Starting phenix.real_space_refine on Sat Feb 7 05:09:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7q9p_13875/02_2026/7q9p_13875.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q9p_13875/02_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 { model { file = "/net/cci-nas-00/data/ceres_data/7q9p_13875/02_2026/7q9p_13875.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q9p_13875/02_2026/7q9p_13875.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7q9p_13875/02_2026/7q9p_13875.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q9p_13875/02_2026/7q9p_13875.map" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 30 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 dihedrals: 24 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 dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 7.30, per 1000 atoms: 0.24 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: 2.92 Conformation dependent library (CDL) restraints added in 1.2 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: 1.39 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: 8.01 Time building geometry restraints manager: 3.73 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: 18250 17.81 - 35.62: 729 35.62 - 53.43: 184 53.43 - 71.24: 48 71.24 - 89.05: 18 Dihedral angle restraints: 19229 sinusoidal: 8147 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 19226 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: 6.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.690 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 30.840 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 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 : 10.947 89.053 11969 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 covalent geometry : bond 0.00454 (31204) covalent geometry : angle 0.66341 (42481) SS BOND : bond 0.00312 ( 48) SS BOND : angle 0.95905 ( 96) hydrogen bonds : bond 0.14405 ( 1248) hydrogen bonds : angle 7.38599 ( 3444) link_BETA1-4 : bond 0.00254 ( 12) link_BETA1-4 : angle 1.35844 ( 36) link_NAG-ASN : bond 0.00332 ( 40) link_NAG-ASN : angle 1.73591 ( 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 : 0.864 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: 0.1987 time to fit residues: 195.2587 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 : 1.128 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: B 484 ASN B 495 GLN ** B 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 853 ASN A 910 GLN A 925 ASN A 946 GLN A 950 ASN H 78 ASN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.102068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.070352 restraints weight = 192935.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.072722 restraints weight = 110159.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.073981 restraints weight = 74752.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.074991 restraints weight = 57609.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.075524 restraints weight = 47543.099| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 31304 Z= 0.144 Angle : 0.630 11.071 42733 Z= 0.325 Chirality : 0.045 0.331 4944 Planarity : 0.004 0.055 5405 Dihedral : 6.605 59.981 5199 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.53 % Favored : 95.23 % Rotamer: Outliers : 0.06 % Allowed : 2.01 % 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: -0.44 (0.13), residues: 3753 helix: 1.16 (0.19), residues: 722 sheet: 0.08 (0.15), residues: 1031 loop : -1.04 (0.13), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 354 TYR 0.035 0.002 TYR A 263 PHE 0.029 0.002 PHE B 756 TRP 0.016 0.001 TRP H 105 HIS 0.006 0.001 HIS A1045 Details of bonding type rmsd covalent geometry : bond 0.00310 (31204) covalent geometry : angle 0.61709 (42481) SS BOND : bond 0.00351 ( 48) SS BOND : angle 1.74071 ( 96) hydrogen bonds : bond 0.04326 ( 1248) hydrogen bonds : angle 6.04443 ( 3444) link_BETA1-4 : bond 0.00349 ( 12) link_BETA1-4 : angle 0.98251 ( 36) link_NAG-ASN : bond 0.00356 ( 40) link_NAG-ASN : angle 1.98750 ( 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 418 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 416 time to evaluate : 1.185 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: B 55 PHE cc_start: 0.8368 (m-80) cc_final: 0.7186 (m-10) REVERT: B 272 PHE cc_start: 0.8706 (m-80) cc_final: 0.7857 (m-80) REVERT: B 313 SER cc_start: 0.9472 (t) cc_final: 0.9125 (p) REVERT: B 314 ASN cc_start: 0.9183 (m110) cc_final: 0.8189 (p0) REVERT: B 782 VAL cc_start: 0.7218 (m) cc_final: 0.6952 (m) REVERT: B 802 ILE cc_start: 0.6958 (pt) cc_final: 0.6755 (pt) REVERT: B 803 LEU cc_start: 0.8805 (mp) cc_final: 0.8589 (tp) REVERT: B 866 MET cc_start: 0.9070 (mpp) cc_final: 0.8777 (mmm) REVERT: B 897 MET cc_start: 0.6687 (mmt) cc_final: 0.6126 (mmt) REVERT: B 999 GLN cc_start: 0.9146 (tp-100) cc_final: 0.8811 (tp-100) REVERT: C 41 LYS cc_start: 0.7711 (mttt) cc_final: 0.7359 (tptt) REVERT: C 128 ILE cc_start: 0.8874 (mp) cc_final: 0.8668 (mp) REVERT: C 168 PHE cc_start: 0.8996 (t80) cc_final: 0.8663 (t80) REVERT: C 223 LEU cc_start: 0.9329 (mp) cc_final: 0.8707 (tp) REVERT: C 348 TYR cc_start: 0.9262 (p90) cc_final: 0.8656 (p90) REVERT: C 420 TYR cc_start: 0.8494 (t80) cc_final: 0.7989 (t80) REVERT: C 737 MET cc_start: 0.9076 (tpp) cc_final: 0.8830 (tpp) REVERT: C 819 LEU cc_start: 0.9398 (mt) cc_final: 0.9058 (mt) REVERT: C 858 LEU cc_start: 0.8839 (mt) cc_final: 0.8393 (tp) REVERT: C 870 TYR cc_start: 0.8598 (m-80) cc_final: 0.8208 (m-80) REVERT: C 928 ILE cc_start: 0.9083 (mm) cc_final: 0.8804 (mm) REVERT: C 966 ASN cc_start: 0.9479 (m-40) cc_final: 0.9066 (m-40) REVERT: C 1059 PHE cc_start: 0.8210 (m-10) cc_final: 0.7900 (m-10) REVERT: C 1110 GLN cc_start: 0.8996 (mt0) cc_final: 0.8672 (mp10) REVERT: A 53 ASP cc_start: 0.7837 (t70) cc_final: 0.7524 (t70) REVERT: A 55 PHE cc_start: 0.7875 (m-80) cc_final: 0.7415 (m-80) REVERT: A 169 GLU cc_start: 0.9103 (pm20) cc_final: 0.8809 (mp0) REVERT: A 420 TYR