Starting phenix.real_space_refine on Fri Mar 6 16:35:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e3l_30983/03_2026/7e3l_30983_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e3l_30983/03_2026/7e3l_30983.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7e3l_30983/03_2026/7e3l_30983.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e3l_30983/03_2026/7e3l_30983.map" model { file = "/net/cci-nas-00/data/ceres_data/7e3l_30983/03_2026/7e3l_30983_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e3l_30983/03_2026/7e3l_30983_neut.cif" } resolution = 3.6 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= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 122 5.16 5 C 20739 2.51 5 N 5461 2.21 5 O 6317 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32639 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 986, 7564 Classifications: {'peptide': 986} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 48, 'TRANS': 937} Chain breaks: 10 Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 172 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 5, 'ASN:plan1': 4, 'GLU:plan': 10, 'GLN:plan1': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 93 Chain: "B" Number of atoms: 7562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 986, 7562 Classifications: {'peptide': 986} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 48, 'TRANS': 937} Chain breaks: 10 Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 173 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 5, 'ASN:plan1': 4, 'GLU:plan': 9, 'GLN:plan1': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 94 Chain: "C" Number of atoms: 7573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 986, 7573 Classifications: {'peptide': 986} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 48, 'TRANS': 937} Chain breaks: 10 Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 5, 'ASN:plan1': 4, 'GLU:plan': 9, 'GLN:plan1': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 89 Chain: "H" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1616 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 209} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1604 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 203} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "F" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1616 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 209} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1604 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 203} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "D" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1616 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 209} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1604 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 203} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 7.34, per 1000 atoms: 0.22 Number of scatterers: 32639 At special positions: 0 Unit cell: (133.66, 134.48, 261.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 122 16.00 O 6317 8.00 N 5461 7.00 C 20739 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.06 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.06 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.06 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.27 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 101 " - pdb=" SG CYS H 106 " distance=2.04 Simple disulfide: pdb=" SG CYS H 150 " - pdb=" SG CYS H 206 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.04 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.04 Simple disulfide: pdb=" SG CYS F 101 " - pdb=" SG CYS F 106 " distance=2.03 Simple disulfide: pdb=" SG CYS F 150 " - pdb=" SG CYS F 206 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 89 " distance=2.04 Simple disulfide: pdb=" SG CYS G 135 " - pdb=" SG CYS G 195 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS D 101 " - pdb=" SG CYS D 106 " distance=2.03 Simple disulfide: pdb=" SG CYS D 150 " - pdb=" SG CYS D 206 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 89 " distance=2.04 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 195 " distance=2.04 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 Links applied NAG-ASN " NAG A1301 " - " ASN A 122 " " NAG A1302 " - " ASN A 234 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 603 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 234 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 603 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 709 " Time building additional restraints: 2.61 Conformation dependent library (CDL) restraints added in 1.2 seconds 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7968 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 80 sheets defined 20.9% alpha, 25.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.787A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.747A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 4.044A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.242A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.637A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 removed outlier: 3.623A pdb=" N GLY A 744 " --> pdb=" O MET A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 4.266A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.314A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.665A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.832A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.527A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.787A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 removed outlier: 3.747A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 4.044A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.241A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.636A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 removed outlier: 3.509A pdb=" N GLY B 744 " --> pdb=" O MET B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 4.223A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.720A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.255A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.644A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.786A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 370 removed outlier: 3.747A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 4.044A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.242A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.637A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.298A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.327A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.516A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.675A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.363A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.107A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 168 No H-bonds generated for 'chain 'H' and resid 166 through 168' Processing helix chain 'H' and resid 195 through 200 removed outlier: 3.608A pdb=" N GLY H 200 " --> pdb=" O SER H 196 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 32 No H-bonds generated for 'chain 'L' and resid 30 through 32' Processing helix chain 'L' and resid 122 through 128 removed outlier: 3.530A pdb=" N SER L 128 " --> pdb=" O GLU L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 190 Processing helix chain 'F' and resid 87 through 91 removed outlier: 4.107A pdb=" N THR F 91 " --> pdb=" O SER F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 168 No H-bonds generated for 'chain 