Starting phenix.real_space_refine on Sun Jul 5 22:34:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7q9p_13875/07_2026/7q9p_13875.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q9p_13875/07_2026/7q9p_13875.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7q9p_13875/07_2026/7q9p_13875.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7q9p_13875/07_2026/7q9p_13875.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7q9p_13875/07_2026/7q9p_13875.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q9p_13875/07_2026/7q9p_13875.map" model { file = "/net/cci-nas-00/data/ceres_data/7q9p_13875/07_2026/7q9p_13875.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q9p_13875/07_2026/7q9p_13875.cif" } resolution = 4.5 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= 0.003 sd= 0.025 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 132 5.16 5 C 19400 2.51 5 N 5010 2.21 5 O 5952 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30494 Number of models: 1 Model: "" Number of chains: 24 Chain: "B" Number of atoms: 8148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8148 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 52, 'TRANS': 987} Chain breaks: 6 Chain: "C" Number of atoms: 8118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1036, 8118 Classifications: {'peptide': 1036} Link IDs: {'PTRANS': 51, 'TRANS': 984} Chain breaks: 6 Chain: "A" Number of atoms: 8154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8154 Classifications: {'peptide': 1041} Link IDs: {'PTRANS': 52, 'TRANS': 988} Chain breaks: 6 Chain: "H" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 946 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 6, 'TRANS': 115} Chain: "L" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 836 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 99} Chain: "E" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 946 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 6, 'TRANS': 115} Chain: "F" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 836 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 99} Chain: "J" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 946 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 6, 'TRANS': 115} Chain: "K" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 836 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 99} Chain: "D" 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: "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: "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: "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: "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 Chain: "A" 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 Time building chain proxies: 7.04, per 1000 atoms: 0.23 Number of scatterers: 30494 At special positions: 0 Unit cell: (160.19, 184.26, 221.61, 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 132 16.00 O 5952 8.00 N 5010 7.00 C 19400 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.03 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " distance=2.03 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 587 " distance=2.03 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.03 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.03 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.02 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS C 376 " - pdb=" SG CYS C 429 " distance=2.03 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 522 " distance=2.03 Simple disulfide: pdb=" SG CYS C 477 " - pdb=" SG CYS C 485 " distance=2.03 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 587 " distance=2.03 Simple disulfide: pdb=" SG CYS C 614 " - pdb=" SG CYS C 646 " distance=2.03 Simple disulfide: pdb=" SG CYS C 659 " - pdb=" SG CYS C 668 " distance=2.03 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 757 " distance=2.02 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.03 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=2.02 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 587 " distance=2.03 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 646 " distance=2.03 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 97 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 97 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 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-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 279 " " NAG A1303 " - " ASN A 328 " " NAG A1304 " - " ASN A 600 " " NAG A1305 " - " ASN A 613 " " NAG A1306 " - " ASN A 654 " " NAG A1307 " - " ASN A 706 " " NAG A1308 " - " ASN A1071 " " NAG A1309 " - " ASN A 165 " " NAG A1310 " - " ASN A 340 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 279 " " NAG B1303 " - " ASN B 328 " " NAG B1304 " - " ASN B 600 " " NAG B1305 " - " ASN B 613 " " NAG B1306 " - " ASN B 654 " " NAG B1307 " - " ASN B 706 " " NAG B1308 " - " ASN B1071 " " NAG B1309 " - " ASN B 165 " " NAG B1310 " - " ASN B 340 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 279 " " NAG C1303 " - " ASN C 600 " " NAG C1304 " - " ASN C 613 " " NAG C1305 " - " ASN C 654 " " NAG C1306 " - " ASN C 706 " " NAG C1307 " - " ASN C1071 " " NAG C1308 " - " ASN C 340 " " NAG D 1 " - " ASN B 714 " " NAG G 1 " - " ASN B 798 " " NAG I 1 " - " ASN B1095 " " NAG M 1 " - " ASN B1131 " " NAG N 1 " - " ASN C 714 " " NAG O 1 " - " ASN C 798 " " NAG P 1 " - " ASN C1095 " " NAG Q 1 " - " ASN C1131 " " NAG R 1 " - " ASN A 714 " " NAG S 1 " - " ASN A 798 " " NAG T 1 " - " ASN A1095 " " NAG U 1 " - " ASN A1131 " Time building additional restraints: 2.93 Conformation dependent library (CDL) restraints added in 1.5 seconds 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7116 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 69 sheets defined 21.7% alpha, 32.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 335 through 340 Processing helix chain 'B' and resid 361 through 367 Processing helix chain 'B' and resid 382 through 386 removed outlier: 3.507A pdb=" N ASN B 385 " --> pdb=" O THR B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 407 removed outlier: 3.918A pdb=" N ARG B 405 " --> pdb=" O ASP B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 435 through 440 Processing helix chain 'B' and resid 734 through 741 Processing helix chain 'B' and resid 743 through 752 removed outlier: 3.771A pdb=" N GLN B 752 " --> pdb=" O ASN B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 780 Processing helix chain 'B' and resid 813 through 823 Processing helix chain 'B' and resid 863 through 882 Processing helix chain 'B' and resid 883 through 888 removed outlier: 3.887A pdb=" N ALA B 887 " --> pdb=" O TRP B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 906 Processing helix chain 'B' and resid 909 through 916 removed outlier: 4.068A pdb=" N LEU B 913 " --> pdb=" O THR B 909 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 938 Processing helix chain 'B' and resid 939 through 941 No H-bonds generated for 'chain 'B' and resid 939 through 941' Processing helix chain 'B' and resid 942 through 963 removed outlier: 3.653A pdb=" N LEU B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 973 through 981 Processing helix chain 'B' and resid 982 through 1029 removed outlier: 4.330A pdb=" N VAL B 988 " --> pdb=" O PRO B 984 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLN B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG B 992 " --> pdb=" O VAL B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1137 through 1144 removed outlier: 3.952A pdb=" N GLU B1141 " --> pdb=" O PRO B1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 335 through 340 Processing helix chain 'C' and resid 362 through 367 Processing helix chain 'C' and resid 381 through 386 removed outlier: 3.720A pdb=" N LEU C 384 " --> pdb=" O PRO C 381 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASN C 385 " --> pdb=" O THR C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 407 removed outlier: 3.894A pdb=" N ARG C 405 " --> pdb=" O ASP C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 419 Processing helix chain 'C' and resid 435 through 440 Processing helix chain 'C' and resid 499 through 502 Processing helix chain 'C' and resid 734 through 741 Processing helix chain 'C' and resid 743 through 752 removed outlier: 3.883A pdb=" N GLN C 752 " --> pdb=" O ASN C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 780 Processing helix chain 'C' and resid 814 through 823 Processing helix chain 'C' and resid 863 through 882 Processing helix chain 'C' and resid 883 through 888 removed outlier: 4.011A pdb=" N ALA C 887 " --> pdb=" O TRP C 883 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 906 Processing helix chain 'C' and resid 909 through 916 removed outlier: 4.318A pdb=" N LEU C 913 " --> pdb=" O THR C 909 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 938 Processing helix chain 'C' and resid 939 through 941 No H-bonds generated for 'chain 'C' and resid 939 through 941' Processing helix chain 'C' and resid 942 through 963 removed outlier: 3.531A pdb=" N VAL C 948 " --> pdb=" O LYS C 944 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 981 Processing helix chain 'C' and resid 982 through 1029 removed outlier: 4.290A pdb=" N VAL C 988 " --> pdb=" O PRO C 984 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLN C 989 " --> pdb=" O GLU C 985 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG C 992 " --> pdb=" O VAL C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1144 removed outlier: 3.759A pdb=" N GLU C1141 " --> pdb=" O PRO C1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 361 through 367 Processing helix chain 'A' and resid 380 through 387 removed outlier: 3.654A pdb=" N LEU A 384 " --> pdb=" O PRO A 381 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASN A 385 " --> pdb=" O THR A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 removed outlier: 3.858A