cc_start: 0.8557 (t80) cc_final: 0.7548 (t80) REVERT: A 583 ASP cc_start: 0.8751 (m-30) cc_final: 0.8298 (t0) REVERT: A 729 THR cc_start: 0.8006 (m) cc_final: 0.7700 (t) REVERT: A 744 THR cc_start: 0.9314 (p) cc_final: 0.9061 (p) REVERT: A 752 GLN cc_start: 0.7880 (tm-30) cc_final: 0.7307 (tm-30) REVERT: A 767 ILE cc_start: 0.9185 (mt) cc_final: 0.8981 (mt) REVERT: A 951 GLN cc_start: 0.9042 (mt0) cc_final: 0.8633 (mt0) REVERT: A 961 LYS cc_start: 0.9403 (mttt) cc_final: 0.9115 (mmtm) REVERT: A 1003 THR cc_start: 0.8717 (m) cc_final: 0.8202 (m) REVERT: A 1025 LYS cc_start: 0.8927 (mttm) cc_final: 0.8610 (mmtt) REVERT: A 1039 PHE cc_start: 0.6400 (t80) cc_final: 0.5782 (t80) REVERT: A 1059 PHE cc_start: 0.8569 (m-80) cc_final: 0.7915 (m-10) REVERT: A 1108 GLU cc_start: 0.8916 (tt0) cc_final: 0.8289 (tm-30) REVERT: K 90 LEU cc_start: 0.7935 (tp) cc_final: 0.7715 (mt) outliers start: 2 outliers final: 0 residues processed: 418 average time/residue: 0.1857 time to fit residues: 127.4223 Evaluate side-chains 286 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 286 time to evaluate : 1.067 ------------------------------------------------------------------------------- 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: 20.0000 chunk 325 optimal weight: 10.0000 chunk 176 optimal weight: 8.9990 chunk 249 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 chunk 333 optimal weight: 50.0000 chunk 271 optimal weight: 5.9990 chunk 302 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 310 optimal weight: 0.3980 chunk 97 optimal weight: 9.9990 overall best weight: 4.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 781 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** 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** C1020 ASN ** C1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1055 HIS C1116 ASN ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 GLN ** A 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.094115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.066309 restraints weight = 201059.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.068172 restraints weight = 123051.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.067937 restraints weight = 82458.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.068164 restraints weight = 77645.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.068333 restraints weight = 74899.756| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 31304 Z= 0.297 Angle : 0.779 12.949 42733 Z= 0.414 Chirality : 0.048 0.267 4944 Planarity : 0.006 0.076 5405 Dihedral : 6.393 59.592 5199 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.36 % Favored : 94.43 % Rotamer: Outliers : 0.24 % Allowed : 3.90 % Favored : 95.86 % 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: -0.97 (0.13), residues: 3753 helix: -0.00 (0.18), residues: 699 sheet: -0.06 (0.15), residues: 1032 loop : -1.18 (0.13), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.039 0.001 ARG C 400 TYR 0.049 0.003 TYR C 738 PHE 0.046 0.003 PHE B1049 TRP 0.019 0.002 TRP J 38 HIS 0.020 0.002 HIS C1055 Details of bonding type rmsd covalent geometry : bond 0.00597 (31204) covalent geometry : angle 0.76533 (42481) SS BOND : bond 0.01639 ( 48) SS BOND : angle 1.71041 ( 96) hydrogen bonds : bond 0.05647 ( 1248) hydrogen bonds : angle 6.64343 ( 3444) link_BETA1-4 : bond 0.00417 ( 12) link_BETA1-4 : angle 1.61123 ( 36) link_NAG-ASN : bond 0.00436 ( 40) link_NAG-ASN : angle 2.35264 ( 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 368 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 360 time to evaluate : 0.866 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: 0.8475 (m-80) cc_final: 0.7322 (m-10) REVERT: B 272 PHE cc_start: 0.8455 (m-80) cc_final: 0.7652 (m-80) REVERT: B 749 LEU cc_start: 0.9017 (mt) cc_final: 0.8795 (mp) REVERT: B 803 LEU cc_start: 0.9165 (mp) cc_final: 0.8959 (tp) REVERT: B 999 GLN cc_start: 0.9384 (tp-100) cc_final: 0.9037 (tp-100) REVERT: C 41 LYS cc_start: 0.7715 (mttt) cc_final: 0.7286 (mmtt) REVERT: C 128 ILE cc_start: 0.9076 (mp) cc_final: 0.8775 (mp) REVERT: C 168 PHE cc_start: 0.9095 (t80) cc_final: 0.8730 (t80) REVERT: C 223 LEU cc_start: 0.9341 (mp) cc_final: 0.8816 (tp) REVERT: C 420 TYR cc_start: 0.8910 (t80) cc_final: 0.8115 (t80) REVERT: C 737 MET cc_start: 0.9491 (tpp) cc_final: 0.9288 (tpp) REVERT: C 817 ASP cc_start: 0.8876 (m-30) cc_final: 0.8606 (m-30) REVERT: C 870 TYR cc_start: 0.8561 (m-80) cc_final: 0.8289 (m-80) REVERT: C 931 ILE cc_start: 0.8822 (mm) cc_final: 0.8519 (mm) REVERT: C 932 GLN cc_start: 0.8960 (tm-30) cc_final: 0.8697 (tm-30) REVERT: C 1110 GLN cc_start: 0.9152 (mt0) cc_final: 0.8718 (mp10) REVERT: A 54 LEU cc_start: 0.6614 (tp) cc_final: 0.6320 (tp) REVERT: A 55 PHE cc_start: 0.8140 (m-80) cc_final: 0.7547 (m-10) REVERT: A 348 TYR cc_start: 0.9721 (p90) cc_final: 0.9503 (p90) REVERT: A 420 TYR cc_start: 0.8723 (t80) cc_final: 0.7634 (t80) REVERT: A 583 ASP cc_start: 0.9032 (m-30) cc_final: 0.8661 (t0) REVERT: A 717 ILE cc_start: 0.8234 (mm) cc_final: 0.7896 (mm) REVERT: A 736 THR cc_start: 0.9245 (m) cc_final: 0.9029 (p) REVERT: A 744 THR cc_start: 0.9456 (p) cc_final: 0.9249 (p) REVERT: A 752 GLN cc_start: 0.8444 (tm-30) cc_final: 0.7934 (tm-30) REVERT: A 893 ILE cc_start: 0.6388 (tt) cc_final: 0.6088 (tt) REVERT: A 999 GLN cc_start: 0.8806 (tp40) cc_final: 0.8530 (tp-100) REVERT: A 1003 THR cc_start: 0.8989 (m) cc_final: 0.8621 (m) REVERT: A 1025 LYS cc_start: 0.8946 (mttm) cc_final: 0.8630 (mmtt) REVERT: A 1108 GLU cc_start: 0.9215 (tt0) cc_final: 0.8582 (tm-30) REVERT: J 120 THR cc_start: 0.7750 (p) cc_final: 0.7527 (p) REVERT: K 90 LEU cc_start: 0.8223 (tp) cc_final: 0.7847 (mt) outliers start: 8 outliers final: 5 residues processed: 368 average time/residue: 0.1676 time to fit residues: 102.7355 Evaluate side-chains 258 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 253 time to evaluate : 1.208 ------------------------------------------------------------------------------- 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: 7.9990 chunk 345 optimal weight: 40.0000 chunk 304 optimal weight: 0.9980 chunk 105 optimal weight: 7.9990 chunk 315 optimal weight: 20.0000 chunk 173 optimal weight: 0.7980 chunk 237 optimal weight: 7.9990 chunk 104 optimal weight: 20.0000 chunk 250 optimal weight: 20.0000 chunk 308 optimal weight: 10.0000 chunk 122 optimal weight: 20.0000 overall best weight: 5.