Starting phenix.real_space_refine on Thu Mar 5 10:45:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t9a_25754/03_2026/7t9a_25754.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t9a_25754/03_2026/7t9a_25754.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7t9a_25754/03_2026/7t9a_25754.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t9a_25754/03_2026/7t9a_25754.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7t9a_25754/03_2026/7t9a_25754.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t9a_25754/03_2026/7t9a_25754.map" } resolution = 3.54 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= 0.001 sd= 0.033 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 131 5.16 5 C 13459 2.51 5 N 3572 2.21 5 O 4355 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21517 Number of models: 1 Model: "" Number of chains: 41 Chain: "A" Number of atoms: 3418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3418 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 23, 'TRANS': 410} Chain breaks: 3 Chain: "B" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 958 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "J" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 943 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "K" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "C" Number of atoms: 3410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3410 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 23, 'TRANS': 409} Chain breaks: 3 Chain: "D" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 958 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "M" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 943 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "N" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "E" Number of atoms: 3418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3418 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 23, 'TRANS': 410} Chain breaks: 4 Chain: "F" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 958 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "O" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 943 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "P" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "H" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1052 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 3, 'TRANS': 128} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TYS:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "L" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 799 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} 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: "Q" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "T" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} 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: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} 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: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} 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: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} 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: "c" 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: "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: "e" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "f" 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: "h" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} 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: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} 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: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" 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: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 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: "E" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "F" 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 Time building chain proxies: 5.08, per 1000 atoms: 0.24 Number of scatterers: 21517 At special positions: 0 Unit cell: (120.51, 129.78, 188.49, 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 131 16.00 O 4355 8.00 N 3572 7.00 C 13459 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.05 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.05 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.02 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.02 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.05 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.05 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.02 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.04 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.02 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.02 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.02 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.06 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.05 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.04 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.04 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.04 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.08 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 ALPHA1-3 " BMA Q 3 " - " MAN Q 4 " " BMA S 3 " - " MAN S 7 " " MAN S 4 " - " MAN S 5 " " BMA Y 3 " - " MAN Y 4 " " BMA e 3 " - " MAN e 4 " ALPHA1-6 " BMA S 3 " - " MAN S 4 " " MAN S 4 " - " MAN S 6 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " BETA1-6 " NAG T 1 " - " FUC T 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG U 1 " - " FUC U 2 " " NAG a 1 " - " FUC a 2 " " NAG b 1 " - " FUC b 2 " " NAG h 1 " - " FUC h 2 " " NAG i 1 " - " FUC i 2 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 234 " " NAG A 603 " - " ASN A 137 " " NAG A 604 " - " ASN A 355 " " NAG A 605 " - " ASN A 276 " " NAG A 606 " - " ASN A 392 " " NAG A 607 " - " ASN A 339 " " NAG A 608 " - " ASN A 295 " " NAG A 609 " - " ASN A 448 " " NAG