Starting phenix.real_space_refine on Mon Sep 14 01:09:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6zhd_11218/09_2026/6zhd_11218.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zhd_11218/09_2026/6zhd_11218.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6zhd_11218/09_2026/6zhd_11218.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zhd_11218/09_2026/6zhd_11218.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6zhd_11218/09_2026/6zhd_11218.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zhd_11218/09_2026/6zhd_11218.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6zhd_11218/09_2026/6zhd_11218.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6zhd_11218/09_2026/6zhd_11218.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 117 5.16 5 C 17150 2.51 5 N 4408 2.21 5 O 5252 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26927 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 7646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 987, 7646 Classifications: {'peptide': 987} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 49, 'TRANS': 937} Chain breaks: 9 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 5, 'ASN:plan1': 4, 'GLU:plan': 4, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 51 Chain: "B" Number of atoms: 7677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 7677 Classifications: {'peptide': 992} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 49, 'TRANS': 942} Chain breaks: 8 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 3, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 55 Chain: "C" Number of atoms: 7659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 990, 7659 Classifications: {'peptide': 990} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 49, 'TRANS': 940} Chain breaks: 7 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 3, 'GLU:plan': 6, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 48 Chain: "D" Number of atoms: 1007 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 128, 1001 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 2, 'TRANS': 125} Conformer: "B" Number of residues, atoms: 128, 1001 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 2, 'TRANS': 125} bond proxies already assigned to first conformer: 1019 Chain: "E" Number of atoms: 1007 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 128, 1001 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 2, 'TRANS': 125} Conformer: "B" Number of residues, atoms: 128, 1001 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 2, 'TRANS': 125} bond proxies already assigned to first conformer: 1019 Chain: "F" Number of atoms: 1007 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 128, 1001 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 2, 'TRANS': 125} Conformer: "B" Number of residues, atoms: 128, 1001 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 2, 'TRANS': 125} bond proxies already assigned to first conformer: 1019 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 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 chiralities: 8 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 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 chiralities: 8 Time building chain proxies: 6.66, per 1000 atoms: 0.25 Number of scatterers: 26927 At special positions: 0 Unit cell: (129.32, 135.68, 218.36, 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 117 16.00 O 5252 8.00 N 4408 7.00 C 17150 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.05 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.05 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.06 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.05 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.05 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.06 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.05 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.07 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.06 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.01 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.06 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.05 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.05 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.06 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.05 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 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 D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.05 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.05 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 BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1310 " - " ASN A 603 " " NAG A1311 " - " ASN A 616 " " NAG A1312 " - " ASN A 657 " " NAG A1313 " - " ASN A 709 " " NAG A1318 " - " ASN A1074 " " NAG A1323 " - " ASN A 165 " " NAG A1324 " - " ASN A 343 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 709 " " NAG B1313 " - " ASN B1074 " " NAG B1318 " - " ASN B 343 " " NAG C1401 " - " ASN C 343 " " NAG C1402 " - " ASN C 61 " " NAG C1405 " - " ASN C 234 " " NAG C1408 " - " ASN C 331 " " NAG C1409 " - " ASN C 603 " " NAG C1410 " - " ASN C 616 " " NAG C1411 " - " ASN C 657 " " NAG C1424 " - " ASN C 165 " " NAG G 1 " - " ASN A 122 " " NAG H 1 " - " ASN A 234 " " NAG I 1 " - " ASN A 282 " " NAG J 1 " - " ASN A 331 " " NAG K 1 " - " ASN A 717 " " NAG L 1 " - " ASN A 801 " " NAG M 1 " - " ASN A1098 " " NAG N 1 " - " ASN A1134 " " NAG O 1 " - " ASN B 717 " " NAG P 1 " - " ASN B 801 " " NAG Q 1 " - " ASN B1098 " " NAG R 1 " - " ASN B1134 " " NAG S 1 " - " ASN C 122 " " NAG T 1 " - " ASN C 282 " " NAG U 1 " - " ASN C 709 " " NAG V 1 " - " ASN C 717 " " NAG W 1 " - " ASN C 801 " " NAG X 1 " - " ASN C1074 " " NAG Y 1 " - " ASN C1098 " " NAG Z 1 " - " ASN C1134 " Time building additional restraints: 2.06 Conformation dependent library (CDL) restraints added in 1.1 seconds 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6260 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 54 sheets defined 25.5% alpha, 29.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.960A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 384 through 389 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.275A 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 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.650A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.097A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.673A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.669A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.405A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.093A 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 337 through 343 removed outlier: 4.033A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 384 through 389 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.275A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.675A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.649A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.114A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.696A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.636A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.413A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.092A 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 337 through 343 removed outlier: 4.025A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 384 through 389 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.283A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.645A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.103A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.661A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.635A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.324A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.085A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 31 Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'D' and resid 105 through 111 Processing helix chain 'E' and resid 28 through 31 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 105 through 111 Processing helix chain 'F' and resid 28 through 31 Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'F' and resid 105 through 111 