pdb=" N ARG A 405 " --> pdb=" O ASP A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 435 through 440 Processing helix chain 'A' and resid 734 through 741 Processing helix chain 'A' and resid 743 through 752 removed outlier: 3.651A pdb=" N GLN A 752 " --> pdb=" O ASN A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 780 Processing helix chain 'A' and resid 813 through 823 Processing helix chain 'A' and resid 863 through 882 Processing helix chain 'A' and resid 883 through 888 removed outlier: 4.022A pdb=" N ALA A 887 " --> pdb=" O TRP A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 907 Processing helix chain 'A' and resid 909 through 916 removed outlier: 3.971A pdb=" N LEU A 913 " --> pdb=" O THR A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 938 Processing helix chain 'A' and resid 939 through 941 No H-bonds generated for 'chain 'A' and resid 939 through 941' Processing helix chain 'A' and resid 942 through 964 Processing helix chain 'A' and resid 973 through 981 Processing helix chain 'A' and resid 982 through 1029 removed outlier: 4.343A pdb=" N VAL A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN A 989 " --> pdb=" O GLU A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1144 removed outlier: 3.729A pdb=" N GLU A1141 " --> pdb=" O PRO A1137 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 92 removed outlier: 3.694A pdb=" N THR H 92 " --> pdb=" O ALA H 89 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.162A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 92 removed outlier: 3.703A pdb=" N THR E 92 " --> pdb=" O ALA E 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 83 removed outlier: 4.160A pdb=" N PHE F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 92 removed outlier: 3.641A pdb=" N THR J 92 " --> pdb=" O ALA J 89 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 83 removed outlier: 4.132A pdb=" N PHE K 83 " --> pdb=" O PRO K 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 21 through 22 Processing sheet with id=AA2, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.688A pdb=" N ASN B 61 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N TYR B 266 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.024A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.067A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 11.241A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 9.820A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.315A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.347A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 9.476A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 10.845A pdb=" N PHE B 140 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N SER B 155 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N GLY B 142 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N MET B 153 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N TYR B 144 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N SER B 151 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.067A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N SER B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N LEU B 141 " --> pdb=" O SER B 244 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LEU B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL B 143 " --> pdb=" O LEU B 246 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 308 through 315 removed outlier: 5.533A pdb=" N ILE B 309 " --> pdb=" O THR B 596 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N THR B 596 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLN B 311 " --> pdb=" O VAL B 594 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL B 594 " --> pdb=" O GLN B 311 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLY B 591 " --> pdb=" O GLN B 610 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 321 through 325 removed outlier: 4.504A pdb=" N GLU B 321 " --> pdb=" O CYS B 535 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 351 through 355 Processing sheet with id=AA9, first strand: chain 'B' and resid 358 through 359 removed outlier: 6.726A pdb=" N CYS B 358 " --> pdb=" O CYS B 522 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AB2, first strand: chain 'B' and resid 470 through 471 Processing sheet with id=AB3, first strand: chain 'B' and resid 651 through 652 removed outlier: 6.454A pdb=" N ALA B 669 " --> pdb=" O PRO B 662 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 699 through 701 removed outlier: 3.731A pdb=" N LYS C 787 " --> pdb=" O ASN B 700 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 708 through 725 removed outlier: 6.602A pdb=" N SER B 708 " --> pdb=" O THR B1073 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR B1073 " --> pdb=" O SER B 708 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ALA B 710 " --> pdb=" O ASN B1071 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASN B1071 " --> pdb=" O ALA B 710 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLU B1069 " --> pdb=" O PRO B 712 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ASN B 714 " --> pdb=" O ALA B1067 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N TYR B1064 " --> pdb=" O HIS B1045 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N HIS B1045 " --> pdb=" O TYR B1064 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 730 through 733 removed outlier: 4.385A pdb=" N LYS B 730 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 785 through 787 removed outlier: 6.041A pdb=" N ILE B 785 " --> pdb=" O ASN A 700 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 1117 through 1122 removed outlier: 4.988A pdb=" N ALA B1084 " --> pdb=" O SER B1120 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 1091 through 1094 Processing sheet with id=AC1, first strand: chain 'C' and resid 21 through 22 Processing sheet with id=AC2, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.308A pdb=" N ASN C 61 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N TYR C 266 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.685A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 83 through 85 removed outlier: 5.948A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 11.328A pdb=" N VAL C 126 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 9.829A pdb=" N GLU C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 11.257A pdb=" N ILE C 128 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 8.597A pdb=" N THR C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N VAL C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ASN C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 11.327A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 9.440A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 10.895A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 8.728A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N GLY C 142 " --> pdb=" O MET C 153 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N MET C 153 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N TYR C 144 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N SER C 151 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 308 through 316 removed outlier: 5.462A pdb=" N ILE C 309 " --> pdb=" O THR C 596 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N THR C 596 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N GLN C 311 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL C 594 " --> pdb=" O GLN C 311 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLY C 591 " --> pdb=" O GLN C 610 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 322 through 325 removed outlier: 5.435A pdb=" N ASP C 571 " --> pdb=" O ILE C 584 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLY C 563 " --> pdb=" O ASP C 571 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 351 through 355 removed outlier: 3.863A pdb=" N ASN C 391 " --> pdb=" O GLU C 513 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 358 through 359 removed outlier: 6.408A pdb=" N CYS C 358 " --> pdb=" O CYS C 522 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 449 through 451 Processing sheet with id=AD1, first strand: chain 'C' and resid 470 through 471 Processing sheet with id=AD2, first strand: chain 'C' and resid 651 through 652 removed outlier: 6.496A pdb=" N ILE C 667 " --> pdb=" O ILE C 663 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 708 through 712 Processing sheet with id=AD4, first strand: chain 'C' and resid 715 through 725 removed outlier: 6.101A pdb=" N TYR C1064 " --> pdb=" O HIS C1045 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N HIS C1045 " --> pdb=" O TYR C1064 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 731 through 733 Processing sheet with id=AD6, first strand: chain 'C' and resid 804 through 805 removed outlier: 3.950A pdb=" N ARG C 812 " --> pdb=" O ASP C 805 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 1117 through 1122 removed outlier: 4.537A pdb=" N ALA C1084 " --> pdb=" O SER C1120 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 1091 through 1094 Processing sheet with id=AD9, first strand: chain 'A' and resid 21 through 22 Processing sheet with id=AE1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.856A pdb=" N ASN A 61 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N TYR A 266 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.447A pdb=" N THR A 271 " --> pdb=" O ASP A 287 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ASP A 287 " --> pdb=" O THR A 271 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU A 273 " --> pdb=" O ALA A 285 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ALA A 285 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LYS A 275 " --> pdb=" O THR A 283 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.551A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 