A 610 " - " ASN A 301 " " NAG A 611 " - " ASN A 197 " " NAG A 612 " - " ASN A 133 " " NAG B 701 " - " ASN B 637 " " NAG B 702 " - " ASN B 625 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 234 " " NAG C 603 " - " ASN C 137 " " NAG C 604 " - " ASN C 355 " " NAG C 605 " - " ASN C 276 " " NAG C 606 " - " ASN C 392 " " NAG C 607 " - " ASN C 339 " " NAG C 608 " - " ASN C 295 " " NAG C 609 " - " ASN C 448 " " NAG C 610 " - " ASN C 301 " " NAG C 611 " - " ASN C 197 " " NAG C 612 " - " ASN C 133 " " NAG D 701 " - " ASN D 625 " " NAG D 702 " - " ASN D 637 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 234 " " NAG E 603 " - " ASN E 137 " " NAG E 604 " - " ASN E 355 " " NAG E 605 " - " ASN E 276 " " NAG E 606 " - " ASN E 392 " " NAG E 607 " - " ASN E 339 " " NAG E 608 " - " ASN E 295 " " NAG E 609 " - " ASN E 448 " " NAG E 610 " - " ASN E 301 " " NAG E 611 " - " ASN E 197 " " NAG E 612 " - " ASN E 133 " " NAG F 701 " - " ASN F 637 " " NAG F 702 " - " ASN F 625 " " NAG G 1 " - " ASN A 386 " " NAG I 1 " - " ASN A 332 " " NAG Q 1 " - " ASN A 262 " " NAG R 1 " - " ASN A 156 " " NAG S 1 " - " ASN A 160 " " NAG T 1 " - " ASN B 618 " " NAG U 1 " - " ASN B 611 " " NAG V 1 " - " ASN C 160 " " NAG W 1 " - " ASN C 386 " " NAG X 1 " - " ASN C 332 " " NAG Y 1 " - " ASN C 262 " " NAG Z 1 " - " ASN C 156 " " NAG a 1 " - " ASN D 618 " " NAG b 1 " - " ASN D 611 " " NAG c 1 " - " ASN E 386 " " NAG d 1 " - " ASN E 332 " " NAG e 1 " - " ASN E 262 " " NAG f 1 " - " ASN E 156 " " NAG g 1 " - " ASN E 160 " " NAG h 1 " - " ASN F 618 " " NAG i 1 " - " ASN F 611 " Time building additional restraints: 2.11 Conformation dependent library (CDL) restraints added in 1.0 seconds 5072 Ramachandran restraints generated. 2536 Oldfield, 0 Emsley, 2536 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4760 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 36 sheets defined 19.1% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.115A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS A 117 " --> pdb=" O ASP A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.535A pdb=" N THR A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.593A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 526 removed outlier: 4.401A pdb=" N GLY B 525 " --> pdb=" O GLY B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 532 Processing helix chain 'B' and resid 534 through 540 Processing helix chain 'B' and resid 572 through 596 Processing helix chain 'B' and resid 618 through 623 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 662 removed outlier: 3.504A pdb=" N ILE B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 61 through 64 Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'K' and resid 79 through 83 Processing helix chain 'C' and resid 99 through 115 Processing helix chain 'C' and resid 139 through 151 Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.952A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 526 removed outlier: 4.382A pdb=" N GLY D 525 " --> pdb=" O GLY D 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 527 through 532 Processing helix chain 'D' and resid 534 through 540 Processing helix chain 'D' and resid 572 through 596 removed outlier: 3.514A pdb=" N LEU D 576 " --> pdb=" O GLY D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 625 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 639 through 662 Processing helix chain 'M' and resid 28 through 32 Processing helix chain 'M' and resid 61 through 64 Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 Processing helix chain 'E' and resid 99 through 115 Processing helix chain 'E' and resid 139 through 151 Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 335 through 350 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 475 through 484 removed outlier: 3.962A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 527 through 532 Processing helix chain 'F' and resid 534 through 540 Processing helix chain 'F' and resid 572 through 596 Processing helix chain 'F' and resid 618 through 623 Processing helix chain 'F' and resid 627 through 633 Processing helix chain 'F' and resid 635 through 637 No H-bonds generated for 'chain 'F' and resid 635 through 637' Processing helix chain 'F' and resid 638 through 662 removed outlier: 3.638A pdb=" N ALA F 662 " --> pdb=" O GLN F 658 " (cutoff:3.500A) Processing helix chain 'O' and resid 28 through 32 Processing helix chain 'O' and resid 61 through 64 Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'P' and resid 79 through 83 removed outlier: 3.508A pdb=" N GLU P 83 " --> pdb=" O ALA P 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 52A through 54 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 removed outlier: 4.129A pdb=" N THR H 87 " --> pdb=" O THR H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 29 through 31 No H-bonds generated for 'chain 'L' and resid 29 through 31' Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.394A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.712A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA5, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.466A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 312 removed outlier: 6.889A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 315 through 323A current: chain 'A' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 385 current: chain 'A' and resid 466 through 470 Processing sheet with id=AA7, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AA8, first strand: chain 'J' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 11 through 12 current: chain 'J' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 57 through 59 current: chain 'J' and resid 100H through 103 Processing sheet with id=AA9, first strand: chain 'K' and resid 12 through 13 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 12 through 13 current: chain 'K' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 45 through 48 