90) REVERT: A 862 HIS cc_start: 0.8692 (OUTLIER) cc_final: 0.8392 (m90) REVERT: A 966 GLU cc_start: 0.8970 (OUTLIER) cc_final: 0.8609 (mp0) REVERT: A 972 LYS cc_start: 0.9129 (OUTLIER) cc_final: 0.8848 (ttmm) REVERT: B 720 ARG cc_start: 0.8579 (ttm170) cc_final: 0.8014 (ttm170) REVERT: B 722 MET cc_start: 0.8921 (tpp) cc_final: 0.8467 (tpp) REVERT: B 731 PHE cc_start: 0.8628 (OUTLIER) cc_final: 0.7977 (p90) REVERT: B 798 TRP cc_start: 0.7514 (m100) cc_final: 0.6501 (m100) REVERT: B 862 HIS cc_start: 0.8699 (OUTLIER) cc_final: 0.8390 (m90) REVERT: B 966 GLU cc_start: 0.8939 (OUTLIER) cc_final: 0.8376 (mp0) REVERT: C 731 PHE cc_start: 0.8554 (OUTLIER) cc_final: 0.7771 (p90) REVERT: C 966 GLU cc_start: 0.8967 (OUTLIER) cc_final: 0.8126 (mt-10) REVERT: C 972 LYS cc_start: 0.9113 (OUTLIER) cc_final: 0.8855 (ttmm) REVERT: D 722 MET cc_start: 0.8861 (tpp) cc_final: 0.8399 (tpp) REVERT: D 731 PHE cc_start: 0.8653 (OUTLIER) cc_final: 0.7865 (p90) REVERT: D 787 MET cc_start: 0.8673 (mmm) cc_final: 0.8365 (mmm) REVERT: D 966 GLU cc_start: 0.8974 (OUTLIER) cc_final: 0.8509 (mp0) REVERT: D 972 LYS cc_start: 0.9104 (OUTLIER) cc_final: 0.8858 (ttmm) REVERT: D 1081 MET cc_start: 0.8153 (mmp) cc_final: 0.7943 (mmp) REVERT: E 731 PHE cc_start: 0.8598 (OUTLIER) cc_final: 0.7876 (p90) REVERT: E 787 MET cc_start: 0.8664 (mmm) cc_final: 0.8322 (mmm) REVERT: E 966 GLU cc_start: 0.9016 (OUTLIER) cc_final: 0.8717 (mp0) REVERT: E 972 LYS cc_start: 0.9140 (OUTLIER) cc_final: 0.8816 (ttmm) REVERT: F 731 PHE cc_start: 0.8658 (OUTLIER) cc_final: 0.7935 (p90) REVERT: F 862 HIS cc_start: 0.8590 (OUTLIER) cc_final: 0.8239 (m90) REVERT: F 966 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8679 (mp0) REVERT: G 722 MET cc_start: 0.8904 (tpp) cc_final: 0.8431 (tpp) REVERT: G 731 PHE cc_start: 0.8718 (OUTLIER) cc_final: 0.8025 (p90) REVERT: G 966 GLU cc_start: 0.8951 (OUTLIER) cc_final: 0.8447 (mt-10) REVERT: G 972 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8865 (ttmm) outliers start: 79 outliers final: 15 residues processed: 314 average time/residue: 0.1767 time to fit residues: 90.4434 Evaluate side-chains 273 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 236 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 731 PHE Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 862 HIS Chi-restraints excluded: chain A residue 966 GLU Chi-restraints excluded: chain A residue 972 LYS Chi-restraints excluded: chain A residue 1074 MET Chi-restraints excluded: chain B residue 731 PHE Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain B residue 862 HIS Chi-restraints excluded: chain B residue 966 GLU Chi-restraints excluded: chain B residue 1074 MET Chi-restraints excluded: chain C residue 731 PHE Chi-restraints excluded: chain C residue 788 LEU Chi-restraints excluded: chain C residue 966 GLU Chi-restraints excluded: chain C residue 972 LYS Chi-restraints excluded: chain D residue 731 PHE Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 966 GLU Chi-restraints excluded: chain D residue 972 LYS Chi-restraints excluded: chain D residue 1074 MET Chi-restraints excluded: chain E residue 731 PHE Chi-restraints excluded: chain E residue 788 LEU Chi-restraints excluded: chain E residue 862 HIS Chi-restraints excluded: chain E residue 966 GLU Chi-restraints excluded: chain E residue 972 LYS Chi-restraints excluded: chain E residue 1074 MET Chi-restraints excluded: chain F residue 731 PHE Chi-restraints excluded: chain F residue 788 LEU Chi-restraints excluded: chain F residue 862 HIS Chi-restraints excluded: chain F residue 966 GLU Chi-restraints excluded: chain F residue 1074 MET Chi-restraints excluded: chain F residue 1081 MET Chi-restraints excluded: chain G residue 731 PHE Chi-restraints excluded: chain G residue 788 LEU Chi-restraints excluded: chain G residue 841 PHE Chi-restraints excluded: chain G residue 966 GLU Chi-restraints excluded: chain G residue 972 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 178 optimal weight: 1.9990 chunk 134 optimal weight: 0.0060 chunk 287 optimal weight: 8.9990 chunk 150 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 352 optimal weight: 5.9990 chunk 327 optimal weight: 50.0000 chunk 7 optimal weight: 9.9990 chunk 303 optimal weight: 0.0570 chunk 266 optimal weight: 30.0000 chunk 162 optimal weight: 7.9990 overall best weight: 2.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1087 ASN B1087 ASN C1087 ASN E1087 ASN F1087 ASN G1087 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.081661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.052280 restraints weight = 125763.951| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 3.23 r_work: 0.2848 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 28749 Z= 0.176 Angle : 0.612 10.680 39403 Z= 0.308 Chirality : 0.043 0.142 4998 Planarity : 0.004 0.057 5173 Dihedral : 4.238 23.417 4543 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 1.13 % Allowed : 4.52 % Favored : 94.35 % Rotamer: Outliers : 4.86 % Allowed : 21.99 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.13), residues: 4340 helix: 2.70 (0.10), residues: 2940 sheet: -1.37 (0.24), residues: 406 loop : -2.10 (0.19), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 720 TYR 0.009 0.001 TYR F 715 PHE 0.015 0.002 PHE G1076 TRP 0.018 0.001 TRP B 798 HIS 0.009 0.002 HIS D1057 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 (28749) covalent geometry : angle 0.61228 / 0.31 (39403) hydrogen bonds : bond 0.03878 / 2.84 ( 2482) hydrogen bonds : angle 3.74997 / 2.79 ( 7320) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8680 Ramachandran restraints generated. 4340 Oldfield, 0 Emsley, 4340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8680 Ramachandran restraints generated. 4340 Oldfield, 0 Emsley, 4340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 251 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 716 HIS cc_start: 0.8475 (m90) cc_final: 0.8243 (m-70) REVERT: A 731 PHE cc_start: 0.8810 (OUTLIER) cc_final: 0.8092 (p90) REVERT: A 736 HIS cc_start: 0.9502 (OUTLIER) cc_final: 0.9227 (t70) REVERT: B 731 PHE cc_start: 0.8694 (OUTLIER) cc_final: 0.8039 (p90) REVERT: B 736 HIS cc_start: 0.9555 (OUTLIER) cc_final: 0.9303 (t70) REVERT: B 787 MET cc_start: 0.8530 (mmm) cc_final: 0.8278 (mmm) REVERT: B 794 VAL cc_start: 0.9337 (OUTLIER) cc_final: 0.8774 (p) REVERT: B 798 TRP cc_start: 0.7571 (m100) cc_final: 0.6545 (m100) REVERT: B 966 GLU cc_start: 0.8982 (OUTLIER) cc_final: 0.8513 (mt-10) REVERT: C 731 PHE cc_start: 0.8688 (OUTLIER) cc_final: 0.7948 (p90) REVERT: C 736 HIS cc_start: 0.9580 (OUTLIER) cc_final: 0.9301 (t70) REVERT: C 966 GLU cc_start: 0.8982 (OUTLIER) cc_final: 0.8515 (mt-10) REVERT: D 731 PHE cc_start: 0.8805 (OUTLIER) cc_final: 0.8025 (p90) REVERT: D 736 HIS cc_start: 0.9577 (OUTLIER) cc_final: 0.9307 (t70) REVERT: D 787 MET cc_start: 0.8684 (mmm) cc_final: 0.8352 (mmm) REVERT: D 966 GLU cc_start: 0.8979 (OUTLIER) cc_final: 0.8385 (mp0) REVERT: D 1074 MET cc_start: 0.9500 (OUTLIER) cc_final: 0.9227 (mtm) REVERT: E 731 PHE cc_start: 0.8734 (OUTLIER) cc_final: 0.8038 (p90) REVERT: E 736 HIS cc_start: 0.9578 (OUTLIER) cc_final: 0.9308 (t70) REVERT: E 787 MET cc_start: 0.8648 (mmm) cc_final: 0.7993 (mmm) REVERT: E 966 GLU cc_start: 0.8998 (OUTLIER) cc_final: 0.8265 (mt-10) REVERT: F 731 PHE cc_start: 0.8738 (OUTLIER) cc_final: 0.8005 (p90) REVERT: F 736 HIS cc_start: 0.9588 (OUTLIER) cc_final: 0.9304 (t70) REVERT: F 966 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8673 (mp0) REVERT: G 716 HIS cc_start: 0.8523 (m90) cc_final: 0.8307 (m-70) REVERT: G 722 MET cc_start: 0.8970 (tpp) cc_final: 0.8543 (tpp) REVERT: G 731 PHE cc_start: 0.8763 (OUTLIER) cc_final: 0.8041 (p90) REVERT: G 736 HIS cc_start: 0.9594 (OUTLIER) cc_final: 0.9331 (t70) REVERT: G 798 TRP cc_start: 0.7528 (m100) cc_final: 0.7127 (m100) REVERT: G 966 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8477 (mt-10) outliers start: 96 outliers final: 27 residues processed: 335 average time/residue: 0.1717 time to fit residues: 94.7931 Evaluate side-chains 284 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 235 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 731 PHE Chi-restraints excluded: chain A residue 736 HIS Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain A residue 1041 GLU Chi-restraints excluded: chain A residue 1074 MET Chi-restraints excluded: chain B residue 731 PHE Chi-restraints excluded: chain B residue 736 HIS Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 946 THR Chi-restraints excluded: chain B residue 966 GLU Chi-restraints excluded: chain B residue 1041 GLU Chi-restraints excluded: chain B residue 1074 MET Chi-restraints excluded: chain C residue 731 PHE Chi-restraints excluded: chain C residue 736 HIS Chi-restraints excluded: chain C residue 788 LEU Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain C residue 946 THR Chi-restraints excluded: chain C residue 966 GLU Chi-restraints excluded: chain C residue 1041 GLU Chi-restraints excluded: chain D residue 731 PHE Chi-restraints excluded: chain D residue 736 HIS Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 946 THR Chi-restraints excluded: chain D residue 966 GLU Chi-restraints excluded: chain D residue 1041 GLU Chi-restraints excluded: chain D residue 1074 MET Chi-restraints excluded: chain E residue 731 PHE Chi-restraints excluded: chain E residue 736 HIS Chi-restraints excluded: chain E residue 788 LEU Chi-restraints excluded: chain E residue 946 THR Chi-restraints excluded: chain E residue 966 GLU Chi-restraints excluded: chain E residue 1041 GLU Chi-restraints excluded: chain E residue 1074 MET Chi-restraints excluded: chain F residue 731 PHE Chi-restraints excluded: chain F residue 736 HIS Chi-restraints excluded: chain F residue 788 LEU Chi-restraints excluded: chain F residue 946 THR Chi-restraints excluded: chain F residue 966 GLU Chi-restraints excluded: chain F residue 1074 MET Chi-restraints excluded: chain G residue 731 PHE Chi-restraints excluded: chain G residue 736 HIS Chi-restraints excluded: chain G residue 788 LEU Chi-restraints excluded: chain G residue 841 PHE Chi-restraints excluded: chain G residue 946 THR Chi-restraints excluded: chain G residue 966 GLU Chi-restraints excluded: chain G residue 1041 GLU Chi-restraints excluded: chain G residue 1074 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 23 optimal weight: 50.0000 chunk 329 optimal weight: 20.0000 chunk 42 optimal weight: 5.9990 chunk 251 optimal weight: 9.9990 chunk 222 optimal weight: 10.0000 chunk 87 optimal weight: 0.0870 chunk 6 optimal weight: 50.0000 chunk 224 optimal weight: 1.9990 chunk 211 optimal weight: 10.0000 chunk 283 optimal weight: 10.0000 chunk 237 optimal weight: 3.9990 overall best weight: 4.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 777 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.080712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.051280 restraints weight = 125259.549| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 3.17 r_work: 0.2791 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 28749 Z= 0.247 Angle : 0.644 10.331 39403 Z= 0.329 Chirality : 0.045 0.192 4998 Planarity : 0.004 0.063 5173 Dihedral : 4.289 19.627 4543 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 1.13 % Allowed : 5.28 % Favored : 93.59 % Rotamer: Outliers : 5.07 % Allowed : 21.48 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.13), residues: 4340 helix: 2.69 (0.10), residues: 2947 sheet: -1.35 (0.24), residues: 406 loop : -2.26 (0.19), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 720 TYR 0.012 0.002 TYR G 715 PHE 0.018 0.002 PHE E1076 TRP 0.018 0.001 TRP A 798 HIS 0.012 0.001 HIS D1057 Details of bonding type rmsd/Z covalent geometry : bond 0.00594 / 0.25 (28749) covalent geometry : angle 0.64440 / 0.33 (39403) hydrogen bonds : bond 0.04079 / 2.98 ( 2482) hydrogen bonds : angle 3.74657 / 2.79 ( 7320) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8680 Ramachandran restraints generated. 4340 Oldfield, 0 Emsley, 4340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8680 Ramachandran restraints generated. 4340 Oldfield, 0 Emsley, 4340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 238 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 716 HIS cc_start: 0.8596 (m90) cc_final: 0.8379 (m-70) REVERT: A 731 PHE cc_start: 0.8837 (OUTLIER) cc_final: 0.8134 (p90) REVERT: A 736 HIS cc_start: 0.9528 (OUTLIER) cc_final: 0.9261 (t70) REVERT: A 972 LYS cc_start: 0.9290 (OUTLIER) cc_final: 0.8967 (ttmm) REVERT: A 1074 MET cc_start: 0.9471 (OUTLIER) cc_final: 0.9231 (mtm) REVERT: B 731 PHE cc_start: 0.8703 (OUTLIER) cc_final: 0.8013 (p90) REVERT: B 736 HIS cc_start: 0.9587 (OUTLIER) cc_final: 0.9334 (t70) REVERT: B 787 MET cc_start: 0.8545 (mmm) cc_final: 0.8229 (mmm) REVERT: B 798 TRP cc_start: 0.7702 (m100) cc_final: 0.6798 (m100) REVERT: B 862 HIS cc_start: 0.8718 (OUTLIER) cc_final: 0.8376 (m90) REVERT: B 966 GLU cc_start: 0.8972 (OUTLIER) cc_final: 0.8595 (mt-10) REVERT: B 1074 MET cc_start: 0.9474 (OUTLIER) cc_final: 0.9185 (mtm) REVERT: C 731 PHE cc_start: 0.8772 (OUTLIER) cc_final: 0.8073 (p90) REVERT: C 736 HIS cc_start: 0.9589 (OUTLIER) cc_final: 0.9310 (t70) REVERT: C 787 MET cc_start: 0.8607 (mmm) cc_final: 0.8375 (mmm) REVERT: C 966 GLU cc_start: 0.8955 (OUTLIER) cc_final: 0.8537 (mt-10) REVERT: C 972 LYS cc_start: 0.9262 (OUTLIER) cc_final: 0.8989 (ttmm) REVERT: C 1049 MET cc_start: 0.9064 (OUTLIER) cc_final: 0.8730 (mmm) REVERT: D 731 PHE cc_start: 0.8839 (OUTLIER) cc_final: 0.8085 (p90) REVERT: D 736 HIS cc_start: 0.9594 (OUTLIER) cc_final: 0.9323 (t70) REVERT: D 966 GLU cc_start: 0.8992 (OUTLIER) cc_final: 0.8660 (mt-10) REVERT: D 972 LYS cc_start: 0.9290 (OUTLIER) cc_final: 0.8987 (ttmm) REVERT: D 1074 MET cc_start: 0.9491 (OUTLIER) cc_final: 0.9264 (mtm) REVERT: E 731 PHE cc_start: 0.8790 (OUTLIER) cc_final: 0.8107 (p90) REVERT: E 736 HIS cc_start: 0.9593 (OUTLIER) cc_final: 0.9338 (t70) REVERT: E 966 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8274 (mt-10) REVERT: E 972 LYS cc_start: 0.9279 (OUTLIER) cc_final: 0.8916 (ttmm) REVERT: F 731 PHE cc_start: 0.8787 (OUTLIER) cc_final: 0.8115 (p90) REVERT: F 736 HIS cc_start: 0.9603 (OUTLIER) cc_final: 0.9319 (t70) REVERT: F 966 GLU cc_start: 0.8970 (OUTLIER) cc_final: 0.8519 (mt-10) REVERT: F 1049 MET cc_start: 0.9055 (OUTLIER) cc_final: 0.8834 (mmm) REVERT: F 1074 MET cc_start: 0.9472 (OUTLIER) cc_final: 0.9209 (mtm) REVERT: G 731 PHE cc_start: 0.8789 (OUTLIER) cc_final: 0.8079 (p90) REVERT: G 736 HIS cc_start: 0.9615 (OUTLIER) cc_final: 0.9354 (t70) REVERT: G 966 GLU cc_start: 0.8952 (OUTLIER) cc_final: 0.8484 (mt-10) REVERT: G 1049 MET cc_start: 0.9078 (OUTLIER) cc_final: 0.8804 (mmm) REVERT: G 1074 MET cc_start: 0.9468 (OUTLIER) cc_final: 0.9186 (mtm) outliers start: 100 outliers final: 46 residues processed: 323 average time/residue: 0.1728 time to fit residues: 92.1097 Evaluate side-chains 316 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 237 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 731 PHE Chi-restraints excluded: chain A residue 736 HIS Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain A residue 948 SER Chi-restraints excluded: chain A residue 972 LYS Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 1074 MET Chi-restraints excluded: chain B residue 731 PHE Chi-restraints excluded: chain B residue 736 HIS Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain B residue 862 HIS Chi-restraints excluded: chain B residue 887 LEU Chi-restraints excluded: chain B residue 946 THR Chi-restraints excluded: chain B residue 948 SER Chi-restraints excluded: chain B residue 966 GLU Chi-restraints excluded: chain B residue 1041 GLU Chi-restraints excluded: chain B residue 1074 MET Chi-restraints excluded: chain C residue 731 PHE Chi-restraints excluded: chain C residue 736 HIS Chi-restraints excluded: chain C residue 788 LEU Chi-restraints excluded: chain C residue 862 HIS Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 887 LEU Chi-restraints excluded: chain C residue 946 THR Chi-restraints excluded: chain C residue 948 SER Chi-restraints excluded: chain C residue 966 GLU Chi-restraints excluded: chain C residue 972 LYS Chi-restraints excluded: chain C residue 1030 LEU Chi-restraints excluded: chain C residue 1041 GLU Chi-restraints excluded: chain C residue 1049 MET Chi-restraints excluded: chain D residue 731 PHE Chi-restraints excluded: chain D residue 736 HIS Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 887 LEU Chi-restraints