11.303A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.812A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.222A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.247A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 9.359A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 10.820A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 8.677A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N GLY A 142 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N MET A 153 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N TYR A 144 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N SER A 151 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 308 through 316 removed outlier: 5.809A pdb=" N ILE A 309 " --> pdb=" O THR A 596 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N THR A 596 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLN A 311 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL A 594 " --> pdb=" O GLN A 311 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLY A 591 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 321 through 325 removed outlier: 6.667A pdb=" N GLU A 321 " --> pdb=" O ASN A 537 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N ASN A 539 " --> pdb=" O GLU A 321 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE A 323 " --> pdb=" O ASN A 539 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 351 through 355 Processing sheet with id=AE7, first strand: chain 'A' and resid 358 through 359 removed outlier: 6.725A pdb=" N CYS A 358 " --> pdb=" O CYS A 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AE9, first strand: chain 'A' and resid 470 through 471 Processing sheet with id=AF1, first strand: chain 'A' and resid 651 through 652 removed outlier: 6.516A pdb=" N ALA A 669 " --> pdb=" O PRO A 662 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'A' and resid 708 through 712 Processing sheet with id=AF3, first strand: chain 'A' and resid 715 through 725 removed outlier: 7.065A pdb=" N GLY A1056 " --> pdb=" O SER A1052 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N SER A1052 " --> pdb=" O GLY A1056 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL A1058 " --> pdb=" O PRO A1050 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU A1060 " --> pdb=" O SER A1048 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N SER A1048 " --> pdb=" O LEU A1060 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL A1062 " --> pdb=" O LEU A1046 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'A' and resid 731 through 733 Processing sheet with id=AF5, first strand: chain 'A' and resid 1117 through 1122 removed outlier: 4.537A pdb=" N ALA A1084 " --> pdb=" O SER A1120 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'A' and resid 1091 through 1094 Processing sheet with id=AF7, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AF8, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.738A pdb=" N VAL H 12 " --> pdb=" O THR H 120 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N TRP H 36 " --> pdb=" O SER H 52 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N SER H 52 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N TRP H 38 " --> pdb=" O ILE H 50 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.738A pdb=" N VAL H 12 " --> pdb=" O THR H 120 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N CYS H 97 " --> pdb=" O TRP H 113 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N TRP H 113 " --> pdb=" O CYS H 97 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ARG H 99 " --> pdb=" O ASP H 111 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.659A pdb=" N THR L 72 " --> pdb=" O SER L 65 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.441A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 10 through 12 Processing sheet with id=AG4, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AG5, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.719A pdb=" N VAL E 12 " --> pdb=" O THR E 120 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N TRP E 36 " --> pdb=" O SER E 52 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N SER E 52 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TRP E 38 " --> pdb=" O ILE E 50 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.719A pdb=" N VAL E 12 " --> pdb=" O THR E 120 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.679A pdb=" N THR F 72 " --> pdb=" O SER F 65 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.447A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'F' and resid 10 through 13 Processing sheet with id=AH1, first strand: chain 'J' and resid 4 through 7 removed outlier: 5.388A pdb=" N GLU J 16 " --> pdb=" O SER J 86 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER J 86 " --> pdb=" O GLU J 16 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.603A pdb=" N VAL J 12 " --> pdb=" O THR J 120 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N TRP J 36 " --> pdb=" O SER J 52 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N SER J 52 " --> pdb=" O TRP J 36 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N TRP J 38 " --> pdb=" O ILE J 50 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.603A pdb=" N VAL J 12 " --> pdb=" O THR J 120 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N CYS J 97 " --> pdb=" O TRP J 113 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N TRP J 113 " --> pdb=" O CYS J 97 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ARG J 99 " --> pdb=" O ASP J 111 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR J 109 " --> pdb=" O THR J 101 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'K' and resid 4 through 7 removed outlier: 3.640A pdb=" N THR K 72 " --> pdb=" O SER K 65 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.467A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'K' and resid 10 through 13 1288 hydrogen bonds defined for protein. 3444 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: 9.45 Time building geometry restraints manager: 3.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9639 1.34 - 1.46: 7411 1.46 - 1.58: 13986 1.58 - 1.70: 3 1.70 - 1.82: 165 Bond restraints: 31204 Sorted by residual: bond pdb=" CB VAL A 698 " pdb=" CG1 VAL A 698 " ideal model delta sigma weight residual 1.521 1.620 -0.099 3.30e-02 9.18e+02 9.02e+00 bond pdb=" C GLY A 697 " pdb=" N VAL A 698 " ideal model delta sigma weight residual 1.332 1.361 -0.029 1.36e-02 5.41e+03 4.67e+00 bond pdb=" N LEU B 229 " pdb=" CA LEU B 229 " ideal model delta sigma weight residual 1.463 1.437 0.025 1.22e-02 6.72e+03 4.32e+00 bond pdb=" CB VAL C 698 " pdb=" CG1 VAL C 698 " ideal model delta sigma weight residual 1.521 1.585 -0.064 3.30e-02 9.18e+02 3.79e+00 bond pdb=" CG LEU C 696 " pdb=" CD1 LEU C 696 " ideal model delta sigma weight residual 1.521 1.581 -0.060 3.30e-02 9.18e+02 3.32e+00 ... (remaining 31199 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.45: 42472 6.45 - 12.91: 3 12.91 - 19.36: 4 19.36 - 25.82: 1 25.82 - 32.27: 1 Bond angle restraints: 42481 Sorted by residual: angle pdb=" N VAL B 317 " pdb=" CA VAL B 317 " pdb=" C VAL B 317 " ideal model delta sigma weight residual 108.17 75.90 32.27 1.46e+00 4.69e-01 4.89e+02 angle pdb=" N GLN B 318 " pdb=" CA GLN B 318 " pdb=" C GLN B 318 " ideal model delta sigma weight residual 108.45 85.56 22.89 1.93e+00 2.68e-01 1.41e+02 angle pdb=" N VAL C 698 " pdb=" CA VAL C 698 " pdb=" C VAL C 698 " ideal model delta sigma weight residual 107.80 92.42 15.38 1.45e+00 4.76e-01 1.13e+02 angle pdb=" N THR L 69 " pdb=" CA THR L 69 " pdb=" C THR L 69 " ideal model delta sigma weight residual 112.04 98.16 13.88 1.44e+00 4.82e-01 9.29e+01 angle pdb=" N VAL C 698 " pdb=" CA VAL C 698 " pdb=" CB VAL C 698 " ideal model delta sigma weight residual 111.46 123.29 -11.83 1.26e+00 6.30e-01 8.81e+01 ... (remaining 42476 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 17301 17.81 - 35.62: 654 35.62 - 53.43: 124 53.43 - 71.24: 40 71.24 - 89.05: 18 Dihedral angle restraints: 18137 sinusoidal: 7055 harmonic: 11082 Sorted by residual: dihedral pdb=" N THR L 69 " pdb=" C THR L 69 " pdb=" CA THR L 69 " pdb=" CB THR L 69 " ideal model delta harmonic sigma weight residual 123.40 100.21 23.19 0 2.50e+00 1.60e-01 8.61e+01 dihedral pdb=" N VAL B 317 " pdb=" C VAL B 317 " pdb=" CA VAL B 317 " pdb=" CB VAL B 317 " ideal model delta harmonic sigma weight residual 123.40 106.86 16.54 0 2.50e+00 1.60e-01 4.37e+01 dihedral pdb=" CA LEU A 696 " pdb=" C LEU A 696 " pdb=" N GLY A 697 " pdb=" CA GLY A 697 " ideal model delta harmonic sigma weight residual -180.00 -148.33 -31.67 0 5.00e+00 4.00e-02 4.01e+01 ... (remaining 18134 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 4858 0.117 - 0.234: 82 0.234 - 0.351: 2 0.351 - 0.468: 1 0.468 - 0.585: 1 Chirality restraints: 4944 Sorted by residual: chirality pdb=" C1 NAG S 2 " pdb=" O4 NAG S 1 " pdb=" C2 NAG S 2 " pdb=" O5 NAG S 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.34 -0.06 2.00e-02 2.50e+03 9.90e+00 chirality pdb=" CA THR L 69 " pdb=" N THR L 69 " pdb=" C THR L 69 " pdb=" CB THR L 69 " both_signs ideal model delta sigma weight residual False 2.53 3.11 -0.59 2.00e-01 2.50e+01 8.56e+00 chirality pdb=" CA VAL B 317 " pdb=" N VAL B 317 " pdb=" C VAL B 317 " pdb=" CB VAL B 317 " both_signs ideal model delta sigma weight residual False 2.44 2.88 -0.43 2.00e-01 2.50e+01 4.72e+00 ... (remaining 4941 not shown) Planarity restraints: 5445 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1303 " 0.025 2.00e-02 2.50e+03 2.09e-02 5.48e+00 pdb=" C7 NAG B1303 " -0.009 2.00e-02 2.50e+03 pdb=" C8 NAG B1303 " 0.020 2.00e-02 2.50e+03 pdb=" N2 NAG B1303 " -0.033 2.00e-02 2.50e+03 pdb=" O7 NAG B1303 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 963 " -0.011 2.00e-02 2.50e+03 2.15e-02 4.63e+00 pdb=" C LEU A 963 " 0.037 2.00e-02 2.50e+03 pdb=" O LEU A 963 " -0.014 2.00e-02 2.50e+03 pdb=" N SER A 964 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 962 " 0.010 