Starting phenix.real_space_refine on Sat Aug 8 03:54:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vna_65205/08_2026/9vna_65205.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vna_65205/08_2026/9vna_65205.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vna_65205/08_2026/9vna_65205.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vna_65205/08_2026/9vna_65205.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vna_65205/08_2026/9vna_65205.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vna_65205/08_2026/9vna_65205.map" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.019 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: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 120 5.16 5 C 16564 2.51 5 N 4036 2.21 5 O 4320 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25044 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 6197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 764, 6197 Classifications: {'peptide': 764} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 19, 'TRANS': 744} Chain breaks: 17 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 2, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 46 Chain: "A" Number of atoms: 6197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 764, 6197 Classifications: {'peptide': 764} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 19, 'TRANS': 744} Chain breaks: 17 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 2, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 46 Chain: "C" Number of atoms: 6197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 764, 6197 Classifications: {'peptide': 764} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 19, 'TRANS': 744} Chain breaks: 17 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 2, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 46 Chain: "D" Number of atoms: 6197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 764, 6197 Classifications: {'peptide': 764} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 19, 'TRANS': 744} Chain breaks: 17 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 2, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 46 Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Unusual residues: {' CA': 1, 'CLR': 1, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Unusual residues: {' CA': 1, 'CLR': 1, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Unusual residues: {' CA': 1, 'CLR': 1, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Unusual residues: {' CA': 1, 'CLR': 1, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.89, per 1000 atoms: 0.24 Number of scatterers: 25044 At special positions: 0 Unit cell: (135.915, 135.915, 156.91, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 120 16.00 O 4320 8.00 N 4036 7.00 C 16564 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 929 " - pdb=" SG CYS B 940 " distance=2.04 Simple disulfide: pdb=" SG CYS A 929 " - pdb=" SG CYS A 940 " distance=2.03 Simple disulfide: pdb=" SG CYS C 929 " - pdb=" SG CYS C 940 " distance=2.03 Simple disulfide: pdb=" SG CYS D 929 " - pdb=" SG CYS D 940 " distance=2.03 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: 2.20 Conformation dependent library (CDL) restraints added in 993.2 milliseconds 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5864 Finding SS restraints... Secondary structure from input PDB file: 161 helices and 6 sheets defined 74.7% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'B' and resid 125 through 136 removed outlier: 3.712A pdb=" N LEU B 129 " --> pdb=" O ASP B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 175 Processing helix chain 'B' and resid 189 through 201 removed outlier: 3.526A pdb=" N GLY B 193 " --> pdb=" O MET B 189 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG B 197 " --> pdb=" O GLY B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 220 removed outlier: 3.508A pdb=" N VAL B 220 " --> pdb=" O TRP B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 288 Processing helix chain 'B' and resid 310 through 322 Processing helix chain 'B' and resid 404 through 416 Processing helix chain 'B' and resid 427 through 436 removed outlier: 3.874A pdb=" N TRP B 436 " --> pdb=" O LEU B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 446 Processing helix chain 'B' and resid 458 through 469 Processing helix chain 'B' and resid 470 through 481 removed outlier: 3.521A pdb=" N VAL B 474 " --> pdb=" O ARG B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 500 Processing helix chain 'B' and resid 502 through 516 Processing helix chain 'B' and resid 518 through 532 Processing helix chain 'B' and resid 561 through 571 Processing helix chain 'B' and resid 574 through 584 removed outlier: 4.047A pdb=" N GLN B 583 " --> pdb=" O VAL B 579 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR B 584 " --> pdb=" O ILE B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 602 removed outlier: 3.862A pdb=" N LEU B 592 " --> pdb=" O THR B 588 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY B 593 " --> pdb=" O LEU B 589 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA B 594 " --> pdb=" O ALA B 590 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER B 595 " --> pdb=" O ALA B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 636 Processing helix chain 'B' and resid 637 through 645 Processing helix chain 'B' and resid 656 through 663 Processing helix chain 'B' and resid 665 through 670 removed outlier: 3.693A pdb=" N ILE B 669 " --> pdb=" O ASP B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 684 Processing helix chain 'B' and resid 691 through 701 removed outlier: 3.598A pdb=" N ILE B 695 " --> pdb=" O LYS B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 708 removed outlier: 3.646A pdb=" N VAL B 705 " --> pdb=" O ILE B 701 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLY B 706 " --> pdb=" O ILE B 702 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N CYS B 707 " --> pdb=" O PRO B 703 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY B 708 " --> pdb=" O LEU B 704 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 701 through 708' Processing helix chain 'B' and resid 725 through 731 Processing helix chain 'B' and resid 733 through 758 Processing helix chain 'B' and resid 765 through 790 Processing helix chain 'B' and resid 791 through 795 removed outlier: 3.786A pdb=" N PHE B 794 " --> pdb=" O VAL B 791 " (cutoff:3.500A) Processing helix chain 'B' and resid 796 through 817 removed outlier: 3.635A pdb=" N VAL B 800 " --> pdb=" O ASP B 796 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 847 removed outlier: 4.092A pdb=" N LEU B 843 " --> pdb=" O PHE B 839 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ILE B 844 " --> pdb=" O THR B 840 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N HIS B 845 " --> pdb=" O LEU B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 853 through 860 Processing helix chain 'B' and resid 863 through 890 Processing helix chain 'B' and resid 895 through 904 Processing helix chain 'B' and resid 904 through 910 removed outlier: 3.596A pdb=" N ALA B 910 " --> pdb=" O GLU B 906 " (cutoff:3.500A) Processing helix chain 'B' and resid 952 through 969 removed outlier: 3.676A pdb=" N THR B 956 " --> pdb=" O PRO B 952 " (cutoff:3.500A) Proline residue: B 958 - end of helix Processing helix chain 'B' and resid 969 through 986 Processing helix chain 'B' and resid 989 through 1008 removed outlier: 4.208A pdb=" N TYR B 999 " --> pdb=" O LYS B 995 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N PHE B1000 " --> pdb=" O PHE B 996 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU B1001 " --> pdb=" O GLN B 997 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG B1008 " --> pdb=" O GLU B1004 " (cutoff:3.500A) Processing helix chain 'B' and resid 1012 through 1024 removed outlier: 4.359A pdb=" N VAL B1017 " --> pdb=" O PHE B1013 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N PHE B1018 " --> pdb=" O PRO B1014 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA B1019 " --> pdb=" O PHE B1015 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE B1021 " --> pdb=" O VAL B1017 " (cutoff:3.500A) Processing helix chain 'B' and resid 1054 through 1067 removed outlier: 4.151A pdb=" N VAL B1058 " --> pdb=" O ALA B1054 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N MET B1059 " --> pdb=" O TRP B1055 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS B1066 " --> pdb=" O ASN B1062 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE B1067 " --> pdb=" O TYR B1063 " (cutoff:3.500A) Processing helix chain 'B' and resid 1077 through 1104 Processing helix chain 'A' and resid 125 through 136 removed outlier: 3.695A pdb=" N LEU A 129 " --> pdb=" O ASP A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 175 Processing helix chain 'A' and resid 189 through 201 removed outlier: 3.521A pdb=" N GLY A 193 " --> pdb=" O MET A 189 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG A 197 " --> pdb=" O GLY A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 220 removed outlier: 3.531A pdb=" N VAL A 220 " --> pdb=" O TRP A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 288 Processing helix chain 'A' and resid 310 through 322 Processing helix chain 'A' and resid 404 through 416 Processing helix chain 'A' and resid 427 through 436 removed outlier: 3.900A pdb=" N TRP A 436 " --> pdb=" O LEU A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 446 Processing helix chain 'A' and resid 458 through 469 Processing helix chain 'A' and resid 470 through 481 Processing