Starting phenix.real_space_refine on Mon Aug 25 14:43:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xmx_33307/08_2025/7xmx_33307_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xmx_33307/08_2025/7xmx_33307.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xmx_33307/08_2025/7xmx_33307.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xmx_33307/08_2025/7xmx_33307.map" model { file = "/net/cci-nas-00/data/ceres_data/7xmx_33307/08_2025/7xmx_33307_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xmx_33307/08_2025/7xmx_33307_neut.cif" } resolution = 3.62 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= 0.002 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 127 5.16 5 C 18232 2.51 5 N 4743 2.21 5 O 5625 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 53 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28727 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1008, 7774 Classifications: {'peptide': 1008} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 54, 'TRANS': 953} Chain breaks: 9 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 3, 'PHE:plan': 3, 'ASN:plan1': 1, 'TRP:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 78 Chain: "B" Number of atoms: 7789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1011, 7789 Classifications: {'peptide': 1011} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 54, 'TRANS': 956} Chain breaks: 9 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 3, 'PHE:plan': 2, 'GLU:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 72 Chain: "C" Number of atoms: 7710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1000, 7710 Classifications: {'peptide': 1000} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 54, 'TRANS': 945} Chain breaks: 10 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 5, 'PHE:plan': 3, 'GLU:plan': 2, 'TRP:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 75 Chain: "E" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 903 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 113} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 803 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 102} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 903 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 113} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "I" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 803 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 102} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 903 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 113} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "L" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 803 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 102} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 6.54, per 1000 atoms: 0.23 Number of scatterers: 28727 At special positions: 0 Unit cell: (136.77, 206.61, 184.3, 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 127 16.00 O 5625 8.00 N 4743 7.00 C 18232 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, 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=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 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 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.02 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 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 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 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=1.75 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.05 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 89 " distance=2.06 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.05 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 89 " distance=2.06 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 95 " distance=2.05 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 89 " distance=2.06 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 A1098 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 657 " " NAG A1304 " - " ASN A 801 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A 603 " " NAG A1308 " - " ASN A 165 " " NAG B1301 " - " ASN B1098 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 657 " " NAG B1304 " - " ASN B 801 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " ASN B1074 " " NAG B1307 " - " ASN B 603 " " NAG B1308 " - " ASN B 616 " " NAG C1301 " - " ASN C1098 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 657 " " NAG C1304 " - " ASN C 801 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C1074 " " NAG C1307 " - " ASN C 603 " " NAG C1308 " - " ASN C 616 " Time building additional restraints: 2.16 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6864 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 59 sheets defined 23.0% alpha, 26.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 4.458A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.216A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.203A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASP A 389 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 408 removed outlier: 4.009A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 427 through 430 removed outlier: 3.759A pdb=" N THR A 430 " --> pdb=" O ASP A 427 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 427 through 430' Processing helix chain 'A' and resid 619 through 623 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 757 removed outlier: 3.542A pdb=" N GLY A 757 " --> pdb=" O LEU A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 4.099A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.789A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.550A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.501A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 946 removed outlier: 4.154A pdb=" N LEU A 945 " --> pdb=" O PRO A 942 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY A 946 " --> pdb=" O SER A 943 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 942 through 946' Processing helix chain 'A' and resid 947 through 968 removed outlier: 3.899A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER A 968 " --> pdb=" O LYS A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 983 removed outlier: 3.980A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 3.747A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.856A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.222A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.132A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASP B 389 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 408 removed outlier: 4.009A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 408' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 427 through 430 removed outlier: 3.744A pdb=" N THR B 430 " --> pdb=" O ASP B 427 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 427 through 430' Processing helix chain 'B' and resid 619 through 623 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 757 removed outlier: 3.542A pdb=" N GLY B 757 " --> pdb=" O LEU B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 4.099A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.788A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.551A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.602A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 946 removed outlier: 4.154A pdb=" N LEU B 945 " --> pdb=" O PRO B 942 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY B 946 " --> pdb=" O SER B 943 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 942 through 946' Processing helix chain 'B' and resid 947 through 968 removed outlier: 3.899A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER B 968 " --> pdb=" O LYS B 964 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 983 removed outlier: 3.980A 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 1140 through 1146 removed outlier: 3.927A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 383 through 390 removed outlier: 4.357A pdb=" N ASN C 388 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP C 389 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 408 removed outlier: 4.009A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 405 through 408' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 427 through 430 removed outlier: 3.731A pdb=" N THR C 430 " --> pdb=" O ASP C 427 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 427 through 430' Processing helix chain 'C' and resid 619 through 623 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 757 Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.511A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.788A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.550A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.670A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 946 removed outlier: 4.154A pdb=" N LEU C 945 " --> pdb=" O PRO C 942 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY C 946 " --> pdb=" O SER C 943 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 942 through 946' Processing helix chain 'C' and