Starting phenix.real_space_refine on Tue Jun 24 19:59:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xmx_33307/06_2025/7xmx_33307_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xmx_33307/06_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_33307/06_2025/7xmx_33307.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xmx_33307/06_2025/7xmx_33307.map" model { file = "/net/cci-nas-00/data/ceres_data/7xmx_33307/06_2025/7xmx_33307_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xmx_33307/06_2025/7xmx_33307_neut.cif" } resolution = 3.62 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 1.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 5} 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: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 3} 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: {'GLN:plan1': 2, 'TYR:plan': 1, 'TRP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 5} 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: {'PHE:plan': 1, 'ASN:plan1': 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: {'PHE:plan': 1, 'ASN:plan1': 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: {'PHE:plan': 1, 'ASN:plan1': 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: 18.44, per 1000 atoms: 0.64 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: 6.69 Conformation dependent library (CDL) restraints added in 3.6 seconds 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: 4.25 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: 13.79 Time building geometry restraints manager: 7.99 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 1147 or resid 1301 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 1147 or resid 1301 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 1147 or resid 1301 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: 3.920 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: 1.310 Check model and map are aligned: 0.220 Set scattering table: 0.280 Process input model: 67.370 Find NCS groups from input model: 1.640 Set up NCS constraints: 0.140 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:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.030 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.019 0.002 TRP F 99 HIS 0.006 0.001 HIS A1064 PHE 0.031 0.002 PHE C 970 TYR 0.041 0.002 TYR B 160 ARG 0.012 0.001 ARG B 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00689 ( 24) link_NAG-ASN : angle 2.04038 ( 72) hydrogen bonds : bond 0.24410 ( 1076) hydrogen bonds : angle 8.97770 ( 2919) SS BOND : bond 0.04790 ( 37) SS BOND : angle 4.43794 ( 74) covalent geometry : bond 0.01155 (29359) covalent geometry : angle 1.29707 (39981) *********************** 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 : 2.641 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: 0.2288 (m-80) cc_final: -0.1279 (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: 0.1336 (tp) REVERT: A 788 ILE cc_start: 0.1992 (mm) cc_final: -0.0746 (tt) REVERT: A 902 MET cc_start: -0.0488 (tpt) cc_final: -0.0721 (ptt) REVERT: A 1098 ASN cc_start: 0.2561 (p0) cc_final: 0.0149 (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: 0.6102 (mm) REVERT: C 469 SER cc_start: 0.1543 (OUTLIER) cc_final: 0.0470 (t) REVERT: F 66 SER cc_start: 0.2828 (p) cc_final: 0.2512 (t) REVERT: H 78 MET cc_start: 0.0117 (ttp) cc_final: -0.0709 (ptm) REVERT: H 82 MET cc_start: 0.0146 (OUTLIER) cc_final: -0.0362 (mtp) REVERT: K 81 GLN cc_start: 0.2430 (OUTLIER) cc_final: 0.1057 (mt0) outliers start: 42 outliers final: 9 residues processed: 318 average time/residue: 0.4280 time to fit residues: 218.7325 Evaluate side-chains 181 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 169 time to evaluate : 2.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 309 optimal weight: 0.9990 chunk 278 optimal weight: 1.9990 chunk 154 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 187 optimal weight: 0.6980 chunk 148 optimal weight: 3.9990 chunk 287 optimal weight: 0.8980 chunk 111 optimal weight: 7.9990 chunk 174 optimal weight: 0.7980 chunk 214 optimal weight: 0.9980 chunk 333 optimal weight: 20.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 A 992 GLN B 122 ASN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN B 613 GLN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS C 207 HIS C 343 ASN C 437 ASN C 487 ASN C 613 GLN H 73 ASN I 1 GLN K 81 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5098 r_free = 0.5098 target = 0.250886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4905 r_free = 0.4905 target = 0.231254 restraints weight = 70648.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4883 r_free = 0.4883 target = 0.229703 restraints weight = 89752.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4891 r_free = 0.4891 target = 0.230390 restraints weight = 78189.021| |-----------------------------------------------------------------------------| r_work (final): 0.4882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0354 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 29420 Z= 0.172 Angle : 0.645 10.908 40127 Z= 0.345 Chirality : 0.047 0.262 4615 Planarity : 0.005 0.068 5166 Dihedral : 7.077 88.565 4478 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.66 % Allowed : 9.16 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.13), residues: 3626 helix: 2.04 (0.20), residues: 626 sheet: 0.75 (0.18), residues: 834 loop : -1.57 (0.12), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 104 HIS 0.012 0.001 HIS A1064 PHE 0.021 0.002 PHE A 400 TYR 0.022 0.002 TYR C1067 ARG 0.011 0.001 ARG E 71 Details of bonding type rmsd link_NAG-ASN : bond 0.01163 ( 24) link_NAG-ASN : angle 2.33646 ( 72) hydrogen bonds : bond 0.07800 ( 1076) hydrogen bonds : angle 6.47515 ( 2919) SS BOND : bond 0.00782 ( 37) SS BOND : angle 1.51285 ( 74) covalent geometry : bond 0.00334 (29359) covalent geometry : angle 0.63487 (39981) *********************** 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 241 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 189 time to evaluate : 2.786 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: symmetry clash REVERT: A 269 TYR cc_start: 0.2848 (m-80) cc_final: -0.0629 (p90) REVERT: A 816 SER cc_start: -0.0303 (OUTLIER) cc_final: -0.0854 (p) REVERT: A 902 MET cc_start: 0.0197 (tpt) cc_final: -0.0660 (ptt) REVERT: B 153 MET cc_start: -0.0450 (ttp) cc_final: -0.1987 (mtm) REVERT: B 197 ILE cc_start: 0.1994 (mm) cc_final: 0.1428 (tt) REVERT: B 902 MET cc_start: 0.1805 (ptm) cc_final: 0.1423 (ptm) REVERT: C 343 ASN cc_start: 0.0324 (OUTLIER) cc_final: -0.1307 (m-40) REVERT: E 78 MET cc_start: 0.0989 (tpp) cc_final: 0.0584 (mmm) REVERT: H 78 MET cc_start: 0.0869 (ttp) cc_final: 0.0531 (ttp) REVERT: H 82 MET cc_start: 0.0260 (mpp) cc_final: -0.0617 (mmm) REVERT: K 78 MET cc_start: 0.2503 (OUTLIER) cc_final: 0.1649 (tpp) REVERT: K 81 GLN cc_start: 0.2355 (OUTLIER) cc_final: 0.2059 (mt0) outliers start: 52 outliers final: 21 residues processed: 233 average time/residue: 0.3624 time to fit residues: 141.3256 Evaluate side-chains 172 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 147 time to evaluate : 2.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 577 ARG 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 199 optimal weight: 0.0980 chunk 208 optimal weight: 10.0000 chunk 340 optimal weight: 20.0000 chunk 144 optimal weight: 4.9990 chunk 156 optimal weight: 0.8980 chunk 301 optimal weight: 10.0000 chunk 233 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 181 optimal weight: 1.9990 chunk 332 optimal weight: 20.0000 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B 755 GLN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1054 GLN ** C 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1064 HIS F 1 GLN F 80 GLN ** I 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5112 r_free = 0.5112 target = 0.252197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4957 r_free = 0.4957 target = 0.236272 restraints weight = 72954.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4934 r_free = 0.4934 target = 0.234772 restraints weight = 75939.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.4914 r_free = 0.4914 target = 0.232896 restraints weight = 67081.534| |-----------------------------------------------------------------------------| r_work (final): 0.4908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1106 moved from start: 0.4215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 29420 Z= 0.243 Angle : 0.807 16.223 40127 Z= 0.433 Chirality : 0.053 0.238 4615 Planarity : 0.006 0.117 5166 Dihedral : 7.132 76.047 4466 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.85 % Favored : 94.13 % Rotamer: Outliers : 2.74 % Allowed : 11.91 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.13), residues: 3626 helix: 0.43 (0.20), residues: 636 sheet: 0.68 (0.18), residues: 876 loop : -1.57 (0.12), residues: 2114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 886 HIS 0.018 0.002 HIS A1048 PHE 0.058 0.003 PHE B 318 TYR 0.039 0.003 TYR C 917 ARG 0.051 0.001 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00565 ( 24) link_NAG-ASN : angle 2.53256 ( 72) hydrogen bonds : bond 0.07047 ( 1076) hydrogen bonds : angle 6.55267 ( 2919) SS BOND : bond 0.00697 ( 37) SS BOND : angle 2.09751 ( 74) covalent geometry : bond 0.00511 (29359) covalent geometry : angle 0.79643 (39981) *********************** 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 288 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 202 time to evaluate : 3.941 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 538 CYS cc_start: 0.3923 (OUTLIER) cc_final: 0.3149 (t) REVERT: A 710 ASN cc_start: 0.3605 (m-40) cc_final: 0.3230 (m-40) REVERT: A 896 ILE cc_start: 0.0429 (OUTLIER) cc_final: -0.0597 (mt) REVERT: A 902 MET cc_start: 0.1470 (tpt) cc_final: -0.0166 (ptt) REVERT: A 1005 GLN cc_start: 0.0831 (OUTLIER) cc_final: 0.0321 (tt0) REVERT: A 1050 MET cc_start: 0.3563 (pmm) cc_final: 0.3266 (pmm) REVERT: A 1066 THR cc_start: 0.4958 (p) cc_final: 0.4729 (p) REVERT: B 237 ARG cc_start: 0.3064 (tmt-80) cc_final: 0.2553 (tpt-90) REVERT: B 906 PHE cc_start: 0.3080 (OUTLIER) cc_final: 0.2393 (m-80) REVERT: B 1067 TYR cc_start: 0.0308 (OUTLIER) cc_final: -0.1515 (t80) REVERT: C 456 PHE cc_start: 0.3151 (m-80) cc_final: 0.2803 (m-80) REVERT: C 517 LEU cc_start: -0.0101 (OUTLIER) cc_final: -0.0769 (mt) REVERT: C 797 PHE cc_start: 0.1790 (m-80) cc_final: 0.1386 (m-10) REVERT: C 964 LYS cc_start: 0.4159 (tmtt) cc_final: 0.3535 (tmmt) REVERT: E 43 LYS cc_start: 0.3182 (mmtt) cc_final: 0.2826 (ttpt) REVERT: E 105 ASP cc_start: -0.0189 (OUTLIER) cc_final: -0.0609 (m-30) REVERT: F 35 SER cc_start: 0.0838 (OUTLIER) cc_final: 0.0137 (m) REVERT: F 86 ASP cc_start: 0.2297 (m-30) cc_final: 0.1772 (t0) REVERT: H 32 ASN cc_start: 0.3445 (m-40) cc_final: 0.3207 (p0) REVERT: H 78 MET cc_start: 0.0675 (ttp) cc_final: 0.0157 (mtp) REVERT: H 82 MET cc_start: -0.0089 (mpp) cc_final: -0.0778 (mmt) REVERT: K 78 MET cc_start: 0.2479 (tpp) cc_final: 0.2126 (tpp) REVERT: K 81 GLN cc_start: 0.2130 (OUTLIER) cc_final: 0.1851 (mt0) outliers start: 86 outliers final: 42 residues processed: 271 average time/residue: 0.3892 time to fit residues: 177.1340 Evaluate side-chains 211 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 160 time to evaluate : 2.