helix chain 'A' and resid 489 through 500 Processing helix chain 'A' and resid 502 through 516 Processing helix chain 'A' and resid 518 through 532 Processing helix chain 'A' and resid 561 through 571 Processing helix chain 'A' and resid 574 through 584 removed outlier: 4.045A pdb=" N GLN A 583 " --> pdb=" O VAL A 579 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR A 584 " --> pdb=" O ILE A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 602 removed outlier: 3.845A pdb=" N LEU A 592 " --> pdb=" O THR A 588 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLY A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA A 594 " --> pdb=" O ALA A 590 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N SER A 595 " --> pdb=" O ALA A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 636 Processing helix chain 'A' and resid 637 through 645 Processing helix chain 'A' and resid 656 through 662 Processing helix chain 'A' and resid 665 through 670 removed outlier: 3.625A pdb=" N ILE A 669 " --> pdb=" O ASP A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 684 Processing helix chain 'A' and resid 691 through 701 removed outlier: 3.607A pdb=" N ILE A 695 " --> pdb=" O LYS A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 708 removed outlier: 3.650A pdb=" N VAL A 705 " --> pdb=" O ILE A 701 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLY A 706 " --> pdb=" O ILE A 702 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N CYS A 707 " --> pdb=" O PRO A 703 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY A 708 " --> pdb=" O LEU A 704 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 701 through 708' Processing helix chain 'A' and resid 725 through 731 Processing helix chain 'A' and resid 733 through 759 removed outlier: 3.652A pdb=" N ASP A 759 " --> pdb=" O VAL A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 790 Processing helix chain 'A' and resid 791 through 795 removed outlier: 3.786A pdb=" N PHE A 794 " --> pdb=" O VAL A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 817 removed outlier: 3.630A pdb=" N VAL A 800 " --> pdb=" O ASP A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 842 Processing helix chain 'A' and resid 842 through 847 Processing helix chain 'A' and resid 853 through 860 Processing helix chain 'A' and resid 863 through 890 Processing helix chain 'A' and resid 895 through 904 Processing helix chain 'A' and resid 904 through 910 removed outlier: 3.600A pdb=" N ALA A 910 " --> pdb=" O GLU A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 969 removed outlier: 3.660A pdb=" N THR A 956 " --> pdb=" O PRO A 952 " (cutoff:3.500A) Proline residue: A 958 - end of helix Processing helix chain 'A' and resid 969 through 986 Processing helix chain 'A' and resid 989 through 1008 removed outlier: 4.209A pdb=" N TYR A 999 " --> pdb=" O LYS A 995 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N PHE A1000 " --> pdb=" O PHE A 996 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A1001 " --> pdb=" O GLN A 997 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG A1008 " --> pdb=" O GLU A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1024 removed outlier: 4.362A pdb=" N VAL A1017 " --> pdb=" O PHE A1013 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N PHE A1018 " --> pdb=" O PRO A1014 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA A1019 " --> pdb=" O PHE A1015 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE A1021 " --> pdb=" O VAL A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1054 through 1067 removed outlier: 4.144A pdb=" N VAL A1058 " --> pdb=" O ALA A1054 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N MET A1059 " --> pdb=" O TRP A1055 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS A1066 " --> pdb=" O ASN A1062 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE A1067 " --> pdb=" O TYR A1063 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1104 Processing helix chain 'C' and resid 125 through 136 removed outlier: 3.700A pdb=" N LEU C 129 " --> pdb=" O ASP C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 175 Processing helix chain 'C' and resid 188 through 201 removed outlier: 4.177A pdb=" N ILE C 192 " --> pdb=" O LEU C 188 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG C 197 " --> pdb=" O GLY C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 220 removed outlier: 3.515A pdb=" N VAL C 220 " --> pdb=" O TRP C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 288 Processing helix chain 'C' and resid 310 through 322 Processing helix chain 'C' and resid 404 through 416 Processing helix chain 'C' and resid 427 through 436 removed outlier: 3.874A pdb=" N TRP C 436 " --> pdb=" O LEU C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 446 Processing helix chain 'C' and resid 458 through 468 Processing helix chain 'C' and resid 470 through 481 removed outlier: 3.517A pdb=" N VAL C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 500 Processing helix chain 'C' and resid 502 through 516 Processing helix chain 'C' and resid 518 through 532 Processing helix chain 'C' and resid 561 through 571 Processing helix chain 'C' and resid 574 through 584 removed outlier: 4.048A pdb=" N GLN C 583 " --> pdb=" O VAL C 579 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR C 584 " --> pdb=" O ILE C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 602 removed outlier: 3.860A pdb=" N LEU C 592 " --> pdb=" O THR C 588 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY C 593 " --> pdb=" O LEU C 589 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA C 594 " --> pdb=" O ALA C 590 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER C 595 " --> pdb=" O ALA C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 636 Processing helix chain 'C' and resid 637 through 645 Processing helix chain 'C' and resid 656 through 663 Processing helix chain 'C' and resid 665 through 670 removed outlier: 3.633A pdb=" N ILE C 669 " --> pdb=" O ASP C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 684 Processing helix chain 'C' and resid 691 through 701 removed outlier: 3.599A pdb=" N ILE C 695 " --> pdb=" O LYS C 691 " (cutoff:3.500A) Processing helix chain 'C' and resid 701 through 708 removed outlier: 3.645A pdb=" N VAL C 705 " --> pdb=" O ILE C 701 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLY C 706 " --> pdb=" O ILE C 702 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N CYS C 707 " --> pdb=" O PRO C 703 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY C 708 " --> pdb=" O LEU C 704 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 701 through 708' Processing helix chain 'C' and resid 725 through 731 Processing helix chain 'C' and resid 733 through 758 Processing helix chain 'C' and resid 765 through 790 Processing helix chain 'C' and resid 791 through 795 removed outlier: 3.786A pdb=" N PHE C 794 " --> pdb=" O VAL C 791 " (cutoff:3.500A) Processing helix chain 'C' and resid 796 through 817 removed outlier: 3.635A pdb=" N VAL C 800 " --> pdb=" O ASP C 796 " (cutoff:3.500A) Processing helix chain 'C' and resid 821 through 847 removed outlier: 4.089A pdb=" N LEU C 843 " --> pdb=" O PHE C 839 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ILE C 844 " --> pdb=" O THR C 840 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N HIS C 845 " --> pdb=" O LEU C 841 " (cutoff:3.500A) Processing helix chain 'C' and resid 853 through 860 Processing helix chain 'C' and resid 863 through 890 Processing helix chain 'C' and resid 895 through 904 Processing helix chain 'C' and resid 904 through 910 removed outlier: 3.594A pdb=" N ALA C 910 " --> pdb=" O GLU C 906 " (cutoff:3.500A) Processing helix chain 'C' and resid 952 through 969 removed outlier: 3.673A pdb=" N THR C 956 " --> pdb=" O PRO C 952 " (cutoff:3.500A) Proline residue: C 958 - end of helix Processing helix chain 'C' and resid 969 through 986 Processing helix chain 'C' and resid 989 through 1008 removed outlier: 4.208A pdb=" N TYR C 999 " --> pdb=" O LYS C 995 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N PHE C1000 " --> pdb=" O PHE C 996 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU C1001 " --> pdb=" O GLN C 997 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG C1008 " --> pdb=" O GLU C1004 " (cutoff:3.500A) Processing helix chain 'C' and resid 1012 through 1024 removed outlier: 4.360A pdb=" N VAL C1017 " --> pdb=" O PHE C1013 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N PHE C1018 " --> pdb=" O PRO C1014 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA C1019 " --> pdb=" O PHE C1015 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE C1021 " --> pdb=" O VAL C1017 " (cutoff:3.500A) Processing helix chain 'C' and resid 1054 through 1067 removed outlier: 4.151A pdb=" N VAL C1058 " --> pdb=" O ALA C1054 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N MET C1059 " --> pdb=" O TRP C1055 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS C1066 " --> pdb=" O ASN C1062 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE C1067 " --> pdb=" O TYR C1063 " (cutoff:3.500A) Processing helix chain 'C' and resid 1077 through 1104 Processing helix chain 'D' and resid 125 through 136 removed outlier: 3.700A pdb=" N LEU D 129 " --> pdb=" O ASP D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 175 Processing helix chain 'D' and resid 188 through 201 removed outlier: 4.163A pdb=" N ILE D 192 " --> pdb=" O LEU D 188 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG D 197 " --> pdb=" O GLY D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 220 removed