'F' and resid 166 through 168' Processing helix chain 'F' and resid 195 through 200 removed outlier: 3.609A pdb=" N GLY F 200 " --> pdb=" O SER F 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 32 No H-bonds generated for 'chain 'G' and resid 30 through 32' Processing helix chain 'G' and resid 122 through 128 removed outlier: 3.529A pdb=" N SER G 128 " --> pdb=" O GLU G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 190 Processing helix chain 'D' and resid 87 through 91 removed outlier: 4.107A pdb=" N THR D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 168 No H-bonds generated for 'chain 'D' and resid 166 through 168' Processing helix chain 'D' and resid 195 through 200 removed outlier: 3.608A pdb=" N GLY D 200 " --> pdb=" O SER D 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 32 No H-bonds generated for 'chain 'E' and resid 30 through 32' Processing helix chain 'E' and resid 122 through 128 removed outlier: 3.530A pdb=" N SER E 128 " --> pdb=" O GLU E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 190 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.583A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.019A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 10.820A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 9.743A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 49 removed outlier: 6.803A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 52 through 55 removed outlier: 3.875A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.920A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 128 through 129 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 3.728A pdb=" N TYR A 313 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 327 Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 565 through 567 removed outlier: 6.344A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.591A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY A 667 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 727 removed outlier: 7.206A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB9, first strand: chain 'A' and resid 788 through 789 removed outlier: 5.717A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1123 Processing sheet with id=AC2, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.605A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 48 through 49 removed outlier: 6.818A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 52 through 55 removed outlier: 3.831A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.840A pdb=" N ILE B 105 " --> pdb=" O GLN B 239 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 95 through 96 removed outlier: 3.506A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 128 through 129 Processing sheet with id=AC8, first strand: chain 'B' and resid 311 through 319 removed outlier: 3.732A pdb=" N TYR B 313 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD3, first strand: chain 'B' and resid 539 through 542 Processing sheet with id=AD4, first strand: chain 'B' and resid 553 through 554 removed outlier: 3.832A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.687A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY B 667 " --> pdb=" O ILE B 670 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.636A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 718 through 727 removed outlier: 7.128A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD9, first strand: chain 'B' and resid 788 through 790 removed outlier: 5.739A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'B' and resid 1120 through 1123 Processing sheet with id=AE2, first strand: chain 'C' and resid 29 through 31 Processing sheet with id=AE3, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.075A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 10.791A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 9.595A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 48 through 49 removed outlier: 6.938A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 52 through 55 removed outlier: 3.902A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.949A pdb=" N ILE C 105 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE C 119 " --> pdb=" O TRP C 104 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 128 through 129 Processing sheet with id=AE8, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.692A pdb=" N TYR C 313 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 324 through 325 removed outlier: 7.041A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AF2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF3, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.537A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY C 667 " --> pdb=" O ILE C 670 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.591A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 718 through 727 removed outlier: 7.148A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF8, first strand: chain 'C' and resid 1120 through 1123 Processing sheet with id=AF9, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AG1, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.889A pdb=" N VAL H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N TRP H 50 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AG3, first strand: chain 'H' and resid 130 through 134 removed outlier: 3.897A pdb=" N GLY H 149 " --> pdb=" O LEU H 134 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'H' and resid 163 through 164 removed outlier: 3.682A pdb=" N VAL H 208 " --> pdb=" O VAL H 217 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL H 217 " --> pdb=" O VAL H 208 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.638A pdb=" N SER L 64 " --> pdb=" O THR L 75 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.277A pdb=" N LEU L 11 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'L' and resid 115 through 119 removed outlier: 4.088A pdb=" N SER L 115 " --> pdb=" O ASN L 138 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASN L 138 " --> pdb=" O SER L 115 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL L 134 " --> pdb=" O PHE L 119 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'L' and resid 146 through 151 removed outlier: 3.542A pdb=" N LYS L 146 " --> pdb=" O THR L 198 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN L 148 " --> pdb=" O GLU L 196 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU L 196 " --> pdb=" O GLN L 148 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N CYS L 195 " --> pdb=" O LYS L 208 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS L 208 " --> pdb=" O CYS L 195 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AH1, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.889A pdb=" N VAL F 34 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N TRP F 50 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N TRP F 36 " --> pdb=" O ILE F 48 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'F' and resid 10 through 12 Processing sheet with id=AH3, first strand: chain 'F' and resid 130 through 134 removed outlier: 3.897A pdb=" N GLY F 149 " --> pdb=" O LEU F 134 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N TYR F 186 " --> pdb=" O ASP F 154 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'F' and resid 163 through 164 removed outlier: 3.682A pdb=" N VAL F 208 " --> pdb=" O VAL F 217 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL F 217 " --> pdb=" O VAL F 208 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'G' and resid 4 through 7 removed