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 577 ARG 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 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 1067 TYR Chi-restraints excluded: chain B residue 28 TYR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 1005 GLN 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 C residue 155 SER Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1018 ILE 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 94 TYR 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 254 optimal weight: 0.2980 chunk 214 optimal weight: 10.0000 chunk 199 optimal weight: 0.9990 chunk 340 optimal weight: 10.0000 chunk 283 optimal weight: 7.9990 chunk 218 optimal weight: 20.0000 chunk 22 optimal weight: 0.9990 chunk 328 optimal weight: 9.9990 chunk 174 optimal weight: 0.9990 chunk 326 optimal weight: 20.0000 chunk 312 optimal weight: 10.0000 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 532 ASN A 755 GLN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 HIS ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN B1036 GLN ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 ASN ** C 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 717 ASN C 955 ASN C1010 GLN C1058 HIS H 30 ASN H 73 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5132 r_free = 0.5132 target = 0.254355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.5063 r_free = 0.5063 target = 0.247662 restraints weight = 78740.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.5057 r_free = 0.5057 target = 0.247148 restraints weight = 106247.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.5058 r_free = 0.5058 target = 0.247327 restraints weight = 101510.061| |-----------------------------------------------------------------------------| r_work (final): 0.5062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1320 moved from start: 0.5508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 29420 Z= 0.214 Angle : 0.750 15.955 40127 Z= 0.396 Chirality : 0.051 0.266 4615 Planarity : 0.006 0.067 5166 Dihedral : 6.896 78.475 4462 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.38 % Favored : 94.59 % Rotamer: Outliers : 3.06 % Allowed : 13.60 % Favored : 83.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.13), residues: 3626 helix: 0.06 (0.19), residues: 650 sheet: 0.61 (0.17), residues: 895 loop : -1.64 (0.13), residues: 2081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 886 HIS 0.011 0.002 HIS A1064 PHE 0.041 0.003 PHE C 392 TYR 0.034 0.002 TYR E 33 ARG 0.020 0.001 ARG A 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00503 ( 24) link_NAG-ASN : angle 2.64018 ( 72) hydrogen bonds : bond 0.05872 ( 1076) hydrogen bonds : angle 6.45968 ( 2919) SS BOND : bond 0.01021 ( 37) SS BOND : angle 2.13914 ( 74) covalent geometry : bond 0.00456 (29359) covalent geometry : angle 0.73675 (39981) *********************** 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 283 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 187 time to evaluate : 3.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.0812 (OUTLIER) cc_final: 0.0416 (m-80) REVERT: A 275 PHE cc_start: 0.3130 (OUTLIER) cc_final: 0.2006 (m-80) REVERT: A 703 ASN cc_start: 0.3166 (OUTLIER) cc_final: 0.2459 (p0) REVERT: A 902 MET cc_start: 0.0924 (tpt) cc_final: 0.0331 (ptt) REVERT: A 1005 GLN cc_start: 0.1292 (OUTLIER) cc_final: 0.0900 (tt0) REVERT: A 1106 GLN cc_start: 0.2401 (OUTLIER) cc_final: 0.1567 (pm20) REVERT: B 1067 TYR cc_start: -0.0241 (OUTLIER) cc_final: -0.1200 (t80) REVERT: B 1123 SER cc_start: 0.1916 (OUTLIER) cc_final: 0.1600 (t) REVERT: C 91 TYR cc_start: -0.0084 (OUTLIER) cc_final: -0.0893 (m-80) REVERT: C 670 ILE cc_start: 0.2286 (OUTLIER) cc_final: 0.1766 (tp) REVERT: C 818 ILE cc_start: 0.4626 (OUTLIER) cc_final: 0.4409 (mm) REVERT: C 1050 MET cc_start: 0.1738 (ptm) cc_final: 0.1441 (ptm) REVERT: E 43 LYS cc_start: 0.3723 (mmtt) cc_final: 0.3307 (ttpt) REVERT: F 35 SER cc_start: 0.0573 (OUTLIER) cc_final: 0.0077 (m) REVERT: H 78 MET cc_start: 0.1498 (ttp) cc_final: 0.0878 (mtm) REVERT: H 82 MET cc_start: -0.0072 (mpp) cc_final: -0.0339 (mmt) REVERT: K 78 MET cc_start: 0.1910 (tpp) cc_final: 0.1695 (tpp) outliers start: 96 outliers final: 47 residues processed: 269 average time/residue: 0.3834 time to fit residues: 173.0558 Evaluate side-chains 203 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 145 time to evaluate : 2.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1106 GLN 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 549 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 761 THR 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 1005 GLN 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 91 TYR 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 781 VAL Chi-restraints excluded: chain C residue 818 ILE 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 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 1095 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 35 SER 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 Chi-restraints excluded: chain L residue 89 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 48 optimal weight: 3.9990 chunk 335 optimal weight: 20.0000 chunk 227 optimal weight: 8.9990 chunk 344 optimal weight: 20.0000 chunk 325 optimal weight: 50.0000 chunk 89 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 90 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 205 optimal weight: 0.3980 chunk 122 optimal weight: 0.0170 overall best weight: 0.6422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 755 GLN A 920 GLN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 HIS ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 493 GLN ** C 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 717 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5126 r_free = 0.5126 target = 0.253475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4956 r_free = 0.4956 target = 0.236322 restraints weight = 74270.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4946 r_free = 0.4946 target = 0.236124 restraints weight = 97047.