outlier: 3.523A pdb=" N VAL D 220 " --> pdb=" O TRP D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 288 Processing helix chain 'D' and resid 310 through 322 Processing helix chain 'D' and resid 404 through 416 Processing helix chain 'D' and resid 427 through 436 removed outlier: 3.880A pdb=" N TRP D 436 " --> pdb=" O LEU D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 446 Processing helix chain 'D' and resid 458 through 469 Processing helix chain 'D' and resid 470 through 481 Processing helix chain 'D' and resid 489 through 500 Processing helix chain 'D' and resid 502 through 516 Processing helix chain 'D' and resid 518 through 532 Processing helix chain 'D' and resid 561 through 571 Processing helix chain 'D' and resid 574 through 584 removed outlier: 4.046A pdb=" N GLN D 583 " --> pdb=" O VAL D 579 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR D 584 " --> pdb=" O ILE D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 602 removed outlier: 3.860A pdb=" N LEU D 592 " --> pdb=" O THR D 588 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLY D 593 " --> pdb=" O LEU D 589 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA D 594 " --> pdb=" O ALA D 590 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER D 595 " --> pdb=" O ALA D 591 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 636 Processing helix chain 'D' and resid 637 through 645 Processing helix chain 'D' and resid 656 through 663 Processing helix chain 'D' and resid 665 through 670 removed outlier: 3.635A pdb=" N ILE D 669 " --> pdb=" O ASP D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 671 through 684 Processing helix chain 'D' and resid 691 through 701 removed outlier: 3.600A pdb=" N ILE D 695 " --> pdb=" O LYS D 691 " (cutoff:3.500A) Processing helix chain 'D' and resid 701 through 708 removed outlier: 3.644A pdb=" N VAL D 705 " --> pdb=" O ILE D 701 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLY D 706 " --> pdb=" O ILE D 702 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N CYS D 707 " --> pdb=" O PRO D 703 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY D 708 " --> pdb=" O LEU D 704 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 701 through 708' Processing helix chain 'D' and resid 725 through 731 Processing helix chain 'D' and resid 733 through 759 removed outlier: 3.654A pdb=" N ASP D 759 " --> pdb=" O VAL D 755 " (cutoff:3.500A) Processing helix chain 'D' and resid 765 through 790 Processing helix chain 'D' and resid 791 through 795 removed outlier: 3.786A pdb=" N PHE D 794 " --> pdb=" O VAL D 791 " (cutoff:3.500A) Processing helix chain 'D' and resid 796 through 817 removed outlier: 3.635A pdb=" N VAL D 800 " --> pdb=" O ASP D 796 " (cutoff:3.500A) Processing helix chain 'D' and resid 821 through 847 removed outlier: 4.090A pdb=" N LEU D 843 " --> pdb=" O PHE D 839 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ILE D 844 " --> pdb=" O THR D 840 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N HIS D 845 " --> pdb=" O LEU D 841 " (cutoff:3.500A) Processing helix chain 'D' and resid 853 through 860 Processing helix chain 'D' and resid 863 through 890 Processing helix chain 'D' and resid 895 through 904 Processing helix chain 'D' and resid 904 through 910 removed outlier: 3.598A pdb=" N ALA D 910 " --> pdb=" O GLU D 906 " (cutoff:3.500A) Processing helix chain 'D' and resid 952 through 969 removed outlier: 3.673A pdb=" N THR D 956 " --> pdb=" O PRO D 952 " (cutoff:3.500A) Proline residue: D 958 - end of helix Processing helix chain 'D' and resid 969 through 986 Processing helix chain 'D' and resid 989 through 1008 removed outlier: 4.209A pdb=" N TYR D 999 " --> pdb=" O LYS D 995 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N PHE D1000 " --> pdb=" O PHE D 996 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU D1001 " --> pdb=" O GLN D 997 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG D1008 " --> pdb=" O GLU D1004 " (cutoff:3.500A) Processing helix chain 'D' and resid 1012 through 1024 removed outlier: 4.360A pdb=" N VAL D1017 " --> pdb=" O PHE D1013 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N PHE D1018 " --> pdb=" O PRO D1014 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA D1019 " --> pdb=" O PHE D1015 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE D1021 " --> pdb=" O VAL D1017 " (cutoff:3.500A) Processing helix chain 'D' and resid 1054 through 1067 removed outlier: 4.151A pdb=" N VAL D1058 " --> pdb=" O ALA D1054 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N MET D1059 " --> pdb=" O TRP D1055 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS D1066 " --> pdb=" O ASN D1062 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE D1067 " --> pdb=" O TYR D1063 " (cutoff:3.500A) Processing helix chain 'D' and resid 1077 through 1104 Processing sheet with id=AA1, first strand: chain 'B' and resid 144 through 146 removed outlier: 6.195A pdb=" N LEU B 144 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N PHE B 304 " --> pdb=" O LEU B 144 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ILE B 146 " --> pdb=" O PHE B 304 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N VAL B 328 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N CYS B 303 " --> pdb=" O VAL B 328 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N VAL B 327 " --> pdb=" O LYS B 395 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 178 through 181 Processing sheet with id=AA3, first strand: chain 'A' and resid 144 through 146 removed outlier: 6.144A pdb=" N LEU A 144 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N PHE A 304 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ILE A 146 " --> pdb=" O PHE A 304 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N VAL A 328 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N CYS A 303 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N VAL A 327 " --> pdb=" O LYS A 395 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 178 through 181 removed outlier: 5.924A pdb=" N ALA A 211 " --> pdb=" O HIS A 259 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N LEU A 261 " --> pdb=" O ALA A 211 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N GLY A 213 " --> pdb=" O LEU A 261 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 259 through 262 removed outlier: 3.904A pdb=" N VAL C 210 " --> pdb=" O ALA C 177 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N ASN C 143 " --> pdb=" O TRP C 178 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N LEU C 180 " --> pdb=" O ASN C 143 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL C 145 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LEU C 144 " --> pdb=" O VAL C 302 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N PHE C 304 " --> pdb=" O LEU C 144 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE C 146 " --> pdb=" O PHE C 304 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N VAL C 328 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N CYS C 303 " --> pdb=" O VAL C 328 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N VAL C 327 " --> pdb=" O LYS C 395 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 259 through 262 removed outlier: 3.905A pdb=" N VAL D 210 " --> pdb=" O ALA D 177 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N ASN D 143 " --> pdb=" O TRP D 178 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N LEU D 180 " --> pdb=" O ASN D 143 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL D 145 " --> pdb=" O LEU D 180 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LEU D 144 " --> pdb=" O VAL D 302 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N PHE D 304 " --> pdb=" O LEU D 144 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ILE D 146 " --> pdb=" O PHE D 304 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N VAL D 328 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N CYS D 303 " --> pdb=" O VAL D 328 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N VAL D 327 " --> pdb=" O LYS D 395 " (cutoff:3.500A) 1518 hydrogen bonds defined for protein. 4521 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.71 Time building geometry restraints manager: 2.