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.647A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 8.819A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.568A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.581A pdb=" N ASN A 125 " --> pdb=" O ASN A 122 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.549A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 324 through 327 removed outlier: 6.655A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.489A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.559A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.864A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.955A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.193A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.681A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.378A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.654A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 8.888A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.575A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.584A pdb=" N ASN B 125 " --> pdb=" O ASN B 122 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.585A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.129A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.476A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 653 through 655 removed outlier: 6.548A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.857A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.798A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.194A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 788 through 790 removed outlier: 5.760A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.379A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.652A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 8.827A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.878A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.736A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.580A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 324 through 328 removed outlier: 4.137A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.487A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.558A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.865A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.952A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.187A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.377A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 2 through 7 Processing sheet with id=AF2, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.183A pdb=" N GLY D 10 " --> pdb=" O THR D 124 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N SER D 126 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N MET D 12 " --> pdb=" O SER D 126 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ARG D 38 " --> pdb=" O PHE D 47 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N PHE D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.183A pdb=" N GLY D 10 " --> pdb=" O THR D 124 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N SER D 126 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N MET D 12 " --> pdb=" O SER D 126 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 2 through 7 Processing sheet with id=AF5, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.183A pdb=" N GLY E 10 " --> pdb=" O THR E 124 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N SER E 126 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N MET E 12 " --> pdb=" O SER E 126 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ARG E 38 " --> pdb=" O PHE E 47 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N PHE E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.183A pdb=" N GLY E 10 " --> pdb=" O THR E 124 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N SER E 126 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N MET E 12 " --> pdb=" O SER E 126 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 2 through 7 Processing sheet with id=AF8, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.183A pdb=" N GLY F 10 " --> pdb=" O THR F 124 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N SER F 126 " --> pdb=" O GLY F 10 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N MET F 12 " --> pdb=" O SER F 126 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ARG F 38 " --> pdb=" O PHE F 47 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N PHE F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.183A pdb=" N GLY F 10 " --> pdb=" O THR F 124 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N SER F 126 " --> pdb=" O GLY F 10 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N MET F 12 " --> pdb=" O SER F 126 " (cutoff:3.500A) 1189 hydrogen bonds defined for protein. 3156 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.12 Time building geometry restraints manager: 2.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4910 1.32 - 1.45: 8300 1.45 - 1.58: 14161 1.58 - 1.70: 0 1.70 - 1.83: 150 Bond restraints: 27521 Sorted by residual: bond pdb=" CA SER A 968 " pdb=" CB SER A 968 " ideal model delta sigma weight residual 1.531 1.479 0.052 1.58e-02 4.01e+03 1.09e+01 bond pdb=" C PHE B 759 " pdb=" O PHE B 759 " ideal model delta sigma weight residual 1.236 1.199 0.038 1.18e-02 7.18e+03 1.01e+01 bond pdb=" CA SER B 968 " pdb=" CB SER B 968 " ideal model delta sigma weight residual 1.531 1.481 0.050 1.58e-02 4.01e+03 9.94e+00 bond pdb=" CA SER C 596 " pdb=" CB SER C 596 " ideal model delta sigma weight residual 1.532 1.481 0.051 1.74e-02 3.30e+03 8.49e+00 bond pdb=" CA SER B1003 " pdb=" CB SER B1003 " ideal model delta sigma weight residual 1.528 1.483 0.045 1.56e-02 4.11e+03 8.49e+00 ... (remaining 27516 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 31716 1.98 - 3.96: 5093 3.96 - 5.94: 551 5.94 - 7.92: 69 7.92 - 9.90: 16 Bond angle restraints: 37445 Sorted by residual: angle pdb=" C PRO C 600 " pdb=" CA PRO C 600 " pdb=" CB PRO C 600 " ideal model delta sigma weight residual 111.44 101.87 9.57 1.51e+00 4.39e-01 4.02e+01 angle pdb=" C GLN A 913 " pdb=" CA GLN A 913 " pdb=" CB GLN A 913 " ideal model delta sigma weight residual 110.85 100.95 9.90 1.70e+00 3.46e-01 3.39e+01 angle pdb=" CA THR B 961 " pdb=" CB THR B 961 " pdb=" OG1 THR B 961 " ideal model delta sigma weight residual 109.60 101.11 8.49 1.50e+00 4.44e-01 3.21e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 117.24 -6.54 1.22e+00 6.72e-01 2.87e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 117.20 -6.50 1.22e+00 6.72e-01 2.84e+01 ... (remaining 37440 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 14551 17.55 - 35.10: 981 35.10 - 52.65: 194 52.65 - 70.20: 37 70.20 - 87.76: 26 Dihedral angle restraints: 15789 sinusoidal: 6038 harmonic: 9751 Sorted by residual: dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual 93.00 -179.24 -87.76 1 1.00e+01 1.00e-02 9.22e+01 dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual 93.00 -179.78 -87.22 1 1.00e+01 1.00e-02 9.13e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 -179.82 -87.18 1 1.00e+01 1.00e-02 9.13e+01 ... (remaining 15786 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.201: 4235 0.201 - 0.402: 193 0.402 - 0.603: 11 0.603 - 0.804: 0 0.804 - 1.006: 1 Chirality restraints: 4440 Sorted by residual: chirality pdb=" C1 NAG Y 2 " pdb=" O4 NAG Y 1 " pdb=" C2 NAG Y 2 " pdb=" O5 NAG Y 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-02 2.50e+03 1.33e+02 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-02 2.50e+03 1.24e+02 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-02 2.50e+03 1.18e+02 ... (remaining 4437 not shown) Planarity restraints: 4780 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1410 " 0.292 2.00e-02 2.50e+03 2.48e-01 7.69e+02 pdb=" C7 NAG C1410 " -0.074 2.00e-02 2.50e+03 pdb=" C8 NAG C1410 " 0.180 2.00e-02 2.50e+03 pdb=" N2 NAG C1410 " -0.428 2.00e-02 2.50e+03 pdb=" O7 NAG C1410 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG L 1 " -0.225 2.00e-02 2.50e+03 1.84e-01 4.24e+02 pdb=" C7 NAG L 1 " 0.065 2.00e-02 2.50e+03 pdb=" C8 NAG L 1 " -0.163 2.00e-02 2.50e+03 pdb=" N2 NAG L 1 " 0.295 2.00e-02 2.50e+03 pdb=" O7 NAG L 1 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1308 " 0.221 2.00e-02 2.50e+03 1.81e-01 4.08e+02 pdb=" C7 NAG B1308 " -0.064 2.00e-02 2.50e+03 pdb=" C8 NAG B1308 " 0.160 2.00e-02 2.50e+03 pdb=" N2 NAG B1308 " -0.290 2.00e-02 2.50e+03 pdb=" O7 NAG B1308 " -0.027 2.00e-02 2.50e+03 ... (remaining 4777 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 83 2.56 - 3.14: 21053 3.14 - 3.73: 40323 3.73 - 4.31: 61219 4.31 - 4.90: 98348 Nonbonded interactions: 221026 Sorted by model distance: nonbonded pdb=" O ASN A 81 " pdb=" NE2 GLN A 239 " model vdw 1.973 3.120 nonbonded pdb=" NH1 ARG C 328 " pdb=" OD2 ASP C 578 " model vdw 2.190 3.120 nonbonded pdb=" OH TYR B 200 " pdb=" OH TYR C 396 " model vdw 2.200 3.040 nonbonded pdb=" OH TYR B 200 " pdb=" OE1 GLU C 516 " model vdw 2.214 3.040 nonbonded pdb=" OE1 GLU E 6 " pdb=" OE1 GLN E 119 " model vdw 2.240 3.040 ... (remaining 221021 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 66 or resid 82 through 96 or (resi \ d 97 and (name N or name CA or name C or name O or name CB )) or resid 98 or (re \ sid 99 and (name N or name CA or name C or name O or name CB )) or resid 100 thr \ ough 110 or (resid 111 through 113 and (name N or name CA or name C or name O or \ name CB )) or resid 116 through 128 or (resid 129 and (name N or name CA or nam \ e C or name O or name CB )) or resid 130 through 134 or (resid 135 through 138 a \ nd (name N or name CA or name C or name O or name CB )) or resid 139 through 140 \ or resid 166 through 168 or (resid 169 and (name N or name CA or name C or name \ O or name CB )) or resid 170 through 172 or resid 187 or (resid 188 and (name N \ or name CA or name C or name O or name CB )) or resid 189 through 210 or (resid \ 211 through 215 and (name N or name CA or name C or name O or name CB )) or res \ id 216 through 241 or (resid 242 through 263 and (name N or name CA or name C or \ name O or name CB )) or resid 265 through 280 or (resid 281 and (name N or name \ CA or name C or name O or name CB )) or resid 282 through 567 or (resid 568 and \ (name N or name CA or name C or name O or name CB )) or resid 569 through 570 o \ r (resid 571 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 72 through 581 or (resid 582 through 583 and (name N or name CA or name C or nam \ e O or name CB )) or resid 584 through 585 or (resid 586 and (name N or name CA \ or name C or name O or name CB )) or resid 587 through 660 or (resid 661 and (na \ me N or name CA or name C or name O or name CB )) or resid 662 through 676 or re \ sid 690 through 747 or (resid 748 and (name N or name CA or name C or name O or \ name CB )) or resid 749 through 810 or (resid 811 and (name N or name CA or name \ C or name O or name CB )) or resid 812 through 827 or resid 856 through 939 or \ (resid 940 and (name N or name CA or name C or name O or name CB )) or resid 941 \ through 984 or (resid 985 and (name N or name CA or name C or name O or name CB \ )) or resid 986 through 1143 or (resid 1144 through 1146 and (name N or name CA \ or name C or name O or name CB )) or resid 1147 through 1324)) selection = (chain 'B' and (resid 27 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 52 or (resid 53 and (name N or nam \ e CA or name C or name O or name CB )) or resid 54 through 66 or resid 82 throug \ h 95 or (resid 96 through 97 and (name N or name CA or name C or name O or name \ CB )) or resid 98 through 111 or (resid 112 through 113 and (name N or name CA o \ r name C or name O or name CB )) or resid 116 through 124 or (resid 125 and (nam \ e N or name CA or name C or name O or name CB )) or resid 126 through 131 or (re \ sid 132 and (name N or name CA or name C or name O or name CB )) or resid 133 or \ (resid 134 through 138 and (name N or name CA or name C or name O or name CB )) \ or resid 139 through 140 or resid 166 through 168 or (resid 169 and (name N or \ name CA or name C or name O or name CB )) or resid 170 through 171 or (resid 172 \ and (name N or name CA or name C or name O or name CB )) or resid 187 through 1 \ 96 or resid 200 through 210 or (resid 211 and (name N or name CA or name C or na \ me O or name CB )) or (resid 215 and (name N or name CA or name C or name O or n \ ame CB )) or resid 216 through 263 or resid 265 through 528 or (resid 529 and (n \ ame N or name CA or name C or name O or name CB )) or resid 530 through 660 or ( \ resid 661 and (name N or name CA or name C or name O or name CB )) or resid 662 \ through 747 or (resid 748 and (name N or name CA or name C or name O or name CB \ )) or resid 749 through 810 or (resid 811 and (name N or name CA or name C or na \ me O or name CB )) or resid 812 through 827 or resid 856 through 939 or (resid 9 \ 40 and (name N or name CA or name C or name O or name CB )) or resid 941 through \ 984 or (resid 985 and (name N or name CA or name C or name O or name CB )) or r \ esid 986 through 1141 or (resid 1142 and (name N or name CA or name C or name O \ or name CB )) or resid 1143 through 1144 or (resid 1145 through 1146 and (name N \ or name CA or name C or name O or name CB )) or resid 1147 through 1308)) selection = (chain 'C' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 95 or (resi \ d 96 through 97 and (name N or name CA or name C or name O or name CB )) or resi \ d 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or re \ sid 100 through 110 or (resid 111 through 113 and (name N or name CA or name C o \ r name O or name CB )) or resid 116 through 124 or (resid 125 and (name N or nam \ e CA or name C or name O or name CB )) or resid 126 through 128 or (resid 129 an \ d (name N or name CA or name C or name O or name CB )) or resid 130 through 133 \ or (resid 134 through 138 and (name N or name CA or name C or name O or name CB \ )) or resid 139 through 140 or resid 166 through 187 or (resid 188 and (name N o \ r name CA or name C or name O or name CB )) or resid 189 through 196 or resid 20 \ 0 through 211 or (resid 215 and (name N or name CA or name C or name O or name C \ B )) or resid 216 through 528 or (resid 529 and (name N or name CA or name C or \ name O or name CB )) or resid 530 through 567 or (resid 568 and (name N or name \ CA or name C or name O or name CB )) or resid 569 through 570 or (resid 571 and \ (name N or name CA or name C or name O or name CB )) or resid 572 through 581 or \ (resid 582 through 583 and (name N or name CA or name C or name O or name CB )) \ or resid 584 through 585 or (resid 586 and (name N or name CA or name C or name \ O or name CB )) or resid 587 through 1141 or (resid 1142 and (name N or name CA \ or name C or name O or name CB )) or resid 1143 or (resid 1144 through 1146 and \ (name N or name CA or name C or name O or name CB )) or resid 1147 through 1424 \ )) } ncs_group { reference = (chain 'D' and (resid 1 through 88 or resid 90 through 128)) selection = (chain 'E' and (resid 1 through 88 or resid 90 through 128)) selection = (chain 'F' and (resid 1 through 88 or resid 90 through 128)) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 25.750 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 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 : 0.008 0.052 27629 Z= 0.528 Angle : 1.482 12.056 37727 Z= 0.951 Chirality : 0.103 1.006 4440 Planarity : 0.011 0.248 4734 Dihedral : 12.865 86.121 9403 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.64 % Favored : 96.33 % Rotamer: Outliers : 0.74 % Allowed : 4.36 % Favored : 94.90 % Cbeta Deviations : 0.32 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.13), residues: 3296 helix: -0.62 (0.18), residues: 671 sheet: 0.18 (0.17), residues: 812 loop : -0.95 (0.13), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.002 ARG B 328 TYR 0.051 0.006 TYR A 28 PHE 0.043 0.006 PHE B 565 TRP 0.019 0.005 TRP C 64 HIS 0.062 0.004 HIS C 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00847 / 0.53 (27521) covalent geometry : angle 1.46105 / 0.95 (37445) SS BOND : bond 0.01630 / 1.07 ( 42) SS BOND : angle 3.28998 / 2.04 ( 84) hydrogen bonds : bond 0.13363 / 8.82 ( 1177) hydrogen bonds : angle 6.96408 / 4.78 ( 3156) link_BETA1-4 : bond 0.00657 / 0.41 ( 20) link_BETA1-4 : angle 2.47361 / 1.59 ( 60) link_NAG-ASN : bond 0.01032 / 0.69 ( 46) link_NAG-ASN : angle 3.43967 / 2.22 ( 138) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 252 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 TYR cc_start: 0.9376 (p90) cc_final: 0.9101 (t80) REVERT: A 386 LYS cc_start: 0.9649 (mmpt) cc_final: 0.9410 (ptpt) REVERT: A 979 ASP cc_start: 0.9664 (m-30) cc_final: 0.9165 (t0) REVERT: A 1107 ARG cc_start: 0.9626 (OUTLIER) cc_final: 0.9347 (ptp-170) REVERT: B 117 LEU cc_start: 0.9409 (mp) cc_final: 0.9144 (tt) REVERT: B 224 GLU cc_start: 0.9652 (OUTLIER) cc_final: 0.9408 (pm20) REVERT: B 229 LEU cc_start: 0.9150 (mt) cc_final: 0.8692 (tp) REVERT: B 869 MET cc_start: 0.9391 (mtp) cc_final: 0.9002 (mtp) REVERT: C 117 LEU cc_start: 0.9374 (mp) cc_final: 0.9038 (tp) REVERT: C 869 MET cc_start: 0.9411 (mtt) cc_final: 0.9181 (mpp) REVERT: D 18 LEU cc_start: 0.4388 (tp) cc_final: 0.3800 (tt) REVERT: D 48 VAL cc_start: 0.8833 (t) cc_final: 0.8600 (t) REVERT: D 73 ASP cc_start: 0.9134 (t0) cc_final: 0.8798 (p0) REVERT: D 84 ASN cc_start: 0.6698 (m-40) cc_final: 0.6312 (m-40) REVERT: D 95 TYR cc_start: 0.9281 (m-80) cc_final: 0.8991 (m-80) REVERT: E 27 ARG cc_start: 0.8659 (ttt180) cc_final: 0.7939 (ptt90) REVERT: E 83 MET cc_start: 0.5893 (mtp) cc_final: 0.5241 (mpp) REVERT: E 88 TYR cc_start: 0.8369 (t80) cc_final: 0.8120 (m-10) REVERT: E 102 VAL cc_start: 0.9046 (t) cc_final: 0.8836 (t) REVERT: E 112 TRP cc_start: 0.8654 (t-100) cc_final: 0.8354 (t-100) REVERT: F 3 GLN cc_start: 0.9304 (tt0) cc_final: 0.9099 (mp10) REVERT: F 67 ARG cc_start: 0.8136 (mtm110) cc_final: 0.7540 (mtm110) REVERT: F 81 LEU cc_start: 0.9490 (tp) cc_final: 0.9041 (tp) REVERT: F 83 MET cc_start: 0.8899 (mtp) cc_final: 0.8631 (mpp) REVERT: F 115 ASP cc_start: 0.8520 (m-30) cc_final: 0.8226 (m-30) outliers start: 21 outliers final: 1 residues processed: 271 average time/residue: 0.2003 time to fit residues: 81.5797 Evaluate side-chains 126 residues out of total 2902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 123 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 226 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 9.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN A 804 GLN A 935 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN C 388 ASN C 607 GLN C 901 GLN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN D 82 GLN E 1 GLN ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.057053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.036104 restraints weight = 207407.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.037773 restraints weight = 79846.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.038872 restraints weight = 45454.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.039587 restraints weight = 31512.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.040022 restraints weight = 24887.291| |-----------------------------------------------------------------------------| r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2769 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2769 r_free = 0.2769 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2769 r_free = 0.2769 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2769 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 27629 Z= 0.182 Angle : 0.653 10.842 37727 Z= 0.330 Chirality : 0.044 0.204 4440 Planarity : 0.004 0.034 4734 Dihedral : 4.790 36.816 3616 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.95 % Allowed : 7.14 % Favored : 91.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.14), residues: 3296 helix: 1.09 (0.20), residues: 687 sheet: 0.33 (0.17), residues: 805 loop : -0.41 (0.14), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 19 TYR 0.025 0.001 TYR B 200 PHE 0.015 0.001 PHE C 135 TRP 0.026 0.002 TRP D 117 HIS 0.009 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.18 (27521) covalent geometry : angle 0.63654 / 0.33 (37445) SS BOND : bond 0.00267 / 0.17 ( 42) SS BOND : angle 0.76984 / 0.49 ( 84) hydrogen bonds : bond 0.04816 / 3.12 ( 1177) hydrogen bonds : angle 5.70208 / 3.94 ( 3156) link_BETA1-4 : bond 0.00233 / 0.14 ( 20) link_BETA1-4 : angle 1.37435 / 0.94 ( 60) link_NAG-ASN : bond 0.00338 / 0.21 ( 46) link_NAG-ASN : angle 2.36415 / 1.54 ( 138) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 133 time to evaluate : 0.983 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 979 ASP cc_start: 0.9199 (m-30) cc_final: 0.8644 (t0) REVERT: B 117 LEU cc_start: 0.9169 (mp) cc_final: 0.8848 (tt) REVERT: B 229 LEU cc_start: 0.9021 (mt) cc_final: 0.8516 (tp) REVERT: B 869 MET cc_start: 0.9205 (mtp) cc_final: 0.8769 (mtp) REVERT: B 900 MET cc_start: 0.9139 (mtt) cc_final: 0.8906 (mtt) REVERT: C 104 TRP cc_start: 0.8703 (m-90) cc_final: 0.8310 (m-90) REVERT: C 117 LEU cc_start: 0.8793 (mp) cc_final: 0.8420 (tt) REVERT: C 427 ASP cc_start: 0.9205 (m-30) cc_final: 0.8797 (t0) REVERT: C 571 ASP cc_start: 0.8046 (t70) cc_final: 0.7476 (t70) REVERT: C 740 MET cc_start: 0.9121 (tpp) cc_final: 0.8543 (tpp) REVERT: C 756 TYR cc_start: 0.9264 (m-80) cc_final: 0.8940 (m-80) REVERT: C 869 MET cc_start: 0.9259 (mtt) cc_final: 0.8987 (mtm) REVERT: C 990 GLU cc_start: 0.9015 (tm-30) cc_final: 0.8760 (pp20) REVERT: D 34 MET cc_start: 0.7024 (tpp) cc_final: 0.6718 (tpt) REVERT: D 73 ASP cc_start: 0.9229 (t0) cc_final: 0.8837 (p0) REVERT: D 76 LYS cc_start: 0.9366 (tptp) cc_final: 0.9119 (tptp) REVERT: D 117 TRP cc_start: 0.7473 (m-90) cc_final: 0.6749 (m-90) REVERT: E 27 ARG cc_start: 0.8150 (ttt180) cc_final: 0.7889 (ptt90) REVERT: F 34 MET cc_start: 0.8902 (mmm) cc_final: 0.8687 (mmm) REVERT: F 46 GLU cc_start: 0.8945 (tt0) cc_final: 0.8704 (pm20) REVERT: F 81 LEU cc_start: 0.9432 (tp) cc_final: 0.8844 (tp) REVERT: F 83 MET cc_start: 0.8679 (mtp) cc_final: 0.8433 (mpp) outliers start: 27 outliers final: 14 residues processed: 158 average time/residue: 0.1760 time to fit residues: 44.3685 Evaluate side-chains 122 residues out of total 2902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 912 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 153 optimal weight: 2.9990 chunk 217 optimal weight: 0.0870 chunk 63 optimal weight: 3.9990 chunk 133 optimal weight: 10.0000 chunk 224 optimal weight: 5.9990 chunk 313 optimal weight: 20.0000 chunk 262 optimal weight: 4.9990 chunk 146 optimal weight: 9.9990 chunk 170 optimal weight: 0.1980 chunk 53 optimal weight: 9.9990 chunk 172 optimal weight: 1.9990 overall best weight: 1.8564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 218 GLN ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 955 ASN A1048 HIS B 901 GLN B1048 HIS C 955 ASN C1005 GLN C1048 HIS E 1 GLN ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.056815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.036049 restraints weight = 195273.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.037697 restraints weight = 77477.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.038761 restraints weight = 44651.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.039397 restraints weight = 31119.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.039909 restraints weight = 25024.067| |-----------------------------------------------------------------------------| r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2769 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2769 r_free = 0.2769 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2769 r_free = 0.2769 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2769 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27629 Z= 0.145 Angle : 0.561 9.645 37727 Z= 0.285 Chirality : 0.043 0.220 4440 Planarity : 0.003 0.042 4734 Dihedral : 4.260 28.437 3607 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.27 % Allowed : 8.23 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.14), residues: 3296 helix: 1.93 (0.21), residues: 670 sheet: 0.34 (0.17), residues: 831 loop : -0.20 (0.14), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 408 TYR 0.021 0.001 TYR D 116 PHE 0.019 0.001 PHE B 168 TRP 0.016 0.001 TRP D 117 HIS 0.007 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (27521) covalent geometry : angle 0.54712 / 0.28 (37445) SS BOND : bond 0.00439 / 0.21 ( 42) SS BOND : angle 0.84106 / 0.49 ( 84) hydrogen bonds : bond 0.04058 / 2.61 ( 1177) hydrogen bonds : angle 