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4955 r_free = 0.4955 target = 0.237065 restraints weight = 67009.914| |-----------------------------------------------------------------------------| r_work (final): 0.4956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1255 moved from start: 0.5708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 29420 Z= 0.131 Angle : 0.632 21.692 40127 Z= 0.324 Chirality : 0.047 0.517 4615 Planarity : 0.005 0.116 5166 Dihedral : 6.195 67.076 4458 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.62 % Allowed : 15.42 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.13), residues: 3626 helix: 0.86 (0.20), residues: 641 sheet: 0.66 (0.17), residues: 889 loop : -1.55 (0.13), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 886 HIS 0.005 0.001 HIS C1048 PHE 0.038 0.001 PHE C 565 TYR 0.022 0.001 TYR B1067 ARG 0.017 0.000 ARG C 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00434 ( 24) link_NAG-ASN : angle 3.62162 ( 72) hydrogen bonds : bond 0.04758 ( 1076) hydrogen bonds : angle 5.88732 ( 2919) SS BOND : bond 0.00552 ( 37) SS BOND : angle 1.96171 ( 74) covalent geometry : bond 0.00271 (29359) covalent geometry : angle 0.60787 (39981) *********************** 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 242 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 160 time to evaluate : 2.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 902 MET cc_start: 0.0748 (tpt) cc_final: 0.0438 (ptt) REVERT: A 905 ARG cc_start: 0.2956 (tpp-160) cc_final: 0.2509 (tpp-160) REVERT: A 915 VAL cc_start: -0.1406 (OUTLIER) cc_final: -0.2706 (p) REVERT: B 197 ILE cc_start: 0.1608 (OUTLIER) cc_final: 0.1295 (mm) REVERT: B 906 PHE cc_start: 0.2460 (OUTLIER) cc_final: 0.0526 (m-80) REVERT: B 1123 SER cc_start: 0.1981 (OUTLIER) cc_final: 0.1605 (t) REVERT: C 91 TYR cc_start: -0.0431 (OUTLIER) cc_final: -0.1084 (m-80) REVERT: C 493 GLN cc_start: 0.1546 (OUTLIER) cc_final: 0.0627 (pp30) REVERT: C 670 ILE cc_start: 0.1765 (OUTLIER) cc_final: 0.1374 (tp) REVERT: C 964 LYS cc_start: 0.4123 (OUTLIER) cc_final: 0.3549 (tmtt) REVERT: E 43 LYS cc_start: 0.3474 (mmtt) cc_final: 0.2992 (ttpt) REVERT: F 35 SER cc_start: 0.0618 (OUTLIER) cc_final: 0.0188 (m) REVERT: F 86 ASP cc_start: 0.1313 (OUTLIER) cc_final: 0.0967 (m-30) REVERT: H 78 MET cc_start: 0.0981 (ttp) cc_final: 0.0424 (mtp) REVERT: H 82 MET cc_start: -0.0217 (mpp) cc_final: -0.0533 (mmt) REVERT: K 81 GLN cc_start: 0.2216 (OUTLIER) cc_final: 0.1383 (mt0) outliers start: 82 outliers final: 42 residues processed: 229 average time/residue: 0.3992 time to fit residues: 152.5500 Evaluate side-chains 199 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 146 time to evaluate : 2.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 197 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 788 ILE Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 1005 GLN 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 91 TYR Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 643 PHE Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 782 PHE Chi-restraints excluded: chain C residue 869 MET 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 1114 ILE Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain E residue 94 TYR 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 F residue 86 ASP 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 81 GLN 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 302 optimal weight: 7.9990 chunk 305 optimal weight: 9.9990 chunk 295 optimal weight: 0.9980 chunk 204 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 165 optimal weight: 0.6980 chunk 282 optimal weight: 3.9990 chunk 99 optimal weight: 0.0980 chunk 276 optimal weight: 0.9980 chunk 244 optimal weight: 0.9980 chunk 241 optimal weight: 30.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 GLN A1005 GLN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 920 GLN ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 755 GLN C 901 GLN C 926 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5140 r_free = 0.5140 target = 0.254921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.5050 r_free = 0.5050 target = 0.246124 restraints weight = 78553.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.5053 r_free = 0.5053 target = 0.246563 restraints weight = 95561.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.5045 r_free = 0.5045 target = 0.245885 restraints weight = 73702.853| |-----------------------------------------------------------------------------| r_work (final): 0.5031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1219 moved from start: 0.5951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 29420 Z= 0.127 Angle : 0.598 10.535 40127 Z= 0.309 Chirality : 0.045 0.274 4615 Planarity : 0.004 0.060 5166 Dihedral : 5.956 63.407 4458 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.16 % Favored : 94.82 % Rotamer: Outliers : 2.49 % Allowed : 15.93 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.14), residues: 3626 helix: 1.19 (0.20), residues: 635 sheet: 0.66 (0.17), residues: 864 loop : -1.51 (0.13), residues: 2127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 353 HIS 0.004 0.001 HIS A1064 PHE 0.019 0.001 PHE C 565 TYR 0.023 0.001 TYR B1067 ARG 0.009 0.000 ARG A 577 Details of bonding type rmsd link_NAG-ASN : bond 0.00737 ( 24) link_NAG-ASN : angle 2.62527 ( 72) hydrogen bonds : bond 0.04427 ( 1076) hydrogen bonds : angle 5.61822 ( 2919) SS BOND : bond 0.00411 ( 37) SS BOND : angle 2.19664 ( 74) covalent geometry : bond 0.00266 (29359) covalent geometry : angle 0.58134 (39981) *********************** 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 242 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 164 time to evaluate : 3.128 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 275 PHE cc_start: 0.2676 (OUTLIER) cc_final: 0.1589 (m-80) REVERT: A 719 THR cc_start: 0.6317 (p) cc_final: 0.5876 (m) REVERT: A 915 VAL cc_start: -0.1576 (OUTLIER) cc_final: -0.2852 (p) REVERT: B 197 ILE cc_start: 0.1738 (mm) cc_final: 0.1465 (mm) REVERT: B 906 PHE cc_start: 0.2190 (OUTLIER) cc_final: 0.0458 (m-80) REVERT: B 1123 SER cc_start: 0.2032 (OUTLIER) cc_final: 0.1649 (t) REVERT: C 91 TYR cc_start: -0.0266 (OUTLIER) cc_final: -0.1042 (m-80) REVERT: C 460 ASN cc_start: 0.4370 (m-40) cc_final: 0.3985 (p0) REVERT: C 670 ILE cc_start: 0.1889 (OUTLIER) cc_final: 0.1427 (tp) REVERT: C 964 LYS cc_start: 0.4122 (OUTLIER) cc_final: 0.3585 (tmtt) REVERT: E 43 LYS cc_start: 0.3650 (mmtt) cc_final: 0.3138 (ttpt) REVERT: F 35 SER cc_start: 0.0800 (OUTLIER) cc_final: 0.0363 (m) REVERT: H 78 MET cc_start: 0.0885 (ttp) cc_final: 0.0329 (mtp) REVERT: H 82 MET cc_start: -0.0323 (mpp) cc_final: -0.0890 (mmt) REVERT: K 81 GLN cc_start: 0.2481 (OUTLIER) cc_final: 0.1800 (mt0) outliers start: 78 outliers final: 49 residues processed: 233 average time/residue: 0.3769 time to fit residues: 150.5894 Evaluate side-chains 213 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 155 time to evaluate : 2.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 474 GLN Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1032 CYS 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 140 PHE 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 896 ILE Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 1005 GLN 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 91 TYR 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 643 PHE Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 869 MET 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 1116 THR Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain E residue 94 TYR 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 81 GLN Chi-restraints excluded: chain K residue 105 ASP 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 222 optimal weight: 9.9990 chunk 357 optimal weight: 2.9990 chunk 228 optimal weight: 9.9990 chunk 152 optimal weight: 5.9990 chunk 269 optimal weight: 1.9990 chunk 321 optimal weight: 2.9990 chunk 238 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 200 optimal weight: 0.3980 chunk 288 optimal weight: 3.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 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** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 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** C 901 GLN C 926 GLN C1088 HIS H 30 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5133 r_free = 0.5133 target = 0.254316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.5044 r_free = 0.5044 target = 0.245661 restraints weight = 78962.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.5038 r_free = 0.5038 target = 0.245388 restraints weight = 97008.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.5032 r_free = 0.5032 target = 0.244848 restraints weight = 89073.534| |-----------------------------------------------------------------------------| r_work (final): 0.5036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1548 moved from start: 0.6608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 29420 Z= 0.198 Angle : 0.737 30.448 40127 Z= 0.380 Chirality : 0.053 1.304 4615 Planarity : 0.005 0.069 5166 Dihedral : 6.385 61.733 4458 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.09 % Favored : 93.85 % Rotamer: Outliers : 2.94 % Allowed : 16.31 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.13), residues: 3626 helix: 0.35 (0.19), residues: 651 sheet: 0.51 (0.17), residues: 883 loop : -1.60 (0.13), residues: 2092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 104 HIS 0.008 0.001 HIS A1064 PHE 0.040 0.002 PHE B1052 TYR 0.030 0.002 TYR B 917 ARG 0.008 0.001 ARG B 905 Details of bonding type rmsd link_NAG-ASN : bond 0.01075 ( 24) link_NAG-ASN : angle 4.25178 ( 72) hydrogen bonds : bond 0.05180 ( 1076) hydrogen bonds : angle 6.10858 ( 2919) SS BOND : bond 0.01275 ( 37) SS BOND : angle 2.86860 ( 74) covalent geometry : bond 0.00422 (29359) covalent geometry : angle 0.70549 (39981) *********************** 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 263 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 171 time to evaluate : 2.689 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: 0.3010 (OUTLIER) cc_final: 0.1876 (m-80) REVERT: A 719 THR cc_start: 0.6278 (p) cc_final: 0.5949 (m) REVERT: A 756 TYR cc_start: -0.0793 (OUTLIER) cc_final: -0.1069 (m-10) REVERT: A 915 VAL cc_start: -0.0933 (OUTLIER) cc_final: -0.2304 (p) REVERT: B 28 TYR cc_start: 0.0620 (OUTLIER) cc_final: 0.0260 (p90) REVERT: B 366 SER cc_start: 0.1033 (OUTLIER) cc_final: 0.0488 (p) REVERT: B 675 GLN cc_start: 0.1462 (tp40) cc_final: 0.1257 (tp40) REVERT: B 906 PHE cc_start: 0.2876 (OUTLIER) cc_final: 0.1022 (m-80) REVERT: B 1123 SER cc_start: 0.3021 (OUTLIER) cc_final: 0.2467 (t) REVERT: C 91 TYR cc_start: -0.0206 (OUTLIER) cc_final: -0.1018 (m-80) REVERT: C 460 ASN cc_start: 0.4243 (m-40) cc_final: 0.3989 (p0) REVERT: C 505 TYR cc_start: 0.0794 (OUTLIER) cc_final: -0.0988 (t80) REVERT: C 670 ILE cc_start: 0.2399 (OUTLIER) cc_final: 0.2192 (tp) REVERT: C 860 VAL cc_start: 0.2127 (OUTLIER) cc_final: 0.1749 (t) REVERT: C 926 GLN cc_start: 0.1257 (OUTLIER) cc_final: 0.0996 (pt0) REVERT: C 964 LYS cc_start: 0.4352 (OUTLIER) cc_final: 0.3711 (tmtt) REVERT: F 35 SER cc_start: 0.0808 (OUTLIER) cc_final: 0.0405 (m) REVERT: H 78 MET cc_start: 0.1322 (ttp) cc_final: 0.0633 (mtp) REVERT: H 82 MET cc_start: -0.0315 (mpp) cc_final: -0.0628 (mmm) REVERT: K 81 GLN cc_start: 0.2351 (OUTLIER) cc_final: 0.1738 (mt0) outliers start: 92 outliers final: 62 residues processed: 252 average time/residue: 0.3472 time to fit residues: 149.2168 Evaluate side-chains 233 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 156 time to evaluate : 2.966 ------------------------------------------------------------------------------- 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 551 VAL 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 716 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 28 TYR Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 366 SER 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 776 LYS Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 91 TYR 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 505 TYR Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 782 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 926 GLN Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1048 HIS Chi-restraints excluded: chain C residue 1049 LEU Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1062 PHE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain E residue 94 TYR 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 81 GLN 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 44 optimal weight: 6.9990 chunk 113 optimal weight: 4.9990 chunk 238 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 157 optimal weight: 1.9990 chunk 236 optimal weight: 20.0000 chunk 172 optimal weight: 0.0980 chunk 96 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 137 optimal weight: 0.8980 chunk 138 optimal weight: 5.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** C 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN C 901 GLN C 926 GLN ** C1036 GLN ** 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 = 0.5133 r_free = 0.5133 target = 0.254582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.4973 r_free = 0.4973 target = 0.238475 restraints weight = 75872.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.4951 r_free = 0.4951 target = 0.237363 restraints weight = 67202.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 72)----------------| | r_work = 0.4944 r_free = 0.4944 target = 0.236321 restraints weight = 53652.179| |-----------------------------------------------------------------------------| r_work (final): 0.4959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1786 moved from start: 0.7326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 29420 Z= 0.187 Angle : 0.709 12.498 40127 Z= 0.373 Chirality : 0.049 0.328 4615 Planarity : 0.005 0.075 5166 Dihedral : 6.501 59.199 4458 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.26 % Favored : 93.68 % Rotamer: Outliers : 3.22 % Allowed : 16.60 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.13), residues: 3626 helix: 0.17 (0.20), residues: 642 sheet: 0.35 (0.18), residues: 888 loop : -1.73 (0.13), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 104 HIS 0.007 0.001 HIS A1088 PHE 0.031 0.002 PHE C1095 TYR 0.031 0.002 TYR A 904 ARG 0.009 0.001 ARG A 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00745 ( 24) link_NAG-ASN : angle 2.37983 ( 72) hydrogen bonds : bond 0.05072 ( 1076) hydrogen bonds : angle 6.18235 ( 2919) SS BOND : bond 0.00415 ( 37) SS BOND : angle 2.29138 ( 74) covalent geometry : bond 0.00403 (29359) covalent geometry : angle 0.69589 (39981) *********************** 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 271 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 170 time to evaluate : 2.727 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 719 THR cc_start: 0.6469 (p) cc_final: 0.6211 (m) REVERT: A 756 TYR cc_start: -0.0852 (OUTLIER) cc_final: -0.1218 (m-10) REVERT: B 28 TYR cc_start: 0.0940 (OUTLIER) cc_final: 0.0399 (p90) REVERT: B 366 SER cc_start: 0.0860 (OUTLIER) cc_final: 0.0380 (p) REVERT: B 906 PHE cc_start: 0.2734 (OUTLIER) cc_final: 0.1685 (m-80) REVERT: C 91 TYR cc_start: -0.0680 (OUTLIER) cc_final: -0.1646 (m-80) REVERT: C 377 PHE cc_start: -0.0079 (t80) cc_final: -0.0626 (t80) REVERT: C 460 ASN cc_start: 0.4508 (m-40) cc_final: 0.3759 (p0) REVERT: C 505 TYR cc_start: -0.0097 (OUTLIER) cc_final: -0.1679 (t80) REVERT: C 670 ILE cc_start: 0.2482 (OUTLIER) cc_final: 0.2273 (tp) REVERT: C 860 VAL cc_start: 0.2239 (OUTLIER) cc_final: 0.1932 (t) REVERT: C 906 PHE cc_start: 0.0796 (OUTLIER) cc_final: -0.0055 (m-80) REVERT: C 1050 MET cc_start: 0.2162 (ptm) cc_final: 0.1748 (ptm) REVERT: E 105 ASP cc_start: 0.1826 (OUTLIER) cc_final: 0.1532 (t0) REVERT: F 35 SER cc_start: 0.0963 (OUTLIER) cc_final: 0.0358 (m) REVERT: H 78 MET cc_start: 0.0465 (ttp) cc_final: -0.0154 (mtp) REVERT: H 82 MET cc_start: -0.0363 (mpp) cc_final: -0.0708 (mmm) REVERT: K 81 GLN cc_start: 0.2181 (OUTLIER) cc_final: 0.1501 (mt0) outliers start: 101 outliers final: 70 residues processed: 256 average time/residue: 0.3584 time to fit residues: 154.2618 Evaluate side-chains 239 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 157 time to evaluate : 2.677 ------------------------------------------------------------------------------- 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 551 VAL 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 716 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1008 VAL 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 1067 TYR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain B residue 28 TYR Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 366 SER 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 776 LYS Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1052 PHE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1138 TYR Chi-restraints excluded: chain C residue 91 TYR 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 505 TYR Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 670 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 781 VAL Chi-restraints excluded: chain C residue 782 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1033 VAL 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 1114 ILE Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain E residue 94 TYR 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 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 81 GLN 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 295 optimal weight: 0.7980 chunk 286 optimal weight: 6.9990 chunk 161 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 112 optimal weight: 0.0670 chunk 137 optimal weight: 30.0000 chunk 142 optimal weight: 30.0000 chunk 38 optimal weight: 10.0000 chunk 236 optimal weight: 20.0000 chunk 205 optimal weight: 6.9990 chunk 284 optimal weight: 0.6980 overall best weight: 0.9122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN ** B1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5142 r_free = 0.5142 target = 0.254886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.5073 r_free = 0.5073 target = 0.248345 restraints weight = 79179.