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3875 1.32 - 1.44: 7313 1.44 - 1.56: 14272 1.56 - 1.69: 0 1.69 - 1.81: 184 Bond restraints: 25644 Sorted by residual: bond pdb=" C PRO D 938 " pdb=" O PRO D 938 " ideal model delta sigma weight residual 1.233 1.192 0.040 1.16e-02 7.43e+03 1.22e+01 bond pdb=" N LYS D 937 " pdb=" CA LYS D 937 " ideal model delta sigma weight residual 1.453 1.484 -0.031 9.20e-03 1.18e+04 1.10e+01 bond pdb=" N LYS A 937 " pdb=" CA LYS A 937 " ideal model delta sigma weight residual 1.453 1.481 -0.028 9.20e-03 1.18e+04 9.22e+00 bond pdb=" N LYS B 937 " pdb=" CA LYS B 937 " ideal model delta sigma weight residual 1.453 1.481 -0.028 9.20e-03 1.18e+04 9.00e+00 bond pdb=" N GLU B 935 " pdb=" CA GLU B 935 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.06e-02 8.90e+03 8.18e+00 ... (remaining 25639 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 33448 1.20 - 2.39: 1045 2.39 - 3.59: 218 3.59 - 4.79: 82 4.79 - 5.99: 15 Bond angle restraints: 34808 Sorted by residual: angle pdb=" CA THR A 930 " pdb=" CB THR A 930 " pdb=" OG1 THR A 930 " ideal model delta sigma weight residual 109.60 103.61 5.99 1.50e+00 4.44e-01 1.59e+01 angle pdb=" CA LEU B 939 " pdb=" C LEU B 939 " pdb=" O LEU B 939 " ideal model delta sigma weight residual 121.99 117.49 4.50 1.14e+00 7.69e-01 1.56e+01 angle pdb=" CA PRO D 938 " pdb=" C PRO D 938 " pdb=" O PRO D 938 " ideal model delta sigma weight residual 121.34 116.91 4.43 1.14e+00 7.69e-01 1.51e+01 angle pdb=" CA LEU A 939 " pdb=" C LEU A 939 " pdb=" O LEU A 939 " ideal model delta sigma weight residual 121.87 117.41 4.46 1.16e+00 7.43e-01 1.48e+01 angle pdb=" CA GLU A 942 " pdb=" C GLU A 942 " pdb=" O GLU A 942 " ideal model delta sigma weight residual 121.19 117.15 4.04 1.10e+00 8.26e-01 1.35e+01 ... (remaining 34803 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 13488 17.96 - 35.91: 1350 35.91 - 53.87: 336 53.87 - 71.82: 106 71.82 - 89.78: 8 Dihedral angle restraints: 15288 sinusoidal: 6304 harmonic: 8984 Sorted by residual: dihedral pdb=" CB GLU B 622 " pdb=" CG GLU B 622 " pdb=" CD GLU B 622 " pdb=" OE1 GLU B 622 " ideal model delta sinusoidal sigma weight residual 0.00 89.78 -89.78 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU D 622 " pdb=" CG GLU D 622 " pdb=" CD GLU D 622 " pdb=" OE1 GLU D 622 " ideal model delta sinusoidal sigma weight residual 0.00 89.75 -89.75 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU A 622 " pdb=" CG GLU A 622 " pdb=" CD GLU A 622 " pdb=" OE1 GLU A 622 " ideal model delta sinusoidal sigma weight residual 0.00 89.74 -89.74 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 15285 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 3001 0.034 - 0.069: 709 0.069 - 0.103: 204 0.103 - 0.137: 70 0.137 - 0.172: 12 Chirality restraints: 3996 Sorted by residual: chirality pdb=" CA VAL A 941 " pdb=" N VAL A 941 " pdb=" C VAL A 941 " pdb=" CB VAL A 941 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.38e-01 chirality pdb=" CA VAL B 941 " pdb=" N VAL B 941 " pdb=" C VAL B 941 " pdb=" CB VAL B 941 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.34e-01 chirality pdb=" CA VAL D 941 " pdb=" N VAL D 941 " pdb=" C VAL D 941 " pdb=" CB VAL D 941 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 6.99e-01 ... (remaining 3993 not shown) Planarity restraints: 4220 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN C 934 " -0.012 2.00e-02 2.50e+03 2.28e-02 5.18e+00 pdb=" C ASN C 934 " 0.039 2.00e-02 2.50e+03 pdb=" O ASN C 934 " -0.014 2.00e-02 2.50e+03 pdb=" N GLU C 935 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU C 906 " -0.033 5.00e-02 4.00e+02 4.99e-02 3.98e+00 pdb=" N PRO C 907 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO C 907 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 907 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 906 " 0.033 5.00e-02 4.00e+02 4.98e-02 3.97e+00 pdb=" N PRO D 907 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO D 907 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 907 " 0.028 5.00e-02 4.00e+02 ... (remaining 4217 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 7727 2.83 - 3.35: 24931 3.35 - 3.87: 39332 3.87 - 4.38: 43842 4.38 - 4.90: 75490 Nonbonded interactions: 191322 Sorted by model distance: nonbonded pdb=" O ASN C 934 " pdb=" OD1 ASN C 934 " model vdw 2.313 3.040 nonbonded pdb=" O GLN A 642 " pdb=" OE1 GLN A 642 " model vdw 2.429 3.040 nonbonded pdb=" O GLN D 642 " pdb=" OE1 GLN D 642 " model vdw 2.429 3.040 nonbonded pdb=" O GLN C 642 " pdb=" OE1 GLN C 642 " model vdw 2.429 3.040 nonbonded pdb=" O GLN B 642 " pdb=" OE1 GLN B 642 " model vdw 2.430 3.040 ... (remaining 191317 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and resid 102 through 1104) selection = (chain 'B' and resid 102 through 1104) selection = (chain 'C' and resid 102 through 1104) selection = (chain 'D' and resid 102 through 1104) } 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: 2.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.420 Check model and map are aligned: 0.090 Set scattering table: 0.040 Process input model: 23.270 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 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 : 0.003 0.044 25648 Z= 0.176 Angle : 0.539 5.985 34816 Z= 0.306 Chirality : 0.035 0.172 3996 Planarity : 0.004 0.050 4220 Dihedral : 15.923 89.781 9412 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.87 % Allowed : 16.70 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.16), residues: 2912 helix: 2.14 (0.11), residues: 2080 sheet: -0.04 (0.52), residues: 84 loop : -0.97 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 278 TYR 0.009 0.001 TYR A 793 PHE 0.017 0.001 PHE A 779 TRP 0.012 0.001 TRP B 898 HIS 0.005 0.001 HIS A1080 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.18 (25644) covalent geometry : angle 0.53858 / 0.31 (34808) SS BOND : bond 0.00221 / 0.11 ( 4) SS BOND : angle 0.87260 / 0.55 ( 8) hydrogen bonds : bond 0.15595 / 10.42 ( 1518) hydrogen bonds : angle 5.61629 / 4.05 ( 4521) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 284 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 189 MET cc_start: 0.6143 (ttm) cc_final: 0.5916 (tmm) REVERT: D 189 MET cc_start: 0.6189 (ttm) cc_final: 0.5885 (tmm) outliers start: 23 outliers final: 16 residues processed: 294 average time/residue: 0.1644 time to fit residues: 78.9996 Evaluate side-chains 273 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 257 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 199 ASN Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 929 CYS Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 929 CYS Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 940 CYS Chi-restraints excluded: chain D residue 199 ASN Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 929 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 197 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 52.0249 > 50:) chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 7.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 199 ASN B 500 HIS B 642 GLN A 199 ASN A 642 GLN C 199 ASN C 500 HIS C 642 GLN C 934 ASN ** C 973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 ASN D 500 HIS D 571 GLN D 642 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.226138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.156962 restraints weight = 26149.945| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 2.30 r_work: 0.3283 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 25648 Z= 0.201 Angle : 0.557 8.180 34816 Z= 0.294 Chirality : 0.041 0.164 3996 Planarity : 0.005 0.054 4220 Dihedral : 6.651 59.809 3813 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.38 % Allowed : 16.67 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.78 (0.15), residues: 2912 helix: 1.93 (0.11), residues: 2084 sheet: 0.61 (0.52), residues: 84 loop : -0.92 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 816 TYR 0.011 0.001 TYR B 793 PHE 0.019 0.002 PHE C 951 TRP 0.017 0.001 TRP D 682 HIS 0.006 0.001 HIS B1080 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.20 (25644) covalent geometry : angle 0.55717 / 0.29 (34808) SS BOND : bond 0.00089 / 0.04 ( 4) SS BOND : angle 0.78079 / 0.47 ( 8) hydrogen bonds : bond 0.06471 / 4.24 ( 1518) hydrogen bonds : angle 4.21240 / 3.01 ( 4521) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 302 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 189 MET cc_start: 0.4422 (ttp) cc_final: 0.3869 (tmm) REVERT: B 431 LYS cc_start: 0.7608 (mtpp) cc_final: 0.7147 (mtmm) REVERT: B 631 GLU cc_start: 0.7131 (mm-30) cc_final: 0.6847 (mm-30) REVERT: A 620 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7649 (mm-30) REVERT: A 631 GLU cc_start: 0.7131 (mm-30) cc_final: 0.6844 (mm-30) REVERT: C 189 MET cc_start: 0.4671 (ttm) cc_final: 0.4335 (tmm) REVERT: C 219 MET cc_start: 0.4409 (ttt) cc_final: 0.4100 (ttt) REVERT: C 431 LYS cc_start: 0.7626 (mtpp) cc_final: 0.7169 (mtmm) REVERT: C 631 GLU cc_start: 0.7136 (mm-30) cc_final: 0.6853 (mm-30) REVERT: C 843 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8576 (mp) REVERT: D 189 MET cc_start: 0.4580 (ttm) cc_final: 0.4248 (tmm) REVERT: D 431 LYS cc_start: 0.7636 (mtpp) cc_final: 0.7185 (mtmm) outliers start: 63 outliers final: 40 residues processed: 346 average time/residue: 0.1567 time to fit residues: 89.2438 Evaluate side-chains 328 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 287 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 326 CYS Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 656 CYS Chi-restraints excluded: chain B residue 698 CYS Chi-restraints excluded: chain B residue 763 VAL Chi-restraints excluded: chain B residue 788 MET Chi-restraints excluded: chain B residue 1013 PHE Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 656 CYS Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 929 CYS Chi-restraints excluded: chain A residue 940 CYS Chi-restraints excluded: chain A residue 1013 PHE Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 326 CYS Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 763 VAL Chi-restraints excluded: chain C residue 788 MET Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain C residue 940 CYS Chi-restraints excluded: chain C residue 1013 PHE Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 326 CYS Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 656 CYS Chi-restraints excluded: chain D residue 698 CYS Chi-restraints excluded: chain D residue 763 VAL Chi-restraints excluded: chain D residue 788 MET Chi-restraints excluded: chain D residue 929 CYS Chi-restraints excluded: chain D residue 940 CYS Chi-restraints excluded: chain D residue 1013 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 138 optimal weight: 0.7980 chunk 196 optimal weight: 0.7980 chunk 12 optimal weight: 10.0000 chunk 167 optimal weight: 6.9990 chunk 285 optimal weight: 0.5980 chunk 234 optimal weight: 20.0000 chunk 157 optimal weight: 9.9990 chunk 241 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 158 optimal weight: 9.