outlier: 3.639A pdb=" N SER G 64 " --> pdb=" O THR G 75 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.278A pdb=" N LEU G 11 " --> pdb=" O GLU G 106 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N TYR G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'G' and resid 115 through 119 removed outlier: 4.087A pdb=" N SER G 115 " --> pdb=" O ASN G 138 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASN G 138 " --> pdb=" O SER G 115 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL G 134 " --> pdb=" O PHE G 119 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N TYR G 174 " --> pdb=" O ASN G 139 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'G' and resid 146 through 151 removed outlier: 3.542A pdb=" N LYS G 146 " --> pdb=" O THR G 198 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN G 148 " --> pdb=" O GLU G 196 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU G 196 " --> pdb=" O GLN G 148 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N CYS G 195 " --> pdb=" O LYS G 208 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS G 208 " --> pdb=" O CYS G 195 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AI1, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.890A pdb=" N VAL D 34 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N TRP D 50 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N TRP D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'D' and resid 10 through 12 Processing sheet with id=AI3, first strand: chain 'D' and resid 130 through 134 removed outlier: 3.896A pdb=" N GLY D 149 " --> pdb=" O LEU D 134 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N TYR D 186 " --> pdb=" O ASP D 154 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'D' and resid 163 through 164 removed outlier: 3.682A pdb=" N VAL D 208 " --> pdb=" O VAL D 217 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL D 217 " --> pdb=" O VAL D 208 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.639A pdb=" N SER E 64 " --> pdb=" O THR E 75 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.278A pdb=" N LEU E 11 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N TYR E 50 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'E' and resid 115 through 119 removed outlier: 4.087A pdb=" N SER E 115 " --> pdb=" O ASN E 138 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASN E 138 " --> pdb=" O SER E 115 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL E 134 " --> pdb=" O PHE E 119 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N TYR E 174 " --> pdb=" O ASN E 139 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'E' and resid 146 through 151 removed outlier: 3.542A pdb=" N LYS E 146 " --> pdb=" O THR E 198 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN E 148 " --> pdb=" O GLU E 196 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU E 196 " --> pdb=" O GLN E 148 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N CYS E 195 " --> pdb=" O LYS E 208 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS E 208 " --> pdb=" O CYS E 195 " (cutoff:3.500A) 1212 hydrogen bonds defined for protein. 3204 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: 8.94 Time building geometry restraints manager: 3.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 10367 1.34 - 1.47: 8501 1.47 - 1.60: 14348 1.60 - 1.73: 0 1.73 - 1.86: 155 Bond restraints: 33371 Sorted by residual: bond pdb=" N ASN G 94 " pdb=" CA ASN G 94 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.29e-02 6.01e+03 1.05e+01 bond pdb=" N ASN L 94 " pdb=" CA ASN L 94 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.29e-02 6.01e+03 1.04e+01 bond pdb=" N ASN E 94 " pdb=" CA ASN E 94 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.29e-02 6.01e+03 1.00e+01 bond pdb=" N ASP H 108 " pdb=" CA ASP H 108 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.16e-02 7.43e+03 9.34e+00 bond pdb=" N ASP D 108 " pdb=" CA ASP D 108 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.16e-02 7.43e+03 9.24e+00 ... (remaining 33366 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 43974 2.22 - 4.44: 1362 4.44 - 6.66: 126 6.66 - 8.88: 20 8.88 - 11.10: 3 Bond angle restraints: 45485 Sorted by residual: angle pdb=" O PHE C 329 " pdb=" C PHE C 329 " pdb=" N PRO C 330 " ideal model delta sigma weight residual 121.88 117.23 4.65 7.10e-01 1.98e+00 4.29e+01 angle pdb=" O PHE A 329 " pdb=" C PHE A 329 " pdb=" N PRO A 330 " ideal model delta sigma weight residual 121.88 117.31 4.57 7.10e-01 1.98e+00 4.15e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 118.40 -7.70 1.22e+00 6.72e-01 3.98e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 117.72 -7.02 1.22e+00 6.72e-01 3.31e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 117.56 -6.86 1.22e+00 6.72e-01 3.16e+01 ... (remaining 45480 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 18272 17.99 - 35.97: 1442 35.97 - 53.96: 236 53.96 - 71.94: 42 71.94 - 89.93: 44 Dihedral angle restraints: 20036 sinusoidal: 7661 harmonic: 12375 Sorted by residual: dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual 93.00 179.44 -86.44 1 1.00e+01 1.00e-02 9.00e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 178.80 -85.80 1 1.00e+01 1.00e-02 8.90e+01 dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual 93.00 178.71 -85.71 1 1.00e+01 1.00e-02 8.88e+01 ... (remaining 20033 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 4993 0.104 - 0.209: 267 0.209 - 0.313: 8 0.313 - 0.417: 6 0.417 - 0.522: 2 Chirality restraints: 5276 Sorted by residual: chirality pdb=" CA CYS C 649 " pdb=" N CYS C 649 " pdb=" C CYS C 649 " pdb=" CB CYS C 649 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.80e+00 chirality pdb=" CA CYS B 649 " pdb=" N CYS B 649 " pdb=" C CYS B 649 " pdb=" CB CYS B 649 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.74e+00 chirality pdb=" CA CYS B 617 " pdb=" N CYS B 617 " pdb=" C CYS B 617 " pdb=" CB CYS B 617 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.05e+00 ... (remaining 5273 not shown) Planarity restraints: 5882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS B 649 " -0.018 2.00e-02 2.50e+03 3.78e-02 1.43e+01 pdb=" C CYS B 649 " 0.065 2.00e-02 2.50e+03 pdb=" O CYS B 649 " -0.025 2.00e-02 2.50e+03 pdb=" N LEU B 650 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS C 649 " 0.018 2.00e-02 2.50e+03 3.78e-02 1.43e+01 pdb=" C CYS C 649 " -0.065 2.00e-02 2.50e+03 pdb=" O CYS C 649 " 0.025 2.00e-02 2.50e+03 pdb=" N LEU C 650 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY E 67 " 0.015 2.00e-02 2.50e+03 3.05e-02 9.30e+00 pdb=" C GLY E 67 " -0.053 2.00e-02 2.50e+03 pdb=" O GLY E 67 " 0.020 2.00e-02 2.50e+03 pdb=" N SER E 68 " 0.018 2.00e-02 2.50e+03 ... (remaining 5879 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 2876 2.73 - 3.28: 31554 3.28 - 3.82: 49629 3.82 - 4.36: 58540 4.36 - 4.90: 104134 Nonbonded interactions: 246733 Sorted by model distance: nonbonded pdb=" O PRO A1053 " pdb=" NE2 GLN A1054 " model vdw 2.193 3.120 nonbonded pdb=" NH1 ARG C1091 " pdb=" O ASP C1118 " model vdw 2.202 3.120 nonbonded pdb=" OG SER C 721 " pdb=" OG1 THR C1066 " model vdw 2.208 3.040 nonbonded pdb=" O PRO B1053 " pdb=" NE2 GLN B1054 " model vdw 2.210 3.120 nonbonded pdb=" N GLU E 80 " pdb=" OD2 ASP E 83 " model vdw 2.211 3.120 ... (remaining 246728 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 130 or (resid 131 through 132 and (name N or na \ me CA or name C or name O or name CB )) or resid 133 through 165 or (resid 166 a \ nd (name N or name CA or name