current: chain 'K' and resid 96 through 98 No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'K' and resid 19 through 24 Processing sheet with id=AB2, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.445A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.589A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 75 through 76 Processing sheet with id=AB5, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB6, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AB7, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.539A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 259 through 261 current: chain 'C' and resid 284 through 312 removed outlier: 6.839A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 315 through 323A current: chain 'C' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 381 through 385 current: chain 'C' and resid 466 through 470 Processing sheet with id=AB9, first strand: chain 'M' and resid 3 through 6 Processing sheet with id=AC1, first strand: chain 'M' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 11 through 12 current: chain 'M' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 57 through 59 current: chain 'M' and resid 100H through 103 Processing sheet with id=AC2, first strand: chain 'N' and resid 12 through 13 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 12 through 13 current: chain 'N' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 45 through 48 current: chain 'N' and resid 96 through 98 No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'N' and resid 19 through 24 Processing sheet with id=AC4, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.401A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.522A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR E 244 " --> pdb=" O ILE E 84 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AC7, first strand: chain 'E' and resid 91 through 94 removed outlier: 3.522A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AC9, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.425A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 259 through 261 current: chain 'E' and resid 284 through 312 removed outlier: 3.750A pdb=" N ASN E 301 " --> pdb=" O ILE E 323A" (cutoff:3.500A) removed outlier: 5.994A pdb=" N LYS E 305 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N THR E 320 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ILE E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N TYR E 318 " --> pdb=" O ILE E 307 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE E 309 " --> pdb=" O ALA E 316 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N ALA E 316 " --> pdb=" O ILE E 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 315 through 323A current: chain 'E' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 381 through 385 current: chain 'E' and resid 466 through 470 Processing sheet with id=AD2, first strand: chain 'O' and resid 3 through 6 Processing sheet with id=AD3, first strand: chain 'O' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 11 through 12 current: chain 'O' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 57 through 59 current: chain 'O' and resid 100H through 103 Processing sheet with id=AD4, first strand: chain 'P' and resid 12 through 13 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 12 through 13 current: chain 'P' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 45 through 48 current: chain 'P' and resid 96 through 98 No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'P' and resid 19 through 24 Processing sheet with id=AD6, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AD7, first strand: chain 'H' and resid 34 through 39 removed outlier: 6.754A pdb=" N MET H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ARG H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 100J through 103 Processing sheet with id=AD8, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AD9, first strand: chain 'L' and resid 11 through 12 removed outlier: 5.631A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 566 hydrogen bonds defined for protein. 1494 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: 3.73 Time building geometry restraints manager: 2.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.42: 9029 1.42 - 1.66: 12747 1.66 - 1.90: 175 1.90 - 2.14: 0 2.14 - 2.38: 1 Bond restraints: 21952 Sorted by residual: bond pdb=" C SER L 94 " pdb=" N PHE L 96 " ideal model delta sigma weight residual 1.333 2.382 -1.049 1.28e-02 6.10e+03 6.72e+03 bond pdb=" CB ASP K 27B" pdb=" CG ASP K 27B" ideal model delta sigma weight residual 1.516 1.351 0.165 2.50e-02 1.60e+03 4.34e+01 bond pdb=" NE ARG E 503 " pdb=" CZ ARG E 503 " ideal model delta sigma weight residual 1.326 1.398 -0.072 1.10e-02 8.26e+03 4.33e+01 bond pdb=" CB LEU L 33 " pdb=" CG LEU L 33 " ideal model delta sigma weight residual 1.530 1.656 -0.126 2.00e-02 2.50e+03 3.94e+01 bond pdb=" CB LEU K 107 " pdb=" CG LEU K 107 " ideal model delta sigma weight residual 1.530 1.652 -0.122 2.00e-02 2.50e+03 3.71e+01 ... (remaining 21947 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.01: 28759 4.01 - 8.02: 1014 8.02 - 12.02: 28 12.02 - 16.03: 3 16.03 - 20.04: 2 Bond angle restraints: 29806 Sorted by residual: angle pdb=" C SER L 94 " pdb=" N PHE L 96 " pdb=" CA PHE L 96 " ideal model delta sigma weight residual 122.05 102.01 20.04 1.48e+00 4.57e-01 1.83e+02 angle pdb=" O SER L 94 " pdb=" C SER L 94 " pdb=" N PHE L 96 " ideal model delta sigma weight residual 123.34 110.98 12.36 1.37e+00 5.33e-01 8.14e+01 angle pdb=" CA SER L 94 " pdb=" C SER L 94 " pdb=" N PHE L 96 " ideal model delta sigma weight residual 116.50 127.89 -11.39 1.44e+00 4.82e-01 6.26e+01 angle pdb=" C CYS C 239 " pdb=" N PRO C 240 " pdb=" CA PRO C 240 " ideal model delta sigma weight residual 119.56 126.77 -7.21 1.01e+00 9.80e-01 5.10e+01 angle pdb=" C GLU E 492 " pdb=" N PRO E 493 " pdb=" CA PRO E 493 " ideal model