excluded: chain D residue 946 THR Chi-restraints excluded: chain D residue 966 GLU Chi-restraints excluded: chain D residue 972 LYS Chi-restraints excluded: chain D residue 989 THR Chi-restraints excluded: chain D residue 1041 GLU Chi-restraints excluded: chain D residue 1074 MET Chi-restraints excluded: chain E residue 731 PHE Chi-restraints excluded: chain E residue 736 HIS Chi-restraints excluded: chain E residue 788 LEU Chi-restraints excluded: chain E residue 887 LEU Chi-restraints excluded: chain E residue 946 THR Chi-restraints excluded: chain E residue 966 GLU Chi-restraints excluded: chain E residue 972 LYS Chi-restraints excluded: chain E residue 994 THR Chi-restraints excluded: chain E residue 1074 MET Chi-restraints excluded: chain F residue 731 PHE Chi-restraints excluded: chain F residue 736 HIS Chi-restraints excluded: chain F residue 788 LEU Chi-restraints excluded: chain F residue 836 ILE Chi-restraints excluded: chain F residue 866 THR Chi-restraints excluded: chain F residue 887 LEU Chi-restraints excluded: chain F residue 946 THR Chi-restraints excluded: chain F residue 948 SER Chi-restraints excluded: chain F residue 966 GLU Chi-restraints excluded: chain F residue 989 THR Chi-restraints excluded: chain F residue 994 THR Chi-restraints excluded: chain F residue 1049 MET Chi-restraints excluded: chain F residue 1074 MET Chi-restraints excluded: chain G residue 731 PHE Chi-restraints excluded: chain G residue 736 HIS Chi-restraints excluded: chain G residue 788 LEU Chi-restraints excluded: chain G residue 841 PHE Chi-restraints excluded: chain G residue 866 THR Chi-restraints excluded: chain G residue 887 LEU Chi-restraints excluded: chain G residue 924 SER Chi-restraints excluded: chain G residue 946 THR Chi-restraints excluded: chain G residue 948 SER Chi-restraints excluded: chain G residue 966 GLU Chi-restraints excluded: chain G residue 989 THR Chi-restraints excluded: chain G residue 1049 MET Chi-restraints excluded: chain G residue 1074 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 213 optimal weight: 10.0000 chunk 12 optimal weight: 50.0000 chunk 53 optimal weight: 1.9990 chunk 331 optimal weight: 0.0470 chunk 215 optimal weight: 7.9990 chunk 246 optimal weight: 0.7980 chunk 385 optimal weight: 30.0000 chunk 102 optimal weight: 2.9990 chunk 30 optimal weight: 0.0570 chunk 397 optimal weight: 50.0000 chunk 142 optimal weight: 9.9990 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 777 GLN D1087 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.081478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.052631 restraints weight = 124372.258| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 3.20 r_work: 0.2838 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 28749 Z= 0.121 Angle : 0.581 11.798 39403 Z= 0.288 Chirality : 0.041 0.161 4998 Planarity : 0.004 0.058 5173 Dihedral : 4.105 18.238 4543 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 1.13 % Allowed : 4.15 % Favored : 94.72 % Rotamer: Outliers : 4.56 % Allowed : 22.59 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.13), residues: 4340 helix: 2.81 (0.10), residues: 2947 sheet: -1.23 (0.25), residues: 406 loop : -2.30 (0.18), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 720 TYR 0.012 0.001 TYR G 715 PHE 0.011 0.001 PHE B1079 TRP 0.020 0.001 TRP A 798 HIS 0.006 0.001 HIS A1057 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (28749) covalent geometry : angle 0.58071 / 0.29 (39403) hydrogen bonds : bond 0.03506 / 2.57 ( 2482) hydrogen bonds : angle 3.56288 / 2.65 ( 7320) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8680 Ramachandran restraints generated. 4340 Oldfield, 0 Emsley, 4340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8680 Ramachandran restraints generated. 4340 Oldfield, 0 Emsley, 4340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 241 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 731 PHE cc_start: 0.8840 (OUTLIER) cc_final: 0.8107 (p90) REVERT: A 736 HIS cc_start: 0.9517 (OUTLIER) cc_final: 0.9241 (t70) REVERT: A 1081 MET cc_start: 0.8300 (mmp) cc_final: 0.8097 (mmp) REVERT: B 731 PHE cc_start: 0.8707 (OUTLIER) cc_final: 0.8032 (p90) REVERT: B 736 HIS cc_start: 0.9564 (OUTLIER) cc_final: 0.9295 (t70) REVERT: B 787 MET cc_start: 0.8575 (mmm) cc_final: 0.8260 (mmm) REVERT: B 794 VAL cc_start: 0.9381 (OUTLIER) cc_final: 0.8952 (p) REVERT: B 798 TRP cc_start: 0.7547 (m100) cc_final: 0.6795 (m100) REVERT: B 966 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8445 (mt-10) REVERT: C 731 PHE cc_start: 0.8748 (OUTLIER) cc_final: 0.8022 (p90) REVERT: C 736 HIS cc_start: 0.9588 (OUTLIER) cc_final: 0.9294 (t70) REVERT: C 787 MET cc_start: 0.8567 (mmm) cc_final: 0.8307 (mmm) REVERT: C 966 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8477 (mt-10) REVERT: D 731 PHE cc_start: 0.8828 (OUTLIER) cc_final: 0.8121 (p90) REVERT: D 735 LYS cc_start: 0.9128 (tptp) cc_final: 0.8603 (mttp) REVERT: D 736 HIS cc_start: 0.9588 (OUTLIER) cc_final: 0.9270 (t70) REVERT: D 787 MET cc_start: 0.8649 (mmm) cc_final: 0.8360 (mmm) REVERT: D 966 GLU cc_start: 0.8945 (OUTLIER) cc_final: 0.8553 (mt-10) REVERT: E 731 PHE cc_start: 0.8755 (OUTLIER) cc_final: 0.8050 (p90) REVERT: E 736 HIS cc_start: 0.9577 (OUTLIER) cc_final: 0.9309 (t70) REVERT: E 966 GLU cc_start: 0.8944 (OUTLIER) cc_final: 0.8220 (mt-10) REVERT: E 972 LYS cc_start: 0.9167 (OUTLIER) cc_final: 0.8807 (ttmm) REVERT: E 1081 MET cc_start: 0.8092 (tpp) cc_final: 0.7807 (tpp) REVERT: F 731 PHE cc_start: 0.8749 (OUTLIER) cc_final: 0.8041 (p90) REVERT: F 736 HIS cc_start: 0.9581 (OUTLIER) cc_final: 0.9297 (t70) REVERT: F 966 GLU cc_start: 0.8943 (OUTLIER) cc_final: 0.8228 (mt-10) REVERT: G 722 MET cc_start: 0.8996 (tpp) cc_final: 0.8502 (tpp) REVERT: G 731 PHE cc_start: 0.8789 (OUTLIER) cc_final: 0.8102 (p90) REVERT: G 735 LYS cc_start: 0.9157 (tptp) cc_final: 0.8610 (mttp) REVERT: G 736 HIS cc_start: 0.9600 (OUTLIER) cc_final: 0.9295 (t70) REVERT: G 966 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8433 (mt-10) outliers start: 90 outliers final: 41 residues processed: 322 average time/residue: 0.1698 time to fit residues: 90.4841 Evaluate side-chains 302 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 239 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 731 PHE Chi-restraints excluded: chain A residue 736 HIS Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 882 MET Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 948 SER Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 1041 GLU Chi-restraints excluded: chain A residue 1074 MET Chi-restraints excluded: chain B residue 731 PHE Chi-restraints excluded: chain B residue 736 HIS Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 887 LEU Chi-restraints excluded: chain B residue 966 GLU Chi-restraints excluded: chain B residue 1041 GLU Chi-restraints excluded: chain B residue 1074 MET Chi-restraints excluded: chain C residue 731 PHE Chi-restraints excluded: chain C residue 736 HIS Chi-restraints excluded: chain C residue 788 LEU Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain C residue 862 HIS Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 887 LEU Chi-restraints excluded: chain C residue 966 GLU Chi-restraints excluded: chain C residue 1041 GLU Chi-restraints excluded: chain D residue 731 PHE Chi-restraints excluded: chain D residue 736 HIS Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain D residue 887 LEU Chi-restraints excluded: chain D residue 966 GLU Chi-restraints excluded: chain D residue 989 THR Chi-restraints excluded: chain D residue 1041 GLU Chi-restraints excluded: chain E residue 731 PHE Chi-restraints excluded: chain E residue 736 HIS Chi-restraints excluded: chain E residue 788 LEU Chi-restraints excluded: chain E residue 874 THR Chi-restraints excluded: chain E residue 887 LEU Chi-restraints excluded: chain E residue 966 GLU Chi-restraints excluded: chain E residue 972 LYS Chi-restraints excluded: chain E residue 989 THR Chi-restraints excluded: chain E residue 1041 GLU Chi-restraints excluded: chain E residue 1074 MET Chi-restraints excluded: chain F residue 731 PHE Chi-restraints excluded: chain F residue 736 HIS Chi-restraints excluded: chain F residue 788 LEU Chi-restraints excluded: chain F residue 887 LEU Chi-restraints excluded: chain F residue 966 GLU Chi-restraints excluded: chain F residue 989 THR Chi-restraints excluded: chain F residue 1044 ILE Chi-restraints excluded: chain G residue 731 PHE Chi-restraints excluded: chain G residue 736 HIS Chi-restraints excluded: chain G residue 788 LEU Chi-restraints excluded: chain G residue 841 PHE Chi-restraints excluded: chain G residue 866 THR Chi-restraints excluded: chain G residue 874 THR Chi-restraints excluded: chain G residue 887 LEU Chi-restraints excluded: chain G residue 946 THR Chi-restraints excluded: chain G residue 966 GLU Chi-restraints excluded: chain G residue 1041 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 384 optimal weight: 50.0000 chunk 212 optimal weight: 9.9990 chunk 332 optimal weight: 50.0000 chunk 37 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 139 optimal weight: 2.9990 chunk 227 optimal weight: 2.9990 chunk 345 optimal weight: 9.9990 chunk 342 optimal weight: 5.9990 chunk 252 optimal weight: 20.0000 chunk 1 optimal weight: 50.