C or name O or name CB )) or resid 167 through 209 \ or (resid 210 and (name N or name CA or name C or name O or name CB )) or resid \ 211 through 616 or (resid 617 and (name N or name CA or name C or name O or nam \ e CB )) or resid 618 through 648 or (resid 649 and (name N or name CA or name C \ or name O or name CB )) or resid 650 through 661 or (resid 662 and (name N or na \ me CA or name C or name O or name CB )) or resid 663 through 670 or (resid 671 t \ hrough 672 and (name N or name CA or name C or name O or name CB )) or resid 673 \ through 982 or (resid 983 and (name N or name CA or name C or name O or name CB \ )) or resid 984 through 1306)) selection = (chain 'B' and (resid 27 through 89 or (resid 90 and (name N or name CA or name \ C or name O or name CB )) or resid 91 through 130 or (resid 131 through 132 and \ (name N or name CA or name C or name O or name CB )) or resid 133 through 190 or \ (resid 191 and (name N or name CA or name C or name O or name CB )) or resid 19 \ 2 through 226 or (resid 227 and (name N or name CA or name C or name O or name C \ B )) or resid 228 through 810 or (resid 811 and (name N or name CA or name C or \ name O or name CB )) or resid 813 through 1306)) selection = (chain 'C' and (resid 27 through 165 or (resid 166 and (name N or name CA or nam \ e C or name O or name CB )) or resid 167 through 190 or (resid 191 and (name N o \ r name CA or name C or name O or name CB )) or resid 192 through 209 or (resid 2 \ 10 and (name N or name CA or name C or name O or name CB )) or resid 211 through \ 661 or (resid 662 and (name N or name CA or name C or name O or name CB )) or r \ esid 663 through 670 or (resid 671 through 672 and (name N or name CA or name C \ or name O or name CB )) or resid 673 through 737 or (resid 738 and (name N or na \ me CA or name C or name O or name CB )) or resid 739 through 742 or (resid 743 a \ nd (name N or name CA or name C or name O or name CB )) or resid 744 through 748 \ or (resid 749 and (name N or name CA or name C or name O or name CB )) or resid \ 750 through 759 or (resid 760 and (name N or name CA or name C or name O or nam \ e CB )) or resid 761 through 810 or (resid 811 and (name N or name CA or name C \ or name O or name CB )) or resid 813 through 982 or (resid 983 and (name N or na \ me CA or name C or name O or name CB )) or resid 984 through 1306)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'L' } 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 group one per residue 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: 8.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.660 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 31.550 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.090 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5259 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 : 0.006 0.239 33433 Z= 0.339 Angle : 0.895 30.899 45629 Z= 0.527 Chirality : 0.054 0.522 5276 Planarity : 0.005 0.042 5862 Dihedral : 13.393 89.926 11942 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.91 % Favored : 91.00 % Rotamer: Outliers : 0.32 % Allowed : 3.65 % Favored : 96.03 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 5.71 % 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: -2.95 (0.12), residues: 4188 helix: -0.92 (0.17), residues: 672 sheet: -1.45 (0.15), residues: 1218 loop : -2.65 (0.11), residues: 2298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 357 TYR 0.038 0.002 TYR B 873 PHE 0.019 0.002 PHE H 132 TRP 0.022 0.002 TRP D 164 HIS 0.012 0.002 HIS L 190 Details of bonding type rmsd covalent geometry : bond 0.00626 (33371) covalent geometry : angle 0.87660 (45485) SS BOND : bond 0.03840 ( 42) SS BOND : angle 3.92213 ( 84) hydrogen bonds : bond 0.14618 ( 1191) hydrogen bonds : angle 7.96486 ( 3204) link_NAG-ASN : bond 0.00397 ( 20) link_NAG-ASN : angle 2.18661 ( 60) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 342 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 902 MET cc_start: 0.8644 (mmm) cc_final: 0.8386 (tpt) outliers start: 11 outliers final: 2 residues processed: 350 average time/residue: 0.2575 time to fit residues: 133.0427 Evaluate side-chains 173 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 171 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain G residue 54 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 0.3980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 4.9990 chunk 401 optimal weight: 8.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 4.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 690 GLN A 762 GLN A 935 GLN A1071 GLN ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN B 165 ASN B 394 ASN B 414 GLN B 935 GLN B 992 GLN B1071 GLN B1106 GLN C 115 GLN C 394 ASN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C 935 GLN C 965 GLN C1106 GLN ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 ASN ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.093474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.056466 restraints weight = 139054.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.057958 restraints weight = 61823.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.058894 restraints weight = 37521.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.059501 restraints weight = 27489.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.059798 restraints weight = 22709.082| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 33433 Z= 0.190 Angle : 0.654 8.540 45629 Z= 0.342 Chirality : 0.045 0.175 5276 Planarity : 0.005 0.057 5862 Dihedral : 5.988 58.950 4964 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.86 % Allowed : 8.62 % Favored : 90.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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 (0.12), residues: 4188 helix: 0.74 (0.19), residues: 744 sheet: -1.00 (0.15), residues: 1221 loop : -2.00 (0.12), residues: 2223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 46 TYR 0.023 0.002 TYR G 37 PHE 0.020 0.002 PHE C 490 TRP 0.009 0.001 TRP C 104 HIS 0.004 0.001 HIS F 107 Details of bonding type rmsd covalent geometry : bond 0.00445 (33371) covalent geometry : angle 0.64805 (45485) SS BOND : bond 0.00512 ( 42) SS BOND : angle 1.39790 ( 84) hydrogen bonds : bond 0.05527 ( 1191) hydrogen bonds : angle 6.14965 ( 3204) link_NAG-ASN : bond 0.00225 ( 20) link_NAG-ASN : angle 1.97197 ( 60) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 196 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 PHE cc_start: 0.7828 (m-10) cc_final: 0.7554 (m-10) REVERT: B 902 MET cc_start: 0.9231 (tpp) cc_final: 0.8946 (tpt) REVERT: C 740 MET cc_start: 0.8129 (OUTLIER) cc_final: 0.7861 (tmm) REVERT: H 81 MET cc_start: 0.7616 (tmm) cc_final: 0.7297 (tpp) REVERT: F 83 LEU cc_start: 0.8694 (mt) cc_final: 0.8159 (tt) REVERT: F 87 ARG cc_start: 0.7487 (ptp-170) cc_final: 0.7275 (ptp-170) REVERT: G 123 ASP cc_start: 0.8030 (OUTLIER) cc_final: 0.7747 (m-30) REVERT: G 144 GLU cc_start: 0.6134 (pm20) cc_final: 0.5551 (pm20) outliers start: 30 outliers final: 16 residues processed: 217 average time/residue: 0.2463 time to fit residues: 80.7549 Evaluate side-chains 182 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 164 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 74 MET Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain F residue 64 PHE Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain G residue 123 ASP Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 180 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 325 optimal weight: 20.0000 chunk 313 optimal weight: 50.0000 chunk 336 optimal weight: 4.9990 chunk 412 optimal weight: 0.0030 chunk 30 optimal weight: 10.0000 chunk 120 optimal weight: 0.0270 chunk 0 optimal weight: 7.9990 chunk 306 optimal weight: 9.9990 chunk 52 optimal weight: 0.8980 chunk 146 optimal weight: 4.9990 chunk 260 optimal weight: 0.7980 overall best weight: 1.3450 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1071 GLN ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B 784 GLN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 GLN F 209 ASN D 115 GLN ** E 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 161 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.093901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.057349 restraints weight = 138663.