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 801 GLN B 925 ASN B1002 GLN ** B1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 904 ASN C 910 GLN C1051 GLN ** A 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 898 GLN ** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.089701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.057598 restraints weight = 179251.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.059109 restraints weight = 112840.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.060217 restraints weight = 80388.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.061121 restraints weight = 64248.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.061564 restraints weight = 54614.228| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.4669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 31304 Z= 0.300 Angle : 0.749 14.659 42733 Z= 0.398 Chirality : 0.047 0.323 4944 Planarity : 0.005 0.078 5405 Dihedral : 6.117 57.215 5199 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 17.82 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.68 % Favored : 94.16 % Rotamer: Outliers : 0.06 % Allowed : 3.36 % Favored : 96.58 % 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: -1.16 (0.13), residues: 3753 helix: -0.38 (0.18), residues: 678 sheet: -0.09 (0.16), residues: 997 loop : -1.25 (0.13), residues: 2078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 992 TYR 0.024 0.002 TYR A 738 PHE 0.031 0.003 PHE A 272 TRP 0.014 0.002 TRP A 64 HIS 0.013 0.002 HIS B1045 Details of bonding type rmsd covalent geometry : bond 0.00593 (31204) covalent geometry : angle 0.73609 (42481) SS BOND : bond 0.00579 ( 48) SS BOND : angle 1.52748 ( 96) hydrogen bonds : bond 0.05511 ( 1248) hydrogen bonds : angle 6.67541 ( 3444) link_BETA1-4 : bond 0.00273 ( 12) link_BETA1-4 : angle 1.66200 ( 36) link_NAG-ASN : bond 0.00350 ( 40) link_NAG-ASN : angle 2.23930 ( 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 325 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 323 time to evaluate : 0.933 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: 0.8184 (m-80) cc_final: 0.7070 (m-10) REVERT: B 272 PHE cc_start: 0.8681 (m-80) cc_final: 0.7990 (m-10) REVERT: B 745 GLU cc_start: 0.9162 (mp0) cc_final: 0.8548 (tt0) REVERT: B 761 ASN cc_start: 0.8893 (m110) cc_final: 0.8104 (m110) REVERT: B 985 GLU cc_start: 0.9057 (mt-10) cc_final: 0.8855 (mp0) REVERT: B 999 GLN cc_start: 0.9387 (tp-100) cc_final: 0.9005 (tp-100) REVERT: B 1036 ARG cc_start: 0.7782 (mtp85) cc_final: 0.7379 (mtp85) REVERT: B 1078 ILE cc_start: 0.8674 (mt) cc_final: 0.8233 (mm) REVERT: B 1124 ASP cc_start: 0.6882 (p0) cc_final: 0.6662 (p0) REVERT: C 128 ILE cc_start: 0.9078 (mp) cc_final: 0.8767 (mp) REVERT: C 168 PHE cc_start: 0.9039 (t80) cc_final: 0.8626 (t80) REVERT: C 223 LEU cc_start: 0.9373 (mp) cc_final: 0.8906 (tp) REVERT: C 420 TYR cc_start: 0.8798 (t80) cc_final: 0.8315 (t80) REVERT: C 694 MET cc_start: 0.8052 (ppp) cc_final: 0.7623 (ppp) REVERT: C 739 ILE cc_start: 0.9604 (mt) cc_final: 0.9358 (tp) REVERT: C 870 TYR cc_start: 0.8757 (m-80) cc_final: 0.8461 (m-80) REVERT: C 916 ASN cc_start: 0.9318 (t0) cc_final: 0.9082 (t0) REVERT: C 918 LYS cc_start: 0.9398 (mttt) cc_final: 0.9031 (mppt) REVERT: C 930 LYS cc_start: 0.9393 (mmtm) cc_final: 0.9056 (mttt) REVERT: C 931 ILE cc_start: 0.9135 (mm) cc_final: 0.8913 (mm) REVERT: C 932 GLN cc_start: 0.9107 (tm-30) cc_final: 0.8788 (tm-30) REVERT: A 55 PHE cc_start: 0.7873 (m-80) cc_final: 0.7594 (m-10) REVERT: A 117 LEU cc_start: 0.9556 (tp) cc_final: 0.9244 (tp) REVERT: A 583 ASP cc_start: 0.8912 (m-30) cc_final: 0.8583 (t0) REVERT: A 694 MET cc_start: 0.8102 (ppp) cc_final: 0.7822 (ppp) REVERT: A 736 THR cc_start: 0.9082 (m) cc_final: 0.8877 (p) REVERT: A 744 THR cc_start: 0.9468 (p) cc_final: 0.9260 (p) REVERT: A 752 GLN cc_start: 0.8566 (tm-30) cc_final: 0.8013 (tm-30) REVERT: A 816 GLU cc_start: 0.8974 (mt-10) cc_final: 0.7617 (mt-10) REVERT: A 957 ASN cc_start: 0.8942 (m110) cc_final: 0.8691 (m110) REVERT: A 982 ASP cc_start: 0.8549 (m-30) cc_final: 0.8293 (p0) REVERT: A 999 GLN cc_start: 0.8741 (tp40) cc_final: 0.8399 (tp-100) REVERT: A 1003 THR cc_start: 0.8913 (m) cc_final: 0.8591 (m) REVERT: A 1108 GLU cc_start: 0.9108 (tt0) cc_final: 0.8581 (tm-30) REVERT: A 1110 GLN cc_start: 0.9276 (mt0) cc_final: 0.8894 (tm-30) REVERT: J 71 MET cc_start: 0.5604 (ppp) cc_final: 0.5309 (ppp) REVERT: K 90 LEU cc_start: 0.8296 (tp) cc_final: 0.8014 (mt) outliers start: 2 outliers final: 1 residues processed: 325 average time/residue: 0.1698 time to fit residues: 93.0531 Evaluate side-chains 236 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 235 time to evaluate : 1.133 ------------------------------------------------------------------------------- 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: 5.9990 chunk 153 optimal weight: 6.9990 chunk 217 optimal weight: 0.2980 chunk 254 optimal weight: 0.0270 chunk 216 optimal weight: 6.9990 chunk 241 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 chunk 332 optimal weight: 50.0000 chunk 283 optimal weight: 0.9980 chunk 326 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 overall best weight: 2.2642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 925 ASN ** 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 391 ASN ** C 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 687 GLN C 904 ASN ** C 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1033 GLN ** 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** A1055 HIS A1105 ASN E 41 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.091627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.060238 restraints weight = 180468.