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 850 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.079981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.051149 restraints weight = 125199.019| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 3.15 r_work: 0.2779 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 28749 Z= 0.292 Angle : 0.648 12.433 39403 Z= 0.334 Chirality : 0.046 0.168 4998 Planarity : 0.004 0.060 5173 Dihedral : 4.282 17.561 4543 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 1.13 % Allowed : 5.53 % Favored : 93.34 % Rotamer: Outliers : 6.28 % Allowed : 20.67 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.13), residues: 4340 helix: 2.74 (0.10), residues: 2947 sheet: -1.40 (0.25), residues: 406 loop : -2.31 (0.18), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 720 TYR 0.013 0.002 TYR A 715 PHE 0.017 0.002 PHE A1076 TRP 0.021 0.002 TRP A 798 HIS 0.013 0.002 HIS G1057 Details of bonding type rmsd/Z covalent geometry : bond 0.00698 / 0.29 (28749) covalent geometry : angle 0.64776 / 0.33 (39403) hydrogen bonds : bond 0.04259 / 3.12 ( 2482) hydrogen bonds : angle 3.76454 / 2.80 ( 7320) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8680 Ramachandran restraints generated. 4340 Oldfield, 0 Emsley, 4340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8680 Ramachandran restraints generated. 4340 Oldfield, 0 Emsley, 4340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 244 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 731 PHE cc_start: 0.8898 (OUTLIER) cc_final: 0.8286 (p90) REVERT: A 735 LYS cc_start: 0.9074 (tptp) cc_final: 0.8483 (mttp) REVERT: A 736 HIS cc_start: 0.9559 (OUTLIER) cc_final: 0.9245 (t70) REVERT: A 972 LYS cc_start: 0.9336 (OUTLIER) cc_final: 0.9016 (ttmm) REVERT: A 1081 MET cc_start: 0.8264 (mmp) cc_final: 0.7609 (mmp) REVERT: B 731 PHE cc_start: 0.8743 (OUTLIER) cc_final: 0.8106 (p90) REVERT: B 736 HIS cc_start: 0.9608 (OUTLIER) cc_final: 0.9340 (t70) REVERT: B 794 VAL cc_start: 0.9414 (OUTLIER) cc_final: 0.9210 (p) REVERT: B 798 TRP cc_start: 0.7728 (m100) cc_final: 0.7128 (m100) REVERT: B 862 HIS cc_start: 0.8696 (OUTLIER) cc_final: 0.8310 (m90) REVERT: B 966 GLU cc_start: 0.8961 (OUTLIER) cc_final: 0.8635 (mt-10) REVERT: B 1049 MET cc_start: 0.9106 (OUTLIER) cc_final: 0.8655 (mmm) REVERT: B 1074 MET cc_start: 0.9476 (OUTLIER) cc_final: 0.9239 (mtm) REVERT: C 731 PHE cc_start: 0.8780 (OUTLIER) cc_final: 0.8070 (p90) REVERT: C 736 HIS cc_start: 0.9619 (OUTLIER) cc_final: 0.9338 (t70) REVERT: C 966 GLU cc_start: 0.8955 (OUTLIER) cc_final: 0.8558 (mt-10) REVERT: C 1049 MET cc_start: 0.9089 (OUTLIER) cc_final: 0.8722 (mmm) REVERT: D 731 PHE cc_start: 0.8827 (OUTLIER) cc_final: 0.8090 (p90) REVERT: D 736 HIS cc_start: 0.9614 (OUTLIER) cc_final: 0.9338 (t70) REVERT: D 966 GLU cc_start: 0.8984 (OUTLIER) cc_final: 0.8681 (mt-10) REVERT: D 972 LYS cc_start: 0.9349 (OUTLIER) cc_final: 0.9049 (ttmm) REVERT: E 731 PHE cc_start: 0.8807 (OUTLIER) cc_final: 0.8145 (p90) REVERT: E 736 HIS cc_start: 0.9606 (OUTLIER) cc_final: 0.9333 (t70) REVERT: E 787 MET cc_start: 0.8574 (mmm) cc_final: 0.8263 (mmm) REVERT: E 892 MET cc_start: 0.9207 (mmp) cc_final: 0.8991 (mmp) REVERT: E 966 GLU cc_start: 0.9000 (OUTLIER) cc_final: 0.8285 (mt-10) REVERT: E 972 LYS cc_start: 0.9315 (OUTLIER) cc_final: 0.8962 (ttmm) REVERT: E 1034 GLN cc_start: 0.8985 (OUTLIER) cc_final: 0.8556 (mt0) REVERT: E 1049 MET cc_start: 0.9143 (OUTLIER) cc_final: 0.8765 (mmm) REVERT: F 731 PHE cc_start: 0.8817 (OUTLIER) cc_final: 0.8185 (p90) REVERT: F 736 HIS cc_start: 0.9609 (OUTLIER) cc_final: 0.9307 (t70) REVERT: F 966 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8525 (mt-10) REVERT: F 1074 MET cc_start: 0.9344 (mmm) cc_final: 0.8823 (mtt) REVERT: G 731 PHE cc_start: 0.8821 (OUTLIER) cc_final: 0.8137 (p90) REVERT: G 736 HIS cc_start: 0.9625 (OUTLIER) cc_final: 0.9358 (t70) REVERT: G 966 GLU cc_start: 0.8971 (OUTLIER) cc_final: 0.8520 (mt-10) REVERT: G 972 LYS cc_start: 0.9329 (OUTLIER) cc_final: 0.9015 (ttmm) REVERT: G 1049 MET cc_start: 0.9053 (OUTLIER) cc_final: 0.8807 (mmm) REVERT: G 1074 MET cc_start: 0.9489 (OUTLIER) cc_final: 0.9200 (mtm) REVERT: G 1081 MET cc_start: 0.8198 (tpp) cc_final: 0.7880 (tpp) outliers start: 124 outliers final: 54 residues processed: 353 average time/residue: 0.1666 time to fit residues: 97.7345 Evaluate side-chains 329 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 242 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 731 PHE Chi-restraints excluded: chain A residue 736 HIS Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain A residue 948 SER Chi-restraints excluded: chain A residue 972 LYS Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 1041 GLU Chi-restraints excluded: chain B residue 715 TYR Chi-restraints excluded: chain B residue 731 PHE Chi-restraints excluded: chain B residue 736 HIS Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 841 PHE Chi-restraints excluded: chain B residue 862 HIS Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 887 LEU Chi-restraints excluded: chain B residue 946 THR Chi-restraints excluded: chain B residue 966 GLU Chi-restraints excluded: chain B residue 1041 GLU Chi-restraints excluded: chain B residue 1049 MET Chi-restraints excluded: chain B residue 1074 MET Chi-restraints excluded: chain C residue 731 PHE Chi-restraints excluded: chain C residue 736 HIS Chi-restraints excluded: chain C residue 788 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 887 LEU Chi-restraints excluded: chain C residue 946 THR Chi-restraints excluded: chain C residue 948 SER Chi-restraints excluded: chain C residue 966 GLU Chi-restraints excluded: chain C residue 1041 GLU Chi-restraints excluded: chain C residue 1049 MET Chi-restraints excluded: chain D residue 731 PHE Chi-restraints excluded: chain D residue 736 HIS Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain D residue 887 LEU Chi-restraints excluded: chain D residue 946 THR Chi-restraints excluded: chain D residue 948 SER Chi-restraints excluded: chain D residue 954 THR Chi-restraints excluded: chain D residue 966 GLU Chi-restraints excluded: chain D residue 972 LYS Chi-restraints excluded: chain D residue 989 THR Chi-restraints excluded: chain D residue 1041 GLU Chi-restraints excluded: chain E residue 731 PHE Chi-restraints excluded: chain E residue 736 HIS Chi-restraints excluded: chain E residue 788 LEU Chi-restraints excluded: chain E residue 874 THR Chi-restraints excluded: chain E residue 887 LEU Chi-restraints excluded: chain E residue 946 THR Chi-restraints excluded: chain E residue 954 THR Chi-restraints excluded: chain E residue 966 GLU Chi-restraints excluded: chain E residue 972 LYS Chi-restraints excluded: chain E residue 994 THR Chi-restraints excluded: chain E residue 1034 GLN Chi-restraints excluded: chain E residue 1038 GLN Chi-restraints excluded: chain E residue 1041 GLU Chi-restraints excluded: chain E residue 1049 MET Chi-restraints excluded: chain E residue 1074 MET Chi-restraints excluded: chain F residue 731 PHE Chi-restraints excluded: chain F residue 736 HIS Chi-restraints excluded: chain F residue 788 LEU Chi-restraints excluded: chain F residue 866 THR Chi-restraints excluded: chain