2.00e-02 2.50e+03 2.09e-02 4.36e+00 pdb=" C GLN A 962 " -0.036 2.00e-02 2.50e+03 pdb=" O GLN A 962 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU A 963 " 0.012 2.00e-02 2.50e+03 ... (remaining 5442 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 255 2.49 - 3.10: 23757 3.10 - 3.70: 45319 3.70 - 4.30: 69085 4.30 - 4.90: 115495 Nonbonded interactions: 253911 Sorted by model distance: nonbonded pdb=" NZ LYS B1025 " pdb=" O PHE B1039 " model vdw 1.893 3.120 nonbonded pdb=" OE2 GLU A 816 " pdb=" N SER A1052 " model vdw 2.014 3.120 nonbonded pdb=" OG SER J 72 " pdb=" OG SER J 81 " model vdw 2.038 3.040 nonbonded pdb=" OE2 GLU B 816 " pdb=" N SER B1052 " model vdw 2.058 3.120 nonbonded pdb=" OG SER H 72 " pdb=" OG SER H 81 " model vdw 2.061 3.040 ... (remaining 253906 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 13 through 66 or resid 77 through 172 or resid 186 through \ 617 or resid 638 through 1308)) selection = (chain 'B' and (resid 13 through 172 or resid 186 through 245 or resid 261 throu \ gh 617 or resid 638 through 1308)) selection = (chain 'C' and (resid 13 through 617 or resid 638 through 1308)) } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'I' 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' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'F' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.060 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: 0.050 Extract box with map and model: 0.890 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 32.180 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.120 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: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6642 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 : 0.005 0.099 31304 Z= 0.232 Angle : 0.671 32.272 42733 Z= 0.370 Chirality : 0.045 0.585 4944 Planarity : 0.004 0.049 5405 Dihedral : 10.567 89.053 10877 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.40 % Allowed : 4.98 % Favored : 94.62 % Rotamer: Outliers : 1.20 % Allowed : 4.53 % Favored : 94.27 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.75 (0.13), residues: 3753 helix: 0.63 (0.20), residues: 708 sheet: -0.07 (0.16), residues: 1016 loop : -1.13 (0.13), residues: 2029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C1036 TYR 0.017 0.001 TYR C 870 PHE 0.023 0.001 PHE B 303 TRP 0.012 0.001 TRP J 36 HIS 0.005 0.001 HIS A 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.23 (31204) covalent geometry : angle 0.66341 / 0.37 (42481) SS BOND : bond 0.00312 / 0.18 ( 48) SS BOND : angle 0.95905 / 0.69 ( 96) hydrogen bonds : bond 0.14405 / 9.42 ( 1248) hydrogen bonds : angle 7.38599 / 5.06 ( 3444) link_BETA1-4 : bond 0.00254 / 0.19 ( 12) link_BETA1-4 : angle 1.35844 / 0.97 ( 36) link_NAG-ASN : bond 0.00332 / 0.24 ( 40) link_NAG-ASN : angle 1.73591 / 1.20 ( 120) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 593 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 PHE cc_start: 0.8523 (m-80) cc_final: 0.8044 (m-10) REVERT: B 313 SER cc_start: 0.9466 (t) cc_final: 0.9231 (p) REVERT: B 314 ASN cc_start: 0.9156 (m110) cc_final: 0.8300 (p0) REVERT: B 729 THR cc_start: 0.8818 (m) cc_final: 0.8089 (p) REVERT: B 802 ILE cc_start: 0.7381 (pt) cc_final: 0.6961 (pt) REVERT: B 932 GLN cc_start: 0.9171 (mt0) cc_final: 0.8917 (tm-30) REVERT: B 985 GLU cc_start: 0.9194 (mt-10) cc_final: 0.8696 (pt0) REVERT: B 1003 THR cc_start: 0.9549 (m) cc_final: 0.8877 (m) REVERT: C 223 LEU cc_start: 0.9426 (mp) cc_final: 0.8813 (tp) REVERT: C 348 TYR cc_start: 0.9151 (p90) cc_final: 0.8564 (p90) REVERT: C 420 TYR cc_start: 0.8213 (t80) cc_final: 0.7635 (t80) REVERT: C 512 PHE cc_start: 0.4743 (m-80) cc_final: 0.4471 (m-80) REVERT: C 605 VAL cc_start: 0.2549 (m) cc_final: 0.2305 (m) REVERT: C 739 ILE cc_start: 0.9279 (mt) cc_final: 0.8994 (tp) REVERT: C 759 GLN cc_start: 0.9612 (pt0) cc_final: 0.9362 (pt0) REVERT: C 767 ILE cc_start: 0.9289 (mt) cc_final: 0.8793 (mt) REVERT: C 819 LEU cc_start: 0.9453 (mt) cc_final: 0.9074 (mt) REVERT: C 858 LEU cc_start: 0.8919 (mt) cc_final: 0.8021 (tp) REVERT: C 866 MET cc_start: 0.8757 (mtt) cc_final: 0.8365 (mtt) REVERT: C 870 TYR cc_start: 0.8992 (m-80) cc_final: 0.8633 (m-80) REVERT: C 919 LEU cc_start: 0.9371 (tp) cc_final: 0.8948 (tt) REVERT: C 1049 PHE cc_start: 0.7249 (m-80) cc_final: 0.6904 (m-80) REVERT: C 1110 GLN cc_start: 0.9131 (mt0) cc_final: 0.8753 (mp10) REVERT: A 55 PHE cc_start: 0.8273 (m-80) cc_final: 0.7481 (m-80) REVERT: A 348 TYR cc_start: 0.9621 (p90) cc_final: 0.9330 (p90) REVERT: A 420 TYR cc_start: 0.8628 (t80) cc_final: 0.7512 (t80) REVERT: A 729 THR cc_start: 0.7878 (m) cc_final: 0.7135 (t) REVERT: A 760 LEU cc_start: 0.9311 (mt) cc_final: 0.9039 (mt) REVERT: A 875 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.9095 (mm) REVERT: A 961 LYS cc_start: 0.9625 (mttt) cc_final: 0.9328 (mmtm) REVERT: A 1002 GLN cc_start: 0.9054 (mt0) cc_final: 0.8835 (mm-40) REVERT: A 1016 ARG cc_start: 0.8445 (ttp-110) cc_final: 0.8208 (ptp-170) REVERT: A 1026 MET cc_start: 0.8696 (tpp) cc_final: 0.8463 (mmm) REVERT: A 1028 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7959 (mt-10) REVERT: A 1059 PHE cc_start: 0.8798 (m-80) cc_final: 0.7926 (m-10) REVERT: A 1108 GLU cc_start: 0.9033 (tt0) cc_final: 0.8729 (tm-30) REVERT: A 1110 GLN cc_start: 0.9299 (mt0) cc_final: 0.8748 (tp40) REVERT: L 4 MET cc_start: 0.7811 (tpp) cc_final: 0.7529 (mmt) REVERT: L 21 LEU cc_start: 0.5360 (OUTLIER) cc_final: 0.4854 (tt) REVERT: J 71 MET cc_start: 0.7278 (mtp) cc_final: 0.6489 (ttp) REVERT: K 4 MET cc_start: 0.6582 (tpp) cc_final: 0.6372 (ttt) REVERT: K 90 LEU cc_start: 0.8187 (tp) cc_final: 0.7794 (tp) outliers start: 40 outliers final: 9 residues processed: 619 average time/residue: 0.1805 time to fit residues: 177.8980 Evaluate side-chains 336 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 325 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 40.0000 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 0.0980 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 30.0000 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 3.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 495 GLN B 771 GLN B1008 GLN B1085 HIS ** B1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 484 ASN C 610 GLN C 853 ASN C 962 GLN C1008 GLN A 484 ASN A 495 GLN A 610 GLN ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 910 GLN A 925 ASN A 946 GLN A 950 ASN H 78 ASN L 38 GLN E 41 GLN E 78 ASN F 38 GLN J 78 ASN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.102098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.072569 restraints weight = 193004.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.075823 restraints weight = 114912.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.075938 restraints weight = 70151.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.076862 restraints weight = 61242.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.077339 restraints weight = 47560.861| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6705 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.109 31304 Z= 0.152 Angle : 0.634 10.698 42733 Z= 0.328 Chirality : 0.045 0.344 4944 Planarity : 0.004 0.055 5405 Dihedral : 4.503 23.732 4107 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.56 % Favored : 95.20 % Rotamer: Outliers : 0.12 % Allowed : 1.95 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % 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: -0.42 (0.13), residues: 3753 helix: 1.20 (0.19), residues: 722 sheet: 0.09 (0.15), residues: 1031 loop : -1.04 (0.13), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 354 TYR 0.033 0.002 TYR A 263 PHE 0.031 0.002 PHE B 756 TRP 0.016 0.001 TRP H 105 HIS 0.005 0.001 HIS A1045 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (31204) covalent geometry : angle 0.62135 / 0.32 (42481) SS BOND : bond 0.00498 / 0.30 ( 48) SS BOND : angle 1.59111 / 0.96 ( 96) hydrogen bonds : bond 0.04311 / 2.83 ( 1248) hydrogen bonds : angle 6.05407 / 4.20 ( 3444) link_BETA1-4 : bond 0.00355 / 0.25 ( 12) link_BETA1-4 : angle 0.95085 / 0.67 ( 36) link_NAG-ASN : bond 0.00333 / 0.22 ( 40) link_NAG-ASN : angle 2.00245 / 1.51 ( 120) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 416 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 PHE cc_start: 0.8394 (m-80) cc_final: 0.7207 (m-10) REVERT: B 272 PHE cc_start: 0.8644 (m-80) cc_final: 0.7798 (m-80) REVERT: B 313 SER cc_start: 0.9463 (t) cc_final: 0.9069 (p) REVERT: B 314 ASN cc_start: 0.9172 (m110) cc_final: 0.8150 (p0) REVERT: B 782 VAL cc_start: 0.7250 (m) cc_final: 0.6986 (m) REVERT: B 803 LEU cc_start: 0.8796 (mp) cc_final: 0.8578 (tp) REVERT: B 866 MET cc_start: 0.9028 (mpp) cc_final: 0.8778 (mmm) REVERT: B 897 MET cc_start: 0.6704 (mmt) cc_final: 0.6134 (mmt) REVERT: B 999 GLN cc_start: 0.9226 (tp-100) cc_final: 0.8858 (tp-100) REVERT: C 128 ILE cc_start: 0.8864 (mp) cc_final: 0.8647 (mp) REVERT: C 168 PHE cc_start: 0.9026 (t80) cc_final: 0.8739 (t80) REVERT: C 223 LEU cc_start: 0.9272 (mp) cc_final: 0.8610 (tp) REVERT: C 348 TYR cc_start: 0.9302 (p90) cc_final: 0.8720 (p90) REVERT: C 420 TYR cc_start: 0.8549 (t80) cc_final: 0.8006 (t80) REVERT: C 737 MET cc_start: 0.9066 (tpp) cc_final: 0.8825 (tpp) REVERT: C 819 LEU cc_start: 0.9405 (mt) cc_final: 0.9068 (mt) REVERT: C 858 LEU cc_start: 0.8822 (mt) cc_final: 0.8387 (tp) REVERT: C 870 TYR cc_start: 0.8597 (m-80) cc_final: 0.8223 (m-80) REVERT: C 928 ILE cc_start: 0.9070 (mm) cc_final: 0.8806 (mm) REVERT: C 947 ASP cc_start: 0.9176 (m-30) cc_final: 0.8819 (t0) REVERT: C 966 ASN cc_start: 0.9491 (m-40) cc_final: 0.9099 (m-40) REVERT: C 1059 PHE cc_start: 0.8198 (m-10) cc_final: 0.7892 (m-10) REVERT: C 1110 GLN cc_start: 0.8995 (mt0) cc_final: 0.8675 (mp10) REVERT: A 53 ASP cc_start: 0.7719 (t70) cc_final: 0.7409 (t70) REVERT: A 55 PHE cc_start: 0.7941 (m-80) cc_final: 0.7455 (m-80) REVERT: A 169 GLU cc_start: 