5.30514 / 3.68 ( 3156) link_BETA1-4 : bond 0.00226 / 0.13 ( 20) link_BETA1-4 : angle 1.22406 / 0.83 ( 60) link_NAG-ASN : bond 0.00230 / 0.15 ( 46) link_NAG-ASN : angle 1.92512 / 1.27 ( 138) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 128 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 567 ARG cc_start: 0.9284 (OUTLIER) cc_final: 0.9039 (tpp80) REVERT: A 912 THR cc_start: 0.9217 (OUTLIER) cc_final: 0.8794 (p) REVERT: A 979 ASP cc_start: 0.9203 (m-30) cc_final: 0.8660 (t0) REVERT: B 117 LEU cc_start: 0.9154 (mp) cc_final: 0.8887 (tt) REVERT: B 229 LEU cc_start: 0.9040 (mt) cc_final: 0.8538 (tp) REVERT: B 740 MET cc_start: 0.8979 (OUTLIER) cc_final: 0.8709 (ttt) REVERT: B 869 MET cc_start: 0.9206 (mtp) cc_final: 0.8834 (mtp) REVERT: C 117 LEU cc_start: 0.8712 (mp) cc_final: 0.8390 (tt) REVERT: C 427 ASP cc_start: 0.9235 (m-30) cc_final: 0.8865 (t0) REVERT: C 571 ASP cc_start: 0.8005 (t70) cc_final: 0.7426 (t70) REVERT: C 740 MET cc_start: 0.9219 (tpp) cc_final: 0.8799 (tpp) REVERT: D 73 ASP cc_start: 0.9197 (t0) cc_final: 0.8833 (p0) REVERT: D 117 TRP cc_start: 0.7507 (m-90) cc_final: 0.6749 (m-90) REVERT: E 27 ARG cc_start: 0.8175 (ttt180) cc_final: 0.7810 (ptt180) REVERT: F 46 GLU cc_start: 0.8937 (tt0) cc_final: 0.8707 (pm20) REVERT: F 81 LEU cc_start: 0.9395 (tp) cc_final: 0.8761 (tp) outliers start: 36 outliers final: 16 residues processed: 159 average time/residue: 0.1712 time to fit residues: 44.2489 Evaluate side-chains 130 residues out of total 2902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 912 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 141 optimal weight: 8.9990 chunk 14 optimal weight: 5.9990 chunk 278 optimal weight: 0.0270 chunk 80 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 chunk 309 optimal weight: 10.0000 chunk 237 optimal weight: 0.0980 chunk 34 optimal weight: 30.0000 chunk 8 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 180 optimal weight: 6.9990 overall best weight: 1.6042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN E 1 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.056620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.036093 restraints weight = 193691.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.037679 restraints weight = 77329.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.038729 restraints weight = 44819.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.039423 restraints weight = 31373.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.039890 restraints weight = 24800.064| |-----------------------------------------------------------------------------| r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2768 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2768 r_free = 0.2768 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2768 r_free = 0.2768 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2768 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27629 Z= 0.125 Angle : 0.524 9.628 37727 Z= 0.265 Chirality : 0.042 0.229 4440 Planarity : 0.003 0.038 4734 Dihedral : 4.010 29.039 3607 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.27 % Allowed : 8.37 % Favored : 90.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.14), residues: 3296 helix: 2.25 (0.21), residues: 663 sheet: 0.40 (0.17), residues: 859 loop : -0.01 (0.15), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 19 TYR 0.016 0.001 TYR B 200 PHE 0.012 0.001 PHE B 329 TRP 0.015 0.001 TRP D 117 HIS 0.007 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 (27521) covalent geometry : angle 0.51292 / 0.26 (37445) SS BOND : bond 0.00228 / 0.15 ( 42) SS BOND : angle 0.55768 / 0.37 ( 84) hydrogen bonds : bond 0.03724 / 2.39 ( 1177) hydrogen bonds : angle 5.09621 / 3.52 ( 3156) link_BETA1-4 : bond 0.00181 / 0.11 ( 20) link_BETA1-4 : angle 1.19788 / 0.80 ( 60) link_NAG-ASN : bond 0.00181 / 0.11 ( 46) link_NAG-ASN : angle 1.69170 / 1.13 ( 138) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 128 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.9395 (OUTLIER) cc_final: 0.9164 (m) REVERT: A 567 ARG cc_start: 0.9319 (OUTLIER) cc_final: 0.9104 (tpp80) REVERT: A 697 MET cc_start: 0.8902 (ttm) cc_final: 0.8685 (ttm) REVERT: A 912 THR cc_start: 0.9225 (OUTLIER) cc_final: 0.8811 (p) REVERT: A 979 ASP cc_start: 0.9249 (m-30) cc_final: 0.8688 (t0) REVERT: B 117 LEU cc_start: 0.9213 (mp) cc_final: 0.8811 (tt) REVERT: B 229 LEU cc_start: 0.9135 (mt) cc_final: 0.8596 (tp) REVERT: B 468 ILE cc_start: 0.9634 (OUTLIER) cc_final: 0.9220 (mp) REVERT: B 740 MET cc_start: 0.8959 (ttt) cc_final: 0.8700 (ttt) REVERT: B 869 MET cc_start: 0.9223 (mtp) cc_final: 0.8819 (mtp) REVERT: C 427 ASP cc_start: 0.9226 (m-30) cc_final: 0.8874 (t0) REVERT: C 571 ASP cc_start: 0.7963 (t70) cc_final: 0.7451 (t70) REVERT: C 740 MET cc_start: 0.9193 (tpp) cc_final: 0.8596 (tpp) REVERT: C 900 MET cc_start: 0.9054 (mtp) cc_final: 0.8805 (mtt) REVERT: C 957 GLN cc_start: 0.9270 (mt0) cc_final: 0.9040 (tt0) REVERT: D 34 MET cc_start: 0.6573 (tpp) cc_final: 0.6297 (tpt) REVERT: D 73 ASP cc_start: 0.9229 (t0) cc_final: 0.8833 (p0) REVERT: D 117 TRP cc_start: 0.7403 (m-90) cc_final: 0.6570 (m-90) REVERT: F 46 GLU cc_start: 0.8911 (tt0) cc_final: 0.8701 (pm20) REVERT: F 67 ARG cc_start: 0.8547 (ptm-80) cc_final: 0.8136 (ptm160) REVERT: F 81 LEU cc_start: 0.9149 (tp) cc_final: 0.8857 (tp) outliers start: 36 outliers final: 22 residues processed: 160 average time/residue: 0.1826 time to fit residues: 46.1734 Evaluate side-chains 136 residues out of total 2902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain E residue 1 GLN Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 112 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 199 optimal weight: 9.9990 chunk 313 optimal weight: 30.0000 chunk 56 optimal weight: 5.9990 chunk 327 optimal weight: 20.0000 chunk 191 optimal weight: 6.9990 chunk 194 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 49 optimal weight: 6.9990 chunk 175 optimal weight: 7.9990 chunk 243 optimal weight: 3.9990 chunk 326 optimal weight: 2.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1011 GLN ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 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 = 0.3288 r_free = 0.3288 target = 0.055778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.034819 restraints weight = 242162.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.036468 restraints weight = 89598.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.037548 restraints weight = 50407.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.038265 restraints weight = 34796.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.038707 restraints weight = 27286.776| |-----------------------------------------------------------------------------| r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2732 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2732 r_free = 0.2732 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2732 r_free = 0.2732 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2732 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 27629 Z= 0.187 Angle : 0.550 9.556 37727 Z= 0.276 Chirality : 0.042 0.227 4440 Planarity : 0.003 0.038 4734 Dihedral : 3.966 29.170 3607 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.69 % Allowed : 8.55 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.15), residues: 3296 helix: 2.28 (0.21), residues: 674 sheet: 0.43 (0.17), residues: 866 loop : -0.00 (0.15), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1039 TYR 0.024 0.001 TYR F 88 PHE 0.011 0.001 PHE B 329 TRP 0.011 0.001 TRP D 117 HIS 0.007 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.19 (27521) covalent geometry : angle 0.53906 / 0.27 (37445) SS BOND : bond 0.00251 / 0.16 ( 42) SS BOND : angle 0.57277 / 0.39 ( 84) hydrogen bonds : bond 0.03777 / 2.43 ( 1177) hydrogen bonds : angle 5.06963 / 3.50 ( 3156) link_BETA1-4 : bond 0.00157 / 0.08 ( 20) link_BETA1-4 : angle 1.30031 / 0.88 ( 60) link_NAG-ASN : bond 0.00289 / 0.19 ( 46) link_NAG-ASN : angle 1.73751 / 1.18 ( 138) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 114 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.9394 (OUTLIER) cc_final: 0.9164 (m) REVERT: A 387 LEU cc_start: 0.9682 (mt) cc_final: 0.9425 (mp) REVERT: A 912 THR cc_start: 0.9284 (OUTLIER) cc_final: 0.8859 (p) REVERT: A 979 ASP cc_start: 0.9258 (m-30) cc_final: 0.8711 (t0) REVERT: B 224 GLU cc_start: 0.9282 (OUTLIER) cc_final: 0.8650 (pm20) REVERT: B 229 LEU cc_start: 0.9131 (mt) cc_final: 0.8653 (tp) REVERT: B 468 ILE cc_start: 0.9664 (OUTLIER) cc_final: 0.9268 (mp) REVERT: B 740 MET cc_start: 0.8992 (ttt) cc_final: 0.8777 (ttt) REVERT: C 468 ILE cc_start: 0.8222 (OUTLIER) cc_final: 0.7390 (mm) REVERT: C 571 ASP cc_start: 0.7914 (t70) cc_final: 0.7424 (t70) REVERT: C 740 MET cc_start: 0.9179 (tpp) cc_final: 0.8776 (tpp) REVERT: C 900 MET cc_start: 0.9120 (mtp) cc_final: 0.8874 (mtt) REVERT: C 957 GLN cc_start: 0.9269 (OUTLIER) cc_final: 0.9026 (tt0) REVERT: D 34 MET cc_start: 0.6721 (tpp) cc_final: 0.6444 (tpt) REVERT: D 73 ASP cc_start: 0.9235 (t0) cc_final: 0.8839 (p0) REVERT: D 117 TRP cc_start: 0.7465 (m-90) cc_final: 0.6632 (m-90) REVERT: F 67 ARG cc_start: 0.8657 (ptm-80) cc_final: 0.8156 (ptm160) outliers start: 48 outliers final: 27 residues processed: 157 average time/residue: 0.1683 time to fit residues: 42.8787 Evaluate side-chains 138 residues out of total 2902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 105 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain E residue 112 TRP Chi-restraints excluded: chain F residue 79 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 67 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 chunk 126 optimal weight: 0.8980 chunk 331 optimal weight: 0.9990 chunk 167 optimal weight: 0.9980 chunk 97 optimal weight: 10.0000 chunk 231 optimal weight: 1.9990 chunk 178 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 chunk 290 optimal weight: 3.9990 chunk 125 optimal weight: 9.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 519 HIS B 762 GLN ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.056133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.035614 restraints weight = 189479.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.037155 restraints weight = 76993.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.038177 restraints weight = 45062.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.038849 restraints weight = 31959.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.039257 restraints weight = 25354.697| |-----------------------------------------------------------------------------| r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2751 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2751 r_free = 0.2751 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2751 r_free = 0.2751 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2751 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27629 Z= 0.129 Angle : 0.510 9.562 37727 Z= 0.258 Chirality : 0.042 0.229 4440 Planarity : 0.003 0.042 4734 Dihedral : 3.866 29.114 3607 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.51 % Allowed : 9.00 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.15), residues: 3296 helix: 2.37 (0.21), residues: 675 sheet: 0.48 (0.17), residues: 865 loop : 0.04 (0.15), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 567 TYR 0.023 0.001 TYR E 104 PHE 0.011 0.001 PHE B 329 TRP 0.011 0.001 TRP D 117 HIS 0.006 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (27521) covalent geometry : angle 0.50115 / 0.26 (37445) SS BOND : bond 0.00198 / 0.13 ( 42) SS BOND : angle 0.47084 / 0.32 ( 84) hydrogen bonds : bond 0.03558 / 2.29 ( 1177) hydrogen bonds : angle 4.94736 / 3.42 ( 3156) link_BETA1-4 : bond 0.00194 / 0.12 ( 20) link_BETA1-4 : angle 1.13387 / 0.76 ( 60) link_NAG-ASN : bond 0.00175 / 0.11 ( 46) link_NAG-ASN : angle 1.54789 / 1.05 ( 138) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 109 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.9397 (OUTLIER) cc_final: 0.9139 (p) REVERT: A 387 LEU cc_start: 0.9670 (mt) cc_final: 0.9411 (mp) REVERT: A 697 MET cc_start: 0.8893 (ttm) cc_final: 0.8503 (ttm) REVERT: A 900 MET cc_start: 0.9491 (mtm) cc_final: 0.9284 (mtm) REVERT: A 912 THR cc_start: 0.9283 (OUTLIER) cc_final: 0.8873 (p) REVERT: A 979 ASP cc_start: 0.9250 (m-30) cc_final: 0.8725 (t0) REVERT: B 224 GLU cc_start: 0.9271 (OUTLIER) cc_final: 0.8885 (mp0) REVERT: B 229 LEU cc_start: 0.9112 (mt) cc_final: 0.8630 (tp) REVERT: B 468 ILE cc_start: 0.9684 (OUTLIER) cc_final: 0.9313 (mp) REVERT: B 740 MET cc_start: 0.9003 (ttt) cc_final: 0.8751 (ttt) REVERT: B 869 MET cc_start: 0.9285 (mtp) cc_final: 0.9059 (mtp) REVERT: C 468 ILE cc_start: 0.8299 (OUTLIER) cc_final: 0.7475 (mm) REVERT: C 571 ASP cc_start: 0.7862 (t70) cc_final: 0.7373 (t70) REVERT: C 740 MET cc_start: 0.9139 (tpp) cc_final: 0.8756 (tpp) REVERT: C 900 MET cc_start: 0.9056 (mtp) cc_final: 0.8794 (mtt) REVERT: C 957 GLN cc_start: 0.9254 (OUTLIER) cc_final: 0.9011 (tt0) REVERT: D 12 MET cc_start: 0.1697 (pmm) cc_final: 0.1054 (ptp) REVERT: D 34 MET cc_start: 0.6807 (tpp) cc_final: 0.6566 (tpt) REVERT: D 73 ASP cc_start: 0.9210 (t0) cc_final: 0.8818 (p0) REVERT: D 117 TRP cc_start: 0.7449 (m-90) cc_final: 0.6676 (m-90) REVERT: F 67 ARG cc_start: 0.8687 (ptm-80) cc_final: 0.8259 (ptm160) outliers start: 43 outliers final: 27 residues processed: 148 average time/residue: 0.1614 time to fit residues: 39.6391 Evaluate side-chains 133 residues out of total 2902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 100 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain E residue 112 TRP Chi-restraints excluded: chain F residue 79 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 259 optimal weight: 2.9990 chunk 163 optimal weight: 7.9990 chunk 188 optimal weight: 0.7980 chunk 187 optimal weight: 0.8980 chunk 137 optimal weight: 10.0000 chunk 323 optimal weight: 10.0000 chunk 296 optimal weight: 6.9990 chunk 322 optimal weight: 7.9990 chunk 103 optimal weight: 9.9990 chunk 133 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 HIS ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C 957 GLN ** F 3 GLN ** 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 = 0.3268 r_free = 0.3268 target = 0.055111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.034741 restraints weight = 176344.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.036205 restraints weight = 75141.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.037166 restraints weight = 44986.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.037777 restraints weight = 32250.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.038208 restraints weight = 26081.619| |-----------------------------------------------------------------------------| r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2712 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2712 r_free = 0.2712 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2712 r_free = 0.2712 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2712 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 27629 Z= 0.241 Angle : 0.592 9.494 37727 Z= 0.294 Chirality : 0.042 0.225 4440 Planarity : 0.003 0.048 4734 Dihedral : 3.998 29.300 3607 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.72 % Allowed : 9.36 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.15), residues: 3296 helix: 2.36 (0.20), residues: 679 sheet: 0.38 (0.16), residues: 869 loop : -0.03 (0.15), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 567 TYR 0.019 0.001 TYR E 104 PHE 0.015 0.001 PHE C 802 TRP 0.013 0.001 TRP F 53 HIS 0.023 0.002 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.24 (27521) covalent geometry : angle 0.58013 / 0.29 (37445) SS BOND : bond 0.00406 / 0.30 ( 42) SS BOND : angle 0.86079 / 0.54 ( 84) hydrogen bonds : bond 0.03826 / 2.47 ( 1177) hydrogen bonds : angle 5.07624 / 3.50 ( 3156) link_BETA1-4 : bond 0.00224 / 0.12 ( 20) link_BETA1-4 : angle 1.39676 / 0.94 ( 60) link_NAG-ASN : bond 0.00422 / 0.27 ( 46) link_NAG-ASN : angle 1.75597 / 1.21 ( 138) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 101 time to evaluate : 1.079 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 34 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.8059 (mmt90) REVERT: A 63 THR cc_start: 0.9406 (OUTLIER) cc_final: 0.9162 (m) REVERT: A 387 LEU cc_start: 0.9682 (mt) cc_final: 0.9408 (mp) REVERT: A 697 MET cc_start: 0.8833 (ttm) cc_final: 0.8305 (ttm) REVERT: A 740 MET cc_start: 0.8951 (OUTLIER) cc_final: 0.8742 (ttp) REVERT: A 912 THR cc_start: 0.9345 (OUTLIER) cc_final: 0.8926 (p) REVERT: A 979 ASP cc_start: 0.9204 (m-30) cc_final: 0.8828 (t0) REVERT: A 1017 GLU cc_start: 0.8801 (tm-30) cc_final: 0.8529 (tm-30) REVERT: B 224 GLU cc_start: 0.9273 (OUTLIER) cc_final: 0.8654 (pm20) REVERT: B 229 LEU cc_start: 0.9207 (mt) cc_final: 0.8717 (tp) REVERT: B 468 ILE cc_start: 0.9697 (OUTLIER) cc_final: 0.9342 (mp) REVERT: B 725 GLU cc_start: 0.8602 (tt0) cc_final: 0.8043 (tt0) REVERT: B 869 MET cc_start: 0.9317 (mtp) cc_final: 0.9037 (mtp) REVERT: C 468 ILE cc_start: 0.8485 (OUTLIER) cc_final: 0.7745 (mm) REVERT: C 571 ASP cc_start: 0.7882 (t70) cc_final: 0.7420 (t70) REVERT: C 900 MET cc_start: 0.9112 (mtp) cc_final: 0.8858 (mtt) REVERT: D 12 MET cc_start: 0.1633 (pmm) cc_final: 0.0945 (ptp) REVERT: D 34 MET cc_start: 0.6799 (tpp) cc_final: 0.6571 (tpt) REVERT: D 117 TRP cc_start: 0.7339 (m-90) cc_final: 0.6477 (m-90) REVERT: F 46 GLU cc_start: 0.8438 (pm20) cc_final: 0.8232 (pm20) REVERT: F 67 ARG cc_start: 0.8688 (ptm-80) cc_final: 0.8420 (ptm160) REVERT: F 108 ASP cc_start: 0.9136 (t0) cc_final: 0.8791 (m-30) outliers start: 49 outliers final: 35 residues processed: 145 average time/residue: 0.1711 time to fit residues: 41.2155 Evaluate side-chains 136 residues out of total 2902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 94 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain E residue 112 TRP Chi-restraints excluded: chain F residue 79 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 19 optimal weight: 0.4980 chunk 114 optimal weight: 10.0000 chunk 234 optimal weight: 20.0000 chunk 186 optimal weight: 8.9990 chunk 214 optimal weight: 6.9990 chunk 103 optimal weight: 9.9990 chunk 88 optimal weight: 20.0000 chunk 243 optimal weight: 7.9990 chunk 113 optimal weight: 3.9990 chunk 319 optimal weight: 6.9990 chunk 277 optimal weight: 3.9990 overall best weight: 4.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS A 519 HIS B 762 GLN ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.054384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2576 r_free = 0.2576 target = 0.033765 restraints weight = 258366.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.035362 restraints weight = 92625.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.036422 restraints weight = 51457.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.037117 restraints weight = 35268.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.037539 restraints weight = 27583.511| |-----------------------------------------------------------------------------| r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2688 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2688 r_free = 0.2688 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2688 r_free = 0.2688 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2688 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 27629 Z= 0.268 Angle : 0.606 9.454 37727 Z= 0.303 Chirality : 0.042 0.223 4440 Planarity : 0.003 0.037 4734 Dihedral : 4.136 29.012 3607 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.72 % Allowed : 9.64 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.15), residues: 3296 helix: 2.24 (0.20), residues: 679 sheet: 0.19 (0.16), residues: 876 loop : -0.09 (0.15), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 19 TYR 0.019 0.001 TYR B 200 PHE 0.016 0.001 PHE C 802 TRP 0.017 0.001 TRP F 53 HIS 0.006 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00569 / 0.27 (27521) covalent geometry : angle 0.59567 / 0.30 (37445) SS BOND : bond 0.00330 / 0.22 ( 42) SS BOND : angle 0.81195 / 0.56 ( 84) hydrogen bonds : bond 0.03963 / 2.56 ( 1177) hydrogen bonds : angle 5.18480 / 3.58 ( 3156) link_BETA1-4 : bond 0.00234 / 0.12 ( 20) link_BETA1-4 : angle 1.28563 / 0.88 ( 60) link_NAG-ASN : bond 0.00412 / 0.26 ( 46) link_NAG-ASN : angle 1.73006 / 1.20 ( 138) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 98 time to evaluate : 1.037 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 34 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.8002 (mmt90) REVERT: A 63 THR cc_start: 0.9398 (OUTLIER) cc_final: 0.9143 (p) REVERT: A 387 LEU cc_start: 0.9675 (mt) cc_final: 0.9391 (mp) REVERT: A 697 MET cc_start: 0.8864 (ttm) cc_final: 0.8480 (ttm) REVERT: A 740 MET cc_start: 0.8998 (OUTLIER) cc_final: 0.8767 (ttp) REVERT: A 912 THR cc_start: 0.9374 (OUTLIER) cc_final: 0.8947 (p) REVERT: A 979 ASP cc_start: 0.9221 (m-30) cc_final: 0.8867 (t0) REVERT: A 1017 GLU cc_start: 0.8885 (tm-30) cc_final: 0.8582 (tm-30) REVERT: B 224 GLU cc_start: 0.9287 (OUTLIER) cc_final: 0.8700 (pm20) REVERT: B 229 LEU cc_start: 0.9246 (mt) cc_final: 0.8741 (tp) REVERT: B 468 ILE cc_start: 0.9720 (OUTLIER) cc_final: 0.9392 (mp) REVERT: B 725 GLU cc_start: 0.8612 (tt0) cc_final: 0.8061 (tt0) REVERT: B 869 MET cc_start: 0.9295 (mtp) cc_final: 0.8970 (mtp) REVERT: C 468 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.7855 (mm) REVERT: C 571 ASP cc_start: 0.7940 (t70) cc_final: 0.7527 (t70) REVERT: C 900 MET cc_start: 0.9148 (mtp) cc_final: 0.8898 (mtt) REVERT: D 12 MET cc_start: 0.1942 (pmm) cc_final: 0.1445 (ptp) REVERT: D 117 TRP cc_start: 0.7265 (m-90) cc_final: 0.6363 (m-90) REVERT: F 12 MET cc_start: 0.8714 (mmm) cc_final: 0.8150 (tpt) REVERT: F 67 ARG cc_start: 0.8686 (ptm-80) cc_final: 0.8455 (ptm160) outliers start: 49 outliers final: 33 residues processed: 141 average time/residue: 0.1800 time to fit residues: 42.1179 Evaluate side-chains 129 residues out of total 2902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 89 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain F residue 79 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 68 optimal weight: 0.9980 chunk 309 optimal weight: 30.0000 chunk 151 optimal weight: 7.9990 chunk 181 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 237 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 191 optimal weight: 2.9990 chunk 260 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 243 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 39 GLN ** F 39 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 = 0.3280 r_free = 0.3280 target = 0.055512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.035152 restraints weight = 186207.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.036678 restraints weight = 76949.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 69)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.037680 restraints weight = 45299.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.038310 restraints weight = 32063.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.038710 restraints weight = 25794.186| |-----------------------------------------------------------------------------| r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2734 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2734 r_free = 0.2734 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2734 r_free = 0.2734 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2734 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 27629 Z= 0.122 Angle : 0.519 11.364 37727 Z= 0.262 Chirality : 0.042 0.228 4440 Planarity : 0.003 0.037 4734 Dihedral : 3.913 28.718 3607 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.30 % Allowed : 10.38 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.15), residues: 3296 helix: 2.36 (0.20), residues: 681 sheet: 0.30 (0.17), residues: 844 loop : 0.01 (0.15), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 567 TYR 0.019 0.001 TYR F 88 PHE 0.012 0.001 PHE C 802 TRP 0.011 0.001 TRP D 117 HIS 0.006 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (27521) covalent geometry : angle 0.51110 / 0.26 (37445) SS BOND : bond 0.00219 / 0.15 ( 42) SS BOND : angle 0.58506 / 0.38 ( 84) hydrogen bonds : bond 0.03588 / 2.31 ( 1177) hydrogen bonds : angle 4.93290 / 3.40 ( 3156) link_BETA1-4 : bond 0.00231 / 0.15 ( 20) link_BETA1-4 : angle 1.03451 / 0.69 ( 60) link_NAG-ASN : bond 0.00170 / 0.11 ( 46) link_NAG-ASN : angle 1.43430 / 0.98 ( 138) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 