delta sigma weight residual 119.87 127.12 -7.25 1.04e+00 9.25e-01 4.86e+01 ... (remaining 29801 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.68: 13649 21.68 - 43.37: 405 43.37 - 65.05: 143 65.05 - 86.74: 55 86.74 - 108.42: 23 Dihedral angle restraints: 14275 sinusoidal: 6843 harmonic: 7432 Sorted by residual: dihedral pdb=" CA THR E 77 " pdb=" C THR E 77 " pdb=" N ASP E 78 " pdb=" CA ASP E 78 " ideal model delta harmonic sigma weight residual -180.00 -151.57 -28.43 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA ASP C 78 " pdb=" C ASP C 78 " pdb=" N PRO C 79 " pdb=" CA PRO C 79 " ideal model delta harmonic sigma weight residual -180.00 -154.43 -25.57 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA ASN E 94 " pdb=" C ASN E 94 " pdb=" N MET E 95 " pdb=" CA MET E 95 " ideal model delta harmonic sigma weight residual 180.00 155.94 24.06 0 5.00e+00 4.00e-02 2.32e+01 ... (remaining 14272 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.264: 3347 0.264 - 0.528: 248 0.528 - 0.792: 3 0.792 - 1.056: 2 1.056 - 1.320: 1 Chirality restraints: 3601 Sorted by residual: chirality pdb=" C1 FUC b 2 " pdb=" O6 NAG b 1 " pdb=" C2 FUC b 2 " pdb=" O5 FUC b 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.08 -1.32 2.00e-02 2.50e+03 4.36e+03 chirality pdb=" C1 MAN S 6 " pdb=" O6 MAN S 4 " pdb=" C2 MAN S 6 " pdb=" O5 MAN S 6 " both_signs ideal model delta sigma weight residual False 2.40 1.73 0.67 2.00e-02 2.50e+03 1.13e+03 chirality pdb=" C1 MAN S 5 " pdb=" O3 MAN S 4 " pdb=" C2 MAN S 5 " pdb=" O5 MAN S 5 " both_signs ideal model delta sigma weight residual False 2.40 1.91 0.49 2.00e-02 2.50e+03 5.91e+02 ... (remaining 3598 not shown) Planarity restraints: 3736 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG g 1 " 0.327 2.00e-02 2.50e+03 2.78e-01 9.67e+02 pdb=" C7 NAG g 1 " -0.081 2.00e-02 2.50e+03 pdb=" C8 NAG g 1 " 0.174 2.00e-02 2.50e+03 pdb=" N2 NAG g 1 " -0.488 2.00e-02 2.50e+03 pdb=" O7 NAG g 1 " 0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG R 2 " -0.326 2.00e-02 2.50e+03 2.77e-01 9.61e+02 pdb=" C7 NAG R 2 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG R 2 " -0.175 2.00e-02 2.50e+03 pdb=" N2 NAG R 2 " 0.486 2.00e-02 2.50e+03 pdb=" O7 NAG R 2 " -0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 701 " 0.312 2.00e-02 2.50e+03 2.72e-01 9.27e+02 pdb=" C7 NAG D 701 " -0.069 2.00e-02 2.50e+03 pdb=" C8 NAG D 701 " 0.125 2.00e-02 2.50e+03 pdb=" N2 NAG D 701 " -0.489 2.00e-02 2.50e+03 pdb=" O7 NAG D 701 " 0.120 2.00e-02 2.50e+03 ... (remaining 3733 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 6170 2.83 - 3.35: 18758 3.35 - 3.87: 36185 3.87 - 4.38: 43141 4.38 - 4.90: 69274 Nonbonded interactions: 173528 Sorted by model distance: nonbonded pdb=" O5 NAG T 1 " pdb=" O6 NAG T 1 " model vdw 2.315 2.432 nonbonded pdb=" N ASP M 84 " pdb=" OD1 ASP M 84 " model vdw 2.372 3.120 nonbonded pdb=" N ASP J 84 " pdb=" OD1 ASP J 84 " model vdw 2.373 3.120 nonbonded pdb=" N ASP O 84 " pdb=" OD1 ASP O 84 " model vdw 2.375 3.120 nonbonded pdb=" O5 NAG R 2 " pdb=" O6 NAG R 2 " model vdw 2.383 2.432 ... (remaining 173523 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 33 through 57 or resid 68 through 612)) selection = chain 'C' selection = (chain 'E' and (resid 33 through 57 or resid 68 through 612)) } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = (chain 'G' and resid 1) selection = (chain 'I' and resid 1) selection = (chain 'T' and resid 1) selection = (chain 'U' and resid 1) selection = (chain 'V' and resid 1) selection = (chain 'W' and resid 1) selection = (chain 'X' and resid 1) selection = (chain 'Z' and resid 1) selection = (chain 'a' and resid 1) selection = (chain 'b' and resid 1) selection = (chain 'c' and resid 1) selection = (chain 'd' and resid 1) selection = (chain 'f' and resid 1) selection = (chain 'g' and resid 1) selection = (chain 'h' and resid 1) selection = (chain 'i' and resid 1) } ncs_group { reference = chain 'J' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'K' selection = chain 'N' selection = chain 'P' } ncs_group { reference = chain 'Q' selection = chain 'Y' selection = chain 'e' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.960 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: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.670 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 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 : 0.022 1.049 22086 Z= 1.249 Angle : 1.766 20.039 30170 Z= 1.142 Chirality : 0.133 1.320 3601 Planarity : 0.016 0.278 3673 Dihedral : 13.070 108.419 9401 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.71 % Allowed : 3.59 % Favored : 95.70 % Rotamer: Outliers : 2.68 % Allowed : 1.74 % Favored : 95.58 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.95 % 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: 0.35 (0.16), residues: 2536 helix: -0.21 (0.25), residues: 375 sheet: 0.91 (0.18), residues: 800 loop : 0.04 (0.17), residues: 1361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG O 71 TYR 0.052 0.006 TYR N 96 PHE 0.036 0.006 PHE L 98 TRP 0.063 0.007 TRP A 96 HIS 0.009 0.002 HIS F 585 Details of bonding type rmsd covalent geometry : bond 0.02174 (21952) covalent geometry : angle 1.73753 (29806) SS BOND : bond 0.01379 ( 38) SS BOND : angle 2.72983 ( 76) hydrogen bonds : bond 0.16917 ( 566) hydrogen bonds : angle 6.91855 ( 1494) link_ALPHA1-3 : bond 0.06218 ( 5) link_ALPHA1-3 : angle 3.64231 ( 15) link_ALPHA1-6 : bond 0.00632 ( 2) link_ALPHA1-6 : angle 3.57903 ( 6) link_BETA1-4 : bond 0.05908 ( 20) link_BETA1-4 : angle 4.31213 ( 60) link_BETA1-6 : bond 0.01861 ( 6) link_BETA1-6 : angle 5.79527 ( 18) link_NAG-ASN : bond 0.06557 ( 63) link_NAG-ASN : angle 2.81694 ( 189) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5072 Ramachandran restraints generated. 2536 Oldfield, 0 Emsley, 2536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5072 Ramachandran restraints generated. 