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.5063 r_free = 0.5063 target = 0.247404 restraints weight = 94112.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.5065 r_free = 0.5065 target = 0.247743 restraints weight = 90984.098| |-----------------------------------------------------------------------------| r_work (final): 0.5069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1538 moved from start: 0.7474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 29420 Z= 0.131 Angle : 0.628 13.236 40127 Z= 0.326 Chirality : 0.046 0.293 4615 Planarity : 0.005 0.061 5166 Dihedral : 6.102 57.335 4458 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.71 % Favored : 94.24 % Rotamer: Outliers : 2.39 % Allowed : 17.59 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.13), residues: 3626 helix: 0.75 (0.20), residues: 640 sheet: 0.29 (0.17), residues: 883 loop : -1.66 (0.13), residues: 2103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 886 HIS 0.004 0.001 HIS C 655 PHE 0.021 0.001 PHE A 338 TYR 0.026 0.001 TYR B1067 ARG 0.006 0.000 ARG C 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00415 ( 24) link_NAG-ASN : angle 1.99216 ( 72) hydrogen bonds : bond 0.04232 ( 1076) hydrogen bonds : angle 5.76156 ( 2919) SS BOND : bond 0.00637 ( 37) SS BOND : angle 2.70277 ( 74) covalent geometry : bond 0.00280 (29359) covalent geometry : angle 0.61261 (39981) *********************** 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 242 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 167 time to evaluate : 5.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 719 THR cc_start: 0.6113 (p) cc_final: 0.5869 (m) REVERT: A 756 TYR cc_start: -0.0786 (OUTLIER) cc_final: -0.1142 (m-10) REVERT: B 906 PHE cc_start: 0.2633 (OUTLIER) cc_final: 0.1518 (m-80) REVERT: B 1123 SER cc_start: 0.4721 (OUTLIER) cc_final: 0.4185 (t) REVERT: C 91 TYR cc_start: -0.0443 (OUTLIER) cc_final: -0.1394 (m-80) REVERT: C 414 GLN cc_start: 0.3587 (mp10) cc_final: 0.3298 (mp10) REVERT: C 670 ILE cc_start: 0.2137 (OUTLIER) cc_final: 0.1643 (tp) REVERT: C 767 LEU cc_start: 0.6353 (OUTLIER) cc_final: 0.6134 (mm) REVERT: E 78 MET cc_start: 0.1455 (mmm) cc_final: 0.1221 (mmm) REVERT: E 105 ASP cc_start: 0.1123 (OUTLIER) cc_final: 0.0809 (t0) REVERT: F 35 SER cc_start: 0.0823 (OUTLIER) cc_final: 0.0288 (m) REVERT: H 78 MET cc_start: 0.1298 (ttp) cc_final: 0.0631 (mtp) REVERT: H 82 MET cc_start: -0.0385 (mpp) cc_final: -0.0597 (mmm) REVERT: K 34 MET cc_start: 0.3112 (ttp) cc_final: 0.1690 (mmm) REVERT: K 81 GLN cc_start: 0.2174 (OUTLIER) cc_final: 0.1679 (mt0) outliers start: 75 outliers final: 56 residues processed: 231 average time/residue: 0.4874 time to fit residues: 193.8093 Evaluate side-chains 223 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 158 time to evaluate : 3.075 ------------------------------------------------------------------------------- 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 698 SER Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 976 VAL 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 A residue 1117 THR Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 213 VAL 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 743 CYS Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 818 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 912 THR Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 91 TYR 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 643 PHE Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 782 PHE Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 913 GLN 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 1136 THR Chi-restraints excluded: chain E residue 94 TYR 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 H residue 51 ILE Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 94 TYR Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain K residue 81 GLN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 341 optimal weight: 30.0000 chunk 140 optimal weight: 30.0000 chunk 51 optimal weight: 0.0770 chunk 13 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 202 optimal weight: 0.9990 chunk 247 optimal weight: 4.9990 chunk 349 optimal weight: 0.7980 chunk 356 optimal weight: 9.9990 chunk 68 optimal weight: 0.0870 chunk 326 optimal weight: 50.0000 overall best weight: 1.3920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1083 HIS ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** C 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 32 ASN K 30 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5143 r_free = 0.5143 target = 0.254841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.5074 r_free = 0.5074 target = 0.248205 restraints weight = 79371.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.5065 r_free = 0.5065 target = 0.247498 restraints weight = 94766.