F residue 887 LEU Chi-restraints excluded: chain F residue 946 THR Chi-restraints excluded: chain F residue 948 SER Chi-restraints excluded: chain F residue 966 GLU Chi-restraints excluded: chain F residue 989 THR Chi-restraints excluded: chain F residue 994 THR Chi-restraints excluded: chain F residue 1044 ILE Chi-restraints excluded: chain G residue 731 PHE Chi-restraints excluded: chain G residue 736 HIS Chi-restraints excluded: chain G residue 788 LEU Chi-restraints excluded: chain G residue 841 PHE Chi-restraints excluded: chain G residue 862 HIS Chi-restraints excluded: chain G residue 874 THR Chi-restraints excluded: chain G residue 887 LEU Chi-restraints excluded: chain G residue 924 SER Chi-restraints excluded: chain G residue 946 THR Chi-restraints excluded: chain G residue 948 SER Chi-restraints excluded: chain G residue 966 GLU Chi-restraints excluded: chain G residue 972 LYS Chi-restraints excluded: chain G residue 989 THR Chi-restraints excluded: chain G residue 1049 MET Chi-restraints excluded: chain G residue 1074 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 411 optimal weight: 0.9980 chunk 428 optimal weight: 3.9990 chunk 299 optimal weight: 2.9990 chunk 327 optimal weight: 50.0000 chunk 274 optimal weight: 5.9990 chunk 405 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 252 optimal weight: 20.0000 chunk 230 optimal weight: 3.9990 chunk 267 optimal weight: 50.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 846 GLN ** D 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 846 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.080511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.052146 restraints weight = 124291.551| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 3.42 r_work: 0.2785 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 28749 Z= 0.166 Angle : 0.628 13.530 39403 Z= 0.306 Chirality : 0.043 0.162 4998 Planarity : 0.004 0.059 5173 Dihedral : 4.216 19.831 4543 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 1.13 % Allowed : 4.10 % Favored : 94.77 % Rotamer: Outliers : 4.76 % Allowed : 22.95 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.14), residues: 4340 helix: 2.85 (0.10), residues: 2912 sheet: -1.40 (0.25), residues: 406 loop : -2.25 (0.18), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 720 TYR 0.013 0.001 TYR G 715 PHE 0.010 0.001 PHE B 841 TRP 0.022 0.001 TRP A 798 HIS 0.009 0.001 HIS D1057 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (28749) covalent geometry : angle 0.62789 / 0.31 (39403) hydrogen bonds : bond 0.03735 / 2.74 ( 2482) hydrogen bonds : angle 3.64661 / 2.72 ( 7320) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8680 Ramachandran restraints generated. 4340 Oldfield, 0 Emsley, 4340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8680 Ramachandran restraints generated. 4340 Oldfield, 0 Emsley, 4340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 244 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 731 PHE cc_start: 0.8842 (OUTLIER) cc_final: 0.8176 (p90) REVERT: A 735 LYS cc_start: 0.9064 (tptp) cc_final: 0.8488 (mttp) REVERT: A 736 HIS cc_start: 0.9547 (OUTLIER) cc_final: 0.9235 (t70) REVERT: A 1081 MET cc_start: 0.8389 (mmp) cc_final: 0.7770 (mmt) REVERT: B 731 PHE cc_start: 0.8758 (OUTLIER) cc_final: 0.8128 (p90) REVERT: B 736 HIS cc_start: 0.9600 (OUTLIER) cc_final: 0.9334 (t70) REVERT: B 794 VAL cc_start: 0.9425 (OUTLIER) cc_final: 0.9218 (p) REVERT: B 798 TRP cc_start: 0.7749 (m100) cc_final: 0.7144 (m100) REVERT: B 966 GLU cc_start: 0.8973 (OUTLIER) cc_final: 0.8571 (mt-10) REVERT: C 731 PHE cc_start: 0.8776 (OUTLIER) cc_final: 0.8087 (p90) REVERT: C 736 HIS cc_start: 0.9614 (OUTLIER) cc_final: 0.9322 (t70) REVERT: C 966 GLU cc_start: 0.8961 (OUTLIER) cc_final: 0.8520 (mt-10) REVERT: C 1049 MET cc_start: 0.9126 (OUTLIER) cc_final: 0.8765 (mmm) REVERT: D 731 PHE cc_start: 0.8836 (OUTLIER) cc_final: 0.8084 (p90) REVERT: D 736 HIS cc_start: 0.9609 (OUTLIER) cc_final: 0.9332 (t70) REVERT: D 966 GLU cc_start: 0.8997 (OUTLIER) cc_final: 0.8669 (mt-10) REVERT: D 972 LYS cc_start: 0.9255 (OUTLIER) cc_final: 0.8949 (ttmm) REVERT: E 731 PHE cc_start: 0.8821 (OUTLIER) cc_final: 0.8128 (p90) REVERT: E 736 HIS cc_start: 0.9593 (OUTLIER) cc_final: 0.9310 (t70) REVERT: E 892 MET cc_start: 0.9197 (mmp) cc_final: 0.8971 (mmp) REVERT: E 966 GLU cc_start: 0.8994 (OUTLIER) cc_final: 0.8289 (mt-10) REVERT: E 972 LYS cc_start: 0.9212 (OUTLIER) cc_final: 0.8860 (ttmm) REVERT: E 1034 GLN cc_start: 0.8940 (OUTLIER) cc_final: 0.8475 (mt0) REVERT: E 1049 MET cc_start: 0.9137 (OUTLIER) cc_final: 0.8741 (mmm) REVERT: F 731 PHE cc_start: 0.8781 (OUTLIER) cc_final: 0.8127 (p90) REVERT: F 736 HIS cc_start: 0.9608 (OUTLIER) cc_final: 0.9310 (t70) REVERT: F 966 GLU cc_start: 0.8976 (OUTLIER) cc_final: 0.8488 (mt-10) REVERT: F 1049 MET cc_start: 0.9050 (OUTLIER) cc_final: 0.8804 (mmm) REVERT: F 1074 MET cc_start: 0.9313 (mmm) cc_final: 0.8816 (mtt) REVERT: G 731 PHE cc_start: 0.8827 (OUTLIER) cc_final: 0.8140 (p90) REVERT: G 736 HIS cc_start: 0.9619 (OUTLIER) cc_final: 0.9352 (t70) REVERT: G 966 GLU cc_start: 0.8953 (OUTLIER) cc_final: 0.8491 (mt-10) REVERT: G 1074 MET cc_start: 0.9418 (OUTLIER) cc_final: 0.9119 (mtm) REVERT: G 1081 MET cc_start: 0.8181 (tpp) cc_final: 0.7943 (tpp) outliers start: 94 outliers final: 47 residues processed: 327 average time/residue: 0.1638 time to fit residues: 88.7338 Evaluate side-chains 316 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 241 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 731 PHE Chi-restraints excluded: chain A residue 736 HIS Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain A residue 948 SER Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 1041 GLU Chi-restraints excluded: chain B residue 731 PHE Chi-restraints excluded: chain B residue 736 HIS Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 841 PHE Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 887 LEU Chi-restraints excluded: chain B residue 946 THR Chi-restraints excluded: chain B residue 966 GLU Chi-restraints excluded: chain B residue 1041 GLU Chi-restraints excluded: chain C residue 731 PHE Chi-restraints excluded: chain C residue 736 HIS Chi-restraints excluded: chain C residue 788 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 887 LEU Chi-restraints excluded: chain C residue 946 THR Chi-restraints excluded: chain C residue 966 GLU Chi-restraints excluded: chain C residue 1041 GLU Chi-restraints excluded: chain C residue 1049 MET Chi-restraints excluded: chain D residue 731 PHE Chi-restraints excluded: chain D residue 736 HIS Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain D residue 887 LEU Chi-restraints excluded: chain D residue 946 THR Chi-restraints excluded: chain D residue 948 SER Chi-restraints excluded: chain D residue 966 GLU Chi-restraints excluded: chain D residue 972 LYS Chi-restraints excluded: chain D residue 989 THR Chi-restraints excluded: chain D residue 1041 GLU Chi-restraints excluded: chain E residue 731 PHE Chi-restraints excluded: chain E residue 736 HIS Chi-restraints excluded: chain E residue 788 LEU Chi-restraints excluded: chain E residue 874 THR Chi-restraints excluded: chain E residue 887 LEU Chi-restraints excluded: chain E residue 946 THR Chi-restraints excluded: chain E residue 966 GLU Chi-restraints excluded: chain E residue 972 LYS Chi-restraints excluded: chain E residue 1034 GLN Chi-restraints excluded: chain E residue 1041 GLU Chi-restraints excluded: chain E residue 1049 MET Chi-restraints excluded: chain E residue 1074 MET Chi-restraints excluded: chain F residue 731 PHE Chi-restraints excluded: chain F residue 736 HIS Chi-restraints excluded: chain F residue 788 LEU Chi-restraints excluded: chain F residue 866 THR Chi-restraints excluded: chain F residue 887 LEU Chi-restraints excluded: chain F residue 946 THR Chi-restraints excluded: chain F residue 948 SER Chi-restraints excluded: chain F residue 966 GLU Chi-restraints excluded: chain F residue 989 THR Chi-restraints excluded: chain F residue 994 THR Chi-restraints excluded: chain F residue 1044 ILE Chi-restraints excluded: chain F residue 1049 MET Chi-restraints excluded: chain G residue 731 PHE Chi-restraints excluded: chain G residue 736 HIS Chi-restraints excluded: chain G residue 788 LEU Chi-restraints excluded: chain G residue 841 PHE Chi-restraints excluded: chain G residue 874 THR Chi-restraints excluded: chain G residue 887 LEU Chi-restraints excluded: chain G residue 924 SER Chi-restraints excluded: chain G residue 946 THR Chi-restraints excluded: chain G residue 948 SER Chi-restraints excluded: chain G residue 966 GLU Chi-restraints excluded: chain G residue 989 THR Chi-restraints excluded: chain G residue 1074 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 254 optimal weight: 50.0000 chunk 395 optimal weight: 40.0000 chunk 93 optimal weight: 3.9990 chunk 238 optimal weight: 3.9990 chunk 346 optimal weight: 20.0000 chunk 242 optimal weight: 6.9990 chunk 159 optimal weight: 30.0000 chunk 356 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 98 optimal weight: 20.0000 chunk 275 optimal weight: 10.0000 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.080286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.051619 restraints weight = 125308.253| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 3.19 r_work: 0.2804 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 28749 Z= 0.195 Angle : 0.630 12.491 39403 Z= 0.309 Chirality : 0.043 0.162 4998 Planarity : 0.004 0.059 5173 Dihedral : 4.207 23.565 4543 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 1.13 % Allowed : 4.70 % Favored : 94.17 % Rotamer: Outliers : 4.66 % Allowed : 22.85 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.14), residues: 4340 helix: 2.87 (0.10), residues: 2898 sheet: -1.42 (0.25), residues: 406 loop : -2.23 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 720 TYR 0.014 0.001 TYR G 715 PHE 0.010 0.001 PHE B 841 TRP 0.025 0.001 TRP G 798 HIS 0.009 0.001 HIS G1057 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.19 (28749) covalent geometry : angle 0.62987 / 0.31 (39403) hydrogen bonds : bond 0.03716 / 2.72 ( 2482) hydrogen bonds : angle 3.64132 / 2.71 ( 7320) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8680 Ramachandran restraints generated. 4340 Oldfield, 0 Emsley, 4340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8680 Ramachandran restraints generated. 4340 Oldfield, 0 Emsley, 4340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 245 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 731 PHE cc_start: 0.8897 (OUTLIER) cc_final: 0.8260 (p90) REVERT: A 735 LYS cc_start: 0.9056 (tptp) cc_final: 0.8474 (mttp) REVERT: A 736 HIS cc_start: 0.9557 (OUTLIER) cc_final: 0.9233 (t70) REVERT: A 972 LYS cc_start: 0.9235 (OUTLIER) cc_final: 0.8893 (ttmm) REVERT: A 1049 MET cc_start: 0.9156 (OUTLIER) cc_final: 0.8816 (mmm) REVERT: A 1081 MET cc_start: 0.8341 (mmp) cc_final: 0.7684 (mmt) REVERT: B 731 PHE cc_start: 0.8750 (OUTLIER) cc_final: 0.8137 (p90) REVERT: B 736 HIS cc_start: 0.9597 (OUTLIER) cc_final: 0.9308 (t70) REVERT: B 794 VAL cc_start: 0.9429 (OUTLIER) cc_final: 0.9221 (p) REVERT: B 798 TRP cc_start: 0.7791 (m100) cc_final: 0.7195 (m100) REVERT: B 966 GLU cc_start: 0.8955 (OUTLIER) cc_final: 0.8568 (mt-10) REVERT: C 731 PHE cc_start: 0.8824 (OUTLIER) cc_final: 0.8156 (p90) REVERT: C 736 HIS cc_start: 0.9606 (OUTLIER) cc_final: 0.9299 (t70) REVERT: C 966 GLU cc_start: 0.8939 (OUTLIER) cc_final: 0.8519 (mt-10) REVERT: C 972 LYS cc_start: 0.9257 (OUTLIER) cc_final: 0.8946 (ttmm) REVERT: C 1049 MET cc_start: 0.9067 (OUTLIER) cc_final: 0.8726 (mmm) REVERT: D 731 PHE cc_start: 0.8849 (OUTLIER) cc_final: 0.8134 (p90) REVERT: D 736 HIS cc_start: 0.9609 (OUTLIER) cc_final: 0.9320 (t70) REVERT: D 966 GLU cc_start: 0.8968 (OUTLIER) cc_final: 0.8645 (mt-10) REVERT: E 731 PHE cc_start: 0.8835 (OUTLIER) cc_final: 0.8154 (p90) REVERT: E 736 HIS cc_start: 0.9600 (OUTLIER) cc_final: 0.9310 (t70) REVERT: E 892 MET cc_start: 0.9193 (mmp) cc_final: 0.8953 (mmp) REVERT: E 966 GLU cc_start: 0.8963 (OUTLIER) cc_final: 0.8243 (mt-10) REVERT: E 972 LYS cc_start: 0.9249 (OUTLIER) cc_final: 0.8909 (ttmm) REVERT: E 1034 GLN cc_start: 0.8957 (OUTLIER) cc_final: 0.8515 (mt0) REVERT: E 1049 MET cc_start: 0.9100 (OUTLIER) cc_final: 0.8731 (mmm) REVERT: F 731 PHE cc_start: 0.8811 (OUTLIER) cc_final: 0.8170 (p90) REVERT: F 736 HIS cc_start: 0.9606 (OUTLIER) cc_final: 0.9295 (t70) REVERT: F 966 GLU cc_start: 0.8946 (OUTLIER) cc_final: 0.8465 (mt-10) REVERT: F 1049 MET cc_start: 0.9018 (OUTLIER) cc_final: 0.8791 (mmm) REVERT: F 1074 MET cc_start: 0.9305 (mmm) cc_final: 0.8795 (mtt) REVERT: G 731 PHE cc_start: 0.8857 (OUTLIER) cc_final: 0.8144 (p90) REVERT: G 736 HIS cc_start: 0.9607 (OUTLIER) cc_final: 0.9319 (t70) REVERT: G 783 ARG cc_start: 0.9434 (ttt90) cc_final: 0.9134 (tpp80) REVERT: G 966 GLU cc_start: 0.8944 (OUTLIER) cc_final: 0.8494 (mt-10) REVERT: G 972 LYS cc_start: 0.9263 (OUTLIER) cc_final: 0.8943 (ttmm) REVERT: G 1074 MET cc_start: 0.9389 (OUTLIER) cc_final: 0.9125 (mtm) REVERT: G 1081 MET cc_start: 0.8205 (tpp) cc_final: 0.8003 (tpp) outliers start: 92 outliers final: 50 residues processed: 325 average time/residue: 0.1760 time to fit residues: 93.9248 Evaluate side-chains 328 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 247 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 731 PHE Chi-restraints excluded: chain A residue 736 HIS Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain A residue 948 SER Chi-restraints excluded: chain A residue 972 LYS Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 1041 GLU Chi-restraints excluded: chain A residue 1049 MET Chi-restraints excluded: chain B residue 731 PHE Chi-restraints excluded: chain B residue 736 HIS Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 841 PHE Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 887 LEU Chi-restraints excluded: chain B residue 946 THR Chi-restraints excluded: chain B residue 966 GLU Chi-restraints excluded: chain B residue 1041 GLU Chi-restraints excluded: chain C residue 731 PHE Chi-restraints excluded: chain C residue 736 HIS Chi-restraints excluded: chain C residue 788 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 887 LEU Chi-restraints excluded: chain C residue 946 THR Chi-restraints excluded: chain C residue 948 SER Chi-restraints excluded: chain C residue 966 GLU Chi-restraints excluded: chain C residue 972 LYS Chi-restraints excluded: chain C residue 1041 GLU Chi-restraints excluded: chain C residue 1049 MET Chi-restraints excluded: chain D residue 731 PHE Chi-restraints excluded: chain D residue 736 HIS Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain D residue 887 LEU Chi-restraints excluded: chain D residue 946 THR Chi-restraints excluded: chain D residue 948 SER Chi-restraints excluded: chain D residue 966 GLU Chi-restraints excluded: chain D residue 989 THR Chi-restraints excluded: chain D residue 1041 GLU Chi-restraints excluded: chain E residue 731 PHE Chi-restraints excluded: chain E residue 736 HIS Chi-restraints excluded: chain E residue 788 LEU Chi-restraints excluded: chain E residue 874 THR Chi-restraints excluded: chain E residue 887 LEU Chi-restraints excluded: chain E residue 946 THR Chi-restraints excluded: chain E residue 948 SER Chi-restraints excluded: chain E residue 966 GLU Chi-restraints excluded: chain E residue 972 LYS Chi-restraints excluded: chain E residue 994 THR Chi-restraints excluded: chain E residue 1034 GLN Chi-restraints excluded: chain E residue 1041 GLU Chi-restraints excluded: chain E residue 1049 MET Chi-restraints excluded: chain E residue 1074 MET Chi-restraints excluded: chain F residue 731 PHE Chi-restraints excluded: chain F residue 736 HIS Chi-restraints excluded: chain F residue 788 LEU Chi-restraints excluded: chain F residue 866 THR Chi-restraints excluded: chain F residue 887 LEU Chi-restraints excluded: chain F residue 946 THR Chi-restraints excluded: chain F residue 948 SER Chi-restraints excluded: chain F residue 966 GLU Chi-restraints excluded: chain F residue 989 THR Chi-restraints excluded: chain F residue 994 THR Chi-restraints excluded: chain F residue 1044 ILE Chi-restraints excluded: chain F residue 1049 MET Chi-restraints excluded: chain G residue 731 PHE Chi-restraints excluded: chain G residue 736 HIS Chi-restraints excluded: chain G residue 788 LEU Chi-restraints excluded: chain G residue 841 PHE Chi-restraints excluded: chain G residue 874 THR Chi-restraints excluded: chain G residue 887 LEU Chi-restraints excluded: chain G residue 924 SER Chi-restraints excluded: chain G residue 946 THR Chi-restraints excluded: chain G residue 948 SER Chi-restraints excluded: chain G residue 966 GLU Chi-restraints excluded: chain G residue 972 LYS Chi-restraints excluded: chain G residue 989 THR Chi-restraints excluded: chain G residue 1074 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 430 optimal weight: 0.8980 chunk 367 optimal weight: 0.8980 chunk 328 optimal weight: 0.2980 chunk 235 optimal weight: 1.9990 chunk 199 optimal weight: 0.2980 chunk 310 optimal weight: 70.0000 chunk 288 optimal weight: 5.9990 chunk 291 optimal weight: 4.9990 chunk 146 optimal weight: 50.0000 chunk 284 optimal weight: 10.0000 chunk 316 optimal weight: 50.