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.058762 restraints weight = 61028.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.059750 restraints weight = 36776.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.060370 restraints weight = 26848.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.060694 restraints weight = 22118.823| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33433 Z= 0.126 Angle : 0.563 7.887 45629 Z= 0.292 Chirality : 0.043 0.156 5276 Planarity : 0.004 0.046 5862 Dihedral : 5.341 59.277 4961 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.03 % Allowed : 10.72 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -1.18 (0.13), residues: 4188 helix: 1.61 (0.20), residues: 729 sheet: -0.78 (0.14), residues: 1275 loop : -1.64 (0.12), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 995 TYR 0.019 0.001 TYR D 80 PHE 0.032 0.001 PHE B 643 TRP 0.007 0.001 TRP B 104 HIS 0.025 0.001 HIS D 44 Details of bonding type rmsd covalent geometry : bond 0.00291 (33371) covalent geometry : angle 0.55793 (45485) SS BOND : bond 0.00382 ( 42) SS BOND : angle 1.07067 ( 84) hydrogen bonds : bond 0.04653 ( 1191) hydrogen bonds : angle 5.51524 ( 3204) link_NAG-ASN : bond 0.00236 ( 20) link_NAG-ASN : angle 1.84020 ( 60) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 186 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 PHE cc_start: 0.7983 (m-80) cc_final: 0.7659 (m-10) REVERT: A 779 GLN cc_start: 0.8629 (tm-30) cc_final: 0.8428 (tm-30) REVERT: B 449 TYR cc_start: 0.8377 (m-10) cc_final: 0.8117 (m-80) REVERT: H 81 MET cc_start: 0.7779 (tmm) cc_final: 0.7491 (tpp) REVERT: L 214 GLU cc_start: 0.4857 (pp20) cc_final: 0.4590 (pm20) REVERT: F 83 LEU cc_start: 0.8636 (mt) cc_final: 0.7578 (tt) REVERT: E 184 LYS cc_start: 0.3723 (tppt) cc_final: 0.2895 (pttp) outliers start: 36 outliers final: 17 residues processed: 216 average time/residue: 0.2311 time to fit residues: 75.7617 Evaluate side-chains 176 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 159 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 74 MET Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain F residue 64 PHE Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain F residue 209 ASN Chi-restraints excluded: chain D residue 80 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 187 optimal weight: 0.9980 chunk 319 optimal weight: 30.0000 chunk 265 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 244 optimal weight: 5.9990 chunk 210 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 197 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1088 HIS C1048 HIS ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 GLN F 209 ASN ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.092564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.055149 restraints weight = 132805.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.056689 restraints weight = 59633.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.057659 restraints weight = 36489.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.058256 restraints weight = 26788.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.058580 restraints weight = 22143.124| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 33433 Z= 0.165 Angle : 0.574 7.289 45629 Z= 0.295 Chirality : 0.043 0.156 5276 Planarity : 0.004 0.048 5862 Dihedral : 5.192 58.535 4961 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.38 % Allowed : 12.18 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.13), residues: 4188 helix: 1.79 (0.20), residues: 732 sheet: -0.69 (0.14), residues: 1254 loop : -1.38 (0.12), residues: 2202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 815 TYR 0.020 0.001 TYR C 91 PHE 0.019 0.001 PHE A 855 TRP 0.018 0.001 TRP D 36 HIS 0.007 0.001 HIS F 210 Details of bonding type rmsd covalent geometry : bond 0.00392 (33371) covalent geometry : angle 0.56894 (45485) SS BOND : bond 0.00367 ( 42) SS BOND : angle 1.09229 ( 84) hydrogen bonds : bond 0.04836 ( 1191) hydrogen bonds : angle 5.31806 ( 3204) link_NAG-ASN : bond 0.00254 ( 20) link_NAG-ASN : angle 1.84747 ( 60) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 166 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 PHE cc_start: 0.7995 (m-80) cc_final: 0.7671 (m-10) REVERT: A 779 GLN cc_start: 0.8776 (tm-30) cc_final: 0.8502 (tm-30) REVERT: B 449 TYR cc_start: 0.8308 (m-10) cc_final: 0.8055 (m-80) REVERT: B 731 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.8259 (ttm) REVERT: C 200 TYR cc_start: 0.7218 (OUTLIER) cc_final: 0.6874 (p90) REVERT: C 740 MET cc_start: 0.8415 (tmm) cc_final: 0.8037 (tmm) REVERT: H 81 MET cc_start: 0.7673 (tmm) cc_final: 0.7404 (tpp) REVERT: L 184 LYS cc_start: 0.4458 (tptt) cc_final: 0.4216 (tppt) REVERT: L 214 GLU cc_start: 0.4882 (pp20) cc_final: 0.4513 (pm20) REVERT: F 83 LEU cc_start: 0.8478 (mt) cc_final: 0.7541 (tt) REVERT: G 82 GLU cc_start: 0.5914 (pt0) cc_final: 0.5674 (pm20) REVERT: G 144 GLU cc_start: 0.6182 (pm20) cc_final: 0.5895 (pm20) REVERT: G 170 LYS cc_start: 0.0976 (pttm) cc_final: 0.0737 (pttm) REVERT: G 188 GLU cc_start: 0.7895 (tp30) cc_final: 0.7611 (tp30) REVERT: E 184 LYS cc_start: 0.3140 (tppt) cc_final: 0.2059 (pttp) outliers start: 48 outliers final: 28 residues processed: 206 average time/residue: 0.2355 time to fit residues: 74.1660 Evaluate side-chains 182 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 152 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 74 MET Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain F residue 209 ASN Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 126 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 107 optimal weight: 0.0070 chunk 402 optimal weight: 20.0000 chunk 202 optimal weight: 7.9990 chunk 151 optimal weight: 1.9990 chunk 297 optimal weight: 9.9990 chunk 205 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 191 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 134 optimal weight: 5.9990 chunk 339 optimal weight: 10.0000 overall best weight: 1.1202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1048 HIS A1071 GLN B 762 GLN H 62 GLN F 62 GLN F 209 ASN ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.093227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.056062 restraints weight = 133366.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.057634 restraints weight = 59325.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.058632 restraints weight = 36008.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.059226 restraints weight = 26309.