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 571 GLN B 642 GLN B1062 ASN A 642 GLN C 199 ASN C 571 GLN C 642 GLN C 934 ASN ** C 973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1062 ASN D 199 ASN D 642 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.229959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.157614 restraints weight = 26250.698| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.05 r_work: 0.3359 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25648 Z= 0.121 Angle : 0.468 8.327 34816 Z= 0.249 Chirality : 0.037 0.149 3996 Planarity : 0.004 0.059 4220 Dihedral : 5.895 57.692 3793 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.79 % Allowed : 17.31 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.15), residues: 2912 helix: 2.11 (0.11), residues: 2092 sheet: 0.19 (0.48), residues: 108 loop : -0.83 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 816 TYR 0.009 0.001 TYR A 793 PHE 0.014 0.001 PHE B 463 TRP 0.013 0.001 TRP A 682 HIS 0.005 0.001 HIS C1080 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (25644) covalent geometry : angle 0.46833 / 0.25 (34808) SS BOND : bond 0.00040 / 0.02 ( 4) SS BOND : angle 0.67155 / 0.39 ( 8) hydrogen bonds : bond 0.04913 / 3.21 ( 1518) hydrogen bonds : angle 3.77648 / 2.70 ( 4521) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 288 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 189 MET cc_start: 0.4394 (ttp) cc_final: 0.3837 (tmm) REVERT: B 431 LYS cc_start: 0.7612 (mtpp) cc_final: 0.7180 (mtmm) REVERT: B 631 GLU cc_start: 0.7088 (mm-30) cc_final: 0.6696 (tm-30) REVERT: A 438 GLN cc_start: 0.7266 (mp10) cc_final: 0.7029 (mp10) REVERT: A 620 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7180 (tt0) REVERT: A 631 GLU cc_start: 0.7096 (mm-30) cc_final: 0.6752 (tm-30) REVERT: C 189 MET cc_start: 0.4378 (ttm) cc_final: 0.4127 (tmm) REVERT: C 219 MET cc_start: 0.4395 (ttt) cc_final: 0.4068 (ttt) REVERT: C 431 LYS cc_start: 0.7606 (mtpp) cc_final: 0.7174 (mtmm) REVERT: C 463 PHE cc_start: 0.6605 (t80) cc_final: 0.6256 (t80) REVERT: C 620 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7227 (tt0) REVERT: C 631 GLU cc_start: 0.7094 (mm-30) cc_final: 0.6708 (tm-30) REVERT: C 843 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8358 (mp) REVERT: D 189 MET cc_start: 0.4404 (ttm) cc_final: 0.4132 (tmm) REVERT: D 431 LYS cc_start: 0.7612 (mtpp) cc_final: 0.7184 (mtmm) REVERT: D 631 GLU cc_start: 0.7095 (mm-30) cc_final: 0.6704 (tm-30) outliers start: 74 outliers final: 37 residues processed: 340 average time/residue: 0.1603 time to fit residues: 88.8405 Evaluate side-chains 315 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 277 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 457 ASP Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain B residue 656 CYS Chi-restraints excluded: chain B residue 698 CYS Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 1007 ASN Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 656 CYS Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 929 CYS Chi-restraints excluded: chain A residue 940 CYS Chi-restraints excluded: chain A residue 1007 ASN Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 645 VAL Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain C residue 940 CYS Chi-restraints excluded: chain C residue 1007 ASN Chi-restraints excluded: chain D residue 122 CYS Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 656 CYS Chi-restraints excluded: chain D residue 698 CYS Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain D residue 940 CYS Chi-restraints excluded: chain D residue 1007 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 256 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 238 optimal weight: 20.0000 chunk 84 optimal weight: 0.8980 chunk 249 optimal weight: 4.9990 chunk 215 optimal weight: 0.0370 chunk 189 optimal weight: 3.9990 chunk 272 optimal weight: 1.9990 chunk 288 optimal weight: 1.9990 chunk 163 optimal weight: 5.9990 chunk 202 optimal weight: 2.9990 overall best weight: 1.3864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 973 ASN D 973 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.227833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.156876 restraints weight = 26203.163| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 2.08 r_work: 0.3331 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 25648 Z= 0.155 Angle : 0.502 7.086 34816 Z= 0.264 Chirality : 0.039 0.146 3996 Planarity : 0.004 0.059 4220 Dihedral : 5.833 56.932 3786 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.58 % Allowed : 17.38 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.15), residues: 2912 helix: 2.02 (0.11), residues: 2092 sheet: 0.44 (0.49), residues: 108 loop : -0.82 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 816 TYR 0.017 0.001 TYR B 646 PHE 0.017 0.001 PHE A 951 TRP 0.015 0.001 TRP A 898 HIS 0.006 0.001 HIS A1080 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (25644) covalent geometry : angle 0.50224 / 0.26 (34808) SS BOND : bond 0.00051 / 0.02 ( 4) SS BOND : angle 0.86723 / 0.53 ( 8) hydrogen bonds : bond 0.05594 / 3.67 ( 1518) hydrogen bonds : angle 3.76961 / 2.69 ( 4521) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 287 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 189 MET cc_start: 0.4313 (OUTLIER) cc_final: 0.3951 (tmm) REVERT: B 431 LYS cc_start: 0.7635 (mtpp) cc_final: 0.7208 (mtmm) REVERT: B 620 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7287 (tt0) REVERT: B 631 GLU cc_start: 0.7100 (mm-30) cc_final: 0.6683 (tm-30) REVERT: A 620 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7225 (tt0) REVERT: A 631 GLU cc_start: 0.7103 (mm-30) cc_final: 0.6688 (tm-30) REVERT: C 219 MET cc_start: 0.4329 (ttt) cc_final: 0.4026 (ttt) REVERT: C 431 LYS cc_start: 0.7631 (mtpp) cc_final: 0.7203 (mtmm) REVERT: C 620 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7285 (tt0) REVERT: C 631 GLU cc_start: 0.7101 (mm-30) cc_final: 0.6692 (tm-30) REVERT: C 843 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8483 (mp) REVERT: D 431 LYS cc_start: 0.7655 (mtpp) cc_final: 0.7226 (mtmm) REVERT: D 631 GLU cc_start: 0.7108 (mm-30) cc_final: 0.6693 (tm-30) outliers start: 95 outliers final: 63 residues processed: 342 average time/residue: 0.1609 time to fit residues: 90.0536 Evaluate side-chains 343 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 278 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 457 ASP Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain B residue 656 CYS Chi-restraints excluded: chain B residue 698 CYS Chi-restraints excluded: chain B residue 788 MET Chi-restraints excluded: chain B residue 803 THR Chi-restraints excluded: chain B residue 815 PHE Chi-restraints excluded: chain B residue 851 ARG Chi-restraints excluded: chain B residue 985 ILE Chi-restraints excluded: chain B residue 1007 ASN Chi-restraints excluded: chain B residue 1023 MET Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 656 CYS Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain A residue 788 MET Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 940 CYS Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 1007 ASN Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 645 VAL Chi-restraints excluded: chain C residue 803 THR Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain C residue 851 ARG Chi-restraints excluded: chain C residue 940 CYS Chi-restraints excluded: chain C residue 985 ILE Chi-restraints excluded: chain C residue 1007 ASN Chi-restraints excluded: chain C residue 1023 MET Chi-restraints excluded: chain D residue 122 CYS Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 656 CYS Chi-restraints excluded: chain D residue 698 CYS Chi-restraints excluded: chain D residue 803 THR Chi-restraints excluded: chain D residue 851 ARG Chi-restraints excluded: chain D residue 929 CYS Chi-restraints excluded: chain D residue 940 CYS Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 1023 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 213 optimal weight: 1.9990 chunk 267 optimal weight: 0.5980 chunk 183 optimal weight: 4.9990 chunk 242 optimal weight: 10.0000 chunk 160 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 65 optimal weight: 0.5980 chunk 4 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 279 optimal weight: 1.9990 chunk 75 optimal weight: 50.0000 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 642 GLN ** B 973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 642 GLN A 973 ASN C 642 GLN D 642 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.225795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.154007 restraints weight = 26068.966| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 2.01 r_work: 0.3295 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 25648 Z= 0.204 Angle : 0.562 7.944 34816 Z= 0.293 Chirality : 0.041 0.161 3996 Planarity : 0.004 0.058 4220 Dihedral : 6.020 56.233 3785 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.03 % Allowed : 18.48 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.15), residues: 2912 helix: 1.84 (0.11), residues: 2096 sheet: 0.46 (0.49), residues: 108 loop : -0.86 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 885 TYR 0.014 0.001 TYR B 646 PHE 0.020 0.002 PHE A 951 TRP 0.018 0.001 TRP B 898 HIS 0.006 0.001 HIS C1080 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.20 (25644) covalent geometry : angle 0.56200 / 0.29 (34808) SS