resid 947 through 968 removed outlier: 3.899A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER C 968 " --> pdb=" O LYS C 964 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 983 removed outlier: 3.980A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.866A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 64 Processing helix chain 'E' and resid 86 through 90 removed outlier: 3.584A pdb=" N THR E 90 " --> pdb=" O ALA E 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 84 Processing helix chain 'H' and resid 60 through 64 Processing helix chain 'H' and resid 86 through 90 removed outlier: 3.584A pdb=" N THR H 90 " --> pdb=" O ALA H 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 80 through 84 Processing helix chain 'K' and resid 60 through 64 Processing helix chain 'K' and resid 86 through 90 removed outlier: 3.585A pdb=" N THR K 90 " --> pdb=" O ALA K 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 84 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.840A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.491A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 10.218A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.786A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.961A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 103 through 104 removed outlier: 3.860A pdb=" N GLY A 103 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 118 through 121 removed outlier: 3.648A pdb=" N TYR A 170 " --> pdb=" O ILE A 128 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.710A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY A 593 " --> pdb=" O PHE A 318 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL A 610 " --> pdb=" O ILE A 651 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR A 612 " --> pdb=" O CYS A 649 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE A 643 " --> pdb=" O LEU A 650 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 326 removed outlier: 3.738A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.526A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.296A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.786A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.783A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB4, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 3.696A pdb=" N SER A1123 " --> pdb=" O ALA A1087 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1094 through 1096 Processing sheet with id=AB6, first strand: chain 'B' and resid 29 through 31 removed outlier: 4.013A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 42 through 43 removed outlier: 3.535A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 48 through 51 removed outlier: 3.961A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AC1, first strand: chain 'B' and resid 169 through 172 removed outlier: 3.836A pdb=" N TYR B 170 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY B 103 " --> pdb=" O LEU B 242 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 318 removed outlier: 5.712A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY B 593 " --> pdb=" O PHE B 318 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL B 610 " --> pdb=" O ILE B 651 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR B 612 " --> pdb=" O CYS B 649 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE B 643 " --> pdb=" O LEU B 650 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 325 through 327 removed outlier: 6.815A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.393A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.297A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.784A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.784A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AC9, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 3.695A pdb=" N SER B1123 " --> pdb=" O ALA B1087 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1094 through 1096 Processing sheet with id=AD2, first strand: chain 'C' and resid 29 through 31 removed outlier: 3.841A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 48 through 51 removed outlier: 3.961A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AD5, first strand: chain 'C' and resid 169 through 172 removed outlier: 3.766A pdb=" N TYR C 170 " --> pdb=" O ILE C 128 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.711A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY C 593 " --> pdb=" O PHE C 318 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL C 610 " --> pdb=" O ILE C 651 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR C 612 " --> pdb=" O CYS C 649 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE C 643 " --> pdb=" O LEU C 650 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 325 through 327 removed outlier: 6.815A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.322A pdb=" N ILE C 402 " --> pdb=" O TYR C 508 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE1, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.297A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.785A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.783A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE4, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 3.696A pdb=" N SER C1123 " --> pdb=" O ALA C1087 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 1094 through 1096 Processing sheet with id=AE6, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.746A pdb=" N GLN E 3 " --> pdb=" O SER E 25 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER E 7 " --> pdb=" O SER E 21 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.630A pdb=" N THR E 111 " --> pdb=" O TYR E 93 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR E 33 " --> pdb=" O SER E 98 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N MET E 34 " --> pdb=" O ILE E 50 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ILE E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.630A pdb=" N THR E 111 " --> pdb=" O TYR E 93 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 9 through 12 removed outlier: 7.116A pdb=" N VAL F 10 " --> pdb=" O THR F 108 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N TRP F 36 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 9 through 12 removed outlier: 7.116A pdb=" N VAL F 10 " --> pdb=" O THR F 108 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 18 through 22 Processing sheet with id=AF3, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.746A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER H 7 " --> pdb=" O SER H 21 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.202A pdb=" N TYR H 33 " --> pdb=" O SER H 98 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N MET H 34 " --> pdb=" O ILE H 50 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ILE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AF6, first strand: chain 'I' and resid 9 through 12 removed outlier: 7.116A pdb=" N VAL I 10 " --> pdb=" O THR I 108 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 9 through 12 removed outlier: 7.116A pdb=" N VAL I 10 " --> pdb=" O THR I 108 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 18 through 22 Processing sheet with id=AF9, first strand: chain 'K' and resid 3 through 7 removed outlier: 3.746A pdb=" N GLN K 3 " --> pdb=" O SER K 25 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER K 7 " --> pdb=" O SER K 21 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 11 through 12 removed outlier: 4.202A pdb=" N TYR K 33 " --> pdb=" O SER K 98 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N MET K 34 " --> pdb=" O ILE K 50 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ILE K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 11 through 12 Processing sheet with id=AG3, first strand: chain 'L' and resid 9 through 12 removed outlier: 7.116A pdb=" N VAL L 10 " --> pdb=" O THR L 108 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 9 through 12 removed outlier: 7.116A pdb=" N VAL L 10 " --> pdb=" O THR L 108 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 18 through 22 1102 hydrogen bonds defined for protein. 2919 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: 6.71 Time building geometry restraints manager: 2.