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.059603 restraints weight = 21719.939| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 33433 Z= 0.111 Angle : 0.533 9.292 45629 Z= 0.273 Chirality : 0.042 0.160 5276 Planarity : 0.004 0.045 5862 Dihedral : 4.886 59.185 4961 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.38 % Allowed : 12.76 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.13), residues: 4188 helix: 2.08 (0.20), residues: 732 sheet: -0.52 (0.14), residues: 1275 loop : -1.21 (0.12), residues: 2181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 41 TYR 0.016 0.001 TYR B1067 PHE 0.017 0.001 PHE C 490 TRP 0.008 0.001 TRP D 36 HIS 0.012 0.001 HIS F 210 Details of bonding type rmsd covalent geometry : bond 0.00260 (33371) covalent geometry : angle 0.52829 (45485) SS BOND : bond 0.00346 ( 42) SS BOND : angle 0.93472 ( 84) hydrogen bonds : bond 0.04287 ( 1191) hydrogen bonds : angle 5.01498 ( 3204) link_NAG-ASN : bond 0.00256 ( 20) link_NAG-ASN : angle 1.70437 ( 60) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 166 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 PHE cc_start: 0.8017 (m-80) cc_final: 0.7693 (m-10) REVERT: A 779 GLN cc_start: 0.8718 (tm-30) cc_final: 0.8460 (tm-30) REVERT: B 200 TYR cc_start: 0.5847 (OUTLIER) cc_final: 0.5642 (p90) REVERT: B 449 TYR cc_start: 0.8301 (m-10) cc_final: 0.8046 (m-80) REVERT: C 200 TYR cc_start: 0.7190 (OUTLIER) cc_final: 0.6906 (p90) REVERT: C 740 MET cc_start: 0.8445 (tmm) cc_final: 0.8059 (tmm) REVERT: H 81 MET cc_start: 0.7761 (tmm) cc_final: 0.7352 (tpp) REVERT: L 40 LYS cc_start: 0.5373 (mmtm) cc_final: 0.5048 (mmtm) REVERT: L 184 LYS cc_start: 0.4104 (tptt) cc_final: 0.3683 (mmmt) REVERT: L 211 ASN cc_start: 0.7889 (t0) cc_final: 0.7615 (t0) REVERT: L 214 GLU cc_start: 0.4874 (pp20) cc_final: 0.4476 (pm20) REVERT: G 82 GLU cc_start: 0.5963 (OUTLIER) cc_final: 0.5689 (pm20) REVERT: G 144 GLU cc_start: 0.6307 (pm20) cc_final: 0.5703 (pm20) REVERT: G 170 LYS cc_start: 0.0865 (pttm) cc_final: 0.0595 (pttm) REVERT: E 126 LEU cc_start: 0.2995 (OUTLIER) cc_final: 0.2268 (mt) REVERT: E 184 LYS cc_start: 0.2972 (tppt) cc_final: 0.1918 (pttp) outliers start: 48 outliers final: 29 residues processed: 206 average time/residue: 0.2271 time to fit residues: 72.7732 Evaluate side-chains 185 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 152 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 74 MET Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 126 LEU Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain F residue 209 ASN Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 197 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 320 optimal weight: 5.9990 chunk 184 optimal weight: 3.9990 chunk 231 optimal weight: 8.9990 chunk 70 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 363 optimal weight: 9.9990 chunk 274 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 chunk 293 optimal weight: 0.9980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1071 GLN ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 209 ASN ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.091710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.054206 restraints weight = 133102.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.055690 restraints weight = 60499.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.056617 restraints weight = 37022.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.057157 restraints weight = 27204.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.057558 restraints weight = 22675.890| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 33433 Z= 0.200 Angle : 0.581 9.236 45629 Z= 0.298 Chirality : 0.043 0.162 5276 Planarity : 0.004 0.047 5862 Dihedral : 5.004 58.090 4961 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.67 % Allowed : 12.87 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.13), residues: 4188 helix: 2.22 (0.20), residues: 708 sheet: -0.57 (0.14), residues: 1272 loop : -1.10 (0.13), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 815 TYR 0.023 0.001 TYR C 91 PHE 0.028 0.002 PHE B 643 TRP 0.009 0.001 TRP D 36 HIS 0.008 0.001 HIS F 210 Details of bonding type rmsd covalent geometry : bond 0.00470 (33371) covalent geometry : angle 0.57479 (45485) SS BOND : bond 0.00452 ( 42) SS BOND : angle 1.44458 ( 84) hydrogen bonds : bond 0.04972 ( 1191) hydrogen bonds : angle 5.09900 ( 3204) link_NAG-ASN : bond 0.00283 ( 20) link_NAG-ASN : angle 1.83652 ( 60) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 154 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7326 (OUTLIER) cc_final: 0.6745 (t80) REVERT: A 456 PHE cc_start: 0.8039 (m-80) cc_final: 0.7696 (m-10) REVERT: A 779 GLN cc_start: 0.8902 (tm-30) cc_final: 0.8556 (tm-30) REVERT: B 1002 GLN cc_start: 0.8583 (tp40) cc_final: 0.8381 (tp40) REVERT: B 1071 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.8116 (pt0) REVERT: C 200 TYR cc_start: 0.7188 (OUTLIER) cc_final: 0.6831 (p90) REVERT: C 340 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8450 (pp20) REVERT: C 740 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.7948 (tmm) REVERT: H 81 MET cc_start: 0.7754 (tmm) cc_final: 0.7365 (tpp) REVERT: L 211 ASN cc_start: 0.7827 (t0) cc_final: 0.7547 (t0) REVERT: L 214 GLU cc_start: 0.4643 (pp20) cc_final: 0.4249 (pm20) REVERT: G 82 GLU cc_start: 0.6105 (OUTLIER) cc_final: 0.5748 (pm20) REVERT: G 170 LYS cc_start: 0.0883 (pttm) cc_final: 0.0650 (pttm) REVERT: E 184 LYS cc_start: 0.2946 (tppt) cc_final: 0.1585 (pttp) outliers start: 58 outliers final: 41 residues processed: 206 average time/residue: 0.2308 time to fit residues: 73.3528 Evaluate side-chains 193 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 146 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 1071 GLN Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 74 MET Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 126 LEU Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain F residue 64 PHE Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain F residue 209 ASN Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 197 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 64 optimal weight: 0.8980 chunk 282 optimal weight: 0.9990 chunk 351 optimal weight: 50.0000 chunk 314 optimal weight: 40.0000 chunk 381 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 294 optimal weight: 20.0000 chunk 15 optimal weight: 7.9990 chunk 277 optimal weight: 5.9990 chunk 422 optimal weight: 3.9990 chunk 325 optimal weight: 0.8980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1071 GLN B 784 GLN B1048 HIS ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 209 ASN ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 GLN ** 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 = 0.3932 r_free = 0.3932 target = 0.092064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.054906 restraints weight = 133318.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.056373 restraints weight = 61818.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.057285 restraints weight = 38112.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.057874 restraints weight = 28142.