99 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.9395 (OUTLIER) cc_final: 0.9154 (p) REVERT: A 387 LEU cc_start: 0.9641 (mt) cc_final: 0.9360 (mp) REVERT: A 697 MET cc_start: 0.8845 (ttm) cc_final: 0.8507 (ttp) REVERT: A 912 THR cc_start: 0.9351 (OUTLIER) cc_final: 0.8929 (p) REVERT: A 979 ASP cc_start: 0.9175 (m-30) cc_final: 0.8823 (t70) REVERT: A 1017 GLU cc_start: 0.8833 (tm-30) cc_final: 0.8487 (tm-30) REVERT: B 224 GLU cc_start: 0.9253 (OUTLIER) cc_final: 0.8863 (mp0) REVERT: B 229 LEU cc_start: 0.9267 (mt) cc_final: 0.8741 (tp) REVERT: B 468 ILE cc_start: 0.9724 (OUTLIER) cc_final: 0.9412 (mp) REVERT: B 725 GLU cc_start: 0.8577 (tt0) cc_final: 0.8038 (tt0) REVERT: B 957 GLN cc_start: 0.8863 (mt0) cc_final: 0.8542 (tt0) REVERT: C 468 ILE cc_start: 0.8570 (OUTLIER) cc_final: 0.7849 (mm) REVERT: C 571 ASP cc_start: 0.7880 (t70) cc_final: 0.7459 (t70) REVERT: C 725 GLU cc_start: 0.8517 (tt0) cc_final: 0.8099 (tt0) REVERT: C 900 MET cc_start: 0.9068 (mtp) cc_final: 0.8804 (mtt) REVERT: D 12 MET cc_start: 0.2003 (pmm) cc_final: 0.1535 (ptp) REVERT: D 83 MET cc_start: -0.0131 (mtp) cc_final: -0.0429 (mtp) REVERT: D 117 TRP cc_start: 0.7202 (m-90) cc_final: 0.6380 (m-90) REVERT: F 12 MET cc_start: 0.8491 (mmm) cc_final: 0.7921 (tpp) REVERT: F 34 MET cc_start: 0.8951 (mmm) cc_final: 0.8468 (mmm) REVERT: F 67 ARG cc_start: 0.8740 (ptm-80) cc_final: 0.8493 (ptm160) REVERT: F 108 ASP cc_start: 0.9158 (t0) cc_final: 0.8876 (m-30) outliers start: 37 outliers final: 24 residues processed: 133 average time/residue: 0.1593 time to fit residues: 35.6674 Evaluate side-chains 126 residues out of total 2902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 97 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 977 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 251 optimal weight: 7.9990 chunk 177 optimal weight: 6.9990 chunk 165 optimal weight: 0.3980 chunk 88 optimal weight: 7.9990 chunk 152 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 25 optimal weight: 8.9990 chunk 262 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 chunk 35 optimal weight: 20.0000 chunk 17 optimal weight: 1.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.054862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.034557 restraints weight = 186656.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.036064 restraints weight = 77797.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.037033 restraints weight = 46010.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.037578 restraints weight = 32707.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.038054 restraints weight = 26875.268| |-----------------------------------------------------------------------------| r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2709 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2709 r_free = 0.2709 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2709 r_free = 0.2709 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2709 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 27629 Z= 0.204 Angle : 0.562 12.753 37727 Z= 0.280 Chirality : 0.042 0.227 4440 Planarity : 0.003 0.037 4734 Dihedral : 3.950 29.064 3607 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.09 % Allowed : 10.55 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.15), residues: 3296 helix: 2.34 (0.20), residues: 681 sheet: 0.32 (0.17), residues: 827 loop : -0.01 (0.15), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 567 TYR 0.019 0.001 TYR F 88 PHE 0.011 0.001 PHE B 329 TRP 0.012 0.001 TRP F 53 HIS 0.006 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.20 (27521) covalent geometry : angle 0.55223 / 0.28 (37445) SS BOND : bond 0.00267 / 0.18 ( 42) SS BOND : angle 0.78563 / 0.50 ( 84) hydrogen bonds : bond 0.03697 / 2.39 ( 1177) hydrogen bonds : angle 4.99529 / 3.44 ( 3156) link_BETA1-4 : bond 0.00166 / 0.09 ( 20) link_BETA1-4 : angle 1.22197 / 0.82 ( 60) link_NAG-ASN : bond 0.00304 / 0.19 ( 46) link_NAG-ASN : angle 1.58030 / 1.09 ( 138) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 2902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 94 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.9399 (OUTLIER) cc_final: 0.9140 (p) REVERT: A 387 LEU cc_start: 0.9639 (mt) cc_final: 0.9341 (mp) REVERT: A 697 MET cc_start: 0.8837 (ttm) cc_final: 0.8518 (ttp) REVERT: A 912 THR cc_start: 0.9356 (OUTLIER) cc_final: 0.8939 (p) REVERT: A 979 ASP cc_start: 0.9182 (m-30) cc_final: 0.8848 (t0) REVERT: A 1017 GLU cc_start: 0.8856 (tm-30) cc_final: 0.8533 (tm-30) REVERT: B 224 GLU cc_start: 0.9250 (OUTLIER) cc_final: 0.8853 (mp0) REVERT: B 229 LEU cc_start: 0.9237 (mt) cc_final: 0.8713 (tp) REVERT: B 468 ILE cc_start: 0.9724 (OUTLIER) cc_final: 0.9348 (mp) REVERT: B 725 GLU cc_start: 0.8600 (tt0) cc_final: 0.8060 (tt0) REVERT: B 869 MET cc_start: 0.9290 (mtp) cc_final: 0.8926 (mtp) REVERT: C 468 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.7991 (mm) REVERT: C 571 ASP cc_start: 0.7901 (t70) cc_final: 0.7497 (t70) REVERT: C 725 GLU cc_start: 0.8493 (tt0) cc_final: 0.8033 (tt0) REVERT: C 900 MET cc_start: 0.9111 (mtp) cc_final: 0.8853 (mtt) REVERT: D 12 MET cc_start: 0.1807 (pmm) cc_final: 0.1184 (ptp) REVERT: D 34 MET cc_start: 0.6425 (tpp) cc_final: 0.6045 (tpt) REVERT: D 117 TRP cc_start: 0.7149 (m-90) cc_final: 0.6287 (m-90) REVERT: F 12 MET cc_start: 0.8548 (mmm) cc_final: 0.8009 (tpp) REVERT: F 34 MET cc_start: 0.9038 (mmm) cc_final: 0.8515 (mmm) REVERT: F 67 ARG cc_start: 0.8750 (ptm-80) cc_final: 0.8503 (ptm160) outliers start: 31 outliers final: 25 residues processed: 123 average time/residue: 0.1652 time to fit residues: 34.5528 Evaluate side-chains 118 residues out of total 2902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 88 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain F residue 79 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 253 optimal weight: 5.9990 chunk 163 optimal weight: 6.9990 chunk 288 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 308 optimal weight: 10.0000 chunk 251 optimal weight: 6.9990 chunk 195 optimal weight: 2.9990 chunk 295 optimal weight: 0.1980 chunk 277 optimal weight: 0.9980 chunk 313 optimal weight: 40.0000 chunk 58 optimal weight: 2.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.055381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.034628 restraints weight = 236167.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.036265 restraints weight = 88006.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.037354 restraints weight = 49624.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.038077 restraints weight = 34326.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.038546 restraints weight = 26934.004| |-----------------------------------------------------------------------------| r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2731 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2731 r_free = 0.2731 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2731 r_free = 0.2731 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.2731 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 27629 Z= 0.145 Angle : 0.544 19.759 37727 Z= 0.274 Chirality : 0.042 0.322 4440 Planarity : 0.003 0.037 4734 Dihedral : 3.884 29.007 3607 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.30 % Allowed : 10.62 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.15), residues: 3296 helix: 2.36 (0.20), residues: 682 sheet: 0.33 (0.17), residues: 848 loop : 0.03 (0.15), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 27 TYR 0.020 0.001 TYR F 88 PHE 0.011 0.001 PHE B 329 TRP 0.020 0.001 TRP E 53 HIS 0.006 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (27521) covalent geometry : angle 0.52467 / 0.27 (37445) SS BOND : bond 0.00207 / 0.14 ( 42) SS BOND : angle 2.42061 / 1.34 ( 84) hydrogen bonds : bond 0.03609 / 2.34 ( 1177) hydrogen bonds : angle 4.93632 / 3.40 ( 3156) link_BETA1-4 : bond 0.00188 / 0.12 ( 20) link_BETA1-4 : angle 1.05725 / 0.71 ( 60) link_NAG-ASN : bond 0.00183 / 0.12 ( 46) link_NAG-ASN : angle 1.43685 / 0.98 ( 138) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4941.98 seconds wall clock time: 86 minutes 6.01 seconds (5166.01 seconds total)