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.061876 restraints weight = 107917.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.063064 restraints weight = 75153.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.063957 restraints weight = 58890.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.064377 restraints weight = 49667.260| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.4946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 31304 Z= 0.167 Angle : 0.629 12.203 42733 Z= 0.325 Chirality : 0.044 0.229 4944 Planarity : 0.004 0.060 5405 Dihedral : 5.476 52.898 5199 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.33 % Favored : 94.51 % Rotamer: Outliers : 0.03 % Allowed : 2.04 % 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: -0.93 (0.13), residues: 3753 helix: 0.03 (0.18), residues: 700 sheet: -0.00 (0.16), residues: 995 loop : -1.16 (0.13), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1036 TYR 0.023 0.002 TYR A 738 PHE 0.020 0.002 PHE C 562 TRP 0.021 0.001 TRP A 883 HIS 0.018 0.002 HIS C1045 Details of bonding type rmsd covalent geometry : bond 0.00345 (31204) covalent geometry : angle 0.61390 (42481) SS BOND : bond 0.00385 ( 48) SS BOND : angle 1.73530 ( 96) hydrogen bonds : bond 0.04432 ( 1248) hydrogen bonds : angle 6.26969 ( 3444) link_BETA1-4 : bond 0.00221 ( 12) link_BETA1-4 : angle 1.45609 ( 36) link_NAG-ASN : bond 0.00406 ( 40) link_NAG-ASN : angle 2.05347 ( 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 325 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 324 time to evaluate : 1.219 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: B 55 PHE cc_start: 0.8000 (m-80) cc_final: 0.7034 (m-10) REVERT: B 272 PHE cc_start: 0.8581 (m-80) cc_final: 0.7877 (m-10) REVERT: B 315 PHE cc_start: 0.8168 (t80) cc_final: 0.7953 (t80) REVERT: B 745 GLU cc_start: 0.9084 (mp0) cc_final: 0.8560 (tt0) REVERT: B 999 GLN cc_start: 0.9277 (tp-100) cc_final: 0.8791 (tp-100) REVERT: B 1036 ARG cc_start: 0.7722 (mtp85) cc_final: 0.7354 (mtp85) REVERT: B 1078 ILE cc_start: 0.8539 (mt) cc_final: 0.8075 (mm) REVERT: C 128 ILE cc_start: 0.9123 (mp) cc_final: 0.8852 (mp) REVERT: C 168 PHE cc_start: 0.8956 (t80) cc_final: 0.8547 (t80) REVERT: C 223 LEU cc_start: 0.9300 (mp) cc_final: 0.8770 (tp) REVERT: C 717 ILE cc_start: 0.8174 (mm) cc_final: 0.7952 (mm) REVERT: C 739 ILE cc_start: 0.9519 (mt) cc_final: 0.9216 (tp) REVERT: C 870 TYR cc_start: 0.8645 (m-80) cc_final: 0.8374 (m-80) REVERT: C 916 ASN cc_start: 0.9224 (t0) cc_final: 0.8965 (t0) REVERT: C 918 LYS cc_start: 0.9281 (mttt) cc_final: 0.8927 (mppt) REVERT: C 930 LYS cc_start: 0.9370 (mmtm) cc_final: 0.9060 (mttt) REVERT: C 948 VAL cc_start: 0.9494 (m) cc_final: 0.9177 (p) REVERT: A 55 PHE cc_start: 0.7798 (m-80) cc_final: 0.7497 (m-80) REVERT: A 106 PHE cc_start: 0.7868 (m-10) cc_final: 0.7525 (m-80) REVERT: A 117 LEU cc_start: 0.9498 (tp) cc_final: 0.9103 (tp) REVERT: A 583 ASP cc_start: 0.8897 (m-30) cc_final: 0.8616 (t0) REVERT: A 717 ILE cc_start: 0.8423 (mt) cc_final: 0.8138 (pt) REVERT: A 736 THR cc_start: 0.9061 (m) cc_final: 0.8824 (p) REVERT: A 744 THR cc_start: 0.9435 (p) cc_final: 0.9198 (p) REVERT: A 752 GLN cc_start: 0.8492 (tm-30) cc_final: 0.8242 (tm-30) REVERT: A 816 GLU cc_start: 0.8596 (mt-10) cc_final: 0.8388 (mt-10) REVERT: A 952 ASN cc_start: 0.9026 (t0) cc_final: 0.8796 (t0) REVERT: A 957 ASN cc_start: 0.8781 (m110) cc_final: 0.8545 (m110) REVERT: A 999 GLN cc_start: 0.8552 (tp40) cc_final: 0.8191 (tp40) REVERT: A 1003 THR cc_start: 0.8764 (m) cc_final: 0.8531 (m) REVERT: A 1033 GLN cc_start: 0.6146 (tt0) cc_final: 0.5428 (tt0) REVERT: A 1108 GLU cc_start: 0.9077 (tt0) cc_final: 0.8578 (tm-30) REVERT: A 1110 GLN cc_start: 0.9109 (mt0) cc_final: 0.8789 (tm-30) REVERT: J 71 MET cc_start: 0.5487 (ppp) cc_final: 0.5195 (ppp) REVERT: K 90 LEU cc_start: 0.8271 (tp) cc_final: 0.7974 (mt) outliers start: 1 outliers final: 0 residues processed: 325 average time/residue: 0.1841 time to fit residues: 100.0493 Evaluate side-chains 242 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 1.249 ------------------------------------------------------------------------------- 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: 0.0000 chunk 197 optimal weight: 4.9990 chunk 356 optimal weight: 0.9990 chunk 249 optimal weight: 0.7980 chunk 209 optimal weight: 9.9990 chunk 214 optimal weight: 20.0000 chunk 360 optimal weight: 6.9990 chunk 215 optimal weight: 20.0000 chunk 322 optimal weight: 50.0000 chunk 23 optimal weight: 0.4980 chunk 63 optimal weight: 1.9990 overall best weight: 0.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 610 GLN ** 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 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 962 GLN ** C1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1051 GLN ** 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 A1051 GLN E 41 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.093059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.061668 restraints weight = 177226.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.063614 restraints weight = 104216.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.064822 restraints weight = 72985.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.065744 restraints weight = 57492.