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7023 1.33 - 1.45: 6301 1.45 - 1.58: 15870 1.58 - 1.70: 2 1.70 - 1.82: 163 Bond restraints: 29359 Sorted by residual: bond pdb=" N PRO C 337 " pdb=" CD PRO C 337 " ideal model delta sigma weight residual 1.473 1.622 -0.149 1.40e-02 5.10e+03 1.13e+02 bond pdb=" N PRO B 337 " pdb=" CD PRO B 337 " ideal model delta sigma weight residual 1.473 1.615 -0.142 1.40e-02 5.10e+03 1.03e+02 bond pdb=" N VAL C 341 " pdb=" CA VAL C 341 " ideal model delta sigma weight residual 1.458 1.494 -0.036 9.00e-03 1.23e+04 1.62e+01 bond pdb=" N ILE C 402 " pdb=" CA ILE C 402 " ideal model delta sigma weight residual 1.456 1.499 -0.043 1.11e-02 8.12e+03 1.51e+01 bond pdb=" N ILE B 402 " pdb=" CA ILE B 402 " ideal model delta sigma weight residual 1.456 1.499 -0.043 1.11e-02 8.12e+03 1.51e+01 ... (remaining 29354 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 32423 1.61 - 3.22: 6376 3.22 - 4.83: 1050 4.83 - 6.44: 121 6.44 - 8.06: 11 Bond angle restraints: 39981 Sorted by residual: angle pdb=" N THR B 618 " pdb=" CA THR B 618 " pdb=" C THR B 618 " ideal model delta sigma weight residual 113.17 105.81 7.36 1.26e+00 6.30e-01 3.41e+01 angle pdb=" N ASP C 427 " pdb=" CA ASP C 427 " pdb=" C ASP C 427 " ideal model delta sigma weight residual 114.64 107.48 7.16 1.52e+00 4.33e-01 2.22e+01 angle pdb=" N ASP A 427 " pdb=" CA ASP A 427 " pdb=" C ASP A 427 " ideal model delta sigma weight residual 114.64 107.57 7.07 1.52e+00 4.33e-01 2.17e+01 angle pdb=" N ASN B 616 " pdb=" CA ASN B 616 " pdb=" C ASN B 616 " ideal model delta sigma weight residual 110.10 103.23 6.87 1.49e+00 4.50e-01 2.13e+01 angle pdb=" N ASP B 427 " pdb=" CA ASP B 427 " pdb=" C ASP B 427 " ideal model delta sigma weight residual 114.64 107.65 6.99 1.52e+00 4.33e-01 2.12e+01 ... (remaining 39976 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.34: 16247 16.34 - 32.67: 1081 32.67 - 49.01: 319 49.01 - 65.34: 104 65.34 - 81.68: 15 Dihedral angle restraints: 17766 sinusoidal: 7072 harmonic: 10694 Sorted by residual: dihedral pdb=" CB CYS B 738 " pdb=" SG CYS B 738 " pdb=" SG CYS B 760 " pdb=" CB CYS B 760 " ideal model delta sinusoidal sigma weight residual 93.00 11.32 81.68 1 1.00e+01 1.00e-02 8.21e+01 dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 760 " pdb=" CB CYS A 760 " ideal model delta sinusoidal sigma weight residual 93.00 11.34 81.66 1 1.00e+01 1.00e-02 8.21e+01 dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual -86.00 -21.96 -64.04 1 1.00e+01 1.00e-02 5.40e+01 ... (remaining 17763 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2984 0.073 - 0.146: 1174 0.146 - 0.218: 370 0.218 - 0.291: 72 0.291 - 0.364: 15 Chirality restraints: 4615 Sorted by residual: 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 2.15 0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CA TYR K 33 " pdb=" N TYR K 33 " pdb=" C TYR K 33 " pdb=" CB TYR K 33 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.35 2.00e-01 2.50e+01 3.14e+00 chirality pdb=" CA TYR E 33 " pdb=" N TYR E 33 " pdb=" C TYR E 33 " pdb=" CB TYR E 33 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.13e+00 ... (remaining 4612 not shown) Planarity restraints: 5190 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1308 " 0.250 2.00e-02 2.50e+03 2.13e-01 5.66e+02 pdb=" C7 NAG B1308 " -0.064 2.00e-02 2.50e+03 pdb=" C8 NAG B1308 " 0.165 2.00e-02 2.50e+03 pdb=" N2 NAG B1308 " -0.364 2.00e-02 2.50e+03 pdb=" O7 NAG B1308 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1308 " -0.141 2.00e-02 2.50e+03 1.16e-01 1.70e+02 pdb=" C7 NAG A1308 " 0.039 2.00e-02 2.50e+03 pdb=" C8 NAG A1308 " -0.106 2.00e-02 2.50e+03 pdb=" N2 NAG A1308 " 0.186 2.00e-02 2.50e+03 pdb=" O7 NAG A1308 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 525 " -0.022 2.00e-02 2.50e+03 4.52e-02 2.04e+01 pdb=" C CYS A 525 " 0.078 2.00e-02 2.50e+03 pdb=" O CYS A 525 " -0.029 2.00e-02 2.50e+03 pdb=" N GLY A 526 " -0.027 2.00e-02 2.50e+03 ... (remaining 5187 not shown) Histogram of nonbonded interaction distances: 1.41 - 2.11: 3 2.11 - 2.80: 7153 2.80 - 3.50: 36907 3.50 - 4.20: 61898 4.20 - 4.90: 108043 Nonbonded interactions: 214004 Sorted by model distance: nonbonded pdb=" CE2 PHE C 201 " pdb=" CG1 ILE C 231 " model vdw 1.407 3.740 nonbonded pdb=" SG CYS B 336 " pdb=" O VAL B 362 " model vdw 1.631 3.400 nonbonded pdb=" CD2 PHE C 201 " pdb=" CG1 ILE C 231 " model vdw 1.835 3.740 nonbonded pdb=" CE2 PHE C 201 " pdb=" CB ILE C 231 " model vdw 2.207 3.770 nonbonded pdb=" O ASP C 290 " pdb=" OD1 ASP C 290 " model vdw 2.237 3.040 ... (remaining 213999 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 26 through 32 or (resid 33 through 34 and (name N or name \ CA or name C or name O or name CB )) or resid 35 through 66 or resid 81 through \ 105 or (resid 106 and (name N or name CA or name C or name O or name CB )) or re \ sid 107 through 128 or (resid 129 and (name N or name CA or name C or name O or \ name CB )) or resid 130 or (resid 131 through 133 and (name N or name CA or name \ C or name O or name CB )) or resid 134 or (resid 135 and (name N or name CA or \ name C or name O or name CB )) or resid 136 through 165 or resid 167 through 176 \ or resid 190 through 215 or (resid 216 and (name N or name CA or name C or name \ O or name CB )) or resid 217 through 239 or (resid 240 and (name N or name CA o \ r name C or name O or name CB )) or resid 241 or (resid 242 through 243 and (nam \ e N or name CA or name C or name O or name CB )) or resid 265 through 330 or res \ id 336 through 356 or (resid 357 through 358 and (name N or name CA or name C or \ name O or name CB )) or resid 359 through 364 or (resid 365 and (name N or name \ CA or name C or name O or name CB )) or resid 366 through 417 or (resid 418 thr \ ough 419 and (name N or name CA or name C or name O or name CB )) or resid 420 t \ hrough 536 or (resid 537 and (name N or name CA or name C or name O or name CB ) \ ) or resid 538 through 621 or (resid 622 through 623 and (name N or name CA or n \ ame C or name O or name CB )) or resid 624 through 626 or (resid 627 and (name N \ or name CA or name C or name O or name CB )) or resid 640 through 675 or resid \ 691 through 1141 or (resid 1142 and (name N or name CA or name C or name O or na \ me CB )) or resid 1143 through 1308)) selection = (chain 'B' and (resid 26 through 33 or (resid 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 through 66 or resid 81 through 96 or (resi \ d 97 and (name N or name CA or name C or name O or name CB )) or resid 98 throug \ h 132 or (resid 133 and (name N or name CA or name C or name O or name CB )) or \ resid 134 or (resid 135 and (name N or name CA or name C or name O or name CB )) \ or resid 136 through 141 or resid 155 through 165 or resid 167 through 176 or ( \ resid 190 and (name N or name CA or name C or name O or name CB )) or resid 191 \ through 209 or (resid 210 and (name N or name CA or name C or name O or name CB \ )) or resid 211 through 213 or (resid 214 and (name N or name CA or name C or na \ me O or name CB )) or resid 215 through 234 or (resid 235 and (name N or name CA \ or name C or name O or name CB )) or resid 236 through 239 or (resid 240 and (n \ ame N or name CA or name C or name O or name CB )) or resid 241 or (resid 242 th \ rough 243 and (name N or name CA or name C or name O or name CB )) or resid 265 \ through 330 or resid 336 through 356 or (resid 357 through 358 and (name N or na \ me CA or name C or name O or name CB )) or resid 359 through 386 or (resid 387 a \ nd (name N or name CA or name C or name O or name CB )) or resid 388 through 464 \ or (resid 465 and (name N or name CA or name C or name O or name CB )) or resid \ 466 through 514 or (resid 515 and (name N or name CA or name C or name O or nam \ e CB )) or resid 516 through 536 or (resid 537 and (name N or name CA or name C \ or name O or name CB )) or resid 538 through 627 or resid 640 through 675 or res \ id 691 through 1308)) selection = (chain 'C' and (resid 26 through 32 or (resid 33 through 34 and (name N or name \ CA or name C or name O or name CB )) or resid 35 through 105 or (resid 106 and ( \ name N or name CA or name C or name O or name CB )) or resid 107 through 128 or \ (resid 129 and (name N or name CA or name C or name O or name CB )) or resid 130 \ or (resid 131 through 133 and (name N or name CA or name C or name O or name CB \ )) or resid 134 through 157 or (resid 158 and (name N or name CA or name C or n \ ame O or name CB )) or resid 159 through 176 or resid 190 through 209 or (resid \ 210 and (name N or name CA or name C or name O or name CB )) or resid 211 throug \ h 213 or (resid 214 and (name N or name CA or name C or name O or name CB )) or \ resid 215 or (resid 216 and (name N or name CA or name C or name O or name CB )) \ or resid 217 through 234 or (resid 235 and (name N or name CA or name C or name \ O or name CB )) or resid 236 through 243 or resid 265 through 357 or (resid 358 \ and (name N or name CA or name C or name O or name CB )) or resid 359 through 3 \ 64 or (resid 365 and (name N or name CA or name C or name O or name CB )) or res \ id 366 through 386 or (resid 387 and (name N or name CA or name C or name O or n \ ame CB )) or resid 388 through 393 or (resid 394 and (name N or name CA or name \ C or name O or name CB )) or resid 395 through 417 or (resid 418 through 419 and \ (name N or name CA or name C or name O or name CB )) or resid 420 through 621 o \ r (resid 622 through 623 and (name N or name CA or name C or name O or name CB ) \ ) or resid 624 through 626 or (resid 627 and (name N or name CA or name C or nam \ e O or name CB )) or resid 640 through 1308)) } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'F' selection = chain 'I' 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: 2.560 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: 0.530 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 27.080 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.060 