0.9161 (pm20) cc_final: 0.8833 (mp0) REVERT: A 420 TYR cc_start: 0.8532 (t80) cc_final: 0.7414 (t80) REVERT: A 583 ASP cc_start: 0.8817 (m-30) cc_final: 0.8351 (t0) REVERT: A 744 THR cc_start: 0.9308 (p) cc_final: 0.9053 (p) REVERT: A 752 GLN cc_start: 0.7818 (tm-30) cc_final: 0.7285 (tm-30) REVERT: A 951 GLN cc_start: 0.9060 (mt0) cc_final: 0.8715 (mt0) REVERT: A 961 LYS cc_start: 0.9402 (mttt) cc_final: 0.9110 (mmtm) REVERT: A 1003 THR cc_start: 0.8728 (m) cc_final: 0.8173 (m) REVERT: A 1025 LYS cc_start: 0.8918 (mttm) cc_final: 0.8616 (mttt) REVERT: A 1039 PHE cc_start: 0.6401 (t80) cc_final: 0.5817 (t80) REVERT: A 1059 PHE cc_start: 0.8548 (m-80) cc_final: 0.7840 (m-10) REVERT: A 1108 GLU cc_start: 0.8951 (tt0) cc_final: 0.8306 (tm-30) REVERT: L 4 MET cc_start: 0.7832 (tpp) cc_final: 0.7464 (mmt) REVERT: K 90 LEU cc_start: 0.7932 (tp) cc_final: 0.7707 (mt) outliers start: 4 outliers final: 0 residues processed: 418 average time/residue: 0.1726 time to fit residues: 118.0144 Evaluate side-chains 290 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 290 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 324 optimal weight: 10.0000 chunk 325 optimal weight: 20.0000 chunk 176 optimal weight: 0.1980 chunk 249 optimal weight: 7.9990 chunk 91 optimal weight: 8.9990 chunk 333 optimal weight: 50.0000 chunk 271 optimal weight: 0.7980 chunk 302 optimal weight: 3.9990 chunk 122 optimal weight: 8.9990 chunk 310 optimal weight: 10.0000 chunk 97 optimal weight: 9.9990 overall best weight: 4.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 484 ASN ** B 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 ASN B1020 ASN B1055 HIS ** B1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1110 GLN B1116 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1055 HIS C1116 ASN ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 GLN ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 999 GLN A1002 GLN A1008 GLN ** A1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1116 ASN E 41 GLN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.094807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.066693 restraints weight = 201002.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.068149 restraints weight = 129977.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.068637 restraints weight = 83208.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.068692 restraints weight = 75886.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.068851 restraints weight = 70522.943| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 31304 Z= 0.275 Angle : 0.733 12.610 42733 Z= 0.389 Chirality : 0.046 0.318 4944 Planarity : 0.005 0.075 5405 Dihedral : 4.952 24.721 4107 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.20 % Favored : 94.59 % Rotamer: Outliers : 0.21 % Allowed : 3.12 % Favored : 96.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % 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 (0.13), residues: 3753 helix: 0.33 (0.18), residues: 705 sheet: 0.10 (0.16), residues: 998 loop : -1.16 (0.13), residues: 2050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 400 TYR 0.043 0.002 TYR C 738 PHE 0.040 0.002 PHE B1049 TRP 0.019 0.002 TRP E 105 HIS 0.016 0.002 HIS C1055 Details of bonding type rmsd/Z covalent geometry : bond 0.00553 / 0.28 (31204) covalent geometry : angle 0.71843 / 0.39 (42481) SS BOND : bond 0.00572 / 0.36 ( 48) SS BOND : angle 2.20490 / 1.44 ( 96) hydrogen bonds : bond 0.05306 / 3.50 ( 1248) hydrogen bonds : angle 6.45773 / 4.48 ( 3444) link_BETA1-4 : bond 0.00302 / 0.21 ( 12) link_BETA1-4 : angle 1.39650 / 0.98 ( 36) link_NAG-ASN : bond 0.00373 / 0.25 ( 40) link_NAG-ASN : angle 2.07351 / 1.52 ( 120) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 350 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 PHE cc_start: 0.8452 (m-80) cc_final: 0.7279 (m-10) REVERT: B 272 PHE cc_start: 0.8490 (m-80) cc_final: 0.7638 (m-80) REVERT: B 749 LEU cc_start: 0.8992 (mt) cc_final: 0.8770 (mp) REVERT: B 803 LEU cc_start: 0.9124 (mp) cc_final: 0.8916 (tt) REVERT: B 999 GLN cc_start: 0.9362 (tp-100) cc_final: 0.9041 (tp-100) REVERT: B 1036 ARG cc_start: 0.7826 (mtp85) cc_final: 0.7588 (mtp85) REVERT: C 128 ILE cc_start: 0.9080 (mp) cc_final: 0.8766 (mp) REVERT: C 168 PHE cc_start: 0.9095 (t80) cc_final: 0.8734 (t80) REVERT: C 223 LEU cc_start: 0.9333 (mp) cc_final: 0.8823 (tp) REVERT: C 420 TYR cc_start: 0.8857 (t80) cc_final: 0.8126 (t80) REVERT: C 694 MET cc_start: 0.8009 (ppp) cc_final: 0.7712 (ppp) REVERT: C 737 MET cc_start: 0.9490 (tpp) cc_final: 0.9278 (tpp) REVERT: C 870 TYR cc_start: 0.8668 (m-80) cc_final: 0.8344 (m-80) REVERT: C 931 ILE cc_start: 0.8903 (mm) cc_final: 0.8668 (mm) REVERT: C 932 GLN cc_start: 0.8983 (tm-30) cc_final: 0.8769 (tm-30) REVERT: C 1110 GLN cc_start: 0.9152 (mt0) cc_final: 0.8727 (mp10) REVERT: A 54 LEU cc_start: 0.6568 (tp) cc_final: 0.6285 (tp) REVERT: A 55 PHE cc_start: 0.8157 (m-80) cc_final: 0.7678 (m-10) REVERT: A 348 TYR cc_start: 0.9712 (p90) cc_final: 0.9494 (p90) REVERT: A 420 TYR cc_start: 0.8705 (t80) cc_final: 0.7620 (t80) REVERT: A 583 ASP cc_start: 0.9009 (m-30) cc_final: 0.8616 (t0) REVERT: A 704 TYR cc_start: 0.4567 (t80) cc_final: 0.3516 (t80) REVERT: A 717 ILE cc_start: 0.8158 (mm) cc_final: 0.7815 (mm) REVERT: A 738 TYR cc_start: 0.8147 (t80) cc_final: 0.7919 (t80) REVERT: A 744 THR cc_start: 0.9479 (p) cc_final: 0.9268 (p) REVERT: A 752 GLN cc_start: 0.8477 (tm-30) cc_final: 0.7758 (tm-30) REVERT: A 759 GLN cc_start: 0.9283 (pt0) cc_final: 0.9024 (pt0) REVERT: A 875 LEU cc_start: 0.9493 (mm) cc_final: 0.9285 (mm) REVERT: A 999 GLN cc_start: 0.8756 (tp40) cc_final: 0.8500 (tp-100) REVERT: A 1003 THR cc_start: 0.8812 (m) cc_final: 0.8376 (m) REVERT: A 1025 LYS cc_start: 0.8979 (mttm) cc_final: 0.8590 (mmtt) REVERT: A 1039 PHE cc_start: 0.6387 (t80) cc_final: 0.6161 (t80) REVERT: A 1059 PHE cc_start: 0.8639 (m-80) cc_final: 0.8408 (m-10) REVERT: A 1108 GLU cc_start: 0.9258 (tt0) cc_final: 0.8594 (tm-30) REVERT: L 4 MET cc_start: 0.7346 (tpp) cc_final: 0.6632 (mmt) REVERT: J 120 THR cc_start: 0.7745 (p) cc_final: 0.7528 (p) REVERT: K 90 LEU cc_start: 0.8216 (tp) cc_final: 0.7844 (mt) outliers start: 7 outliers final: 5 residues processed: 357 average time/residue: 0.1694 time to fit residues: 100.7425 Evaluate side-chains 267 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 262 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 139 optimal weight: 5.9990 chunk 345 optimal weight: 50.0000 chunk 304 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 315 optimal weight: 8.9990 chunk 173 optimal weight: 0.9990 chunk 237 optimal weight: 5.9990 chunk 104 optimal weight: 20.0000 chunk 250 optimal weight: 9.9990 chunk 308 optimal weight: 6.9990 chunk 122 optimal weight: 20.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 801 GLN B 950 ASN ** B1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1110 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 910 GLN C1020 ASN C1051 GLN ** A 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 898 GLN ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.091216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.059213 restraints weight = 174643.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.060963 restraints weight = 105690.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.062159 restraints weight = 73798.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.062866 restraints weight = 58111.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.063585 restraints weight = 50213.898| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.4427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 31304 Z= 0.256 Angle : 0.697 12.722 42733 Z= 0.369 Chirality : 0.046 0.255 4944 Planarity : 0.005 0.077 5405 Dihedral : 5.078 26.538 4107 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.52 % Favored : 94.30 % Rotamer: Outliers : 0.06 % Allowed : 3.27 % Favored : 96.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % 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: -0.95 (0.13), residues: 3753 helix: -0.01 (0.19), residues: 688 sheet: -0.00 (0.16), residues: 1010 loop : -1.17 (0.13), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.038 0.001 ARG A 992 TYR 0.025 0.002 TYR C 738 PHE 0.043 0.003 PHE B 559 TRP 0.014 0.002 TRP C1099 HIS 0.018 0.002 HIS B1045 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.26 (31204) covalent geometry : angle 0.68553 / 0.37 (42481) SS BOND : bond 0.00485 / 0.32 ( 48) SS BOND : angle 1.55435 / 0.98 ( 96) hydrogen bonds : bond 0.05047 / 3.34 ( 1248) hydrogen bonds : angle 6.42109 / 4.46 ( 3444) link_BETA1-4 : bond 0.00261 / 0.17 ( 12) link_BETA1-4 : angle 1.43781 / 1.00 ( 36) link_NAG-ASN : bond 0.00335 / 0.22 ( 40) link_NAG-ASN : angle 2.05595 / 1.52 ( 120) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 327 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 PHE cc_start: 0.8178 (m-80) cc_final: 0.7064 (m-10) REVERT: B 272 PHE cc_start: 0.8686 (m-80) cc_final: 0.7957 (m-10) REVERT: B 745 GLU cc_start: 0.9156 (mp0) cc_final: 0.8533 (tt0) REVERT: B 999 GLN cc_start: 0.9376 (tp-100) cc_final: 0.8950 (tp-100) REVERT: B 1036 ARG cc_start: 0.7454 (mtp85) cc_final: 0.7164 (mtp85) REVERT: C 128 ILE cc_start: 0.9082 (mp) cc_final: 0.8775 (mp) REVERT: C 168 PHE cc_start: 0.9012 (t80) cc_final: 0.8584 (t80) REVERT: C 223 LEU cc_start: 0.9349 (mp) cc_final: 0.8835 (tp) REVERT: C 290 LEU cc_start: 0.8491 (tt) cc_final: 0.8130 (mt) REVERT: C 717 ILE cc_start: 0.8216 (mm) cc_final: 0.7993 (mm) REVERT: C 737 MET cc_start: 0.9473 (tpp) cc_final: 0.9263 (tpp) REVERT: C 739 ILE cc_start: 0.9553 (mt) cc_final: 0.9339 (tp) REVERT: C 815 ILE cc_start: 0.9559 (mt) cc_final: 0.9327 (mt) REVERT: C 870 TYR cc_start: 0.8767 (m-80) cc_final: 0.8403 (m-80) REVERT: C 918 LYS cc_start: 0.9366 (mttt) cc_final: 0.9002 (mppt) REVERT: C 932 GLN cc_start: 0.9083 (tm-30) cc_final: 0.8798 (tm-30) REVERT: A 55 PHE cc_start: 0.7866 (m-80) cc_final: 0.7537 (m-80) REVERT: A 117 LEU cc_start: 0.9536 (tp) cc_final: 0.9217 (tp) REVERT: A 420 TYR cc_start: 0.8878 (t80) cc_final: 0.7783 (t80) REVERT: A 583 ASP cc_start: 0.8883 (m-30) cc_final: 0.8553 (t0) REVERT: A 717 ILE cc_start: 0.8401 (mm) cc_final: 0.7905 (mm) REVERT: A 738 TYR cc_start: 0.8395 (t80) cc_final: 0.8149 (t80) REVERT: A 744 THR cc_start: 0.9460 (p) cc_final: 0.9243 (p) REVERT: A 752 GLN cc_start: 0.8573 (tm-30) cc_final: 0.7900 (tm-30) REVERT: A 816 GLU cc_start: 0.9048 (mt-10) cc_final: 0.7759 (mt-10) REVERT: A 999 GLN cc_start: 0.8676 (tp40) cc_final: 0.8391 (tp-100) REVERT: A 1003 THR cc_start: 0.8833 (m) cc_final: 0.8516 (m) REVERT: A 1025 LYS cc_start: 0.8942 (mttm) cc_final: 0.8716 (mmtt) REVERT: A 1108 GLU cc_start: 0.9133 (tt0) cc_final: 0.8504 (tm-30) REVERT: J 71 MET cc_start: 0.5833 (ppp) cc_final: 0.5354 (ppp) REVERT: K 90 LEU cc_start: 0.8249 (tp) cc_final: 0.7960 (mt) outliers start: 2 outliers final: 1 residues processed: 329 average time/residue: 0.1704 time to fit residues: 94.2584 Evaluate side-chains 235 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 234 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 102 optimal weight: 0.0170 chunk 153 optimal weight: 6.9990 chunk 217 optimal weight: 8.9990 chunk 254 optimal weight: 0.0570 chunk 216 optimal weight: 7.9990 chunk 241 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 332 optimal weight: 30.0000 chunk 283 optimal weight: 3.9990 chunk 326 optimal weight: 8.9990 chunk 74 optimal weight: 8.9990 overall best weight: 3.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.089797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.058806 restraints weight = 181150.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.060404 restraints weight = 110742.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.061591 restraints weight = 78570.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.062273 restraints weight = 62306.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.062743 restraints weight = 52457.344| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.5017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 31304 Z= 0.238 Angle : 0.680 13.280 42733 Z= 0.358 Chirality : 0.045 0.283 4944 Planarity : 0.005 0.072 5405 Dihedral : 5.069 27.053 4107 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.65 % Favored : 94.19 % Rotamer: Outliers : 0.06 % Allowed : 2.34 % Favored : 97.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.13), residues: 3753 helix: -0.14 (0.18), residues: 694 sheet: -0.03 (0.16), residues: 1003 loop : -1.19 (0.13), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 506 TYR 0.023 0.002 TYR C 738 PHE 0.031 0.002 PHE A1072 TRP 0.023 0.002 TRP A 883 HIS 0.011 0.002 HIS B1045 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.24 (31204) covalent geometry : angle 0.66802 / 0.36 (42481) SS BOND : bond 0.00481 / 0.31 ( 48) SS BOND : angle 1.40435 / 0.89 ( 96) hydrogen bonds : bond 0.04883 / 3.24 ( 1248) hydrogen bonds : angle 6.40692 / 4.45 ( 3444) link_BETA1-4 : bond 0.00257 / 0.18 ( 12) link_BETA1-4 : angle 1.45957 / 1.01 ( 36) link_NAG-ASN : bond 0.00401 / 0.23 ( 40) link_NAG-ASN : angle 2.07427 / 1.50 ( 120) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 311 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 PHE cc_start: 0.8000 (m-80) cc_final: 0.7002 (m-10) REVERT: B 272 PHE cc_start: 0.8585 (m-80) cc_final: 0.7897 (m-10) REVERT: B 745 GLU cc_start: 0.9119 (mp0) cc_final: 0.8614 (tt0) REVERT: B 999 GLN cc_start: 0.9326 (tp-100) cc_final: 0.8858 (tp-100) REVERT: B 1124 ASP cc_start: 0.6871 (p0) cc_final: 0.6584 (p0) REVERT: C 128 ILE cc_start: 0.9122 (mp) cc_final: 0.8832 (mp) REVERT: C 168 PHE cc_start: 0.9012 (t80) cc_final: 0.8601 (t80) REVERT: C 223 LEU cc_start: 0.9329 (mp) cc_final: 0.8779 (tp) REVERT: C 420 TYR cc_start: 0.8592 (t80) cc_final: 0.8112 (t80) REVERT: C 516 HIS cc_start: 0.5564 (m90) cc_final: 0.5011 (m90) REVERT: C 717 ILE cc_start: 0.8242 (mm) cc_final: 0.8009 (mm) REVERT: C 737 MET cc_start: 0.9473 (tpp) cc_final: 0.9271 (tpp) REVERT: C 739 ILE cc_start: 0.9573 (mt) cc_final: 0.9268 (tp) REVERT: C 870 TYR cc_start: 0.8669 (m-80) cc_final: 0.8449 (m-80) REVERT: C 918 LYS cc_start: 0.9333 (mttt) cc_final: 0.8952 (mppt) REVERT: C 989 GLN cc_start: 0.8817 (mm-40) cc_final: 0.8264 (mp10) REVERT: A 55 PHE cc_start: 0.7843 (m-80) cc_final: 0.7484 (m-80) REVERT: A 583 ASP cc_start: 0.8913 (m-30) cc_final: 0.8613 (t0) REVERT: A 738 TYR cc_start: 0.8509 (t80) cc_final: 0.8231 (t80) REVERT: A 744 THR cc_start: 0.9462 (p) cc_final: 0.9244 (p) REVERT: A 752 GLN cc_start: 0.8534 (tm-30) cc_final: 0.8302 (tm-30) REVERT: A 760 LEU cc_start: 0.9168 (mt) cc_final: 0.8634 (mt) REVERT: A 982 ASP cc_start: 0.8429 (m-30) cc_final: 0.8023 (p0) REVERT: A 999 GLN cc_start: 0.8635 (tp40) cc_final: 0.8313 (tp40) REVERT: A 1003 THR cc_start: 0.8858 (m) cc_final: 0.8625 (m) REVERT: A 1108 GLU cc_start: 0.9133 (tt0) cc_final: 0.8468 (tm-30) REVERT: J 71 MET cc_start: 0.5877 (ppp) cc_final: 0.5358 (ppp) REVERT: K 90 LEU cc_start: 0.8312 (tp) cc_final: 0.8015 (mt) outliers start: 2 outliers final: 2 residues processed: 313 average time/residue: 0.1700 time to fit residues: 89.7266 Evaluate side-chains 239 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 237 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 36 optimal weight: 6.9990 chunk 197 optimal weight: 0.9980 chunk 356 optimal weight: 0.7980 chunk 249 optimal weight: 7.9990 chunk 209 optimal weight: 10.0000 chunk 214 optimal weight: 9.9990 chunk 360 optimal weight: 9.9990 chunk 215 optimal weight: 20.0000 chunk 322 optimal weight: 50.0000 chunk 23 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 overall best weight: 2.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 484 ASN ** B 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 HIS ** A 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1105 ASN E 41 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.090502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.058966 restraints weight = 182044.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.060833 restraints weight = 109179.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.062104 restraints weight = 76509.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.062872 restraints weight = 60053.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.063467 restraints weight = 51099.519| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.5302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 31304 Z= 0.175 Angle : 0.621 9.279 42733 Z= 0.323 Chirality : 0.044 0.270 4944 Planarity : 0.004 0.058 5405 Dihedral : 4.857 25.068 4107 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.44 % Favored : 94.40 % Rotamer: Outliers : 0.03 % Allowed : 1.98 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % 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: -0.93 (0.13), residues: 3753 helix: 0.05 (0.18), residues: 696 sheet: 0.00 (0.16), residues: 986 loop : -1.15 (0.13), residues: 2071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 44 TYR 0.025 0.002 TYR L 87 PHE 0.035 0.002 PHE C1049 TRP 0.017 0.001 TRP A 883 HIS 0.019 0.002 HIS C1045 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.18 (31204) covalent geometry : angle 0.60769 / 0.32 (42481) SS BOND : bond 0.00380 / 0.24 ( 48) SS BOND : angle 1.41201 / 0.93 ( 96) hydrogen bonds : bond 0.04396 / 2.92 ( 1248) hydrogen bonds : angle 6.19433 / 4.35 ( 3444) link_BETA1-4 : bond 0.00174 / 0.12 ( 12) link_BETA1-4 : angle 1.32810 / 0.96 ( 36) link_NAG-ASN : bond 0.00363 / 0.22 ( 40) link_NAG-ASN : angle 2.11656 / 1.54 ( 120) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 315 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 PHE cc_start: 0.7953 (m-80) cc_final: 0.6907 (m-10) REVERT: B 272 PHE cc_start: 0.8598 (m-80) cc_final: 0.8021 (m-10) REVERT: B 315 PHE cc_start: 0.8139 (t80) cc_final: 0.7919 (t80) REVERT: B 745 GLU cc_start: 0.9086 (mp0) cc_final: 0.8539 (tt0) REVERT: B 866 MET cc_start: 0.9119 (mpp) cc_final: 0.8348 (ptp) REVERT: B 999 GLN cc_start: 0.9342 (tp-100) cc_final: 0.8905 (tp-100) REVERT: B 1028 GLU cc_start: 0.7552 (mt-10) cc_final: 0.6767 (mt-10) REVERT: B 1124 ASP cc_start: 0.6847 (p0) cc_final: 0.6621 (p0) REVERT: C 168 PHE cc_start: 0.8980 (t80) cc_final: 0.8543 (t80) REVERT: C 223 LEU cc_start: 0.9253 (mp) cc_final: 0.8712 (tp) REVERT: C 516 HIS cc_start: 0.5577 (m90) cc_final: 0.5057 (m90) REVERT: C 737 MET cc_start: 0.9491 (tpp) cc_final: 0.9290 (tpp) REVERT: C 739 ILE cc_start: 0.9598 (mt) cc_final: 0.9379 (tp) REVERT: C 816 GLU cc_start: 0.8778 (mt-10) cc_final: 0.7842 (mt-10) REVERT: C 918 LYS cc_start: 0.9295 (mttt) cc_final: 0.8921 (mppt) REVERT: C 947 ASP cc_start: 0.9197 (t0) cc_final: 0.8970 (t0) REVERT: C 989 GLN cc_start: 0.8829 (mm-40) cc_final: 0.8277 (mp10) REVERT: A 33 THR cc_start: 0.6875 (p) cc_final: 0.6156 (p) REVERT: A 55 PHE cc_start: 0.7711 (m-80) cc_final: 0.7418 (m-80) REVERT: A 583 ASP cc_start: 0.8948 (m-30) cc_final: 0.8675 (t0) REVERT: A 694 MET cc_start: 0.8255 (ppp) cc_final: 0.7973 (ppp) REVERT: A 717 ILE cc_start: 0.8417 (mp) cc_final: 0.8195 (pt) REVERT: A 738 TYR cc_start: 0.8546 (t80) cc_final: 0.8262 (t80) REVERT: A 744 THR cc_start: 0.9450 (p) cc_final: 0.9218 (p) REVERT: A 982 ASP cc_start: 0.8359 (m-30) cc_final: 0.8055 (p0) REVERT: A 999 GLN cc_start: 0.8660 (tp40) cc_final: 0.8282 (tp40) REVERT: A 1003 THR cc_start: 0.8842 (m) cc_final: 0.8599 (m) REVERT: A 1028 GLU cc_start: 0.8274 (pt0) cc_final: 0.8051 (pt0) REVERT: A 1108 GLU cc_start: 0.8934 (tt0) cc_final: 0.8350 (tm-30) REVERT: J 71 MET cc_start: 0.5459 (ppp) cc_final: 0.4797 (ppp) REVERT: K 90 LEU cc_start: 0.8294 (tp) cc_final: 0.8033 (mt) outliers start: 1 outliers final: 0 residues processed: 316 average time/residue: 0.1764 time to fit residues: 92.9124 Evaluate side-chains 241 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 264 optimal weight: 3.9990 chunk 164 optimal weight: 8.9990 chunk 129 optimal weight: 3.9990 chunk 213 optimal weight: 6.9990 chunk 48 optimal weight: 7.9990 chunk 184 optimal weight: 1.9990 chunk 271 optimal weight: 0.9980 chunk 151 optimal weight: 2.9990 chunk 353 optimal weight: 8.9990 chunk 261 optimal weight: 3.9990 chunk 30 optimal weight: 30.