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.066176 restraints weight = 48366.488| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.5090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 31304 Z= 0.124 Angle : 0.595 8.973 42733 Z= 0.306 Chirality : 0.044 0.232 4944 Planarity : 0.004 0.047 5405 Dihedral : 5.018 47.976 5199 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.50 % Favored : 95.34 % Rotamer: Outliers : 0.06 % Allowed : 1.62 % Favored : 98.32 % 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: 0.36 (0.19), residues: 693 sheet: 0.08 (0.16), residues: 1007 loop : -1.08 (0.13), residues: 2053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 564 TYR 0.023 0.001 TYR A 263 PHE 0.024 0.001 PHE C1049 TRP 0.015 0.001 TRP A 64 HIS 0.012 0.001 HIS C1045 Details of bonding type rmsd covalent geometry : bond 0.00268 (31204) covalent geometry : angle 0.58153 (42481) SS BOND : bond 0.00379 ( 48) SS BOND : angle 1.64224 ( 96) hydrogen bonds : bond 0.03940 ( 1248) hydrogen bonds : angle 6.04271 ( 3444) link_BETA1-4 : bond 0.00340 ( 12) link_BETA1-4 : angle 1.22996 ( 36) link_NAG-ASN : bond 0.00192 ( 40) link_NAG-ASN : angle 1.96001 ( 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 340 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 338 time to evaluate : 1.100 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: 0.7932 (m-80) cc_final: 0.6936 (m-10) REVERT: B 272 PHE cc_start: 0.8577 (m-80) cc_final: 0.7968 (m-10) REVERT: B 745 GLU cc_start: 0.9065 (mp0) cc_final: 0.8550 (tt0) REVERT: B 999 GLN cc_start: 0.9329 (tp-100) cc_final: 0.8881 (tp-100) REVERT: B 1028 GLU cc_start: 0.7615 (mt-10) cc_final: 0.6894 (mt-10) REVERT: B 1078 ILE cc_start: 0.8512 (mt) cc_final: 0.8058 (mm) REVERT: C 168 PHE cc_start: 0.8932 (t80) cc_final: 0.8499 (t80) REVERT: C 223 LEU cc_start: 0.9262 (mp) cc_final: 0.8714 (tp) REVERT: C 717 ILE cc_start: 0.8211 (mm) cc_final: 0.7992 (mm) REVERT: C 739 ILE cc_start: 0.9588 (mt) cc_final: 0.9356 (tt) REVERT: C 817 ASP cc_start: 0.8783 (m-30) cc_final: 0.8378 (m-30) REVERT: C 866 MET cc_start: 0.9001 (mtp) cc_final: 0.8797 (mtp) REVERT: C 916 ASN cc_start: 0.9236 (t0) cc_final: 0.8972 (t0) REVERT: C 918 LYS cc_start: 0.9314 (mttt) cc_final: 0.8935 (mppt) REVERT: C 930 LYS cc_start: 0.9396 (mmtm) cc_final: 0.9061 (mttt) REVERT: C 989 GLN cc_start: 0.8726 (mm-40) cc_final: 0.8234 (mp10) REVERT: C 1015 ILE cc_start: 0.9445 (mm) cc_final: 0.8998 (tt) REVERT: A 55 PHE cc_start: 0.7638 (m-80) cc_final: 0.7167 (m-80) REVERT: A 106 PHE cc_start: 0.7845 (m-10) cc_final: 0.7570 (m-80) REVERT: A 117 LEU cc_start: 0.9477 (tp) cc_final: 0.9087 (tp) REVERT: A 583 ASP cc_start: 0.8870 (m-30) cc_final: 0.8602 (t0) REVERT: A 717 ILE cc_start: 0.8451 (mt) cc_final: 0.8176 (pt) REVERT: A 736 THR cc_start: 0.9066 (m) cc_final: 0.8827 (p) REVERT: A 744 THR cc_start: 0.9448 (p) cc_final: 0.9203 (p) REVERT: A 770 GLU cc_start: 0.8586 (tt0) cc_final: 0.8217 (tp30) REVERT: A 952 ASN cc_start: 0.9012 (t0) cc_final: 0.8792 (t0) REVERT: A 957 ASN cc_start: 0.8798 (m110) cc_final: 0.8549 (m110) REVERT: A 999 GLN cc_start: 0.8680 (tp40) cc_final: 0.8168 (tp40) REVERT: A 1003 THR cc_start: 0.8767 (m) cc_final: 0.8476 (m) REVERT: A 1028 GLU cc_start: 0.8439 (pt0) cc_final: 0.8184 (pt0) REVERT: A 1030 VAL cc_start: 0.8225 (t) cc_final: 0.7796 (t) REVERT: A 1033 GLN cc_start: 0.5976 (tt0) cc_final: 0.5157 (tt0) REVERT: A 1108 GLU cc_start: 0.8999 (tt0) cc_final: 0.8551 (tm-30) REVERT: A 1110 GLN cc_start: 0.9075 (mt0) cc_final: 0.8741 (tm-30) REVERT: J 71 MET cc_start: 0.5727 (ppp) cc_final: 0.5481 (ppp) REVERT: K 90 LEU cc_start: 0.8283 (tp) cc_final: 0.7987 (mt) outliers start: 2 outliers final: 1 residues processed: 340 average time/residue: 0.1727 time to fit residues: 98.2998 Evaluate side-chains 259 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 258 time to evaluate : 1.068 ------------------------------------------------------------------------------- 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: 1.9990 chunk 164 optimal weight: 8.9990 chunk 129 optimal weight: 6.9990 chunk 213 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 chunk 184 optimal weight: 8.9990 chunk 271 optimal weight: 2.9990 chunk 151 optimal weight: 20.0000 chunk 353 optimal weight: 30.0000 chunk 261 optimal weight: 4.9990 chunk 30 optimal weight: 30.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 687 GLN ** B 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 925 ASN ** B1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN C 314 ASN ** C 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 516 HIS ** C 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 952 ASN ** C1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 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 781 GLN ** A1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.088597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.060035 restraints weight = 205507.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.060713 restraints weight = 134813.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.061478 restraints weight = 101684.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.062393 restraints weight = 73314.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.062772 restraints weight = 54633.007| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.5801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 31304 Z= 0.287 Angle : 0.746 13.182 42733 Z= 0.398 Chirality : 0.047 0.313 4944 Planarity : 0.005 0.067 5405 Dihedral : 5.487 39.853 5199 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 20.