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 846 GLN C 846 GLN C 921 ASN E 846 GLN G 921 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.082098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.053908 restraints weight = 124256.638| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 3.17 r_work: 0.2848 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 28749 Z= 0.114 Angle : 0.621 15.275 39403 Z= 0.295 Chirality : 0.041 0.148 4998 Planarity : 0.004 0.058 5173 Dihedral : 4.038 16.837 4543 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 1.13 % Allowed : 3.76 % Favored : 95.12 % Rotamer: Outliers : 3.34 % Allowed : 23.61 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.14), residues: 4340 helix: 2.93 (0.10), residues: 2905 sheet: -1.32 (0.26), residues: 406 loop : -2.19 (0.18), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 720 TYR 0.016 0.001 TYR G 715 PHE 0.018 0.001 PHE B 841 TRP 0.028 0.001 TRP G 798 HIS 0.006 0.001 HIS A1057 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (28749) covalent geometry : angle 0.62122 / 0.29 (39403) hydrogen bonds : bond 0.03289 / 2.42 ( 2482) hydrogen bonds : angle 3.51444 / 2.61 ( 7320) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8680 Ramachandran restraints generated. 4340 Oldfield, 0 Emsley, 4340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8680 Ramachandran restraints generated. 4340 Oldfield, 0 Emsley, 4340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 254 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 731 PHE cc_start: 0.8939 (OUTLIER) cc_final: 0.8273 (p90) REVERT: A 735 LYS cc_start: 0.9045 (tptp) cc_final: 0.8500 (mttp) REVERT: A 736 HIS cc_start: 0.9523 (OUTLIER) cc_final: 0.9177 (t70) REVERT: A 783 ARG cc_start: 0.9392 (ttt90) cc_final: 0.9162 (tpp80) REVERT: A 1081 MET cc_start: 0.8296 (mmp) cc_final: 0.7695 (mmt) REVERT: B 731 PHE cc_start: 0.8771 (OUTLIER) cc_final: 0.8125 (p90) REVERT: B 736 HIS cc_start: 0.9576 (OUTLIER) cc_final: 0.9281 (t70) REVERT: B 783 ARG cc_start: 0.9443 (ttt90) cc_final: 0.9186 (tpp80) REVERT: B 787 MET cc_start: 0.8587 (mmm) cc_final: 0.8015 (mmm) REVERT: B 794 VAL cc_start: 0.9428 (OUTLIER) cc_final: 0.8833 (p) REVERT: B 798 TRP cc_start: 0.7771 (m100) cc_final: 0.6967 (m100) REVERT: B 966 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.8368 (mt-10) REVERT: C 722 MET cc_start: 0.8943 (tpp) cc_final: 0.8448 (tpp) REVERT: C 731 PHE cc_start: 0.8829 (OUTLIER) cc_final: 0.8168 (p90) REVERT: C 736 HIS cc_start: 0.9581 (OUTLIER) cc_final: 0.9254 (t70) REVERT: C 783 ARG cc_start: 0.9401 (ttt90) cc_final: 0.9158 (tpp80) REVERT: C 966 GLU cc_start: 0.8879 (OUTLIER) cc_final: 0.8411 (mt-10) REVERT: D 731 PHE cc_start: 0.8889 (OUTLIER) cc_final: 0.8164 (p90) REVERT: D 736 HIS cc_start: 0.9582 (OUTLIER) cc_final: 0.9266 (t70) REVERT: D 783 ARG cc_start: 0.9407 (ttt90) cc_final: 0.9097 (tpp80) REVERT: D 966 GLU cc_start: 0.8943 (OUTLIER) cc_final: 0.8562 (mt-10) REVERT: E 731 PHE cc_start: 0.8852 (OUTLIER) cc_final: 0.8185 (p90) REVERT: E 735 LYS cc_start: 0.9159 (tptp) cc_final: 0.8647 (mttp) REVERT: E 736 HIS cc_start: 0.9567 (OUTLIER) cc_final: 0.9224 (t70) REVERT: E 787 MET cc_start: 0.8447 (mmm) cc_final: 0.8124 (mmm) REVERT: E 966 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8179 (mt-10) REVERT: E 1074 MET cc_start: 0.9280 (OUTLIER) cc_final: 0.8898 (mmm) REVERT: F 731 PHE cc_start: 0.8846 (OUTLIER) cc_final: 0.8194 (p90) REVERT: F 736 HIS cc_start: 0.9590 (OUTLIER) cc_final: 0.9277 (t70) REVERT: F 966 GLU cc_start: 0.8905 (OUTLIER) cc_final: 0.8132 (mt-10) REVERT: F 1074 MET cc_start: 0.9241 (mmm) cc_final: 0.8864 (mtt) REVERT: G 722 MET cc_start: 0.8967 (tpp) cc_final: 0.8374 (tpp) REVERT: G 731 PHE cc_start: 0.8874 (OUTLIER) cc_final: 0.8164 (p90) REVERT: G 735 LYS cc_start: 0.9170 (tptp) cc_final: 0.8652 (mttp) REVERT: G 736 HIS cc_start: 0.9590 (OUTLIER) cc_final: 0.9254 (t70) REVERT: G 783 ARG cc_start: 0.9408 (ttt90) cc_final: 0.9132 (tpp80) REVERT: G 798 TRP cc_start: 0.7854 (m100) cc_final: 0.7452 (m100) REVERT: G 966 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.8395 (mt-10) REVERT: G 1074 MET cc_start: 0.9292 (OUTLIER) cc_final: 0.8898 (mtm) outliers start: 66 outliers final: 34 residues processed: 317 average time/residue: 0.1800 time to fit residues: 92.1573 Evaluate side-chains 299 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 242 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 731 PHE Chi-restraints excluded: chain A residue 736 HIS Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 948 SER Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 1041 GLU Chi-restraints excluded: chain B residue 731 PHE Chi-restraints excluded: chain B residue 736 HIS Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 887 LEU Chi-restraints excluded: chain B residue 966 GLU Chi-restraints excluded: chain C residue 731 PHE Chi-restraints excluded: chain C residue 736 HIS Chi-restraints excluded: chain C residue 788 LEU Chi-restraints excluded: chain C residue 887 LEU Chi-restraints excluded: chain C residue 948 SER Chi-restraints excluded: chain C residue 966 GLU Chi-restraints excluded: chain C residue 1030 LEU Chi-restraints excluded: chain C residue 1041 GLU Chi-restraints excluded: chain D residue 731 PHE Chi-restraints excluded: chain D residue 736 HIS Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 887 LEU Chi-restraints excluded: chain D residue 966 GLU Chi-restraints excluded: chain D residue 989 THR Chi-restraints excluded: chain D residue 1041 GLU Chi-restraints excluded: chain E residue 731 PHE Chi-restraints excluded: chain E residue 736 HIS Chi-restraints excluded: chain E residue 788 LEU Chi-restraints excluded: chain E residue 866 THR Chi-restraints excluded: chain E residue 874 THR Chi-restraints excluded: chain E residue 887 LEU Chi-restraints excluded: chain E residue 948 SER Chi-restraints excluded: chain E residue 966 GLU Chi-restraints excluded: chain E residue 1041 GLU Chi-restraints excluded: chain E residue 1074 MET Chi-restraints excluded: chain F residue 731 PHE Chi-restraints excluded: chain F residue 736 HIS Chi-restraints excluded: chain F residue 788 LEU Chi-restraints excluded: chain F residue 887 LEU Chi-restraints excluded: chain F residue 948 SER Chi-restraints excluded: chain F residue 966 GLU Chi-restraints excluded: chain F residue 989 THR Chi-restraints excluded: chain F residue 994 THR Chi-restraints excluded: chain F residue 1044 ILE Chi-restraints excluded: chain G residue 731 PHE Chi-restraints excluded: chain G residue 736 HIS Chi-restraints excluded: chain G residue 788 LEU Chi-restraints excluded: chain G residue 841 PHE Chi-restraints excluded: chain G residue 874 THR Chi-restraints excluded: chain G residue 887 LEU Chi-restraints excluded: chain G residue 966 GLU Chi-restraints excluded: chain G residue 1074 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 100 optimal weight: 5.9990 chunk 423 optimal weight: 4.9990 chunk 185 optimal weight: 0.0970 chunk 262 optimal weight: 50.0000 chunk 316 optimal weight: 50.0000 chunk 211 optimal weight: 5.9990 chunk 409 optimal weight: 0.1980 chunk 222 optimal weight: 40.0000 chunk 102 optimal weight: 0.4980 chunk 188 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 overall best weight: 2.