BOND : bond 0.00066 / 0.03 ( 4) SS BOND : angle 0.91385 / 0.56 ( 8) hydrogen bonds : bond 0.06430 / 4.22 ( 1518) hydrogen bonds : angle 3.87308 / 2.77 ( 4521) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 283 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 189 MET cc_start: 0.4358 (OUTLIER) cc_final: 0.3982 (tmm) REVERT: B 631 GLU cc_start: 0.6998 (mm-30) cc_final: 0.6701 (mm-30) REVERT: A 301 ILE cc_start: 0.8293 (mm) cc_final: 0.8093 (mm) REVERT: A 631 GLU cc_start: 0.7012 (mm-30) cc_final: 0.6713 (mm-30) REVERT: C 631 GLU cc_start: 0.7020 (mm-30) cc_final: 0.6722 (mm-30) REVERT: C 843 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8594 (mp) REVERT: C 1060 LYS cc_start: 0.7587 (OUTLIER) cc_final: 0.7162 (ttmt) REVERT: D 631 GLU cc_start: 0.7015 (mm-30) cc_final: 0.6714 (mm-30) outliers start: 107 outliers final: 89 residues processed: 346 average time/residue: 0.1557 time to fit residues: 87.5117 Evaluate side-chains 369 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 277 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 457 ASP Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain B residue 656 CYS Chi-restraints excluded: chain B residue 698 CYS Chi-restraints excluded: chain B residue 788 MET Chi-restraints excluded: chain B residue 803 THR Chi-restraints excluded: chain B residue 851 ARG Chi-restraints excluded: chain B residue 985 ILE Chi-restraints excluded: chain B residue 1007 ASN Chi-restraints excluded: chain B residue 1013 PHE Chi-restraints excluded: chain B residue 1023 MET Chi-restraints excluded: chain B residue 1059 MET Chi-restraints excluded: chain B residue 1060 LYS Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 656 CYS Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain A residue 788 MET Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 851 ARG Chi-restraints excluded: chain A residue 929 CYS Chi-restraints excluded: chain A residue 940 CYS Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 1013 PHE Chi-restraints excluded: chain A residue 1023 MET Chi-restraints excluded: chain A residue 1059 MET Chi-restraints excluded: chain A residue 1060 LYS Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 566 ILE Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 645 VAL Chi-restraints excluded: chain C residue 656 CYS Chi-restraints excluded: chain C residue 788 MET Chi-restraints excluded: chain C residue 803 THR Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain C residue 851 ARG Chi-restraints excluded: chain C residue 940 CYS Chi-restraints excluded: chain C residue 985 ILE Chi-restraints excluded: chain C residue 1007 ASN Chi-restraints excluded: chain C residue 1013 PHE Chi-restraints excluded: chain C residue 1023 MET Chi-restraints excluded: chain C residue 1059 MET Chi-restraints excluded: chain C residue 1060 LYS Chi-restraints excluded: chain D residue 122 CYS Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 492 VAL Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 566 ILE Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 656 CYS Chi-restraints excluded: chain D residue 698 CYS Chi-restraints excluded: chain D residue 788 MET Chi-restraints excluded: chain D residue 803 THR Chi-restraints excluded: chain D residue 851 ARG Chi-restraints excluded: chain D residue 929 CYS Chi-restraints excluded: chain D residue 940 CYS Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 1007 ASN Chi-restraints excluded: chain D residue 1013 PHE Chi-restraints excluded: chain D residue 1023 MET Chi-restraints excluded: chain D residue 1059 MET Chi-restraints excluded: chain D residue 1060 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 218 optimal weight: 0.8980 chunk 16 optimal weight: 9.9990 chunk 142 optimal weight: 0.9990 chunk 267 optimal weight: 9.9990 chunk 227 optimal weight: 50.0000 chunk 277 optimal weight: 0.5980 chunk 242 optimal weight: 8.9990 chunk 239 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 205 optimal weight: 0.6980 chunk 191 optimal weight: 10.0000 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 642 GLN ** B 973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 642 GLN C 642 GLN D 642 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.226056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.151450 restraints weight = 25654.510| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 1.98 r_work: 0.3318 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 25648 Z= 0.158 Angle : 0.514 7.437 34816 Z= 0.268 Chirality : 0.039 0.140 3996 Planarity : 0.004 0.059 4220 Dihedral : 5.953 55.005 3785 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.07 % Allowed : 19.42 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.16), residues: 2912 helix: 1.96 (0.11), residues: 2096 sheet: 0.52 (0.49), residues: 108 loop : -0.84 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 816 TYR 0.013 0.001 TYR B 646 PHE 0.016 0.001 PHE C 951 TRP 0.016 0.001 TRP C 898 HIS 0.005 0.001 HIS A1080 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 (25644) covalent geometry : angle 0.51391 / 0.27 (34808) SS BOND : bond 0.00071 / 0.03 ( 4) SS BOND : angle 0.80303 / 0.48 ( 8) hydrogen bonds : bond 0.05560 / 3.64 ( 1518) hydrogen bonds : angle 3.74953 / 2.68 ( 4521) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 279 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 178 TRP cc_start: 0.7511 (m-10) cc_final: 0.7280 (m-10) REVERT: B 189 MET cc_start: 0.4275 (OUTLIER) cc_final: 0.3914 (tmm) REVERT: B 631 GLU cc_start: 0.7178 (mm-30) cc_final: 0.6692 (tm-30) REVERT: B 912 PHE cc_start: 0.8746 (OUTLIER) cc_final: 0.8465 (m-80) REVERT: B 1060 LYS cc_start: 0.7218 (OUTLIER) cc_final: 0.6916 (ttmt) REVERT: A 301 ILE cc_start: 0.8393 (mm) cc_final: 0.8191 (mm) REVERT: A 620 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7236 (tt0) REVERT: A 631 GLU cc_start: 0.7188 (mm-30) cc_final: 0.6709 (tm-30) REVERT: A 1060 LYS cc_start: 0.7334 (OUTLIER) cc_final: 0.7035 (ttmt) REVERT: C 631 GLU cc_start: 0.7168 (mm-30) cc_final: 0.6705 (tm-30) REVERT: C 843 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8512 (mp) REVERT: C 1060 LYS cc_start: 0.7217 (OUTLIER) cc_final: 0.6932 (ttmt) REVERT: D 631 GLU cc_start: 0.7179 (mm-30) cc_final: 0.6711 (tm-30) REVERT: D 1060 LYS cc_start: 0.7206 (OUTLIER) cc_final: 0.6894 (ttmt) outliers start: 108 outliers final: 76 residues processed: 353 average time/residue: 0.1511 time to fit residues: 86.8190 Evaluate side-chains 352 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 269 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 457 ASP Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 656 CYS Chi-restraints excluded: chain B residue 698 CYS Chi-restraints excluded: chain B residue 788 MET Chi-restraints excluded: chain B residue 803 THR Chi-restraints excluded: chain B residue 815 PHE Chi-restraints excluded: chain B residue 851 ARG Chi-restraints excluded: chain B residue 912 PHE Chi-restraints excluded: chain B residue 985 ILE Chi-restraints excluded: chain B residue 1007 ASN Chi-restraints excluded: chain B residue 1023 MET Chi-restraints excluded: chain B residue 1060 LYS Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 656 CYS Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain A residue 788 MET Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 815 PHE Chi-restraints excluded: chain A residue 851 ARG Chi-restraints excluded: chain A residue 929 CYS Chi-restraints excluded: chain A residue 940 CYS Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 1013 PHE Chi-restraints excluded: chain A residue 1023 MET Chi-restraints excluded: chain A residue 1060 LYS Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 566 ILE Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 645 VAL Chi-restraints excluded: chain C residue 656 CYS Chi-restraints excluded: chain C residue 788 MET Chi-restraints excluded: chain C residue 803 THR Chi-restraints excluded: chain C residue 815 PHE Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain C residue 851 ARG Chi-restraints excluded: chain C residue 940 CYS Chi-restraints excluded: chain C residue 985 ILE Chi-restraints excluded: chain C residue 1023 MET Chi-restraints excluded: chain C residue 1060 LYS Chi-restraints excluded: chain D residue 122 CYS Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 492 VAL Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 566 ILE Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 656 CYS Chi-restraints excluded: chain D residue 698 CYS Chi-restraints excluded: chain D residue 803 THR Chi-restraints excluded: chain D residue 815 PHE Chi-restraints excluded: chain D residue 851 ARG Chi-restraints excluded: chain D residue 929 CYS Chi-restraints excluded: chain D residue 940 CYS Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 1023 MET Chi-restraints excluded: chain D residue 1060 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 4 optimal weight: 10.0000 chunk 55 optimal weight: 0.9980 chunk 293 optimal weight: 0.6980 chunk 148 optimal weight: 2.9990 chunk 169 optimal weight: 4.9990 chunk 269 optimal weight: 0.0770 chunk 95 optimal weight: 9.9990 chunk 56 optimal weight: 0.9990 chunk 195 optimal weight: 3.9990 chunk 76 optimal weight: 30.0000 chunk 193 optimal weight: 0.0970 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 642 GLN ** B 973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 642 GLN C 642 GLN D 642 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.231270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.162307 restraints weight = 