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.13 % Favored : 93.74 % Rotamer: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % 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: -1.11 (0.13), residues: 3753 helix: -0.33 (0.18), residues: 679 sheet: -0.12 (0.17), residues: 956 loop : -1.16 (0.13), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 44 TYR 0.025 0.002 TYR C 738 PHE 0.030 0.003 PHE B 315 TRP 0.032 0.002 TRP A 883 HIS 0.025 0.002 HIS C1045 Details of bonding type rmsd covalent geometry : bond 0.00567 (31204) covalent geometry : angle 0.73431 (42481) SS BOND : bond 0.00510 ( 48) SS BOND : angle 1.36093 ( 96) hydrogen bonds : bond 0.05268 ( 1248) hydrogen bonds : angle 6.61482 ( 3444) link_BETA1-4 : bond 0.00393 ( 12) link_BETA1-4 : angle 1.58857 ( 36) link_NAG-ASN : bond 0.00531 ( 40) link_NAG-ASN : angle 2.23870 ( 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 294 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 294 time to evaluate : 1.213 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: B 272 PHE cc_start: 0.8601 (m-80) cc_final: 0.8226 (m-10) REVERT: B 745 GLU cc_start: 0.9112 (mp0) cc_final: 0.8670 (tt0) REVERT: B 985 GLU cc_start: 0.8659 (mp0) cc_final: 0.8447 (mp0) REVERT: B 999 GLN cc_start: 0.9366 (tp-100) cc_final: 0.9039 (tp-100) REVERT: B 1078 ILE cc_start: 0.8772 (mt) cc_final: 0.8386 (mm) REVERT: B 1124 ASP cc_start: 0.7139 (p0) cc_final: 0.6824 (p0) REVERT: C 168 PHE cc_start: 0.9121 (t80) cc_final: 0.8743 (t80) REVERT: C 223 LEU cc_start: 0.9308 (mp) cc_final: 0.8769 (tp) REVERT: C 348 TYR cc_start: 0.9421 (p90) cc_final: 0.8864 (p90) REVERT: C 694 MET cc_start: 0.7790 (ppp) cc_final: 0.7366 (ppp) REVERT: C 717 ILE cc_start: 0.8251 (mm) cc_final: 0.8011 (mm) REVERT: C 817 ASP cc_start: 0.8944 (m-30) cc_final: 0.8504 (m-30) REVERT: C 918 LYS cc_start: 0.9314 (mttt) cc_final: 0.8909 (mppt) REVERT: C 989 GLN cc_start: 0.8980 (mm-40) cc_final: 0.8431 (mp10) REVERT: A 55 PHE cc_start: 0.7845 (m-80) cc_final: 0.7480 (m-80) REVERT: A 106 PHE cc_start: 0.8424 (m-10) cc_final: 0.8063 (m-80) REVERT: A 117 LEU cc_start: 0.9572 (tp) cc_final: 0.9230 (tp) REVERT: A 583 ASP cc_start: 0.9064 (m-30) cc_final: 0.8808 (t0) REVERT: A 694 MET cc_start: 0.8302 (ppp) cc_final: 0.8034 (ppp) REVERT: A 717 ILE cc_start: 0.8509 (mt) cc_final: 0.8189 (pt) REVERT: A 736 THR cc_start: 0.9047 (m) cc_final: 0.8821 (p) REVERT: A 738 TYR cc_start: 0.8506 (t80) cc_final: 0.8296 (t80) REVERT: A 744 THR cc_start: 0.9468 (p) cc_final: 0.9249 (p) REVERT: A 770 GLU cc_start: 0.8795 (tt0) cc_final: 0.8516 (tp30) REVERT: A 952 ASN cc_start: 0.9138 (t0) cc_final: 0.8790 (t0) REVERT: A 999 GLN cc_start: 0.8649 (tp40) cc_final: 0.8301 (tp-100) REVERT: A 1003 THR cc_start: 0.8952 (m) cc_final: 0.8655 (m) REVERT: A 1108 GLU cc_start: 0.9103 (tt0) cc_final: 0.8617 (tm-30) REVERT: K 90 LEU cc_start: 0.8419 (tp) cc_final: 0.8134 (mt) outliers start: 0 outliers final: 0 residues processed: 294 average time/residue: 0.1751 time to fit residues: 86.5069 Evaluate side-chains 219 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 1.136 ------------------------------------------------------------------------------- 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: 8.9990 chunk 224 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 140 optimal weight: 4.9990 chunk 40 optimal weight: 9.9990 chunk 254 optimal weight: 7.9990 chunk 347 optimal weight: 40.0000 chunk 128 optimal weight: 7.9990 chunk 338 optimal weight: 50.0000 chunk 265 optimal weight: 10.0000 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1105 ASN ** 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 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 962 GLN ** A 52 GLN ** 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 821 ASN ** A1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.087156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.060908 restraints weight = 208531.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.061265 restraints weight = 138522.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.061191 restraints weight = 98979.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.061626 restraints weight = 87936.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.061758 restraints weight = 76665.796| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.6516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 31304 Z= 0.307 Angle : 0.772 12.186 42733 Z= 0.412 Chirality : 0.047 0.289 4944 Planarity : 0.005 0.076 5405 Dihedral : 5.825 39.321 5199 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 21.51 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.58 % Favored : 93.29 % Rotamer: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % 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: -1.43 (0.13), residues: 3753 helix: -0.69 (0.18), residues: 700 sheet: -0.38 (0.16), residues: 1010 loop : -1.31 (0.13), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG A1036 TYR 0.024 0.002 TYR C 738 PHE 0.060 0.003 PHE B1039 TRP 0.044 0.002 TRP A 883 HIS 0.023 0.003 HIS C1045 Details of bonding type rmsd covalent geometry : bond 0.00610 (31204) covalent geometry : angle 0.75779 (42481) SS BOND : bond 0.00497 ( 48) SS BOND : angle 1.54975 ( 96) hydrogen bonds : bond 0.05618 ( 1248) hydrogen bonds : angle 6.78978 ( 3444) link_BETA1-4 : bond 0.00288 ( 12) link_BETA1-4 : angle 1.72691 ( 36) link_NAG-ASN : bond 0.00548 ( 40) link_NAG-ASN : angle 2.50151 ( 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 290 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 290 time to evaluate : 1.188 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 272 PHE cc_start: 0.8705 (m-80) cc_final: 0.8274 (m-10) REVERT: B 707 ASN cc_start: 0.9086 (p0) cc_final: 0.8676 (t0) REVERT: B 985 GLU cc_start: 0.8661 (mp0) cc_final: 0.8417 (mp0) REVERT: B 999 GLN cc_start: 0.9400 (tp-100) cc_final: 0.8956 (tp-100) REVERT: B 1078 ILE cc_start: 0.8816 (mt) cc_final: 0.8539 (mm) REVERT: B 1124 ASP cc_start: 0.7332 (p0) cc_final: 0.7085 (p0) REVERT: C 168 PHE cc_start: 0.9070 (t80) cc_final: 0.8703 (t80) REVERT: C 223 LEU cc_start: 0.9149 (mp) cc_final: 0.8630 (tp) REVERT: C 348 TYR cc_start: 0.9462 (p90) cc_final: 0.8940 (p90) REVERT: C 717 ILE cc_start: 0.8192 (mm) cc_final: 0.7969 (mm) REVERT: C 817 ASP cc_start: 0.8787 (m-30) cc_final: 0.8391 (m-30) REVERT: C 918 LYS cc_start: 0.9335 (mttt) cc_final: 0.8939 (mppt) REVERT: C 966 ASN cc_start: 0.9565 (m-40) cc_final: 0.9331 (m-40) REVERT: C 989 GLN cc_start: 0.9039 (mm-40) cc_final: 0.8512 (mp10) REVERT: A 55 PHE cc_start: 0.7841 (m-80) cc_final: 0.7499 (m-10) REVERT: A 106 PHE cc_start: 0.8555 (m-10) cc_final: 0.8237 (m-10) REVERT: A 117 LEU cc_start: 0.9574 (tp) cc_final: 0.9363 (tp) REVERT: A 736 THR