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 921 ASN ** F 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 921 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.081415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.051392 restraints weight = 127314.723| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 3.15 r_work: 0.2816 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 28749 Z= 0.155 Angle : 0.640 19.303 39403 Z= 0.304 Chirality : 0.042 0.170 4998 Planarity : 0.004 0.058 5173 Dihedral : 4.014 17.536 4543 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 1.13 % Allowed : 4.19 % Favored : 94.68 % Rotamer: Outliers : 3.14 % Allowed : 23.20 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.14 (0.14), residues: 4340 helix: 2.95 (0.10), residues: 2905 sheet: -1.33 (0.26), residues: 406 loop : -2.15 (0.18), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 719 TYR 0.015 0.001 TYR F 715 PHE 0.008 0.001 PHE B 841 TRP 0.023 0.001 TRP G 798 HIS 0.008 0.001 HIS G1057 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 (28749) covalent geometry : angle 0.63983 / 0.30 (39403) hydrogen bonds : bond 0.03438 / 2.52 ( 2482) hydrogen bonds : angle 3.53442 / 2.63 ( 7320) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8680 Ramachandran restraints generated. 4340 Oldfield, 0 Emsley, 4340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8680 Ramachandran restraints generated. 4340 Oldfield, 0 Emsley, 4340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 245 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 731 PHE cc_start: 0.8956 (OUTLIER) cc_final: 0.8332 (p90) REVERT: A 735 LYS cc_start: 0.9045 (tptp) cc_final: 0.8467 (mttp) REVERT: A 736 HIS cc_start: 0.9548 (OUTLIER) cc_final: 0.9202 (t70) REVERT: A 783 ARG cc_start: 0.9403 (ttt90) cc_final: 0.9169 (tpp80) REVERT: A 1081 MET cc_start: 0.8245 (mmp) cc_final: 0.7928 (mmt) REVERT: B 731 PHE cc_start: 0.8803 (OUTLIER) cc_final: 0.8196 (p90) REVERT: B 736 HIS cc_start: 0.9595 (OUTLIER) cc_final: 0.9312 (t70) REVERT: B 798 TRP cc_start: 0.7819 (m100) cc_final: 0.7065 (m100) REVERT: B 966 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8503 (mt-10) REVERT: C 722 MET cc_start: 0.8943 (tpp) cc_final: 0.8461 (tpp) REVERT: C 731 PHE cc_start: 0.8853 (OUTLIER) cc_final: 0.8219 (p90) REVERT: C 736 HIS cc_start: 0.9600 (OUTLIER) cc_final: 0.9288 (t70) REVERT: C 783 ARG cc_start: 0.9402 (ttt90) cc_final: 0.9154 (tpp80) REVERT: C 966 GLU cc_start: 0.8922 (OUTLIER) cc_final: 0.8473 (mt-10) REVERT: D 731 PHE cc_start: 0.8879 (OUTLIER) cc_final: 0.8172 (p90) REVERT: D 736 HIS cc_start: 0.9602 (OUTLIER) cc_final: 0.9302 (t70) REVERT: D 779 LEU cc_start: 0.9327 (pt) cc_final: 0.9002 (mm) REVERT: D 783 ARG cc_start: 0.9413 (ttt90) cc_final: 0.9110 (tpp80) REVERT: D 966 GLU cc_start: 0.8939 (OUTLIER) cc_final: 0.8570 (mt-10) REVERT: E 731 PHE cc_start: 0.8863 (OUTLIER) cc_final: 0.8181 (p90) REVERT: E 736 HIS cc_start: 0.9596 (OUTLIER) cc_final: 0.9304 (t70) REVERT: E 787 MET cc_start: 0.8499 (mmm) cc_final: 0.8161 (mmm) REVERT: E 966 GLU cc_start: 0.8943 (OUTLIER) cc_final: 0.8224 (mt-10) REVERT: F 731 PHE cc_start: 0.8847 (OUTLIER) cc_final: 0.8215 (p90) REVERT: F 736 HIS cc_start: 0.9611 (OUTLIER) cc_final: 0.9306 (t70) REVERT: F 966 GLU cc_start: 0.8941 (OUTLIER) cc_final: 0.8215 (mt-10) REVERT: F 1074 MET cc_start: 0.9308 (mmm) cc_final: 0.8815 (mtt) REVERT: G 722 MET cc_start: 0.8974 (tpp) cc_final: 0.8408 (tpp) REVERT: G 731 PHE cc_start: 0.8874 (OUTLIER) cc_final: 0.8171 (p90) REVERT: G 735 LYS cc_start: 0.9175 (tptp) cc_final: 0.8627 (mttp) REVERT: G 736 HIS cc_start: 0.9602 (OUTLIER) cc_final: 0.9271 (t70) REVERT: G 783 ARG cc_start: 0.9420 (ttt90) cc_final: 0.9138 (tpp80) REVERT: G 966 GLU cc_start: 0.8928 (OUTLIER) cc_final: 0.8458 (mt-10) REVERT: G 1074 MET cc_start: 0.9366 (OUTLIER) cc_final: 0.9087 (mtm) outliers start: 62 outliers final: 38 residues processed: 303 average time/residue: 0.1800 time to fit residues: 87.8501 Evaluate side-chains 308 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 249 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 731 PHE Chi-restraints excluded: chain A residue 736 HIS Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 948 SER Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 1041 GLU Chi-restraints excluded: chain B residue 731 PHE Chi-restraints excluded: chain B residue 736 HIS Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain B residue 841 PHE Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 887 LEU Chi-restraints excluded: chain B residue 966 GLU Chi-restraints excluded: chain C residue 731 PHE Chi-restraints excluded: chain C residue 736 HIS Chi-restraints excluded: chain C residue 788 LEU Chi-restraints excluded: chain C residue 887 LEU Chi-restraints excluded: chain C residue 948 SER Chi-restraints excluded: chain C residue 966 GLU Chi-restraints excluded: chain C residue 1030 LEU Chi-restraints excluded: chain C residue 1041 GLU Chi-restraints excluded: chain D residue 731 PHE Chi-restraints excluded: chain D residue 736 HIS Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 887 LEU Chi-restraints excluded: chain D residue 966 GLU Chi-restraints excluded: chain D residue 989 THR Chi-restraints excluded: chain D residue 1041 GLU Chi-restraints excluded: chain E residue 731 PHE Chi-restraints excluded: chain E residue 736 HIS Chi-restraints excluded: chain E residue 788 LEU Chi-restraints excluded: chain E residue 866 THR Chi-restraints excluded: chain E residue 874 THR Chi-restraints excluded: chain E residue 887 LEU Chi-restraints excluded: chain E residue 948 SER Chi-restraints excluded: chain E residue 966 GLU Chi-restraints excluded: chain E residue 1041 GLU Chi-restraints excluded: chain E residue 1074 MET Chi-restraints excluded: chain F residue 731 PHE Chi-restraints excluded: chain F residue 736 HIS Chi-restraints excluded: chain F residue 788 LEU Chi-restraints excluded: chain F residue 887 LEU Chi-restraints excluded: chain F residue 936 ILE Chi-restraints excluded: chain F residue 948 SER Chi-restraints excluded: chain F residue 966 GLU Chi-restraints excluded: chain F residue 989 THR Chi-restraints excluded: chain F residue 994 THR Chi-restraints excluded: chain F residue 1044 ILE Chi-restraints excluded: chain G residue 731 PHE Chi-restraints excluded: chain G residue 736 HIS Chi-restraints excluded: chain G residue 788 LEU Chi-restraints excluded: chain G residue 841 PHE Chi-restraints excluded: chain G residue 874 THR Chi-restraints excluded: chain G residue 887 LEU Chi-restraints excluded: chain G residue 948 SER Chi-restraints excluded: chain G residue 966 GLU Chi-restraints excluded: chain G residue 1074 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 122 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 143 optimal weight: 20.0000 chunk 27 optimal weight: 10.0000 chunk 181 optimal weight: 0.9980 chunk 226 optimal weight: 0.7980 chunk 210 optimal weight: 50.0000 chunk 257 optimal weight: 20.0000 chunk 153 optimal weight: 7.9990 chunk 115 optimal weight: 0.7980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 971 ASN ** F 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 850 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.081688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.052374 restraints weight = 126619.407| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 3.17 r_work: 0.2846 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28749 Z= 0.120 Angle : 0.631 19.243 39403 Z= 0.295 Chirality : 0.041 0.171 4998 Planarity : 0.004 0.058 5173 Dihedral : 3.905 15.515 4543 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 1.13 % Allowed : 3.99 % Favored : 94.88 % Rotamer: Outliers : 3.09 % Allowed : 23.25 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.14), residues: 4340 helix: 2.95 (0.10), residues: 2947 sheet: -1.27 (0.26), residues: 406 loop : -2.19 (0.19), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 783 TYR 0.016 0.001 TYR A 715 PHE 0.008 0.001 PHE B 841 TRP 0.030 0.001 TRP G 798 HIS 0.007 0.001 HIS A1057 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (28749) covalent geometry : angle 0.63099 / 0.29 (39403) hydrogen bonds : bond 0.03181 / 2.34 ( 2482) hydrogen bonds : angle 3.45706 / 2.57 ( 7320) =============================================================================== Job complete usr+sys time: 9341.24 seconds wall clock time: 159 minutes 24.14 seconds (9564.14 seconds total)