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.058216 restraints weight = 23367.037| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 33433 Z= 0.150 Angle : 0.555 9.358 45629 Z= 0.284 Chirality : 0.043 0.156 5276 Planarity : 0.004 0.130 5862 Dihedral : 4.938 59.078 4961 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.72 % Allowed : 13.48 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.13), residues: 4188 helix: 2.12 (0.20), residues: 732 sheet: -0.50 (0.14), residues: 1272 loop : -1.05 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 67 TYR 0.018 0.001 TYR C 91 PHE 0.029 0.001 PHE B 643 TRP 0.007 0.001 TRP D 36 HIS 0.003 0.001 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.00355 (33371) covalent geometry : angle 0.55017 (45485) SS BOND : bond 0.00347 ( 42) SS BOND : angle 1.22432 ( 84) hydrogen bonds : bond 0.04672 ( 1191) hydrogen bonds : angle 4.97115 ( 3204) link_NAG-ASN : bond 0.00240 ( 20) link_NAG-ASN : angle 1.74296 ( 60) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 150 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7243 (OUTLIER) cc_final: 0.6514 (t80) REVERT: A 456 PHE cc_start: 0.8045 (m-80) cc_final: 0.7691 (m-10) REVERT: A 779 GLN cc_start: 0.8894 (tm-30) cc_final: 0.8553 (tm-30) REVERT: B 449 TYR cc_start: 0.8278 (m-10) cc_final: 0.8071 (m-80) REVERT: B 1002 GLN cc_start: 0.8582 (tp40) cc_final: 0.8372 (tp40) REVERT: B 1071 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.8075 (pt0) REVERT: C 200 TYR cc_start: 0.7187 (OUTLIER) cc_final: 0.6801 (p90) REVERT: C 340 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8480 (pp20) REVERT: C 740 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.7922 (tmm) REVERT: C 779 GLN cc_start: 0.8677 (tp40) cc_final: 0.8448 (tm-30) REVERT: L 211 ASN cc_start: 0.7884 (t0) cc_final: 0.7634 (t0) REVERT: L 214 GLU cc_start: 0.4848 (pp20) cc_final: 0.4568 (pm20) REVERT: F 2 MET cc_start: 0.5576 (ttt) cc_final: 0.5314 (ttt) REVERT: G 82 GLU cc_start: 0.6127 (OUTLIER) cc_final: 0.5716 (pm20) REVERT: G 170 LYS cc_start: 0.1133 (pttm) cc_final: 0.0888 (pttm) REVERT: D 68 VAL cc_start: 0.3648 (OUTLIER) cc_final: 0.3392 (p) REVERT: D 83 LEU cc_start: 0.6882 (tp) cc_final: 0.6649 (tp) outliers start: 60 outliers final: 41 residues processed: 203 average time/residue: 0.2167 time to fit residues: 69.4423 Evaluate side-chains 193 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 145 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 1071 GLN Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 74 MET Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 126 LEU Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 197 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 110 optimal weight: 2.9990 chunk 387 optimal weight: 30.0000 chunk 338 optimal weight: 30.0000 chunk 294 optimal weight: 20.0000 chunk 322 optimal weight: 50.0000 chunk 201 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 227 optimal weight: 0.0370 chunk 190 optimal weight: 2.9990 chunk 408 optimal weight: 30.0000 chunk 42 optimal weight: 2.9990 overall best weight: 1.9864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 935 GLN F 209 ASN G 199 HIS ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 165 ASN ** E 43 GLN ** 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 = 0.3930 r_free = 0.3930 target = 0.091947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.054947 restraints weight = 132555.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.056350 restraints weight = 61876.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.057245 restraints weight = 38180.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.057826 restraints weight = 28185.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.058176 restraints weight = 23396.211| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 33433 Z= 0.152 Angle : 0.555 9.954 45629 Z= 0.283 Chirality : 0.043 0.197 5276 Planarity : 0.004 0.090 5862 Dihedral : 4.876 58.814 4961 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.72 % Allowed : 13.94 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.13), residues: 4188 helix: 2.18 (0.20), residues: 729 sheet: -0.42 (0.14), residues: 1266 loop : -1.01 (0.13), residues: 2193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 67 TYR 0.019 0.001 TYR C 91 PHE 0.031 0.001 PHE B 643 TRP 0.007 0.001 TRP H 36 HIS 0.003 0.001 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.00362 (33371) covalent geometry : angle 0.55005 (45485) SS BOND : bond 0.00341 ( 42) SS BOND : angle 1.11377 ( 84) hydrogen bonds : bond 0.04587 ( 1191) hydrogen bonds : angle 4.89492 ( 3204) link_NAG-ASN : bond 0.00242 ( 20) link_NAG-ASN : angle 1.70995 ( 60) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 156 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7214 (OUTLIER) cc_final: 0.6470 (t80) REVERT: A 456 PHE cc_start: 0.8049 (m-80) cc_final: 0.7688 (m-10) REVERT: A 779 GLN cc_start: 0.8931 (tm-30) cc_final: 0.8588 (tm-30) REVERT: B 1002 GLN cc_start: 0.8608 (tp40) cc_final: 0.8386 (tp40) REVERT: B 1071 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.8147 (pt0) REVERT: C 200 TYR cc_start: 0.7173 (OUTLIER) cc_final: 0.6871 (p90) REVERT: C 340 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8470 (pp20) REVERT: C 740 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.7919 (tmm) REVERT: L 40 LYS cc_start: 0.5882 (mmtm) cc_final: 0.5682 (mmmt) REVERT: L 211 ASN cc_start: 0.7735 (t0) cc_final: 0.7449 (t0) REVERT: L 214 GLU cc_start: 0.4758 (pp20) cc_final: 0.4367 (pm20) REVERT: G 82 GLU cc_start: 0.6056 (OUTLIER) cc_final: 0.5601 (pm20) REVERT: G 143 ARG cc_start: 0.7928 (ttp-110) cc_final: 0.7546 (ptp90) REVERT: E 82 GLU cc_start: 0.7865 (tt0) cc_final: 0.7645 (pp20) outliers start: 60 outliers final: 46 residues processed: 209 average time/residue: 0.2235 time to fit residues: 73.4908 Evaluate side-chains 200 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 148 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 1071 GLN Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 74 MET Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain F residue 209 ASN Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 203 SER Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 197 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 182 optimal weight: 0.9990 chunk 147 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 418 optimal weight: 10.0000 chunk 368 optimal weight: 10.0000 chunk 160 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 399 optimal weight: 40.0000 chunk 42 optimal weight: 0.8980 chunk 314 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 954 GLN C1071 GLN ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.092429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.055533 restraints weight = 132113.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.057040 restraints weight = 60938.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.057962 restraints weight = 37609.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.058540 restraints weight = 27842.