2536 Oldfield, 0 Emsley, 2536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 318 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8704 (mp) REVERT: A 215 ILE cc_start: 0.9239 (mt) cc_final: 0.9033 (pt) REVERT: J 28 THR cc_start: 0.8600 (m) cc_final: 0.8348 (p) REVERT: K 94 ARG cc_start: 0.6261 (OUTLIER) cc_final: 0.5631 (tpt170) REVERT: M 3 GLN cc_start: 0.8305 (mt0) cc_final: 0.7990 (mt0) REVERT: N 26 THR cc_start: 0.8860 (t) cc_final: 0.8257 (t) REVERT: N 94 ARG cc_start: 0.5883 (mpt180) cc_final: 0.3607 (mmt180) REVERT: E 69 TRP cc_start: 0.7257 (OUTLIER) cc_final: 0.6103 (m100) REVERT: E 95 MET cc_start: 0.9054 (ptm) cc_final: 0.8767 (ptm) REVERT: E 137 ASN cc_start: 0.8056 (OUTLIER) cc_final: 0.7783 (m-40) REVERT: F 635 ILE cc_start: 0.8977 (OUTLIER) cc_final: 0.8704 (pp) REVERT: O 6 GLU cc_start: 0.7865 (mp0) cc_final: 0.7509 (mp0) REVERT: P 94 ARG cc_start: 0.5913 (OUTLIER) cc_final: 0.4032 (tpp-160) REVERT: H 29 PHE cc_start: 0.5122 (m-10) cc_final: 0.4652 (m-10) REVERT: H 43 LYS cc_start: 0.8849 (mmtt) cc_final: 0.8542 (pttt) REVERT: H 78 LEU cc_start: 0.7352 (tp) cc_final: 0.6917 (tp) REVERT: H 82 MET cc_start: 0.7848 (mtm) cc_final: 0.7631 (mpp) REVERT: L 5 THR cc_start: 0.8802 (p) cc_final: 0.8519 (m) REVERT: L 37 GLN cc_start: 0.6040 (tt0) cc_final: 0.5679 (tt0) REVERT: L 46 LEU cc_start: 0.7230 (tp) cc_final: 0.6760 (tp) REVERT: L 70 ASP cc_start: 0.8341 (t0) cc_final: 0.8055 (t0) REVERT: L 96 PHE cc_start: 0.7241 (OUTLIER) cc_final: 0.6761 (m-80) outliers start: 60 outliers final: 12 residues processed: 366 average time/residue: 0.1778 time to fit residues: 95.0958 Evaluate side-chains 172 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 153 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain K residue 94 ARG Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 169 ARG Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain P residue 94 ARG Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 96 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 247 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN J 3 GLN J 13 GLN J 52 ASN ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN D 577 GLN D 616 ASN D 650 GLN D 653 GLN N 17 GLN ** H 52BASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.083942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.065647 restraints weight = 65875.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.067796 restraints weight = 35848.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.069133 restraints weight = 24807.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.069881 restraints weight = 19684.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.070419 restraints weight = 17147.156| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22086 Z= 0.152 Angle : 0.707 13.359 30170 Z= 0.347 Chirality : 0.048 0.265 3601 Planarity : 0.004 0.039 3673 Dihedral : 9.226 79.058 4799 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.23 % Favored : 96.45 % Rotamer: Outliers : 1.83 % Allowed : 6.38 % Favored : 91.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % 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: 0.51 (0.17), residues: 2538 helix: 1.81 (0.28), residues: 355 sheet: 0.85 (0.18), residues: 774 loop : -0.32 (0.16), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 66 TYR 0.014 0.001 TYR M 100F PHE 0.024 0.002 PHE H 27 TRP 0.022 0.001 TRP C 479 HIS 0.004 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00335 (21952) covalent geometry : angle 0.66989 (29806) SS BOND : bond 0.00292 ( 38) SS BOND : angle 1.01157 ( 76) hydrogen bonds : bond 0.05030 ( 566) hydrogen bonds : angle 5.05700 ( 1494) link_ALPHA1-3 : bond 0.01308 ( 5) link_ALPHA1-3 : angle 2.37069 ( 15) link_ALPHA1-6 : bond 0.01349 ( 2) link_ALPHA1-6 : angle 2.09015 ( 6) link_BETA1-4 : bond 0.00563 ( 20) link_BETA1-4 : angle 2.66562 ( 60) link_BETA1-6 : bond 0.01229 ( 6) link_BETA1-6 : angle 2.56971 ( 18) link_NAG-ASN : bond 0.00453 ( 63) link_NAG-ASN : angle 2.24806 ( 189) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 189 time to evaluate : 0.820 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: J 6 GLU cc_start: 0.8223 (mp0) cc_final: 0.8011 (mp0) REVERT: J 28 THR cc_start: 0.8552 (m) cc_final: 0.8334 (p) REVERT: J 87 THR cc_start: 0.8513 (m) cc_final: 0.8298 (p) REVERT: K 27 ASP cc_start: 0.8589 (OUTLIER) cc_final: 0.8310 (t70) REVERT: K 94 ARG cc_start: 0.5432 (mpt180) cc_final: 0.4387 (mmt180) REVERT: C 475 MET cc_start: 0.7605 (tpp) cc_final: 0.7155 (mmm) REVERT: D 632 ASP cc_start: 0.8412 (t70) cc_final: 0.8154 (t0) REVERT: M 11 LEU cc_start: 0.7510 (tp) cc_final: 0.7092 (mp) REVERT: N 94 ARG cc_start: 0.5312 (mpt180) cc_final: 0.3163 (mmt180) REVERT: E 69 TRP cc_start: 0.8181 (OUTLIER) cc_final: 0.7147 (m100) REVERT: E 77 THR cc_start: 0.7565 (OUTLIER) cc_final: 0.7351 (p) REVERT: P 53 GLN cc_start: 0.8396 (mm-40) cc_final: 0.8060 (mm110) REVERT: P 94 ARG cc_start: 0.5095 (mpt180) cc_final: 0.3676 (tpp-160) REVERT: H 34 MET cc_start: 0.6393 (mtm) cc_final: 0.5402 (mtm) REVERT: H 38 ARG cc_start: 0.8438 (ptt180) cc_final: 0.8019 (ptm160) REVERT: H 67 PHE cc_start: 0.6465 (m-10) cc_final: 0.5921 (m-10) REVERT: H 75 LYS cc_start: 0.8814 (pttp) cc_final: 0.8609 (mmmt) REVERT: H 78 LEU cc_start: 0.7297 (tp) cc_final: 0.6590 (tp) REVERT: H 82 LEU cc_start: 0.7426 (pp) cc_final: 0.6309 (mp) REVERT: L 62 PHE cc_start: 0.7625 (m-80) cc_final: 0.7363 (m-80) REVERT: L 75 ILE cc_start: 0.7964 (mp) cc_final: 0.7224 (tp) REVERT: L 79 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7849 (mm-30) outliers start: 41 outliers final: 16 residues processed: 221 average time/residue: 0.1684 time to fit residues: 56.0137 Evaluate side-chains 169 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 150 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain J residue 101 ASP Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain K residue 27 ASP Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain N residue 81 ASP Chi-restraints excluded: chain N residue 106 VAL Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain L residue 96 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 162 optimal weight: 0.5980 chunk 204 optimal weight: 5.9990 chunk 134 optimal weight: 8.9990 chunk 224 optimal weight: 7.9990 chunk 235 optimal weight: 30.0000 chunk 209 optimal weight: 9.9990 chunk 113 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN A 82 GLN A 103 GLN A 195 ASN J 3 GLN ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 ASN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.079057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.060159 restraints weight = 67168.