cc_start: 0.9063 (m) cc_final: 0.8855 (p) REVERT: A 752 GLN cc_start: 0.8572 (tm-30) cc_final: 0.8331 (tm-30) REVERT: A 770 GLU cc_start: 0.8743 (tt0) cc_final: 0.8390 (tp30) REVERT: A 952 ASN cc_start: 0.9091 (t0) cc_final: 0.8726 (t0) REVERT: A 956 LEU cc_start: 0.9158 (mt) cc_final: 0.8952 (mt) REVERT: A 999 GLN cc_start: 0.8585 (tp40) cc_final: 0.8235 (tp40) REVERT: A 1025 LYS cc_start: 0.9218 (mttm) cc_final: 0.9003 (mttm) REVERT: L 4 MET cc_start: 0.7838 (mmm) cc_final: 0.7139 (mmm) REVERT: K 90 LEU cc_start: 0.8493 (tp) cc_final: 0.8153 (mt) outliers start: 0 outliers final: 0 residues processed: 290 average time/residue: 0.1822 time to fit residues: 88.5271 Evaluate side-chains 207 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 1.235 ------------------------------------------------------------------------------- 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: 0.9990 chunk 0 optimal weight: 20.0000 chunk 68 optimal weight: 0.9990 chunk 186 optimal weight: 10.0000 chunk 83 optimal weight: 8.9990 chunk 256 optimal weight: 10.0000 chunk 306 optimal weight: 9.9990 chunk 157 optimal weight: 9.9990 chunk 175 optimal weight: 4.9990 chunk 225 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 164 ASN B 188 ASN B 314 ASN B 748 ASN ** B 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1105 ASN ** 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 641 GLN ** C 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.086811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.059864 restraints weight = 207553.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.061005 restraints weight = 133362.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.060817 restraints weight = 85630.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.060908 restraints weight = 95191.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.061198 restraints weight = 81383.184| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.6900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 31304 Z= 0.284 Angle : 0.748 12.156 42733 Z= 0.397 Chirality : 0.046 0.213 4944 Planarity : 0.005 0.064 5405 Dihedral : 5.772 38.650 5199 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 21.01 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.39 % Favored : 93.47 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % 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: -1.53 (0.13), residues: 3753 helix: -0.83 (0.18), residues: 702 sheet: -0.45 (0.16), residues: 1004 loop : -1.35 (0.13), residues: 2047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG A1036 TYR 0.024 0.002 TYR A 738 PHE 0.030 0.002 PHE A1039 TRP 0.033 0.002 TRP A 883 HIS 0.032 0.003 HIS A1045 Details of bonding type rmsd covalent geometry : bond 0.00565 (31204) covalent geometry : angle 0.73243 (42481) SS BOND : bond 0.00470 ( 48) SS BOND : angle 1.45016 ( 96) hydrogen bonds : bond 0.05492 ( 1248) hydrogen bonds : angle 6.81430 ( 3444) link_BETA1-4 : bond 0.00225 ( 12) link_BETA1-4 : angle 1.66912 ( 36) link_NAG-ASN : bond 0.00504 ( 40) link_NAG-ASN : angle 2.59275 ( 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 280 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 280 time to evaluate : 1.218 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: B 272 PHE cc_start: 0.8696 (m-80) cc_final: 0.8203 (m-10) REVERT: B 314 ASN cc_start: 0.9245 (m-40) cc_final: 0.8713 (p0) REVERT: B 985 GLU cc_start: 0.8790 (mp0) cc_final: 0.8519 (mp0) REVERT: B 999 GLN cc_start: 0.9431 (tp-100) cc_final: 0.8974 (tp-100) REVERT: B 1124 ASP cc_start: 0.7458 (p0) cc_final: 0.7127 (p0) REVERT: C 223 LEU cc_start: 0.9157 (mp) cc_final: 0.8673 (tp) REVERT: C 348 TYR cc_start: 0.9497 (p90) cc_final: 0.8947 (p90) REVERT: C 817 ASP cc_start: 0.8847 (m-30) cc_final: 0.8472 (m-30) REVERT: C 918 LYS cc_start: 0.9322 (mttt) cc_final: 0.8938 (mppt) REVERT: C 989 GLN cc_start: 0.9066 (mm-40) cc_final: 0.8489 (mp10) REVERT: C 1049 PHE cc_start: 0.7691 (m-10) cc_final: 0.7311 (m-10) REVERT: A 55 PHE cc_start: 0.7813 (m-80) cc_final: 0.7471 (m-10) REVERT: A 106 PHE cc_start: 0.8649 (m-10) cc_final: 0.8392 (m-10) REVERT: A 117 LEU cc_start: 0.9575 (tp) cc_final: 0.9337 (tp) REVERT: A 694 MET cc_start: 0.8465 (ppp) cc_final: 0.8056 (ppp) REVERT: A 717 ILE cc_start: 0.8042 (pt) cc_final: 0.7338 (pt) REVERT: A 736 THR cc_start: 0.9108 (m) cc_final: 0.8902 (p) REVERT: A 770 GLU cc_start: 0.8758 (tt0) cc_final: 0.8372 (tp30) REVERT: A 952 ASN cc_start: 0.9095 (t0) cc_final: 0.8737 (t0) REVERT: A 956 LEU cc_start: 0.9260 (mt) cc_final: 0.9044 (mt) REVERT: A 999 GLN cc_start: 0.8720 (tp40) cc_final: 0.8366 (tp40) REVERT: A 1003 THR cc_start: 0.9221 (m) cc_final: 0.8985 (m) REVERT: K 90 LEU cc_start: 0.8613 (tp) cc_final: 0.8318 (mt) outliers start: 0 outliers final: 0 residues processed: 280 average time/residue: 0.1835 time to fit residues: 86.7952 Evaluate side-chains 197 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 1.202 ------------------------------------------------------------------------------- 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: 7.9990 chunk 266 optimal weight: 10.0000 chunk 263 optimal weight: 0.6980 chunk 116 optimal weight: 8.9990 chunk 41 optimal weight: 6.9990 chunk 150 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 chunk 357 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 88 optimal weight: 0.0170 chunk 3 optimal weight: 8.9990 overall best weight: 0.9022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 641 GLN B 687 GLN ** B 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 932 GLN B1002 GLN ** 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 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 952 ASN C 962 GLN ** A 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.089490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.060348 restraints weight = 179459.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.062434 restraints weight = 107580.