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 65)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.058909 restraints weight = 23139.686| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 33433 Z= 0.120 Angle : 0.544 9.911 45629 Z= 0.277 Chirality : 0.043 0.160 5276 Planarity : 0.004 0.072 5862 Dihedral : 4.773 59.200 4961 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.41 % Allowed : 14.48 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.13), residues: 4188 helix: 2.32 (0.20), residues: 726 sheet: -0.33 (0.14), residues: 1269 loop : -0.96 (0.13), residues: 2193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 408 TYR 0.017 0.001 TYR B 365 PHE 0.026 0.001 PHE B 643 TRP 0.007 0.001 TRP H 36 HIS 0.003 0.000 HIS F 210 Details of bonding type rmsd covalent geometry : bond 0.00285 (33371) covalent geometry : angle 0.53965 (45485) SS BOND : bond 0.00338 ( 42) SS BOND : angle 0.97181 ( 84) hydrogen bonds : bond 0.04306 ( 1191) hydrogen bonds : angle 4.77910 ( 3204) link_NAG-ASN : bond 0.00242 ( 20) link_NAG-ASN : angle 1.63576 ( 60) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 160 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7145 (OUTLIER) cc_final: 0.6418 (t80) REVERT: A 456 PHE cc_start: 0.8074 (m-80) cc_final: 0.7722 (m-10) REVERT: A 779 GLN cc_start: 0.8902 (tm-30) cc_final: 0.8556 (tm-30) REVERT: A 902 MET cc_start: 0.9186 (tpt) cc_final: 0.8964 (tpt) REVERT: B 1071 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.8034 (pt0) REVERT: B 1107 ARG cc_start: 0.7941 (mtt90) cc_final: 0.7724 (mpt-90) REVERT: C 200 TYR cc_start: 0.7191 (OUTLIER) cc_final: 0.6901 (p90) REVERT: C 340 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8504 (pp20) REVERT: C 740 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.7870 (tmm) REVERT: C 779 GLN cc_start: 0.8516 (tm-30) cc_final: 0.8288 (tm-30) REVERT: H 19 LYS cc_start: 0.9327 (tppt) cc_final: 0.9039 (tppt) REVERT: L 211 ASN cc_start: 0.7729 (t0) cc_final: 0.7482 (t0) REVERT: L 214 GLU cc_start: 0.5123 (pp20) cc_final: 0.4769 (pm20) REVERT: F 2 MET cc_start: 0.5276 (ttp) cc_final: 0.5052 (mtp) REVERT: G 82 GLU cc_start: 0.6189 (OUTLIER) cc_final: 0.5685 (pm20) REVERT: G 143 ARG cc_start: 0.7974 (ttp-110) cc_final: 0.7586 (ptp90) REVERT: D 83 LEU cc_start: 0.6814 (tp) cc_final: 0.6541 (tp) REVERT: D 87 ARG cc_start: 0.8692 (ptp90) cc_final: 0.8383 (ptp90) REVERT: E 18 ARG cc_start: 0.7815 (mpt-90) cc_final: 0.7609 (mpt180) REVERT: E 82 GLU cc_start: 0.7891 (tt0) cc_final: 0.7669 (pp20) outliers start: 49 outliers final: 40 residues processed: 203 average time/residue: 0.2407 time to fit residues: 74.8322 Evaluate side-chains 196 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 150 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 1071 GLN Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 74 MET Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 203 SER Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 197 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 264 optimal weight: 0.8980 chunk 332 optimal weight: 50.0000 chunk 371 optimal weight: 0.0870 chunk 164 optimal weight: 0.3980 chunk 301 optimal weight: 20.0000 chunk 304 optimal weight: 20.0000 chunk 334 optimal weight: 9.9990 chunk 150 optimal weight: 2.9990 chunk 252 optimal weight: 0.1980 chunk 303 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1071 GLN L 199 HIS F 209 ASN ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.092963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.056270 restraints weight = 132809.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.057768 restraints weight = 60795.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.058712 restraints weight = 37385.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.059241 restraints weight = 27524.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.059630 restraints weight = 22964.331| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.118 33433 Z= 0.106 Angle : 0.541 11.444 45629 Z= 0.275 Chirality : 0.042 0.163 5276 Planarity : 0.004 0.060 5862 Dihedral : 4.652 58.991 4961 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.47 % Allowed : 14.60 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.13), residues: 4188 helix: 2.32 (0.20), residues: 735 sheet: -0.24 (0.14), residues: 1269 loop : -0.86 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 24 TYR 0.017 0.001 TYR L 50 PHE 0.028 0.001 PHE B 643 TRP 0.033 0.001 TRP H 36 HIS 0.003 0.000 HIS L 190 Details of bonding type rmsd covalent geometry : bond 0.00257 (33371) covalent geometry : angle 0.53760 (45485) SS BOND : bond 0.00342 ( 42) SS BOND : angle 0.92282 ( 84) hydrogen bonds : bond 0.04018 ( 1191) hydrogen bonds : angle 4.65756 ( 3204) link_NAG-ASN : bond 0.00250 ( 20) link_NAG-ASN : angle 1.57701 ( 60) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 160 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.6990 (OUTLIER) cc_final: 0.6425 (t80) REVERT: A 456 PHE cc_start: 0.8115 (m-80) cc_final: 0.7754 (m-10) REVERT: A 779 GLN cc_start: 0.8868 (tm-30) cc_final: 0.8502 (tm-30) REVERT: C 200 TYR cc_start: 0.7192 (OUTLIER) cc_final: 0.6988 (p90) REVERT: C 340 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8505 (pp20) REVERT: C 740 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.7826 (tmm) REVERT: L 197 VAL cc_start: -0.3141 (OUTLIER) cc_final: -0.3446 (m) REVERT: L 211 ASN cc_start: 0.7712 (t0) cc_final: 0.7431 (t0) REVERT: L 214 GLU cc_start: 0.5008 (pp20) cc_final: 0.4661 (pm20) REVERT: F 2 MET cc_start: 0.5114 (ttp) cc_final: 0.4873 (mtp) REVERT: F 74 MET cc_start: 0.7077 (mmm) cc_final: 0.6865 (mpp) REVERT: G 82 GLU cc_start: 0.6076 (OUTLIER) cc_final: 0.5605 (pm20) REVERT: D 68 VAL cc_start: 0.4202 (OUTLIER) cc_final: 0.3998 (p) REVERT: D 83 LEU cc_start: 0.6817 (tp) cc_final: 0.6526 (tp) REVERT: D 87 ARG cc_start: 0.8668 (ptp90) cc_final: 0.8357 (ptp90) REVERT: E 82 GLU cc_start: 0.7872 (tt0) cc_final: 0.7657 (pp20) outliers start: 51 outliers final: 39 residues processed: 204 average time/residue: 0.2303 time to fit residues: 72.3935 Evaluate side-chains 194 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 148 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 74 MET Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain F residue 209 ASN Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 203 SER Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 197 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 169 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 178 optimal weight: 0.9980 chunk 179 optimal weight: 7.9990 chunk 260 optimal weight: 0.9980 chunk 55 optimal weight: 0.3980 chunk 289 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 chunk 245 optimal weight: 0.0010 chunk 274 optimal weight: 6.9990 chunk 269 optimal weight: 0.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 955 ASN ** B1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1071 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.093026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.056276 restraints weight = 133436.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.057814 restraints weight = 60751.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.058761 restraints weight = 37251.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.059287 restraints weight = 27459.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.059670 restraints weight = 22953.448| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.118 33433 Z= 0.140 Angle : 0.678 59.173 45629 Z= 0.363 Chirality : 0.043 0.335 5276 Planarity : 0.004 0.120 5862 Dihedral : 4.668 58.976 4961 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.32 % Allowed : 14.94 % Favored : 83.74 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.13), residues: 4188 helix: 2.32 (0.20), residues: 735 sheet: -0.23 (0.14), residues: 1269 loop : -0.85 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.046 0.001 ARG G 143 TYR 0.027 0.001 TYR G 174 PHE 0.024 0.001 PHE B 643 TRP 0.031 0.001 TRP H 36 HIS 0.002 0.000 HIS L 190 Details of bonding type rmsd covalent geometry : bond 0.00323 (33371) covalent geometry : angle 0.67562 (45485) SS BOND : bond 0.00342 ( 42) SS BOND : angle 0.89844 ( 84) hydrogen bonds : bond 0.04009 ( 1191) hydrogen bonds : angle 4.66108 ( 3204) link_NAG-ASN : bond 0.00246 ( 20) link_NAG-ASN : angle 1.57677 ( 60) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7782.81 seconds wall clock time: 133 minutes 55.80 seconds (8035.80 seconds total)