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.5068 r_free = 0.5068 target = 0.247830 restraints weight = 94613.467| |-----------------------------------------------------------------------------| r_work (final): 0.5072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1645 moved from start: 0.7844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 29420 Z= 0.154 Angle : 0.656 10.944 40127 Z= 0.342 Chirality : 0.047 0.247 4615 Planarity : 0.005 0.059 5166 Dihedral : 6.214 59.036 4458 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.37 % Favored : 93.57 % Rotamer: Outliers : 2.36 % Allowed : 17.68 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.13), residues: 3626 helix: 0.58 (0.20), residues: 640 sheet: 0.24 (0.18), residues: 870 loop : -1.70 (0.13), residues: 2116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 104 HIS 0.018 0.002 HIS C1064 PHE 0.034 0.002 PHE C1095 TYR 0.028 0.001 TYR B1067 ARG 0.007 0.001 ARG A 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00479 ( 24) link_NAG-ASN : angle 1.93805 ( 72) hydrogen bonds : bond 0.04453 ( 1076) hydrogen bonds : angle 5.87823 ( 2919) SS BOND : bond 0.00445 ( 37) SS BOND : angle 1.99173 ( 74) covalent geometry : bond 0.00335 (29359) covalent geometry : angle 0.64681 (39981) ********************** 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 241 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 167 time to evaluate : 2.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 756 TYR cc_start: -0.0818 (OUTLIER) cc_final: -0.1175 (m-10) REVERT: B 366 SER cc_start: 0.0975 (OUTLIER) cc_final: 0.0431 (p) REVERT: B 726 ILE cc_start: 0.4194 (tp) cc_final: 0.3962 (mt) REVERT: B 906 PHE cc_start: 0.2637 (OUTLIER) cc_final: 0.1772 (m-80) REVERT: C 91 TYR cc_start: -0.0406 (OUTLIER) cc_final: -0.1407 (m-80) REVERT: C 414 GLN cc_start: 0.3709 (mp10) cc_final: 0.3460 (mp10) REVERT: C 505 TYR cc_start: 0.1038 (OUTLIER) cc_final: -0.0653 (t80) REVERT: C 670 ILE cc_start: 0.2280 (OUTLIER) cc_final: 0.2045 (tp) REVERT: C 1050 MET cc_start: 0.2426 (ptm) cc_final: 0.1911 (ptm) REVERT: E 78 MET cc_start: 0.1278 (mmm) cc_final: 0.1037 (mmm) REVERT: H 78 MET cc_start: 0.1241 (ttp) cc_final: 0.0645 (mtp) REVERT: H 82 MET cc_start: -0.0253 (mpp) cc_final: -0.0482 (mmm) REVERT: K 81 GLN cc_start: 0.2207 (OUTLIER) cc_final: 0.1402 (mt0) outliers start: 74 outliers final: 59 residues processed: 229 average time/residue: 0.3396 time to fit residues: 133.9613 Evaluate side-chains 220 residues out of total 3212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 154 time to evaluate : 2.876 ------------------------------------------------------------------------------- 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 698 SER Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 976 VAL 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 A residue 1117 THR 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 345 THR Chi-restraints excluded: chain B residue 366 SER 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 818 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1049 LEU Chi-restraints excluded: chain B residue 1052 PHE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 104 TRP 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 505 TYR Chi-restraints excluded: chain C residue 670 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 781 VAL Chi-restraints excluded: chain C residue 782 PHE Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1062 PHE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain E residue 94 TYR Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain F residue 28 ASN Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 94 TYR Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain K residue 81 GLN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 352 optimal weight: 20.0000 chunk 290 optimal weight: 0.0970 chunk 120 optimal weight: 0.9990 chunk 200 optimal weight: 3.9990 chunk 249 optimal weight: 10.0000 chunk 268 optimal weight: 0.9990 chunk 233 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 250 optimal weight: 0.8980 chunk 289 optimal weight: 0.0970 chunk 309 optimal weight: 30.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN B 926 GLN B1106 GLN ** C 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 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 = 0.5144 r_free = 0.5144 target = 0.255340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.5026 r_free = 0.5026 target = 0.243411 restraints weight = 76178.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.5018 r_free = 0.5018 target = 0.243031 restraints weight = 79308.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.5005 r_free = 0.5005 target = 0.241698 restraints weight = 76054.926| |-----------------------------------------------------------------------------| r_work (final): 0.5023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1585 moved from start: 0.7918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 29420 Z= 0.121 Angle : 0.591 9.909 40127 Z= 0.308 Chirality : 0.045 0.239 4615 Planarity : 0.004 0.053 5166 Dihedral : 5.911 57.359 4458 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.96 % Favored : 94.98 % Rotamer: Outliers : 2.07 % Allowed : 17.94 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.14), residues: 3626 helix: 0.94 (0.20), residues: 650 sheet: 0.22 (0.18), residues: 862 loop : -1.63 (0.13), residues: 2114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 886 HIS 0.011 0.001 HIS C1064 PHE 0.027 0.001 PHE C1095 TYR 0.032 0.001 TYR B 473 ARG 0.008 0.000 ARG C 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00357 ( 24) link_NAG-ASN : angle 1.70061 ( 72) hydrogen bonds : bond 0.03902 ( 1076) hydrogen bonds : angle 5.56167 ( 2919) SS BOND : bond 0.00312 ( 37) SS BOND : angle 1.63303 ( 74) covalent geometry : bond 0.00259 (29359) covalent geometry : angle 0.58358 (39981) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8747.11 seconds wall clock time: 154 minutes 11.46 seconds (9251.46 seconds total)