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:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0033 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 : 0.012 0.283 29420 Z= 0.755 Angle : 1.312 27.180 40127 Z= 0.917 Chirality : 0.086 0.364 4615 Planarity : 0.006 0.213 5166 Dihedral : 12.654 80.186 10791 Min Nonbonded Distance : 1.407 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.65 % Favored : 93.27 % Rotamer: Outliers : 1.34 % Allowed : 6.16 % Favored : 92.50 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.13), residues: 3626 helix: 1.27 (0.21), residues: 635 sheet: 0.44 (0.17), residues: 854 loop : -1.79 (0.12), residues: 2137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 237 TYR 0.041 0.002 TYR B 160 PHE 0.031 0.002 PHE C 970 TRP 0.019 0.002 TRP F 99 HIS 0.006 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.01155 (29359) covalent geometry : angle 1.29707 (39981) SS BOND : bond 0.04790 ( 37) SS BOND : angle 4.43794 ( 74) hydrogen bonds : bond 0.24410 ( 1076) hydrogen bonds : angle 8.97770 ( 2919) link_NAG-ASN : bond 0.00689 ( 24) link_NAG-ASN : angle 2.04038 ( 72) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 282 time to evaluate : 0.786 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 269 TYR cc_start: 0.2288 (m-80) cc_final: -0.1277 (p90) REVERT: A 395 VAL cc_start: 0.0452 (t) cc_final: 0.0235 (t) REVERT: A 650 LEU cc_start: 0.1773 (mp) cc_final: 0.1335 (tp) REVERT: A 788 ILE cc_start: 0.1992 (mm) cc_final: 0.0695 (pt) REVERT: A 902 MET cc_start: -0.0488 (tpt) cc_final: -0.0724 (ptt) REVERT: A 1098 ASN cc_start: 0.2561 (p0) cc_final: 0.0150 (t0) REVERT: B 153 MET cc_start: -0.0016 (ttp) cc_final: -0.2122 (ptt) REVERT: B 468 ILE cc_start: 0.6333 (tt) cc_final: 0.6103 (mm) REVERT: C 469 SER cc_start: 0.1543 (OUTLIER) cc_final: 0.0472 (t) REVERT: F 66 SER cc_start: 0.2828 (p) cc_final: 0.2511 (t) REVERT: H 78 MET cc_start: 0.0117 (ttp) cc_final: -0.0707 (ptm) REVERT: H 82 MET cc_start: 0.0146 (OUTLIER) cc_final: -0.0364 (mtp) REVERT: K 81 GLN cc_start: 0.2430 (OUTLIER) cc_final: 0.1057 (mt0) outliers start: 42 outliers final: 11 residues processed: 318 average time/residue: 0.1716 time to fit residues: 87.6467 Evaluate side-chains 182 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 168 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain E residue 19 ARG Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 80 GLN Chi-restraints excluded: chain H residue 19 ARG Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 81 GLN Chi-restraints excluded: chain L residue 77 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 197 optimal weight: 0.0270 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 1.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 414 GLN A 487 ASN A 658 ASN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 992 GLN B 122 ASN B 487 ASN B 895 GLN B1088 HIS C 207 HIS C 343 ASN C 437 ASN C 487 ASN K 81 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5095 r_free = 0.5095 target = 0.250525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4918 r_free = 0.4918 target = 0.232436 restraints weight = 71127.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4896 r_free = 0.4896 target = 0.230964 restraints weight = 98948.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4895 r_free = 0.4895 target = 0.230699 restraints weight = 83418.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4887 r_free = 0.4887 target = 0.230071 restraints weight = 73459.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4891 r_free = 0.4891 target = 0.230436 restraints weight = 65601.200| |-----------------------------------------------------------------------------| r_work (final): 0.4883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0266 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 29420 Z= 0.162 Angle : 0.639 12.089 40127 Z= 0.341 Chirality : 0.046 0.236 4615 Planarity : 0.004 0.068 5166 Dihedral : 7.149 89.466 4486 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.66 % Allowed : 9.13 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.13), residues: 3626 helix: 2.02 (0.20), residues: 641 sheet: 0.79 (0.18), residues: 833 loop : -1.59 (0.12), residues: 2152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 71 TYR 0.025 0.002 TYR I 50 PHE 0.023 0.002 PHE A 400 TRP 0.013 0.001 TRP L 92 HIS 0.008 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00323 (29359) covalent geometry : angle 0.62759 (39981) SS BOND : bond 0.00672 ( 37) SS BOND : angle 1.39665 ( 74) hydrogen bonds : bond 0.07920 ( 1076) hydrogen bonds : angle 6.50435 ( 2919) link_NAG-ASN : bond 0.00576 ( 24) link_NAG-ASN : angle 2.58135 ( 72) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 186 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 TYR cc_start: 0.2719 (m-80) cc_final: -0.0688 (p90) REVERT: A 480 CYS cc_start: -0.1599 (OUTLIER) cc_final: -0.1886 (m) REVERT: A 650 LEU cc_start: 0.1838 (mp) cc_final: 0.1381 (tp) REVERT: A 788 ILE cc_start: 0.1898 (mm) cc_final: -0.0593 (tt) REVERT: A 816 SER cc_start: -0.0396 (OUTLIER) cc_final: -0.0923 (p) REVERT: A 902 MET cc_start: -0.0038 (tpt) cc_final: -0.0773 (ptt) REVERT: B 153 MET cc_start: -0.0429 (ttp) cc_final: -0.1969 (mtm) REVERT: B 645 THR cc_start: 0.0409 (t) cc_final: 0.0172 (p) REVERT: B 902 MET cc_start: 0.1793 (ptm) cc_final: 0.1020 (ptm) REVERT: C 343 ASN cc_start: 0.0208 (OUTLIER) cc_final: -0.1283 (m-40) REVERT: E 78 MET cc_start: 0.0861 (tpp) cc_final: 0.0413 (mmm) REVERT: H 78 MET cc_start: 0.0868 (ttp) cc_final: 0.0520 (ttp) REVERT: H 82 MET cc_start: 0.0253 (mpp) cc_final: -0.0635 (mmm) REVERT: K 34 MET cc_start: 0.3041 (ttm) cc_final: 0.2795 (ttp) REVERT: K 78 MET cc_start: 0.2476 (OUTLIER) cc_final: 0.1616 (tpp) REVERT: K 81 GLN cc_start: 0.2398 (OUTLIER) cc_final: 0.2081 (mt0) outliers start: 52 outliers final: 20 residues processed: 229 average time/residue: 0.1454 time to fit residues: 55.5172 Evaluate side-chains 173 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 80 GLN Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 78 MET Chi-restraints excluded: chain K residue 81 GLN Chi-restraints excluded: chain K residue 105 ASP Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 77 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 107 optimal weight: 8.9990 chunk 310 optimal weight: 7.9990 chunk 284 optimal weight: 0.0020 chunk 258 optimal weight: 1.9990 chunk 135 optimal weight: 8.9990 chunk 121 optimal weight: 7.9990 chunk 361 optimal weight: 0.0010 chunk 153 optimal weight: 4.9990 chunk 236 optimal weight: 0.0000 chunk 129 optimal weight: 6.9990 chunk 363 optimal weight: 50.0000 overall best weight: 1.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 GLN A 955 ASN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1083 HIS A1088 HIS A1135 ASN B 613 GLN B 703 ASN B 755 GLN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1036 GLN B1054 GLN ** C 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN ** C 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 1 GLN F 80 GLN I 1 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5108 r_free = 0.5108 target = 0.251759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4940 r_free = 0.4940 target = 0.234380 restraints weight = 72584.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.4895 r_free = 0.4895 target = 0.231539 restraints weight = 73411.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4885 r_free = 0.4885 target = 0.230282 restraints weight = 67788.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4881 r_free = 0.4881 target = 0.229830 restraints weight = 64157.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4881 r_free = 0.4881 target = 0.229823 restraints weight = 60056.855| |-----------------------------------------------------------------------------| r_work (final): 0.4873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0828 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 29420 Z= 0.176 Angle : 0.680 10.829 40127 Z= 0.364 Chirality : 0.049 0.284 4615 Planarity : 0.005 0.083 5166 Dihedral : 6.545 74.623 4466 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.17 % Allowed : 11.71 % Favored : 86.12 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.13), residues: 3626 helix: 1.20 (0.20), residues: 639 sheet: 0.90 (0.18), residues: 813 loop : -1.47 (0.12), residues: 2174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 319 TYR 0.028 0.002 TYR C 917 PHE 0.037 0.002 PHE B 318 TRP 0.022 0.002 TRP C 886 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00358 (29359) covalent geometry : angle 0.67135 (39981) SS BOND : bond 0.00568 ( 37) SS BOND : angle 1.76825 ( 74) hydrogen bonds : bond 0.06013 ( 1076) hydrogen bonds : angle 5.96872 ( 2919) link_NAG-ASN : bond 0.00425 ( 24) link_NAG-ASN : angle 1.97318 ( 72) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 195 time to evaluate : 0.877 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: A 269 TYR cc_start: 0.2743 (m-80) cc_final: -0.0732 (p90) REVERT: A 902 MET cc_start: 0.0872 (tpt) cc_final: -0.0048 (ptt) REVERT: A 1005 GLN cc_start: 0.0802 (OUTLIER) cc_final: 0.0380 (tt0) REVERT: B 237 ARG cc_start: 0.3198 (tmt-80) cc_final: 0.2860 (tpt-90) REVERT: B 906 PHE cc_start: 0.3069 (OUTLIER) cc_final: 0.2727 (m-80) REVERT: B 1067 TYR cc_start: -0.0295 (OUTLIER) cc_final: -0.1782 (t80) REVERT: C 456 PHE cc_start: 0.3075 (m-80) cc_final: 0.2730 (m-80) REVERT: C 1049 LEU cc_start: 0.1995 (mt) cc_final: 0.1561 (mt) REVERT: E 43 LYS cc_start: 0.3021 (mmtt) cc_final: 0.2665 (ttpt) REVERT: E 78 MET cc_start: 0.0797 (tpp) cc_final: 0.0262 (mmm) REVERT: F 35 SER cc_start: 0.0963 (OUTLIER) cc_final: 0.0230 (m) REVERT: F 86 ASP cc_start: 0.2236 (m-30) cc_final: 0.1753 (t0) REVERT: H 78 MET cc_start: 0.0427 (ttp) cc_final: -0.0078 (mtp) REVERT: H 82 MET cc_start: -0.0014 (mpp) cc_final: -0.0719 (mmt) REVERT: K 34 MET cc_start: 0.2979 (ttm) cc_final: 0.2631 (ttp) REVERT: K 78 MET cc_start: 0.2308 (tpp) cc_final: 0.1930 (tpp) outliers start: 68 outliers final: 34 residues processed: 249 average time/residue: 0.1489 time to fit residues: 62.5621 Evaluate side-chains 188 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 150 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain B residue 28 TYR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1067 TYR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain F residue 28 ASN Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 105 ASP Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 77 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 87 optimal weight: 1.9990 chunk 163 optimal weight: 3.9990 chunk 336 optimal weight: 8.9990 chunk 264 optimal weight: 2.9990 chunk 157 optimal weight: 0.7980 chunk 255 optimal weight: 0.0030 chunk 160 optimal weight: 0.0270 chunk 72 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 111 optimal weight: 10.0000 overall best weight: 1.1652 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 955 ASN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN C 343 ASN ** C 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5112 r_free = 0.5112 target = 0.252104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4949 r_free = 0.4949 target = 0.235254 restraints weight = 72187.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4932 r_free = 0.4932 target = 0.234263 restraints weight = 69894.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4937 r_free = 0.4937 target = 0.234516 restraints weight = 61690.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4932 r_free = 0.4932 target = 0.234177 restraints weight = 48375.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4934 r_free = 0.4934 target = 0.234464 restraints weight = 47073.807| |-----------------------------------------------------------------------------| r_work (final): 0.4929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0902 moved from start: 0.4283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 29420 Z= 0.146 Angle : 0.591 10.857 40127 Z= 0.312 Chirality : 0.046 0.193 4615 Planarity : 0.004 0.070 5166 Dihedral : 6.009 70.402 4459 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.14 % Allowed : 13.21 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.13), residues: 3626 helix: 1.35 (0.20), residues: 647 sheet: 0.99 (0.18), residues: 822 loop : -1.44 (0.12), residues: 2157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 905 TYR 0.033 0.002 TYR B 508 PHE 0.025 0.002 PHE C 970 TRP 0.021 0.001 TRP C 886 HIS 0.005 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00309 (29359) covalent geometry : angle 0.58267 (39981) SS BOND : bond 0.00426 ( 37) SS BOND : angle 1.84517 ( 74) hydrogen bonds : bond 0.05094 ( 1076) hydrogen bonds : angle 5.67907 ( 2919) link_NAG-ASN : bond 0.00349 ( 24) link_NAG-ASN : angle 1.62631 ( 72) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 170 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 710 ASN cc_start: 0.2903 (m-40) cc_final: 0.2566 (m-40) REVERT: A 896 ILE cc_start: 0.0445 (OUTLIER) cc_final: -0.0627 (mt) REVERT: A 902 MET cc_start: 0.0643 (tpt) cc_final: -0.0182 (ptt) REVERT: A 1005 GLN cc_start: 0.1110 (OUTLIER) cc_final: 0.0694 (tt0) REVERT: B 153 MET cc_start: 0.0026 (ttt) cc_final: -0.2589 (mtm) REVERT: B 237 ARG cc_start: 0.2940 (tmt-80) cc_final: 0.2539 (tpt-90) REVERT: B 906 PHE cc_start: 0.2791 (OUTLIER) cc_final: 0.2584 (m-80) REVERT: C 456 PHE cc_start: 0.3324 (m-80) cc_final: 0.3104 (m-80) REVERT: C 1049 LEU cc_start: 0.1853 (OUTLIER) cc_final: 0.1108 (mt) REVERT: E 43 LYS cc_start: 0.3238 (mmtt) cc_final: 0.2928 (ttpt) REVERT: E 78 MET cc_start: 0.0877 (tpp) cc_final: 0.0298 (mmm) REVERT: F 35 SER cc_start: 0.0728 (OUTLIER) cc_final: -0.0066 (m) REVERT: F 86 ASP cc_start: 0.1813 (m-30) cc_final: 0.1547 (t0) REVERT: H 78 MET cc_start: 0.0836 (ttp) cc_final: 0.0215 (mtp) REVERT: H 82 MET cc_start: -0.0022 (mpp) cc_final: -0.0646 (mmt) REVERT: K 34 MET cc_start: 0.3364 (OUTLIER) cc_final: 0.3011 (ttp) REVERT: K 78 MET cc_start: 0.2405 (tpp) cc_final: 0.2011 (tpp) outliers start: 67 outliers final: 35 residues processed: 226 average time/residue: 0.1583 time to fit residues: 59.9433 Evaluate side-chains 190 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 149 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain B residue 28 TYR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1049 LEU Chi-restraints excluded: chain C residue 1062 PHE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain F residue 28 ASN Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain K residue 34 MET Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 105 ASP Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 77 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 123 optimal weight: 2.9990 chunk 295 optimal weight: 0.9990 chunk 248 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 chunk 336 optimal weight: 30.0000 chunk 74 optimal weight: 4.9990 chunk 151 optimal weight: 0.9990 chunk 189 optimal weight: 0.7980 chunk 327 optimal weight: 9.9990 chunk 236 optimal weight: 4.9990 chunk 164 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1048 HIS B 422 ASN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5116 r_free = 0.5116 target = 0.252471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.4937 r_free = 0.4937 target = 0.234141 restraints weight = 72746.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4917 r_free = 0.4917 target = 0.232855 restraints weight = 75202.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4926 r_free = 0.4926 target = 0.233763 restraints weight = 64322.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4926 r_free = 0.4926 target = 0.233865 restraints weight = 50246.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4927 r_free = 0.4927 target = 0.233957 restraints weight = 48439.710| |-----------------------------------------------------------------------------| r_work (final): 0.4925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0979 moved from start: 0.4723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 29420 Z= 0.126 Angle : 0.572 12.932 40127 Z= 0.301 Chirality : 0.045 0.199 4615 Planarity : 0.004 0.066 5166 Dihedral : 5.805 66.573 4459 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.36 % Allowed : 13.76 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.14), residues: 3626 helix: 1.43 (0.20), residues: 654 sheet: 0.94 (0.18), residues: 809 loop : -1.39 (0.12), residues: 2163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 355 TYR 0.033 0.001 TYR B 508 PHE 0.033 0.001 PHE C 392 TRP 0.019 0.001 TRP C 886 HIS 0.004 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00260 (29359) covalent geometry : angle 0.56494 (39981) SS BOND : bond 0.00530 ( 37) SS BOND : angle 1.65587 ( 74) hydrogen bonds : bond 0.04588 ( 1076) hydrogen bonds : angle 5.52829 ( 2919) link_NAG-ASN : bond 0.00385 ( 24) link_NAG-ASN : angle 1.53569 ( 72) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 163 time to evaluate : 0.829 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: A 421 TYR cc_start: 0.1952 (m-80) cc_final: 0.1647 (m-80) REVERT: A 422 ASN cc_start: -0.0395 (m110) cc_final: -0.0851 (m-40) REVERT: A 710 ASN cc_start: 0.3917 (m-40) cc_final: 0.3482 (m110) REVERT: A 896 ILE cc_start: 0.0246 (OUTLIER) cc_final: -0.0753 (mt) REVERT: A 1005 GLN cc_start: 0.1404 (OUTLIER) cc_final: 0.1174 (tt0) REVERT: B 153 MET cc_start: -0.0094 (ttt) cc_final: -0.2782 (mtm) REVERT: B 237 ARG cc_start: 0.3286 (tmt-80) cc_final: 0.2963 (tpt-90) REVERT: C 91 TYR cc_start: -0.1115 (m-80) cc_final: -0.1840 (m-10) REVERT: C 456 PHE cc_start: 0.3627 (m-80) cc_final: 0.3363 (m-80) REVERT: C 655 HIS cc_start: 0.1062 (t70) cc_final: -0.0285 (t-90) REVERT: C 670 ILE cc_start: 0.1621 (OUTLIER) cc_final: 0.1169 (tp) REVERT: C 964 LYS cc_start: 0.3381 (OUTLIER) cc_final: 0.2829 (tmtt) REVERT: C 1049 LEU cc_start: 0.2020 (OUTLIER) cc_final: 0.1530 (mt) REVERT: E 43 LYS cc_start: 0.3242 (mmtt) cc_final: 0.2918 (ttpt) REVERT: E 78 MET cc_start: 0.1043 (tpp) cc_final: 0.0430 (mmm) REVERT: F 35 SER cc_start: 0.0625 (OUTLIER) cc_final: 0.0156 (m) REVERT: F 86 ASP cc_start: 0.1871 (m-30) cc_final: 0.1590 (t0) REVERT: H 78 MET cc_start: 0.0688 (ttp) cc_final: 0.0168 (mtp) REVERT: H 82 MET cc_start: -0.0009 (mpp) cc_final: -0.0658 (mmt) REVERT: K 34 MET cc_start: 0.3376 (OUTLIER) cc_final: 0.3024 (ttp) REVERT: K 78 MET cc_start: 0.2419 (tpp) cc_final: 0.2052 (tpp) outliers start: 74 outliers final: 41 residues processed: 225 average time/residue: 0.1516 time to fit residues: 58.0316 Evaluate side-chains 201 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 153 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain B residue 28 TYR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 1067 TYR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 474 GLN Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1049 LEU Chi-restraints excluded: chain C residue 1062 PHE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain F residue 28 ASN Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain K residue 34 MET Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 105 ASP Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 77 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 198 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 211 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 chunk 237 optimal weight: 40.0000 chunk 241 optimal weight: 0.9980 chunk 362 optimal weight: 8.9990 chunk 285 optimal weight: 5.9990 chunk 31 optimal weight: 9.9990 chunk 199 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 360 ASN A 532 ASN A 755 GLN ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 755 GLN C 955 ASN C1010 GLN C1058 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5133 r_free = 0.5133 target = 0.254347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.5041 r_free = 0.5041 target = 0.245444 restraints weight = 78877.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 78)----------------| | r_work = 0.5026 r_free = 0.5026 target = 0.244431 restraints weight = 97575.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.5021 r_free = 0.5021 target = 0.243913 restraints weight = 91550.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.5018 r_free = 0.5018 target = 0.243615 restraints weight = 88379.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.5021 r_free = 0.5021 target = 0.243957 restraints weight = 77517.955| |-----------------------------------------------------------------------------| r_work (final): 0.5025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1558 moved from start: 0.6275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.118 29420 Z= 0.245 Angle : 0.861 13.001 40127 Z= 0.453 Chirality : 0.055 0.391 4615 Planarity : 0.006 0.116 5166 Dihedral : 6.944 61.607 4459 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.34 % Favored : 93.57 % Rotamer: Outliers : 3.32 % Allowed : 14.59 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.37 (0.13), residues: 3626 helix: -0.56 (0.18), residues: 661 sheet: 0.50 (0.18), residues: 848 loop : -1.71 (0.12), residues: 2117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG A 905 TYR 0.035 0.002 TYR C 917 PHE 0.050 0.003 PHE C 718 TRP 0.029 0.002 TRP B 886 HIS 0.018 0.002 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00528 (29359) covalent geometry : angle 0.84437 (39981) SS BOND : bond 0.00790 ( 37) SS BOND : angle 2.69631 ( 74) hydrogen bonds : bond 0.06231 ( 1076) hydrogen bonds : angle 6.63708 ( 2919) link_NAG-ASN : bond 0.01152 ( 24) link_NAG-ASN : angle 3.12965 ( 72) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 186 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 421 TYR cc_start: 0.2149 (m-80) cc_final: 0.1853 (m-80) REVERT: A 719 THR cc_start: 0.6612 (p) cc_final: 0.6160 (m) REVERT: A 896 ILE cc_start: 0.0636 (OUTLIER) cc_final: -0.0856 (mt) REVERT: A 900 MET cc_start: 0.0802 (mtp) cc_final: -0.0059 (mtp) REVERT: A 1005 GLN cc_start: 0.1426 (OUTLIER) cc_final: 0.1222 (tt0) REVERT: B 28 TYR cc_start: 0.0769 (OUTLIER) cc_final: 0.0296 (p90) REVERT: B 727 LEU cc_start: 0.3756 (mt) cc_final: 0.2730 (mt) REVERT: B 731 MET cc_start: 0.2799 (mmp) cc_final: 0.1291 (mmt) REVERT: B 1067 TYR cc_start: -0.0332 (OUTLIER) cc_final: -0.1152 (t80) REVERT: B 1123 SER cc_start: 0.2499 (OUTLIER) cc_final: 0.2145 (t) REVERT: C 91 TYR cc_start: -0.0565 (m-80) cc_final: -0.2465 (m-80) REVERT: C 129 LYS cc_start: 0.1554 (ptpt) cc_final: 0.1260 (mmmt) REVERT: C 392 PHE cc_start: 0.0640 (OUTLIER) cc_final: 0.0322 (m-80) REVERT: C 655 HIS cc_start: 0.1758 (t70) cc_final: -0.0373 (t-90) REVERT: C 1049 LEU cc_start: 0.2257 (OUTLIER) cc_final: 0.1924 (mt) REVERT: C 1050 MET cc_start: 0.1349 (ptm) cc_final: 0.0981 (ptm) REVERT: E 43 LYS cc_start: 0.3699 (mmtt) cc_final: 0.3185 (ttpt) REVERT: E 78 MET cc_start: 0.1181 (tpp) cc_final: 0.0612 (mmm) REVERT: F 35 SER cc_start: 0.0912 (OUTLIER) cc_final: 0.0463 (m) REVERT: H 78 MET cc_start: 0.0961 (ttp) cc_final: 0.0282 (mtp) REVERT: H 82 MET cc_start: -0.0395 (mpp) cc_final: -0.0674 (mmm) REVERT: K 34 MET cc_start: 0.4061 (ttm) cc_final: 0.3843 (ttp) REVERT: K 78 MET cc_start: 0.2243 (tpp) cc_final: 0.2013 (tpp) outliers start: 104 outliers final: 61 residues processed: 273 average time/residue: 0.1544 time to fit residues: 71.3504 Evaluate side-chains 226 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 157 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 474 GLN Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 741 TYR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1064 HIS Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain B residue 28 TYR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 1067 TYR Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 474 GLN Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 782 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1048 HIS Chi-restraints excluded: chain C residue 1049 LEU Chi-restraints excluded: chain C residue 1062 PHE Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain F residue 28 ASN Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain K residue 105 ASP Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 77 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 241 optimal weight: 3.9990 chunk 271 optimal weight: 3.9990 chunk 160 optimal weight: 0.0270 chunk 182 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 199 optimal weight: 0.2980 chunk 100 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 chunk 249 optimal weight: 0.7980 overall best weight: 0.9840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 920 GLN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 ASN C 493 GLN C 755 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5140 r_free = 0.5140 target = 0.254946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.5068 r_free = 0.5068 target = 0.247978 restraints weight = 78507.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.5063 r_free = 0.5063 target = 0.247541 restraints weight = 94145.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.5064 r_free = 0.5064 target = 0.247735 restraints weight = 98225.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.5061 r_free = 0.5061 target = 0.247449 restraints weight = 81785.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.5062 r_free = 0.5062 target = 0.247573 restraints weight = 76562.592| |-----------------------------------------------------------------------------| r_work (final): 0.5052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1301 moved from start: 0.6430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 29420 Z= 0.137 Angle : 0.643 16.351 40127 Z= 0.339 Chirality : 0.048 0.707 4615 Planarity : 0.005 0.073 5166 Dihedral : 6.153 59.195 4458 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.99 % Favored : 94.98 % Rotamer: Outliers : 2.33 % Allowed : 16.05 % Favored : 81.62 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.13), residues: 3626 helix: 0.49 (0.20), residues: 645 sheet: 0.46 (0.18), residues: 859 loop : -1.54 (0.13), residues: 2122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 66 TYR 0.026 0.001 TYR B1067 PHE 0.026 0.002 PHE A 906 TRP 0.024 0.001 TRP C1102 HIS 0.004 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00287 (29359) covalent geometry : angle 0.62581 (39981) SS BOND : bond 0.00451 ( 37) SS BOND : angle 2.42486 ( 74) hydrogen bonds : bond 0.04468 ( 1076) hydrogen bonds : angle 5.80550 ( 2919) link_NAG-ASN : bond 0.01183 ( 24) link_NAG-ASN : angle 2.62428 ( 72) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 162 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 PHE cc_start: 0.2748 (OUTLIER) cc_final: 0.1585 (m-80) REVERT: A 421 TYR cc_start: 0.1982 (m-80) cc_final: 0.1705 (m-80) REVERT: A 719 THR cc_start: 0.6237 (p) cc_final: 0.5852 (m) REVERT: A 756 TYR cc_start: -0.0979 (OUTLIER) cc_final: -0.1360 (m-10) REVERT: A 873 TYR cc_start: 0.5610 (m-80) cc_final: 0.5247 (m-80) REVERT: B 456 PHE cc_start: 0.2449 (m-80) cc_final: 0.2102 (m-80) REVERT: B 727 LEU cc_start: 0.4312 (mt) cc_final: 0.3997 (mt) REVERT: B 906 PHE cc_start: 0.2558 (OUTLIER) cc_final: 0.0991 (m-80) REVERT: B 1049 LEU cc_start: 0.2286 (mt) cc_final: 0.1556 (mt) REVERT: B 1123 SER cc_start: 0.2464 (OUTLIER) cc_final: 0.2201 (t) REVERT: C 91 TYR cc_start: -0.0870 (m-80) cc_final: -0.2689 (m-80) REVERT: C 129 LYS cc_start: 0.1466 (ptpt) cc_final: 0.1078 (mmmt) REVERT: C 392 PHE cc_start: 0.0739 (OUTLIER) cc_final: 0.0529 (m-80) REVERT: C 493 GLN cc_start: 0.1391 (OUTLIER) cc_final: 0.0643 (pp30) REVERT: C 655 HIS cc_start: 0.1870 (t70) cc_final: -0.0459 (t-90) REVERT: C 670 ILE cc_start: 0.2169 (OUTLIER) cc_final: 0.1727 (tp) REVERT: C 1049 LEU cc_start: 0.2137 (OUTLIER) cc_final: 0.1908 (mt) REVERT: E 43 LYS cc_start: 0.3592 (mmtt) cc_final: 0.3101 (ttpt) REVERT: E 78 MET cc_start: 0.1315 (tpp) cc_final: 0.0565 (mmm) REVERT: E 105 ASP cc_start: 0.1628 (OUTLIER) cc_final: 0.1313 (t0) REVERT: F 35 SER cc_start: 0.0688 (OUTLIER) cc_final: 0.0163 (m) REVERT: H 78 MET cc_start: 0.0943 (ttp) cc_final: 0.0268 (mtp) REVERT: H 82 MET cc_start: -0.0204 (mpp) cc_final: -0.0485 (mmm) REVERT: K 34 MET cc_start: 0.3974 (OUTLIER) cc_final: 0.3774 (ttp) outliers start: 73 outliers final: 48 residues processed: 223 average time/residue: 0.1605 time to fit residues: 60.5015 Evaluate side-chains 215 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 156 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 474 GLN Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 741 TYR Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1064 HIS Chi-restraints excluded: chain A residue 1075 PHE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 474 GLN Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 782 PHE Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1049 LEU Chi-restraints excluded: chain C residue 1062 PHE Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain F residue 28 ASN Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain K residue 34 MET Chi-restraints excluded: chain K residue 105 ASP Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 77 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 156 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 326 optimal weight: 20.0000 chunk 89 optimal weight: 0.6980 chunk 131 optimal weight: 9.9990 chunk 82 optimal weight: 3.9990 chunk 33 optimal weight: 40.0000 chunk 232 optimal weight: 6.9990 chunk 363 optimal weight: 20.0000 chunk 281 optimal weight: 0.3980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 784 GLN ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 493 GLN ** C 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN ** C 755 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 = 0.5138 r_free = 0.5138 target = 0.254724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.5073 r_free = 0.5073 target = 0.248372 restraints weight = 78751.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.5062 r_free = 0.5062 target = 0.247509 restraints weight = 95773.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.5053 r_free = 0.5053 target = 0.246811 restraints weight = 103171.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.5051 r_free = 0.5051 target = 0.246631 restraints weight = 106539.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.5053 r_free = 0.5053 target = 0.246837 restraints weight = 96166.805| |-----------------------------------------------------------------------------| r_work (final): 0.5043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1448 moved from start: 0.6818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 29420 Z= 0.165 Angle : 0.664 16.569 40127 Z= 0.347 Chirality : 0.048 0.644 4615 Planarity : 0.005 0.063 5166 Dihedral : 6.412 72.991 4458 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.68 % Favored : 94.24 % Rotamer: Outliers : 2.55 % Allowed : 16.34 % Favored : 81.10 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.13), residues: 3626 helix: 0.33 (0.19), residues: 662 sheet: 0.46 (0.18), residues: 863 loop : -1.62 (0.13), residues: 2101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 905 TYR 0.028 0.002 TYR B1067 PHE 0.034 0.002 PHE B1052 TRP 0.016 0.001 TRP A 886 HIS 0.007 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00351 (29359) covalent geometry : angle 0.64766 (39981) SS BOND : bond 0.00425 ( 37) SS BOND : angle 2.06956 ( 74) hydrogen bonds : bond 0.04689 ( 1076) hydrogen bonds : angle 5.89988 ( 2919) link_NAG-ASN : bond 0.00423 ( 24) link_NAG-ASN : angle 2.95869 ( 72) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 170 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 719 THR cc_start: 0.6425 (p) cc_final: 0.6131 (m) REVERT: A 756 TYR cc_start: -0.0828 (OUTLIER) cc_final: -0.1202 (m-10) REVERT: A 784 GLN cc_start: 0.2388 (OUTLIER) cc_final: 0.2085 (mm-40) REVERT: A 873 TYR cc_start: 0.5987 (m-80) cc_final: 0.5761 (m-10) REVERT: A 896 ILE cc_start: 0.0583 (OUTLIER) cc_final: -0.0515 (mt) REVERT: B 28 TYR cc_start: 0.1010 (OUTLIER) cc_final: 0.0461 (p90) REVERT: B 328 ARG cc_start: -0.2187 (mtt180) cc_final: -0.2706 (mtp180) REVERT: B 456 PHE cc_start: 0.2489 (m-80) cc_final: 0.2131 (m-80) REVERT: B 770 ILE cc_start: 0.0917 (OUTLIER) cc_final: 0.0627 (mt) REVERT: B 906 PHE cc_start: 0.2677 (OUTLIER) cc_final: 0.1549 (m-80) REVERT: B 1067 TYR cc_start: -0.0569 (OUTLIER) cc_final: -0.1230 (t80) REVERT: B 1123 SER cc_start: 0.3216 (OUTLIER) cc_final: 0.2707 (t) REVERT: C 91 TYR cc_start: -0.0762 (m-80) cc_final: -0.2632 (m-80) REVERT: C 129 LYS cc_start: 0.1395 (ptpt) cc_final: 0.0905 (mmmt) REVERT: C 460 ASN cc_start: 0.4247 (m-40) cc_final: 0.3924 (p0) REVERT: C 493 GLN cc_start: 0.1109 (OUTLIER) cc_final: 0.0539 (pt0) REVERT: C 655 HIS cc_start: 0.2084 (t70) cc_final: -0.0251 (t-90) REVERT: C 818 ILE cc_start: 0.4655 (OUTLIER) cc_final: 0.4357 (mm) REVERT: C 1049 LEU cc_start: 0.2406 (OUTLIER) cc_final: 0.2172 (mt) REVERT: C 1050 MET cc_start: 0.1175 (ptm) cc_final: 0.0563 (ptm) REVERT: E 78 MET cc_start: 0.1228 (tpp) cc_final: 0.0527 (mmm) REVERT: E 105 ASP cc_start: 0.1507 (OUTLIER) cc_final: 0.1200 (t0) REVERT: F 35 SER cc_start: 0.0801 (OUTLIER) cc_final: 0.0216 (m) REVERT: H 78 MET cc_start: 0.0662 (ttp) cc_final: 0.0150 (mtp) REVERT: H 82 MET cc_start: -0.0350 (mpp) cc_final: -0.0574 (mmm) REVERT: K 34 MET cc_start: 0.3975 (OUTLIER) cc_final: 0.3764 (ttp) outliers start: 80 outliers final: 50 residues processed: 239 average time/residue: 0.1511 time to fit residues: 61.0665 Evaluate side-chains 226 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 162 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 474 GLN Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1048 HIS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 28 TYR Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 1067 TYR Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 474 GLN Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 782 PHE Chi-restraints excluded: chain C residue 818 ILE Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1049 LEU Chi-restraints excluded: chain C residue 1062 PHE Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain F residue 28 ASN Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain K residue 34 MET Chi-restraints excluded: chain K residue 105 ASP Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 77 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 62 optimal weight: 6.9990 chunk 133 optimal weight: 20.0000 chunk 91 optimal weight: 0.4980 chunk 90 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 189 optimal weight: 0.0670 chunk 214 optimal weight: 7.9990 chunk 149 optimal weight: 0.5980 chunk 342 optimal weight: 10.0000 chunk 28 optimal weight: 0.5980 chunk 246 optimal weight: 10.0000 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 784 GLN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN B 196 ASN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 755 GLN C 901 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5145 r_free = 0.5145 target = 0.255386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.5079 r_free = 0.5079 target = 0.248941 restraints weight = 78964.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.5071 r_free = 0.5071 target = 0.248203 restraints weight = 89451.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.5072 r_free = 0.5072 target = 0.248392 restraints weight = 85767.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.5070 r_free = 0.5070 target = 0.248161 restraints weight = 71188.