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.062455 restraints weight = 73626.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.063524 restraints weight = 60445.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.063729 restraints weight = 44836.847| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.6841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 31304 Z= 0.132 Angle : 0.638 8.621 42733 Z= 0.330 Chirality : 0.045 0.190 4944 Planarity : 0.004 0.067 5405 Dihedral : 5.160 34.004 5199 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.82 % Favored : 95.04 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % 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: -1.03 (0.13), residues: 3753 helix: 0.08 (0.19), residues: 670 sheet: -0.16 (0.16), residues: 976 loop : -1.19 (0.13), residues: 2107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A1036 TYR 0.018 0.001 TYR J 96 PHE 0.045 0.002 PHE A 756 TRP 0.014 0.001 TRP J 36 HIS 0.018 0.002 HIS A1045 Details of bonding type rmsd covalent geometry : bond 0.00284 (31204) covalent geometry : angle 0.62406 (42481) SS BOND : bond 0.00317 ( 48) SS BOND : angle 1.33125 ( 96) hydrogen bonds : bond 0.04147 ( 1248) hydrogen bonds : angle 6.27880 ( 3444) link_BETA1-4 : bond 0.00261 ( 12) link_BETA1-4 : angle 1.25954 ( 36) link_NAG-ASN : bond 0.00234 ( 40) link_NAG-ASN : angle 2.24530 ( 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 316 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 316 time to evaluate : 1.231 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: B 55 PHE cc_start: 0.7887 (m-80) cc_final: 0.7061 (m-10) REVERT: B 272 PHE cc_start: 0.8542 (m-80) cc_final: 0.8035 (m-10) REVERT: B 773 LYS cc_start: 0.9120 (pttt) cc_final: 0.8759 (pttm) REVERT: B 985 GLU cc_start: 0.8587 (mp0) cc_final: 0.8334 (mp0) REVERT: B 999 GLN cc_start: 0.9270 (tp-100) cc_final: 0.8852 (tp-100) REVERT: B 1028 GLU cc_start: 0.7309 (mt-10) cc_final: 0.7090 (mt-10) REVERT: B 1124 ASP cc_start: 0.7077 (p0) cc_final: 0.6759 (p0) REVERT: C 223 LEU cc_start: 0.9118 (mp) cc_final: 0.8583 (tp) REVERT: C 290 LEU cc_start: 0.8728 (tt) cc_final: 0.8465 (mt) REVERT: C 348 TYR cc_start: 0.9219 (p90) cc_final: 0.8716 (p90) REVERT: C 817 ASP cc_start: 0.8784 (m-30) cc_final: 0.8400 (m-30) REVERT: C 918 LYS cc_start: 0.9241 (mttt) cc_final: 0.8894 (mppt) REVERT: C 989 GLN cc_start: 0.8947 (mm-40) cc_final: 0.8403 (mp10) REVERT: C 1015 ILE cc_start: 0.9546 (mt) cc_final: 0.8876 (tt) REVERT: C 1049 PHE cc_start: 0.7812 (m-10) cc_final: 0.7599 (m-10) REVERT: A 106 PHE cc_start: 0.8167 (m-10) cc_final: 0.7894 (m-80) REVERT: A 117 LEU cc_start: 0.9458 (tp) cc_final: 0.9208 (tp) REVERT: A 169 GLU cc_start: 0.9176 (pm20) cc_final: 0.8880 (mp0) REVERT: A 694 MET cc_start: 0.8450 (ppp) cc_final: 0.8131 (ppp) REVERT: A 744 THR cc_start: 0.9569 (p) cc_final: 0.9359 (p) REVERT: A 770 GLU cc_start: 0.8573 (tt0) cc_final: 0.8235 (tp30) REVERT: A 952 ASN cc_start: 0.9063 (t0) cc_final: 0.8677 (t0) REVERT: A 956 LEU cc_start: 0.9194 (mt) cc_final: 0.8969 (mt) REVERT: A 999 GLN cc_start: 0.8793 (tp40) cc_final: 0.8370 (tp40) REVERT: A 1003 THR cc_start: 0.9047 (m) cc_final: 0.8838 (m) REVERT: L 4 MET cc_start: 0.8488 (mmm) cc_final: 0.8260 (tpt) REVERT: K 90 LEU cc_start: 0.8557 (tp) cc_final: 0.8226 (mt) outliers start: 0 outliers final: 0 residues processed: 316 average time/residue: 0.1702 time to fit residues: 90.6784 Evaluate side-chains 224 residues out of total 3334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 1.176 ------------------------------------------------------------------------------- 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: 3.9990 chunk 39 optimal weight: 50.0000 chunk 28 optimal weight: 7.9990 chunk 318 optimal weight: 30.0000 chunk 307 optimal weight: 0.8980 chunk 246 optimal weight: 2.9990 chunk 241 optimal weight: 7.9990 chunk 95 optimal weight: 1.9990 chunk 303 optimal weight: 4.9990 chunk 178 optimal weight: 0.2980 chunk 280 optimal weight: 2.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 484 ASN ** B 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 652 HIS C 962 GLN A 52 GLN ** A 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1033 GLN ** 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 = 0.4136 r_free = 0.4136 target = 0.089549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.062351 restraints weight = 204225.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.063932 restraints weight = 125693.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.063760 restraints weight = 78649.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.063998 restraints weight = 78960.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.064091 restraints weight = 70352.433| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.6985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 31304 Z= 0.154 Angle : 0.628 8.980 42733 Z= 0.327 Chirality : 0.044 0.224 4944 Planarity : 0.004 0.058 5405 Dihedral : 4.984 33.730 5199 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.36 % Favored : 94.51 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % 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: -0.96 (0.13), residues: 3753 helix: 0.22 (0.19), residues: 651 sheet: -0.19 (0.16), residues: 990 loop : -1.13 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1036 TYR 0.033 0.002 TYR A 446 PHE 0.035 0.002 PHE A 272 TRP 0.014 0.001 TRP J 36 HIS 0.020 0.001 HIS A1045 Details of bonding type rmsd covalent geometry : bond 0.00323 (31204) covalent geometry : angle 0.61500 (42481) SS BOND : bond 0.00359 ( 48) SS BOND : angle 1.25886 ( 96) hydrogen bonds : bond 0.04271 ( 1248) hydrogen bonds : angle 6.24369 ( 3444) link_BETA1-4 : bond 0.00224 ( 12) link_BETA1-4 : angle 1.23427 ( 36) link_NAG-ASN : bond 0.00287 ( 40) link_NAG-ASN : angle 2.17109 ( 120) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7556.79 seconds wall clock time: 131 minutes 1.10 seconds (7861.10 seconds total)