25947.014| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 2.27 r_work: 0.3373 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 25648 Z= 0.107 Angle : 0.478 11.598 34816 Z= 0.247 Chirality : 0.037 0.200 3996 Planarity : 0.004 0.058 4220 Dihedral : 5.790 54.432 3785 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.68 % Allowed : 20.70 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.19 (0.16), residues: 2912 helix: 2.21 (0.11), residues: 2092 sheet: 0.70 (0.50), residues: 108 loop : -0.77 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 816 TYR 0.012 0.001 TYR B 646 PHE 0.013 0.001 PHE A 565 TRP 0.013 0.001 TRP B 567 HIS 0.005 0.001 HIS A1080 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (25644) covalent geometry : angle 0.47652 / 0.25 (34808) SS BOND : bond 0.00819 / 0.43 ( 4) SS BOND : angle 2.90821 / 1.93 ( 8) hydrogen bonds : bond 0.04274 / 2.78 ( 1518) hydrogen bonds : angle 3.54765 / 2.55 ( 4521) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 285 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 178 TRP cc_start: 0.7561 (m-10) cc_final: 0.7352 (m-10) REVERT: B 189 MET cc_start: 0.4295 (OUTLIER) cc_final: 0.4090 (tmm) REVERT: B 526 LYS cc_start: 0.4962 (mmmt) cc_final: 0.4648 (mptt) REVERT: B 620 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7308 (tt0) REVERT: B 631 GLU cc_start: 0.7097 (mm-30) cc_final: 0.6690 (tm-30) REVERT: B 1060 LYS cc_start: 0.7119 (OUTLIER) cc_final: 0.6911 (ttmt) REVERT: A 620 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7261 (tt0) REVERT: A 631 GLU cc_start: 0.7121 (mm-30) cc_final: 0.6711 (tm-30) REVERT: A 1060 LYS cc_start: 0.7114 (OUTLIER) cc_final: 0.6910 (ttmt) REVERT: C 620 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7288 (tt0) REVERT: C 631 GLU cc_start: 0.7110 (mm-30) cc_final: 0.6711 (tm-30) REVERT: C 1060 LYS cc_start: 0.7165 (OUTLIER) cc_final: 0.6940 (ttmt) REVERT: D 620 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7296 (tt0) REVERT: D 631 GLU cc_start: 0.7129 (mm-30) cc_final: 0.6716 (tm-30) REVERT: D 1060 LYS cc_start: 0.7119 (OUTLIER) cc_final: 0.6912 (ttmt) outliers start: 71 outliers final: 51 residues processed: 327 average time/residue: 0.1443 time to fit residues: 76.5172 Evaluate side-chains 330 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 274 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 457 ASP Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain B residue 656 CYS Chi-restraints excluded: chain B residue 698 CYS Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 815 PHE Chi-restraints excluded: chain B residue 851 ARG Chi-restraints excluded: chain B residue 1007 ASN Chi-restraints excluded: chain B residue 1023 MET Chi-restraints excluded: chain B residue 1060 LYS Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 656 CYS Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 815 PHE Chi-restraints excluded: chain A residue 851 ARG Chi-restraints excluded: chain A residue 929 CYS Chi-restraints excluded: chain A residue 940 CYS Chi-restraints excluded: chain A residue 1023 MET Chi-restraints excluded: chain A residue 1060 LYS Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 645 VAL Chi-restraints excluded: chain C residue 656 CYS Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 815 PHE Chi-restraints excluded: chain C residue 851 ARG Chi-restraints excluded: chain C residue 940 CYS Chi-restraints excluded: chain C residue 1023 MET Chi-restraints excluded: chain C residue 1060 LYS Chi-restraints excluded: chain D residue 122 CYS Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 656 CYS Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain D residue 815 PHE Chi-restraints excluded: chain D residue 851 ARG Chi-restraints excluded: chain D residue 929 CYS Chi-restraints excluded: chain D residue 940 CYS Chi-restraints excluded: chain D residue 1023 MET Chi-restraints excluded: chain D residue 1060 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 242 optimal weight: 9.9990 chunk 178 optimal weight: 9.9990 chunk 259 optimal weight: 6.9990 chunk 204 optimal weight: 0.8980 chunk 71 optimal weight: 6.9990 chunk 75 optimal weight: 50.0000 chunk 275 optimal weight: 3.9990 chunk 213 optimal weight: 3.9990 chunk 141 optimal weight: 0.5980 chunk 73 optimal weight: 5.9990 chunk 247 optimal weight: 10.0000 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1080 HIS ** 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 = 0.4376 r_free = 0.4376 target = 0.221953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.149989 restraints weight = 25683.247| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.37 r_work: 0.3235 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 25648 Z= 0.293 Angle : 0.661 10.425 34816 Z= 0.340 Chirality : 0.046 0.236 3996 Planarity : 0.005 0.058 4220 Dihedral : 6.357 56.630 3785 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.66 % Allowed : 19.80 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 1.48 (0.15), residues: 2912 helix: 1.58 (0.11), residues: 2120 sheet: 0.61 (0.49), residues: 108 loop : -0.78 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 885 TYR 0.013 0.002 TYR A 924 PHE 0.024 0.002 PHE D 951 TRP 0.017 0.002 TRP A 898 HIS 0.006 0.001 HIS C1080 Details of bonding type rmsd/Z covalent geometry : bond 0.00747 / 0.29 (25644) covalent geometry : angle 0.65930 / 0.34 (34808) SS BOND : bond 0.00175 / 0.09 ( 4) SS BOND : angle 3.15286 / 2.09 ( 8) hydrogen bonds : bond 0.07398 / 4.86 ( 1518) hydrogen bonds : angle 3.98675 / 2.84 ( 4521) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 277 time to evaluate : 1.165 Fit side-chains REVERT: B 189 MET cc_start: 0.4409 (OUTLIER) cc_final: 0.4054 (tmm) REVERT: B 631 GLU cc_start: 0.7126 (mm-30) cc_final: 0.6834 (mm-30) REVERT: A 631 GLU cc_start: 0.7154 (mm-30) cc_final: 0.6865 (mm-30) REVERT: C 631 GLU cc_start: 0.7147 (mm-30) cc_final: 0.6855 (mm-30) REVERT: D 631 GLU cc_start: 0.7158 (mm-30) cc_final: 0.6869 (mm-30) outliers start: 97 outliers final: 79 residues processed: 341 average time/residue: 0.1504 time to fit residues: 83.9123 Evaluate side-chains 345 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 265 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 457 ASP Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 656 CYS Chi-restraints excluded: chain B residue 698 CYS Chi-restraints excluded: chain B residue 788 MET Chi-restraints excluded: chain B residue 803 THR Chi-restraints excluded: chain B residue 851 ARG Chi-restraints excluded: chain B residue 985 ILE Chi-restraints excluded: chain B residue 1013 PHE Chi-restraints excluded: chain B residue 1023 MET Chi-restraints excluded: chain B residue 1059 MET Chi-restraints excluded: chain B residue 1060 LYS Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 656 CYS Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain A residue 788 MET Chi-restraints excluded: chain A residue 851 ARG Chi-restraints excluded: chain A residue 929 CYS Chi-restraints excluded: chain A residue 940 CYS Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 1023 MET Chi-restraints excluded: chain A residue 1059 MET Chi-restraints excluded: chain A residue 1060 LYS Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 566 ILE Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 645 VAL Chi-restraints excluded: chain C residue 656 CYS Chi-restraints excluded: chain C residue 788 MET Chi-restraints excluded: chain C residue 803 THR Chi-restraints excluded: chain C residue 851 ARG Chi-restraints excluded: chain C residue 940 CYS Chi-restraints excluded: chain C residue 985 ILE Chi-restraints excluded: chain C residue 1013 PHE Chi-restraints excluded: chain C residue 1023 MET Chi-restraints excluded: chain C residue 1060 LYS Chi-restraints excluded: chain D residue 122 CYS Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 566 ILE Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 656 CYS Chi-restraints excluded: chain D residue 698 CYS Chi-restraints excluded: chain D residue 788 MET Chi-restraints excluded: chain D residue 803 THR Chi-restraints excluded: chain D residue 851 ARG Chi-restraints excluded: chain D residue 929 CYS Chi-restraints excluded: chain D residue 940 CYS Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 1013 PHE Chi-restraints excluded: chain D residue 1023 MET Chi-restraints excluded: chain D residue 1060 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 28 optimal weight: 1.9990 chunk 227 optimal weight: 50.0000 chunk 303 optimal weight: 50.0000 chunk 245 optimal weight: 10.0000 chunk 176 optimal weight: 5.9990 chunk 288 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 244 optimal weight: 8.9990 chunk 101 optimal weight: 3.9990 chunk 281 optimal weight: 0.9980 chunk 15 optimal weight: 8.