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.5071 r_free = 0.5071 target = 0.248239 restraints weight = 70041.464| |-----------------------------------------------------------------------------| r_work (final): 0.5074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1344 moved from start: 0.6850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 29420 Z= 0.117 Angle : 0.596 15.177 40127 Z= 0.307 Chirality : 0.047 0.850 4615 Planarity : 0.004 0.053 5166 Dihedral : 6.044 73.249 4458 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.88 % Favored : 95.04 % Rotamer: Outliers : 1.82 % Allowed : 16.98 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.14), residues: 3626 helix: 1.02 (0.20), residues: 648 sheet: 0.58 (0.18), residues: 848 loop : -1.53 (0.13), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 355 TYR 0.025 0.001 TYR B1067 PHE 0.029 0.001 PHE A 906 TRP 0.018 0.001 TRP A 886 HIS 0.004 0.001 HIS C1101 Details of bonding type rmsd covalent geometry : bond 0.00248 (29359) covalent geometry : angle 0.57770 (39981) SS BOND : bond 0.00314 ( 37) SS BOND : angle 1.98243 ( 74) hydrogen bonds : bond 0.03957 ( 1076) hydrogen bonds : angle 5.51425 ( 2919) link_NAG-ASN : bond 0.00373 ( 24) link_NAG-ASN : angle 2.89605 ( 72) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 168 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 GLN cc_start: 0.1827 (pt0) cc_final: 0.1566 (pt0) REVERT: A 719 THR cc_start: 0.5701 (p) cc_final: 0.5369 (m) REVERT: A 756 TYR cc_start: -0.0791 (OUTLIER) cc_final: -0.1151 (m-10) REVERT: A 873 TYR cc_start: 0.5484 (m-80) cc_final: 0.5246 (m-80) REVERT: A 1034 LEU cc_start: 0.0355 (OUTLIER) cc_final: 0.0116 (mm) REVERT: B 456 PHE cc_start: 0.1777 (m-80) cc_final: 0.1543 (m-80) REVERT: B 770 ILE cc_start: 0.1500 (OUTLIER) cc_final: 0.0844 (mt) REVERT: B 1049 LEU cc_start: 0.2507 (mt) cc_final: 0.2186 (tp) REVERT: B 1123 SER cc_start: 0.2122 (OUTLIER) cc_final: 0.1823 (t) REVERT: C 91 TYR cc_start: -0.0677 (m-80) cc_final: -0.2520 (m-80) REVERT: C 129 LYS cc_start: 0.1711 (ptpt) cc_final: 0.1301 (mmmt) REVERT: C 655 HIS cc_start: 0.1357 (t70) cc_final: -0.0849 (t-90) REVERT: C 818 ILE cc_start: 0.4652 (OUTLIER) cc_final: 0.4413 (mm) REVERT: E 43 LYS cc_start: 0.3708 (mmtt) cc_final: 0.3294 (ttpt) REVERT: E 78 MET cc_start: 0.1543 (tpp) cc_final: 0.0829 (mmm) REVERT: E 105 ASP cc_start: 0.1009 (OUTLIER) cc_final: 0.0806 (t0) REVERT: F 35 SER cc_start: 0.0836 (OUTLIER) cc_final: 0.0286 (m) REVERT: H 78 MET cc_start: 0.1255 (ttp) cc_final: 0.0708 (mtp) REVERT: H 82 MET cc_start: -0.0357 (mpp) cc_final: -0.0648 (mmt) outliers start: 57 outliers final: 43 residues processed: 218 average time/residue: 0.1517 time to fit residues: 55.8191 Evaluate side-chains 206 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 156 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 474 GLN Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1048 HIS Chi-restraints excluded: chain A residue 1075 PHE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 474 GLN Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 782 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 818 ILE Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1062 PHE Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain F residue 28 ASN Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain K residue 105 ASP Chi-restraints excluded: chain L residue 77 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 202 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 351 optimal weight: 20.0000 chunk 77 optimal weight: 0.7980 chunk 321 optimal weight: 5.9990 chunk 163 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 170 optimal weight: 0.0980 chunk 232 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 198 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN B 564 GLN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 32 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5145 r_free = 0.5145 target = 0.255240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.5077 r_free = 0.5077 target = 0.248529 restraints weight = 78549.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.5071 r_free = 0.5071 target = 0.248224 restraints weight = 97316.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.5063 r_free = 0.5063 target = 0.247527 restraints weight = 89947.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.5059 r_free = 0.5059 target = 0.247243 restraints weight = 102998.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.5061 r_free = 0.5061 target = 0.247363 restraints weight = 86262.694| |-----------------------------------------------------------------------------| r_work (final): 0.5065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1481 moved from start: 0.7172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29420 Z= 0.139 Angle : 0.619 13.481 40127 Z= 0.320 Chirality : 0.047 0.788 4615 Planarity : 0.004 0.054 5166 Dihedral : 6.095 69.492 4458 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.90 % Favored : 94.02 % Rotamer: Outliers : 1.76 % Allowed : 16.95 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.14), residues: 3626 helix: 0.80 (0.20), residues: 653 sheet: 0.54 (0.18), residues: 817 loop : -1.52 (0.13), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 905 TYR 0.027 0.001 TYR B1067 PHE 0.035 0.002 PHE B 86 TRP 0.014 0.001 TRP A 886 HIS 0.023 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00299 (29359) covalent geometry : angle 0.60604 (39981) SS BOND : bond 0.00333 ( 37) SS BOND : angle 1.68136 ( 74) hydrogen bonds : bond 0.04125 ( 1076) hydrogen bonds : angle 5.61334 ( 2919) link_NAG-ASN : bond 0.00358 ( 24) link_NAG-ASN : angle 2.62369 ( 72) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 170 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 PHE cc_start: 0.2983 (OUTLIER) cc_final: 0.1774 (m-80) REVERT: A 756 TYR cc_start: -0.0802 (OUTLIER) cc_final: -0.1154 (m-10) REVERT: A 1034 LEU cc_start: 0.0581 (OUTLIER) cc_final: 0.0114 (mt) REVERT: B 456 PHE cc_start: 0.2025 (m-80) cc_final: 0.1718 (m-80) REVERT: B 770 ILE cc_start: 0.1627 (OUTLIER) cc_final: 0.1033 (mt) REVERT: B 1049 LEU cc_start: 0.3006 (mt) cc_final: 0.2581 (tp) REVERT: B 1123 SER cc_start: 0.2879 (OUTLIER) cc_final: 0.2414 (t) REVERT: C 91 TYR cc_start: -0.0663 (m-80) cc_final: -0.2497 (m-80) REVERT: C 129 LYS cc_start: 0.1583 (ptpt) cc_final: 0.1364 (mmmt) REVERT: C 655 HIS cc_start: 0.1659 (t70) cc_final: -0.0558 (t-90) REVERT: C 1050 MET cc_start: 0.1569 (ptm) cc_final: 0.1254 (ptm) REVERT: E 78 MET cc_start: 0.1564 (tpp) cc_final: 0.1342 (mmm) REVERT: F 35 SER cc_start: 0.0958 (OUTLIER) cc_final: 0.0382 (m) REVERT: H 78 MET cc_start: 0.0986 (ttp) cc_final: 0.0519 (mtp) REVERT: H 82 MET cc_start: -0.0216 (mpp) cc_final: -0.0522 (mmm) outliers start: 55 outliers final: 44 residues processed: 221 average time/residue: 0.1511 time to fit residues: 57.2862 Evaluate side-chains 211 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 161 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 474 GLN Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1048 HIS Chi-restraints excluded: chain A residue 1075 PHE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 474 GLN Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 782 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1062 PHE Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain F residue 28 ASN Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain K residue 105 ASP Chi-restraints excluded: chain L residue 77 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 16 optimal weight: 7.9990 chunk 246 optimal weight: 9.9990 chunk 343 optimal weight: 20.0000 chunk 184 optimal weight: 0.8980 chunk 239 optimal weight: 30.0000 chunk 321 optimal weight: 0.6980 chunk 356 optimal weight: 7.9990 chunk 117 optimal weight: 0.9990 chunk 91 optimal weight: 0.1980 chunk 126 optimal weight: 6.9990 chunk 218 optimal weight: 20.0000 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A 907 ASN ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5143 r_free = 0.5143 target = 0.255047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.5075 r_free = 0.5075 target = 0.248346 restraints weight = 80005.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.5072 r_free = 0.5072 target = 0.248253 restraints weight = 97082.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.5066 r_free = 0.5066 target = 0.247756 restraints weight = 87122.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.5064 r_free = 0.5064 target = 0.247495 restraints weight = 87501.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.5065 r_free = 0.5065 target = 0.247633 restraints weight = 75354.486| |-----------------------------------------------------------------------------| r_work (final): 0.5069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1728 moved from start: 0.7995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 29420 Z= 0.199 Angle : 0.745 18.548 40127 Z= 0.387 Chirality : 0.052 1.049 4615 Planarity : 0.005 0.082 5166 Dihedral : 6.687 59.346 4458 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.20 % Favored : 92.72 % Rotamer: Outliers : 1.92 % Allowed : 17.08 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.28 (0.13), residues: 3626 helix: -0.03 (0.19), residues: 663 sheet: 0.30 (0.18), residues: 850 loop : -1.68 (0.13), residues: 2113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 815 TYR 0.040 0.002 TYR C1067 PHE 0.049 0.003 PHE C 377 TRP 0.021 0.002 TRP C1102 HIS 0.011 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00424 (29359) covalent geometry : angle 0.73167 (39981) SS BOND : bond 0.00487 ( 37) SS BOND : angle 1.75047 ( 74) hydrogen bonds : bond 0.04957 ( 1076) hydrogen bonds : angle 6.20714 ( 2919) link_NAG-ASN : bond 0.00436 ( 24) link_NAG-ASN : angle 3.05055 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4113.27 seconds wall clock time: 72 minutes 3.70 seconds (4323.70 seconds total)