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 ASN ** C 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 962 GLN ** C1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1051 GLN ** A 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 781 GLN ** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.089577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.060227 restraints weight = 178477.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.062536 restraints weight = 109265.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.063004 restraints weight = 70059.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.063807 restraints weight = 53812.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.063871 restraints weight = 47104.314| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.5638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 31304 Z= 0.189 Angle : 0.634 8.777 42733 Z= 0.332 Chirality : 0.044 0.234 4944 Planarity : 0.005 0.073 5405 Dihedral : 4.842 25.206 4107 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.78 % Favored : 94.06 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % 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: -0.95 (0.13), residues: 3753 helix: 0.07 (0.19), residues: 689 sheet: -0.05 (0.16), residues: 968 loop : -1.14 (0.13), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 44 TYR 0.023 0.002 TYR C 738 PHE 0.023 0.002 PHE C1039 TRP 0.019 0.001 TRP A 883 HIS 0.020 0.002 HIS C1045 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.19 (31204) covalent geometry : angle 0.62266 / 0.33 (42481) SS BOND : bond 0.00413 / 0.26 ( 48) SS BOND : angle 1.34939 / 0.91 ( 96) hydrogen bonds : bond 0.04424 / 2.95 ( 1248) hydrogen bonds : angle 6.24952 / 4.37 ( 3444) link_BETA1-4 : bond 0.00221 / 0.15 ( 12) link_BETA1-4 : angle 1.30492 / 0.91 ( 36) link_NAG-ASN : bond 0.00308 / 0.20 ( 40) link_NAG-ASN : angle 2.01347 / 1.46 ( 120) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 292 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 PHE cc_start: 0.7977 (m-80) cc_final: 0.7017 (m-10) REVERT: B 272 PHE cc_start: 0.8545 (m-80) cc_final: 0.7949 (m-10) REVERT: B 694 MET cc_start: 0.8730 (ppp) cc_final: 0.8484 (tmm) REVERT: B 707 ASN cc_start: 0.8937 (p0) cc_final: 0.8538 (t0) REVERT: B 745 GLU cc_start: 0.9121 (mp0) cc_final: 0.8646 (tt0) REVERT: B 866 MET cc_start: 0.9109 (mpp) cc_final: 0.8416 (ptp) REVERT: B 999 GLN cc_start: 0.9316 (tp-100) cc_final: 0.8890 (tp-100) REVERT: B 1124 ASP cc_start: 0.6881 (p0) cc_final: 0.6681 (p0) REVERT: C 168 PHE cc_start: 0.9020 (t80) cc_final: 0.8622 (t80) REVERT: C 223 LEU cc_start: 0.9248 (mp) cc_final: 0.8739 (tp) REVERT: C 348 TYR cc_start: 0.9273 (p90) cc_final: 0.8778 (p90) REVERT: C 516 HIS cc_start: 0.5693 (m90) cc_final: 0.5195 (m90) REVERT: C 737 MET cc_start: 0.9479 (tpp) cc_final: 0.9234 (tpp) REVERT: C 739 ILE cc_start: 0.9601 (mt) cc_final: 0.9361 (tp) REVERT: C 816 GLU cc_start: 0.8531 (mt-10) cc_final: 0.7364 (mt-10) REVERT: C 817 ASP cc_start: 0.8927 (m-30) cc_final: 0.8518 (m-30) REVERT: C 866 MET cc_start: 0.9057 (mtp) cc_final: 0.8779 (mtt) REVERT: C 918 LYS cc_start: 0.9293 (mttt) cc_final: 0.8910 (mppt) REVERT: C 947 ASP cc_start: 0.9171 (t0) cc_final: 0.8964 (t0) REVERT: C 989 GLN cc_start: 0.8886 (mm-40) cc_final: 0.8338 (mp10) REVERT: C 1049 PHE cc_start: 0.7428 (m-10) cc_final: 0.7135 (m-80) REVERT: A 55 PHE cc_start: 0.7733 (m-80) cc_final: 0.7462 (m-80) REVERT: A 583 ASP cc_start: 0.8994 (m-30) cc_final: 0.8736 (t0) REVERT: A 694 MET cc_start: 0.8243 (ppp) cc_final: 0.7993 (ppp) REVERT: A 717 ILE cc_start: 0.8387 (mp) cc_final: 0.8174 (pt) REVERT: A 738 TYR cc_start: 0.8542 (t80) cc_final: 0.8224 (t80) REVERT: A 744 THR cc_start: 0.9461 (p) cc_final: 0.9230 (p) REVERT: A 869 GLN cc_start: 0.9141 (mt0) cc_final: 0.8777 (tm-30) REVERT: A 999 GLN cc_start: 0.8650 (tp40) cc_final: 0.8264 (tp40) REVERT: A 1003 THR cc_start: 0.8842 (m) cc_final: 0.8607 (m) REVERT: A 1028 GLU cc_start: 0.8366 (pt0) cc_final: 0.7995 (pt0) REVERT: A 1061 HIS cc_start: 0.6753 (m90) cc_final: 0.6495 (m170) REVERT: A 1108 GLU cc_start: 0.9027 (tt0) cc_final: 0.8399 (tm-30) REVERT: J 71 MET cc_start: 0.5792 (ppp) cc_final: 0.5226 (ppp) REVERT: K 90 LEU cc_start: 0.8339 (tp) cc_final: 0.8061 (mt) outliers start: 0 outliers final: 0 residues processed: 292 average time/residue: 0.1764 time to fit residues: 86.1318 Evaluate side-chains 229 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 211 optimal weight: 7.9990 chunk 224 optimal weight: 20.0000 chunk 39 optimal weight: 40.0000 chunk 54 optimal weight: 1.9990 chunk 140 optimal weight: 0.0060 chunk 40 optimal weight: 20.0000 chunk 254 optimal weight: 0.0270 chunk 347 optimal weight: 40.0000 chunk 128 optimal weight: 0.6980 chunk 338 optimal weight: 40.0000 chunk 265 optimal weight: 0.6980 overall best weight: 0.6856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1105 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 962 GLN ** A 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 950 ASN A1051 GLN A1055 HIS A1061 HIS E 41 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.091488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.062135 restraints weight = 179705.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.064077 restraints weight = 110149.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.064723 restraints weight = 81220.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.065823 restraints weight = 58879.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.066106 restraints weight = 47111.684| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.5699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 31304 Z= 0.116 Angle : 0.591 8.697 42733 Z= 0.305 Chirality : 0.044 0.214 4944 Planarity : 0.004 0.043 5405 Dihedral : 4.526 24.309 4107 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.58 % Favored : 95.26 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % 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: -0.74 (0.13), residues: 3753 helix: 0.49 (0.20), residues: 670 sheet: 0.04 (0.16), residues: 980 loop : -1.08 (0.13), residues: 2103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1036 TYR 0.019 0.001 TYR C 738 PHE 0.018 0.001 PHE C1049 TRP 0.021 0.001 TRP A 64 HIS 0.015 0.001 HIS B1045 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 (31204) covalent geometry : angle 0.58126 / 0.30 (42481) SS BOND : bond 0.00263 / 0.17 ( 48) SS BOND : angle 1.31891 / 0.84 ( 96) hydrogen bonds : bond 0.03806 / 2.54 ( 1248) hydrogen bonds : angle 5.99066 / 4.22 ( 3444) link_BETA1-4 : bond 0.00304 / 0.19 ( 12) link_BETA1-4 : angle 1.10449 / 0.79 ( 36) link_NAG-ASN : bond 0.00185 / 0.13 ( 40) link_NAG-ASN : angle 1.76217 / 1.25 ( 120) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 315 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 PHE cc_start: 0.7918 (m-80) cc_final: 0.7030 (m-10) REVERT: B 272 PHE cc_start: 0.8489 (m-80) cc_final: 0.7876 (m-10) REVERT: B 694 MET cc_start: 0.8702 (ppp) cc_final: 0.8453 (tmm) REVERT: B 745 GLU cc_start: 0.9138 (mp0) cc_final: 0.8699 (tt0) REVERT: B 950 ASN cc_start: 0.9207 (t0) cc_final: 0.8927 (t0) REVERT: B 999 GLN cc_start: 0.9320 (tp-100) cc_final: 0.8886 (tp-100) REVERT: B 1124 ASP cc_start: 0.6835 (p0) cc_final: 0.6625 (p0) REVERT: C 168 PHE cc_start: 0.8974 (t80) cc_final: 0.8580 (t80) REVERT: C 223 LEU cc_start: 0.9171 (mp) cc_final: 0.8618 (tp) REVERT: C 739 ILE cc_start: 0.9603 (mt) cc_final: 0.9385 (tt) REVERT: C 817 ASP cc_start: 0.8818 (m-30) cc_final: 0.8428 (m-30) REVERT: C 866 MET cc_start: 0.9115 (mtp) cc_final: 0.8834 (mtt) REVERT: C 918 LYS cc_start: 0.9270 (mttt) cc_final: 0.8925 (mppt) REVERT: C 947 ASP cc_start: 0.9216 (t0) cc_final: 0.9001 (t0) REVERT: C 958 THR cc_start: 0.9308 (p) cc_final: 0.9053 (p) REVERT: C 989 GLN cc_start: 0.8792 (mm-40) cc_final: 0.8277 (mp10) REVERT: C 1049 PHE cc_start: 0.7787 (m-10) cc_final: 0.7489 (m-80) REVERT: A 55 PHE cc_start: 0.7586 (m-80) cc_final: 0.7146 (m-80) REVERT: A 583 ASP cc_start: 0.9011 (m-30) cc_final: 0.8760 (t0) REVERT: A 738 TYR cc_start: 0.8403 (t80) cc_final: 0.7818 (t80) REVERT: A 744 THR cc_start: 0.9460 (p) cc_final: 0.9225 (p) REVERT: A 770 GLU cc_start: 0.8593 (tt0) cc_final: 0.7914 (tp30) REVERT: A 869 GLN cc_start: 0.9081 (mt0) cc_final: 0.8735 (tm-30) REVERT: A 999 GLN cc_start: 0.8671 (tp40) cc_final: 0.8344 (tp40) REVERT: A 1028 GLU cc_start: 0.8499 (pt0) cc_final: 0.8137 (pt0) REVERT: A 1107 TYR cc_start: 0.8209 (t80) cc_final: 0.7976 (t80) REVERT: A 1108 GLU cc_start: 0.8867 (tt0) cc_final: 0.8370 (tm-30) REVERT: J 71 MET cc_start: 0.6025 (ppp) cc_final: 0.5573 (ppp) REVERT: K 90 LEU cc_start: 0.8329 (tp) cc_final: 0.8018 (mt) outliers start: 0 outliers final: 0 residues processed: 315 average time/residue: 0.1760 time to fit residues: 92.8092 Evaluate side-chains 229 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 284 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 68 optimal weight: 1.9990 chunk 186 optimal weight: 0.9980 chunk 83 optimal weight: 9.9990 chunk 256 optimal weight: 10.0000 chunk 306 optimal weight: 5.9990 chunk 157 optimal weight: 0.2980 chunk 175 optimal weight: 6.9990 chunk 225 optimal weight: 3.9990 chunk 30 optimal weight: 30.0000 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 652 HIS C 962 GLN ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 999 GLN ** A1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.090607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.062277 restraints weight = 202077.