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 642 GLN B 973 ASN ** B1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.222914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 112)---------------| | r_work = 0.3659 r_free = 0.3659 target = 0.144811 restraints weight = 25705.471| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 1.65 r_work: 0.3270 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 25648 Z= 0.250 Angle : 0.638 9.219 34816 Z= 0.329 Chirality : 0.044 0.218 3996 Planarity : 0.005 0.058 4220 Dihedral : 6.351 56.067 3785 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.24 % Allowed : 20.63 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 1.37 (0.15), residues: 2912 helix: 1.51 (0.11), residues: 2120 sheet: 0.42 (0.49), residues: 108 loop : -0.83 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 885 TYR 0.012 0.002 TYR A1005 PHE 0.023 0.002 PHE A 951 TRP 0.016 0.002 TRP A 898 HIS 0.005 0.001 HIS B1080 Details of bonding type rmsd/Z covalent geometry : bond 0.00628 / 0.25 (25644) covalent geometry : angle 0.63614 / 0.33 (34808) SS BOND : bond 0.00178 / 0.08 ( 4) SS BOND : angle 2.99803 / 1.98 ( 8) hydrogen bonds : bond 0.06860 / 4.50 ( 1518) hydrogen bonds : angle 3.98419 / 2.83 ( 4521) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 279 time to evaluate : 0.684 Fit side-chains REVERT: B 631 GLU cc_start: 0.6948 (mm-30) cc_final: 0.6638 (mm-30) REVERT: B 912 PHE cc_start: 0.8808 (OUTLIER) cc_final: 0.8318 (m-80) REVERT: B 1060 LYS cc_start: 0.7548 (OUTLIER) cc_final: 0.7144 (ttmt) REVERT: A 631 GLU cc_start: 0.6980 (mm-30) cc_final: 0.6671 (mm-30) REVERT: A 912 PHE cc_start: 0.8861 (OUTLIER) cc_final: 0.8302 (m-80) REVERT: A 1060 LYS cc_start: 0.7549 (OUTLIER) cc_final: 0.7098 (ttmt) REVERT: C 631 GLU cc_start: 0.6970 (mm-30) cc_final: 0.6656 (mm-30) REVERT: C 912 PHE cc_start: 0.8817 (OUTLIER) cc_final: 0.8256 (m-80) REVERT: C 1060 LYS cc_start: 0.7551 (OUTLIER) cc_final: 0.7190 (ttmt) REVERT: D 189 MET cc_start: 0.5692 (mtt) cc_final: 0.5151 (tmm) REVERT: D 631 GLU cc_start: 0.7001 (mm-30) cc_final: 0.6686 (mm-30) REVERT: D 912 PHE cc_start: 0.8817 (OUTLIER) cc_final: 0.8259 (m-80) outliers start: 86 outliers final: 70 residues processed: 340 average time/residue: 0.1331 time to fit residues: 74.4057 Evaluate side-chains 339 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 262 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 457 ASP Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 656 CYS Chi-restraints excluded: chain B residue 698 CYS Chi-restraints excluded: chain B residue 788 MET Chi-restraints excluded: chain B residue 803 THR Chi-restraints excluded: chain B residue 851 ARG Chi-restraints excluded: chain B residue 912 PHE Chi-restraints excluded: chain B residue 929 CYS Chi-restraints excluded: chain B residue 985 ILE Chi-restraints excluded: chain B residue 1013 PHE Chi-restraints excluded: chain B residue 1023 MET Chi-restraints excluded: chain B residue 1060 LYS Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 656 CYS Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain A residue 788 MET Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 851 ARG Chi-restraints excluded: chain A residue 912 PHE Chi-restraints excluded: chain A residue 929 CYS Chi-restraints excluded: chain A residue 940 CYS Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 1013 PHE Chi-restraints excluded: chain A residue 1023 MET Chi-restraints excluded: chain A residue 1060 LYS Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 566 ILE Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 656 CYS Chi-restraints excluded: chain C residue 788 MET Chi-restraints excluded: chain C residue 851 ARG Chi-restraints excluded: chain C residue 912 PHE Chi-restraints excluded: chain C residue 940 CYS Chi-restraints excluded: chain C residue 985 ILE Chi-restraints excluded: chain C residue 1013 PHE Chi-restraints excluded: chain C residue 1023 MET Chi-restraints excluded: chain C residue 1060 LYS Chi-restraints excluded: chain D residue 122 CYS Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 457 ASP Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 492 VAL Chi-restraints excluded: chain D residue 566 ILE Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain D residue 656 CYS Chi-restraints excluded: chain D residue 698 CYS Chi-restraints excluded: chain D residue 788 MET Chi-restraints excluded: chain D residue 851 ARG Chi-restraints excluded: chain D residue 912 PHE Chi-restraints excluded: chain D residue 929 CYS Chi-restraints excluded: chain D residue 940 CYS Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 1013 PHE Chi-restraints excluded: chain D residue 1023 MET Chi-restraints excluded: chain D residue 1060 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 149 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 36 optimal weight: 0.0980 chunk 49 optimal weight: 0.2980 chunk 82 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 213 optimal weight: 0.0030 chunk 23 optimal weight: 4.9990 chunk 291 optimal weight: 0.1980 chunk 197 optimal weight: 0.4980 chunk 107 optimal weight: 6.9990 overall best weight: 0.2190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 642 GLN ** A 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 642 GLN ** C 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 642 GLN ** C1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 642 GLN ** D1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.233435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 245)---------------| | r_work = 0.3839 r_free = 0.3839 target = 0.161862 restraints weight = 26112.093| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 1.67 r_work: 0.3444 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 25648 Z= 0.101 Angle : 0.492 9.662 34816 Z= 0.254 Chirality : 0.037 0.165 3996 Planarity : 0.004 0.059 4220 Dihedral : 5.948 53.966 3785 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.28 % Allowed : 22.62 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.16), residues: 2912 helix: 2.01 (0.11), residues: 2120 sheet: 0.43 (0.49), residues: 108 loop : -0.74 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 816 TYR 0.011 0.001 TYR B 646 PHE 0.013 0.001 PHE C 565 TRP 0.016 0.001 TRP D 567 HIS 0.006 0.001 HIS C 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00199 / 0.10 (25644) covalent geometry : angle 0.49081 / 0.25 (34808) SS BOND : bond 0.00126 / 0.06 ( 4) SS BOND : angle 2.27889 / 1.50 ( 8) hydrogen bonds : bond 0.03795 / 2.46 ( 1518) hydrogen bonds : angle 3.57948 / 2.58 ( 4521) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5824 Ramachandran restraints generated. 2912 Oldfield, 0 Emsley, 2912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 290 time to evaluate : 0.921 Fit side-chains REVERT: B 189 MET cc_start: 0.4099 (ttp) cc_final: 0.3517 (tmm) REVERT: B 631 GLU cc_start: 0.6893 (mm-30) cc_final: 0.6538 (tm-30) REVERT: A 468 LYS cc_start: 0.6328 (mptt) cc_final: 0.6081 (mmtt) REVERT: A 631 GLU cc_start: 0.6912 (mm-30) cc_final: 0.6550 (tm-30) REVERT: A 782 GLU cc_start: 0.7646 (tp30) cc_final: 0.7339 (tp30) REVERT: C 189 MET cc_start: 0.5529 (mtt) cc_final: 0.5240 (tmm) REVERT: C 631 GLU cc_start: 0.6907 (mm-30) cc_final: 0.6555 (tm-30) REVERT: C 782 GLU cc_start: 0.7635 (tp30) cc_final: 0.7335 (tp30) REVERT: C 807 PHE cc_start: 0.8091 (t80) cc_final: 0.6586 (m-10) REVERT: D 189 MET cc_start: 0.5845 (mtt) cc_final: 0.5244 (tmm) REVERT: D 631 GLU cc_start: 0.6918 (mm-30) cc_final: 0.6549 (tm-30) REVERT: D 782 GLU cc_start: 0.7643 (tp30) cc_final: 0.7343 (tp30) REVERT: D 807 PHE cc_start: 0.8099 (t80) cc_final: 0.6582 (m-10) outliers start: 34 outliers final: 24 residues processed: 313 average time/residue: 0.1516 time to fit residues: 76.4542 Evaluate side-chains 309 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 285 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 656 CYS Chi-restraints excluded: chain B residue 851 ARG Chi-restraints excluded: chain B residue 929 CYS Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 656 CYS Chi-restraints excluded: chain A residue 851 ARG Chi-restraints excluded: chain A residue 929 CYS Chi-restraints excluded: chain A residue 940 CYS Chi-restraints excluded: chain A residue 1023 MET Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 656 CYS Chi-restraints excluded: chain C residue 851 ARG Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 656 CYS Chi-restraints excluded: chain D residue 851 ARG Chi-restraints excluded: chain D residue 929 CYS Chi-restraints excluded: chain D residue 940 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 169 optimal weight: 10.0000 chunk 257 optimal weight: 3.9990 chunk 176 optimal weight: 3.9990 chunk 246 optimal weight: 5.9990 chunk 147 optimal weight: 10.0000 chunk 277 optimal weight: 5.9990 chunk 195 optimal weight: 2.9990 chunk 226 optimal weight: 20.0000 chunk 80 optimal weight: 8.9990 chunk 295 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1080 HIS ** 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 = 0.4392 r_free = 0.4392 target = 0.224054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 128)---------------| | r_work = 0.3723 r_free = 0.3723 target = 0.151989 restraints weight = 26103.623| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 1.81 r_work: 0.3286 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 25648 Z= 0.282 Angle : 0.661 9.215 34816 Z= 0.340 Chirality : 0.045 0.212 3996 Planarity : 0.005 0.059 4220 Dihedral : 6.298 55.716 3784 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.66 % Allowed : 22.51 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.16), residues: 2912 helix: 1.63 (0.11), residues: 2120 sheet: 0.38 (0.50), residues: 108 loop : -0.85 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 885 TYR 0.012 0.002 TYR D 924 PHE 0.023 0.002 PHE C 735 TRP 0.017 0.002 TRP A 898 HIS 0.006 0.001 HIS A1080 Details of bonding type rmsd/Z covalent geometry : bond 0.00714 / 0.28 (25644) covalent geometry : angle 0.65976 / 0.34 (34808) SS BOND : bond 0.00173 / 0.09 ( 4) SS BOND : angle 2.83230 / 1.87 ( 8) hydrogen bonds : bond 0.07200 / 4.73 ( 1518) hydrogen bonds : angle 3.97166 / 2.83 ( 4521) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7343.21 seconds wall clock time: 125 minutes 49.16 seconds (7549.16 seconds total)