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.063391 restraints weight = 39220.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.064007 restraints weight = 24220.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.063922 restraints weight = 19041.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.064016 restraints weight = 19738.997| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 22086 Z= 0.243 Angle : 0.698 11.740 30170 Z= 0.346 Chirality : 0.048 0.305 3601 Planarity : 0.004 0.047 3673 Dihedral : 7.063 54.000 4770 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.26 % Favored : 95.51 % Rotamer: Outliers : 1.61 % Allowed : 7.18 % Favored : 91.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.31 (0.16), residues: 2538 helix: 1.92 (0.27), residues: 355 sheet: 0.74 (0.18), residues: 807 loop : -0.57 (0.17), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 617 TYR 0.017 0.002 TYR L 87 PHE 0.022 0.002 PHE L 98 TRP 0.024 0.002 TRP L 35 HIS 0.006 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00569 (21952) covalent geometry : angle 0.67134 (29806) SS BOND : bond 0.00347 ( 38) SS BOND : angle 0.98624 ( 76) hydrogen bonds : bond 0.04923 ( 566) hydrogen bonds : angle 4.87400 ( 1494) link_ALPHA1-3 : bond 0.01250 ( 5) link_ALPHA1-3 : angle 1.45915 ( 15) link_ALPHA1-6 : bond 0.01230 ( 2) link_ALPHA1-6 : angle 1.70894 ( 6) link_BETA1-4 : bond 0.00477 ( 20) link_BETA1-4 : angle 2.10657 ( 60) link_BETA1-6 : bond 0.00632 ( 6) link_BETA1-6 : angle 2.66454 ( 18) link_NAG-ASN : bond 0.00371 ( 63) link_NAG-ASN : angle 1.98725 ( 189) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 164 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.9007 (mtp) cc_final: 0.8732 (mtp) REVERT: A 108 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8641 (mp) REVERT: J 87 THR cc_start: 0.8568 (m) cc_final: 0.8362 (p) REVERT: K 94 ARG cc_start: 0.5658 (mpt180) cc_final: 0.4703 (mmt-90) REVERT: D 616 ASN cc_start: 0.8390 (OUTLIER) cc_final: 0.8188 (t0) REVERT: D 632 ASP cc_start: 0.8544 (t70) cc_final: 0.8233 (t0) REVERT: M 11 LEU cc_start: 0.7787 (tp) cc_final: 0.7262 (mp) REVERT: N 94 ARG cc_start: 0.5639 (mpt180) cc_final: 0.3483 (mmt180) REVERT: E 69 TRP cc_start: 0.8356 (OUTLIER) cc_final: 0.7171 (m100) REVERT: E 95 MET cc_start: 0.8915 (ptm) cc_final: 0.8620 (ptm) REVERT: E 129 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8804 (mt) REVERT: P 45 LYS cc_start: 0.8211 (ttmm) cc_final: 0.8008 (ptmm) REVERT: P 53 GLN cc_start: 0.8591 (mm-40) cc_final: 0.8250 (mm110) REVERT: P 85 ASP cc_start: 0.8517 (m-30) cc_final: 0.8049 (m-30) REVERT: P 94 ARG cc_start: 0.5321 (mpt180) cc_final: 0.3687 (tpp-160) REVERT: H 34 MET cc_start: 0.5994 (mtm) cc_final: 0.5172 (mtm) REVERT: H 38 ARG cc_start: 0.8396 (ptt180) cc_final: 0.7932 (ptm160) REVERT: H 67 PHE cc_start: 0.5891 (m-10) cc_final: 0.5508 (m-10) REVERT: H 78 LEU cc_start: 0.7369 (tp) cc_final: 0.6589 (tp) REVERT: H 82 LEU cc_start: 0.7282 (pp) cc_final: 0.6047 (mp) REVERT: L 35 TRP cc_start: 0.6947 (m100) cc_final: 0.6603 (m100) REVERT: L 62 PHE cc_start: 0.7908 (m-80) cc_final: 0.7514 (m-80) REVERT: L 73 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8133 (pp) REVERT: L 79 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8127 (mm-30) REVERT: L 87 TYR cc_start: 0.7418 (m-80) cc_final: 0.7185 (m-80) REVERT: L 96 PHE cc_start: 0.6018 (OUTLIER) cc_final: 0.5599 (m-80) outliers start: 36 outliers final: 17 residues processed: 192 average time/residue: 0.1747 time to fit residues: 51.4706 Evaluate side-chains 165 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 141 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain F residue 526 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 79 GLU Chi-restraints excluded: chain L residue 96 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 20 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 21 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 193 optimal weight: 6.9990 chunk 200 optimal weight: 3.9990 chunk 230 optimal weight: 0.0270 chunk 45 optimal weight: 3.9990 chunk 198 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 overall best weight: 1.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN B 653 GLN J 3 GLN ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 17 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.076930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.057575 restraints weight = 67963.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.059513 restraints weight = 37399.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.060757 restraints weight = 26384.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.061451 restraints weight = 21254.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.062014 restraints weight = 18703.354| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22086 Z= 0.146 Angle : 0.586 10.682 30170 Z= 0.289 Chirality : 0.045 0.284 3601 Planarity : 0.004 0.051 3673 Dihedral : 5.931 50.957 4766 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.74 % Favored : 96.02 % Rotamer: Outliers : 1.47 % Allowed : 7.85 % Favored : 90.