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.063371 restraints weight = 131587.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.064426 restraints weight = 89921.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.065124 restraints weight = 68930.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.065064 restraints weight = 52924.492| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.5957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 31304 Z= 0.180 Angle : 0.623 8.882 42733 Z= 0.327 Chirality : 0.044 0.187 4944 Planarity : 0.004 0.063 5405 Dihedral : 4.668 25.146 4107 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.62 % Favored : 94.24 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % 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 (0.13), residues: 3753 helix: 0.33 (0.19), residues: 674 sheet: 0.01 (0.16), residues: 987 loop : -1.09 (0.13), residues: 2092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG J 104 TYR 0.023 0.002 TYR A 204 PHE 0.021 0.002 PHE C1039 TRP 0.017 0.001 TRP A 64 HIS 0.016 0.002 HIS C1045 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.18 (31204) covalent geometry : angle 0.61360 / 0.33 (42481) SS BOND : bond 0.00401 / 0.26 ( 48) SS BOND : angle 1.20932 / 0.81 ( 96) hydrogen bonds : bond 0.04275 / 2.86 ( 1248) hydrogen bonds : angle 6.13762 / 4.33 ( 3444) link_BETA1-4 : bond 0.00216 / 0.15 ( 12) link_BETA1-4 : angle 1.23348 / 0.85 ( 36) link_NAG-ASN : bond 0.00290 / 0.19 ( 40) link_NAG-ASN : angle 1.84566 / 1.33 ( 120) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 PHE cc_start: 0.7974 (m-80) cc_final: 0.7089 (m-10) REVERT: B 272 PHE cc_start: 0.8478 (m-80) cc_final: 0.7853 (m-10) REVERT: B 315 PHE cc_start: 0.7564 (t80) cc_final: 0.7328 (t80) REVERT: B 707 ASN cc_start: 0.8993 (p0) cc_final: 0.8528 (t0) REVERT: B 950 ASN cc_start: 0.9237 (t0) cc_final: 0.8907 (t0) REVERT: B 999 GLN cc_start: 0.9271 (tp-100) cc_final: 0.8924 (tp-100) REVERT: C 168 PHE cc_start: 0.9036 (t80) cc_final: 0.8660 (t80) REVERT: C 223 LEU cc_start: 0.9212 (mp) cc_final: 0.8678 (tp) REVERT: C 348 TYR cc_start: 0.9405 (p90) cc_final: 0.8840 (p90) REVERT: C 817 ASP cc_start: 0.8873 (m-30) cc_final: 0.8449 (m-30) REVERT: C 866 MET cc_start: 0.9030 (mtp) cc_final: 0.8828 (mtp) REVERT: C 918 LYS cc_start: 0.9276 (mttt) cc_final: 0.8892 (mppt) REVERT: C 947 ASP cc_start: 0.9186 (t0) cc_final: 0.8972 (t0) REVERT: C 989 GLN cc_start: 0.8916 (mm-40) cc_final: 0.8395 (mp10) REVERT: A 55 PHE cc_start: 0.7707 (m-80) cc_final: 0.7444 (m-80) REVERT: A 583 ASP cc_start: 0.9068 (m-30) cc_final: 0.8816 (t0) REVERT: A 744 THR cc_start: 0.9481 (p) cc_final: 0.9252 (p) REVERT: A 770 GLU cc_start: 0.8631 (tt0) cc_final: 0.8195 (tp30) REVERT: A 869 GLN cc_start: 0.9138 (mt0) cc_final: 0.8779 (tm-30) REVERT: A 999 GLN cc_start: 0.8674 (tp-100) cc_final: 0.8428 (tm-30) REVERT: A 1108 GLU cc_start: 0.8928 (tt0) cc_final: 0.8380 (tm-30) REVERT: J 71 MET cc_start: 0.5748 (ppp) cc_final: 0.5380 (ppp) REVERT: K 90 LEU cc_start: 0.8314 (tp) cc_final: 0.7985 (mt) outliers start: 0 outliers final: 0 residues processed: 283 average time/residue: 0.1721 time to fit residues: 83.0194 Evaluate side-chains 213 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 42 optimal weight: 20.0000 chunk 266 optimal weight: 7.9990 chunk 263 optimal weight: 6.9990 chunk 116 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 150 optimal weight: 10.0000 chunk 118 optimal weight: 7.9990 chunk 357 optimal weight: 30.0000 chunk 25 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 3 optimal weight: 8.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 687 GLN B 748 ASN ** B 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 925 ASN ** C 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 952 ASN ** C 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1105 ASN E 41 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.088012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.059555 restraints weight = 204776.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.061117 restraints weight = 126604.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.061331 restraints weight = 87773.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.062181 restraints weight = 73268.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.062105 restraints weight = 54879.903| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.6592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 31304 Z= 0.253 Angle : 0.720 14.954 42733 Z= 0.383 Chirality : 0.046 0.328 4944 Planarity : 0.005 0.115 5405 Dihedral : 5.231 35.125 4107 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 19.12 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.10 % Favored : 93.76 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.13), residues: 3753 helix: -0.36 (0.18), residues: 671 sheet: -0.18 (0.16), residues: 968 loop : -1.17 (0.13), residues: 2114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 34 TYR 0.045 0.002 TYR B 263 PHE 0.037 0.002 PHE A 903 TRP 0.033 0.002 TRP A 883 HIS 0.022 0.003 HIS C1045 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.25 (31204) covalent geometry : angle 0.70947 / 0.38 (42481) SS BOND : bond 0.00445 / 0.28 ( 48) SS BOND : angle 1.26903 / 0.87 ( 96) hydrogen bonds : bond 0.05044 / 3.34 ( 1248) hydrogen bonds : angle 6.56886 / 4.66 ( 3444) link_BETA1-4 : bond 0.00230 / 0.15 ( 12) link_BETA1-4 : angle 1.49229 / 1.02 ( 36) link_NAG-ASN : bond 0.00445 / 0.29 ( 40) link_NAG-ASN : angle 2.11732 / 1.52 ( 120) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7506 Ramachandran restraints generated. 3753 Oldfield, 0 Emsley, 3753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 1.215 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: B 272 PHE cc_start: 0.8630 (m-80) cc_final: 0.8282 (m-10) REVERT: B 932 GLN cc_start: 0.9168 (pt0) cc_final: 0.8815 (pp30) REVERT: B 950 ASN cc_start: 0.9299 (t0) cc_final: 0.8908 (t0) REVERT: B 957 ASN cc_start: 0.8951 (m110) cc_final: 0.8645 (m-40) REVERT: B 999 GLN cc_start: 0.9317 (tp-100) cc_final: 0.8953 (tp-100) REVERT: C 223 LEU cc_start: 0.9144 (mp) cc_final: 0.8634 (tp) REVERT: C 348 TYR cc_start: 0.9470 (p90) cc_final: 0.8906 (p90) REVERT: C 717 ILE cc_start: 0.8108 (mm) cc_final: 0.7898 (mm) REVERT: C 817 ASP cc_start: 0.8898 (m-30) cc_final: 0.8446 (m-30) REVERT: C 866 MET cc_start: 0.9011 (mtp) cc_final: 0.8759 (mtp) REVERT: C 918 LYS cc_start: 0.9255 (mttt) cc_final: 0.8867 (mppt) REVERT: C 947 ASP cc_start: 0.9185 (t0) cc_final: 0.8956 (t0) REVERT: C 989 GLN cc_start: 0.9023 (mm-40) cc_final: 0.8505 (mp10) REVERT: C 1007 GLN cc_start: 0.9351 (mp10) cc_final: 0.9121 (mp10) REVERT: C 1047 MET cc_start: 0.7983 (ppp) cc_final: 0.7741 (ppp) REVERT: C 1049 PHE cc_start: 0.7584 (m-80) cc_final: 0.7174 (m-80) REVERT: A 55 PHE cc_start: 0.7781 (m-80) cc_final: 0.7419 (m-80) REVERT: A 744 THR cc_start: 0.9519 (p) cc_final: 0.9316 (p) REVERT: A 770 GLU cc_start: 0.8763 (tt0) cc_final: 0.8437 (tp30) REVERT: A 999 GLN cc_start: 0.8784 (tp-100) cc_final: 0.8540 (tm-30) REVERT: A 1039 PHE cc_start: 0.7009 (t80) cc_final: 0.6698 (t80) REVERT: A 1108 GLU cc_start: 0.9096 (tt0) cc_final: 0.8549 (tm-30) REVERT: K 90 LEU cc_start: 0.8552 (tp) cc_final: 0.8262 (mt) outliers start: 0 outliers final: 0 residues processed: 269 average time/residue: 0.1740 time to fit residues: 79.0753 Evaluate side-chains 196 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 78 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 318 optimal weight: 5.9990 chunk 307 optimal weight: 0.9990 chunk 246 optimal weight: 40.0000 chunk 241 optimal weight: 9.9990 chunk 95 optimal weight: 6.9990 chunk 303 optimal weight: 0.9980 chunk 178 optimal weight: 0.0170 chunk 280 optimal weight: 4.9990 overall best weight: 1.8024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 687 GLN ** B 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 925 ASN ** B1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 952 ASN ** C1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.089017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.057834 restraints weight = 178894.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.059622 restraints weight = 108360.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.060914 restraints weight = 76021.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.061664 restraints weight = 59467.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.062149 restraints weight = 50401.006| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.6667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 31304 Z= 0.149 Angle : 0.628 8.261 42733 Z= 0.327 Chirality : 0.044 0.211 4944 Planarity : 0.004 0.049 5405 Dihedral : 4.846 25.624 4107 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.14 % Favored : 94.72 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.05 % 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: -0.95 (0.13), residues: 3753 helix: 0.15 (0.19), residues: 669 sheet: -0.12 (0.16), residues: 982 loop : -1.14 (0.13), residues: 2102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 506 TYR 0.024 0.001 TYR C1004 PHE 0.030 0.002 PHE B 885 TRP 0.016 0.001 TRP A 883 HIS 0.015 0.002 HIS C1045 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 (31204) covalent geometry : angle 0.61815 / 0.32 (42481) SS BOND : bond 0.00327 / 0.21 ( 48) SS BOND : angle 1.12628 / 0.74 ( 96) hydrogen bonds : bond 0.04211 / 2.83 ( 1248) hydrogen bonds : angle 6.23141 / 4.39 ( 3444) link_BETA1-4 : bond 0.00230 / 0.16 ( 12) link_BETA1-4 : angle 1.23341 / 0.86 ( 36) link_NAG-ASN : bond 0.00228 / 0.16 ( 40) link_NAG-ASN : angle 1.88570 / 1.33 ( 120) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6897.09 seconds wall clock time: 119 minutes 48.02 seconds (7188.02 seconds total)