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.25 (0.17), residues: 2538 helix: 2.14 (0.28), residues: 358 sheet: 0.67 (0.18), residues: 803 loop : -0.67 (0.17), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 103 TYR 0.011 0.001 TYR L 87 PHE 0.015 0.001 PHE E 176 TRP 0.017 0.001 TRP E 479 HIS 0.004 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00336 (21952) covalent geometry : angle 0.56161 (29806) SS BOND : bond 0.00259 ( 38) SS BOND : angle 1.01490 ( 76) hydrogen bonds : bond 0.03974 ( 566) hydrogen bonds : angle 4.45470 ( 1494) link_ALPHA1-3 : bond 0.01211 ( 5) link_ALPHA1-3 : angle 1.67848 ( 15) link_ALPHA1-6 : bond 0.01108 ( 2) link_ALPHA1-6 : angle 1.36995 ( 6) link_BETA1-4 : bond 0.00353 ( 20) link_BETA1-4 : angle 1.65575 ( 60) link_BETA1-6 : bond 0.00439 ( 6) link_BETA1-6 : angle 2.33215 ( 18) link_NAG-ASN : bond 0.00209 ( 63) link_NAG-ASN : angle 1.73185 ( 189) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 149 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.8996 (mtp) cc_final: 0.8738 (mtp) REVERT: J 87 THR cc_start: 0.8566 (m) cc_final: 0.8343 (p) REVERT: K 94 ARG cc_start: 0.5625 (mpt180) cc_final: 0.4489 (mmt180) REVERT: D 632 ASP cc_start: 0.8534 (t70) cc_final: 0.8242 (t0) REVERT: M 11 LEU cc_start: 0.7748 (tp) cc_final: 0.7230 (mp) REVERT: N 94 ARG cc_start: 0.5526 (mpt180) cc_final: 0.3488 (mmt180) REVERT: E 69 TRP cc_start: 0.8404 (OUTLIER) cc_final: 0.7062 (m100) REVERT: E 95 MET cc_start: 0.8766 (ptm) cc_final: 0.8445 (ptm) REVERT: P 94 ARG cc_start: 0.5156 (mpt180) cc_final: 0.3518 (tpp-160) REVERT: H 34 MET cc_start: 0.5716 (mtm) cc_final: 0.5241 (mtm) REVERT: H 38 ARG cc_start: 0.8501 (ptt180) cc_final: 0.8000 (ptm160) REVERT: H 67 PHE cc_start: 0.5961 (m-10) cc_final: 0.5375 (m-10) REVERT: H 82 LEU cc_start: 0.7204 (pp) cc_final: 0.6099 (mp) REVERT: L 62 PHE cc_start: 0.7824 (m-80) cc_final: 0.7470 (m-80) REVERT: L 79 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7812 (mm-30) REVERT: L 90 GLN cc_start: 0.8381 (pp30) cc_final: 0.8168 (pp30) outliers start: 33 outliers final: 16 residues processed: 179 average time/residue: 0.1610 time to fit residues: 45.2318 Evaluate side-chains 149 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 132 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain K residue 27 ASP Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain N residue 106 VAL Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain F residue 526 SER Chi-restraints excluded: chain O residue 43 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 181 optimal weight: 9.9990 chunk 76 optimal weight: 4.9990 chunk 146 optimal weight: 10.0000 chunk 201 optimal weight: 5.9990 chunk 241 optimal weight: 5.9990 chunk 20 optimal weight: 0.0020 chunk 167 optimal weight: 5.9990 chunk 37 optimal weight: 0.6980 chunk 1 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 overall best weight: 2.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 105 GLN ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 39 GLN P 38 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.075987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.056498 restraints weight = 68077.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.058423 restraints weight = 38145.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.059634 restraints weight = 26982.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.060433 restraints weight = 21854.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.060851 restraints weight = 19101.088| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22086 Z= 0.179 Angle : 0.597 10.481 30170 Z= 0.292 Chirality : 0.045 0.299 3601 Planarity : 0.004 0.049 3673 Dihedral : 5.633 50.738 4761 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.29 % Favored : 95.51 % Rotamer: Outliers : 1.34 % Allowed : 8.30 % Favored : 90.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.17 (0.17), residues: 2538 helix: 2.18 (0.28), residues: 359 sheet: 0.68 (0.19), residues: 776 loop : -0.79 (0.16), residues: 1403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 350 TYR 0.014 0.001 TYR L 87 PHE 0.015 0.002 PHE H 29 TRP 0.044 0.001 TRP L 35 HIS 0.005 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00419 (21952) covalent geometry : angle 0.57412 (29806) SS BOND : bond 0.00266 ( 38) SS BOND : angle 1.05739 ( 76) hydrogen bonds : bond 0.04119 ( 566) hydrogen bonds : angle 4.45779 ( 1494) link_ALPHA1-3 : bond 0.01209 ( 5) link_ALPHA1-3 : angle 1.51376 ( 15) link_ALPHA1-6 : bond 0.01069 ( 2) link_ALPHA1-6 : angle 1.43962 ( 6) link_BETA1-4 : bond 0.00358 ( 20) link_BETA1-4 : angle 1.61523 ( 60) link_BETA1-6 : bond 0.00304 ( 6) link_BETA1-6 : angle 2.23930 ( 18) link_NAG-ASN : bond 0.00257 ( 63) link_NAG-ASN : angle 1.68266 ( 189) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 158 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.9001 (mtp) cc_final: 0.8718 (mtp) REVERT: A 370 GLU cc_start: 0.7841 (mp0) cc_final: 0.7604 (mp0) REVERT: A 475 MET cc_start: 0.8906 (tpp) cc_final: 0.8605 (tpp) REVERT: J 87 THR cc_start: 0.8546 (m) cc_final: 0.8334 (p) REVERT: K 94 ARG cc_start: 0.5672 (mpt180) cc_final: 0.5205 (tpt170) REVERT: D 632 ASP cc_start: 0.8623 (t70) cc_final: 0.8282 (t0) REVERT: M 11 LEU cc_start: 0.7807 (tp) cc_final: 0.7299 (mp) REVERT: N 94 ARG cc_start: 0.5678 (mpt180) cc_final: 0.3402 (mmt180) REVERT: E 69 TRP cc_start: 0.8406 (OUTLIER) cc_final: 0.7190 (m100) REVERT: E 95 MET cc_start: 0.8850 (ptm) cc_final: 0.8547 (ptm) REVERT: O 3 GLN cc_start: 0.7735 (OUTLIER) cc_final: 0.7400 (mm110) REVERT: P 45 LYS cc_start: 0.8260 (ttmm) cc_final: 0.7747 (tttp) REVERT: P 94 ARG cc_start: 0.5297 (mpt180) cc_final: 0.3575 (tpp-160) REVERT: P 107 LEU cc_start: 0.6938 (mp) cc_final: 0.6155 (mt) REVERT: H 38 ARG cc_start: 0.8539 (ptt180) cc_final: 0.7859 (ptm160) REVERT: H 43 LYS cc_start: 0.6422 (pptt) cc_final: 0.5904 (pptt) REVERT: H 67 PHE cc_start: 0.6230 (m-10) cc_final: 0.5623 (m-10) REVERT: H 78 LEU cc_start: 0.7562 (tp) cc_final: 0.7162 (tp) REVERT: H 82 LEU cc_start: 0.7336 (pp) cc_final: 0.6262 (mp) REVERT: L 35 TRP cc_start: 0.7164 (m100) cc_final: 0.6249 (m100) REVERT: L 79 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7858 (mm-30) REVERT: L 87 TYR cc_start: 0.7447 (m-80) cc_final: 0.6816 (m-80) outliers start: 30 outliers final: 17 residues processed: 181 average time/residue: 0.1673 time to fit residues: 46.7680 Evaluate side-chains 160 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain K residue 27 ASP Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain D residue 543 LEU Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 105 GLN Chi-restraints excluded: chain N residue 81 ASP Chi-restraints excluded: chain N residue 106 VAL Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain F residue 526 SER Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 43 LYS Chi-restraints excluded: chain L residue 79 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 144 optimal weight: 8.9990 chunk 74 optimal weight: 10.0000 chunk 93 optimal weight: 4.9990 chunk 252 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 121 optimal weight: 0.0980 chunk 187 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 152 optimal weight: 8.9990 chunk 68 optimal weight: 8.9990 chunk 8 optimal weight: 3.9990 overall best weight: 3.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 3 GLN ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 79 GLN N 79 GLN E 99 ASN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.075792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.056576 restraints weight = 68305.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.058397 restraints weight = 39589.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.059579 restraints weight = 28543.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.060239 restraints weight = 23252.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.060778 restraints weight = 20611.318| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 22086 Z= 0.232 Angle : 0.629 10.651 30170 Z= 0.308 Chirality : 0.046 0.285 3601 Planarity : 0.004 0.050 3673 Dihedral : 5.748 49.857 4760 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.53 % Favored : 95.31 % Rotamer: Outliers : 1.34 % Allowed : 9.24 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % 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: -0.07 (0.17), residues: 2538 helix: 1.92 (0.28), residues: 365 sheet: 0.44 (0.18), residues: 791 loop : -0.90 (0.16), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 77 TYR 0.013 0.001 TYR J 100G PHE 0.016 0.002 PHE E 53 TRP 0.022 0.002 TRP L 35 HIS 0.006 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00550 (21952) covalent geometry : angle 0.60684 (29806) SS BOND : bond 0.00326 ( 38) SS BOND : angle 1.05571 ( 76) hydrogen bonds : bond 0.04438 ( 566) hydrogen bonds : angle 4.59136 ( 1494) link_ALPHA1-3 : bond 0.01170 ( 5) link_ALPHA1-3 : angle 1.56743 ( 15) link_ALPHA1-6 : bond 0.01048 ( 2) link_ALPHA1-6 : angle 1.44521 ( 6) link_BETA1-4 : bond 0.00331 ( 20) link_BETA1-4 : angle 1.63406 ( 60) link_BETA1-6 : bond 0.00299 ( 6) link_BETA1-6 : angle 2.20152 ( 18) link_NAG-ASN : bond 0.00265 ( 63) link_NAG-ASN : angle 1.75662 ( 189) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 149 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.9025 (mtp) cc_final: 0.8761 (mtp) REVERT: A 475 MET cc_start: 0.8977 (tpp) cc_final: 0.8711 (tpp) REVERT: J 87 THR cc_start: 0.8524 (m) cc_final: 0.8241 (p) REVERT: K 94 ARG cc_start: 0.5626 (mpt180) cc_final: 0.5328 (tpt170) REVERT: C 475 MET cc_start: 0.8100 (mmt) cc_final: 0.7765 (mmm) REVERT: D 632 ASP cc_start: 0.8653 (t70) cc_final: 0.8325 (t0) REVERT: M 11 LEU cc_start: 0.7697 (tp) cc_final: 0.7201 (mp) REVERT: N 94 ARG cc_start: 0.5789 (mpt180) cc_final: 0.3446 (mmt180) REVERT: E 95 MET cc_start: 0.8903 (ptm) cc_final: 0.8605 (ptm) REVERT: O 3 GLN cc_start: 0.7699 (OUTLIER) cc_final: 0.7492 (mm110) REVERT: P 94 ARG cc_start: 0.5327 (mpt180) cc_final: 0.3566 (tpp-160) REVERT: P 107 LEU cc_start: 0.6708 (mp) cc_final: 0.5970 (mt) REVERT: H 38 ARG cc_start: 0.8518 (ptt180) cc_final: 0.7829 (ptm160) REVERT: H 43 LYS cc_start: 0.6443 (pptt) cc_final: 0.6029 (pptt) REVERT: H 67 PHE cc_start: 0.6322 (m-10) cc_final: 0.5841 (m-10) REVERT: H 78 LEU cc_start: 0.7680 (tp) cc_final: 0.7445 (tp) REVERT: H 82 LEU cc_start: 0.7300 (pp) cc_final: 0.6238 (mp) REVERT: L 79 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7855 (mm-30) REVERT: L 89 GLN cc_start: 0.7272 (tm-30) cc_final: 0.7033 (tp40) REVERT: L 90 GLN cc_start: 0.8445 (pp30) cc_final: 0.7344 (pm20) outliers start: 30 outliers final: 20 residues processed: 173 average time/residue: 0.1673 time to fit residues: 44.6497 Evaluate side-chains 159 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain K residue 26 THR Chi-restraints excluded: chain K residue 27 ASP Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain N residue 81 ASP Chi-restraints excluded: chain N residue 106 VAL Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain F residue 526 SER Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 43 LYS Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain L residue 75 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 75 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 183 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 89 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.076978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.057986 restraints weight = 67305.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.059861 restraints weight = 38190.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.061060 restraints weight = 27245.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.061808 restraints weight = 22090.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.062298 restraints weight = 19371.746| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22086 Z= 0.137 Angle : 0.557 10.390 30170 Z= 0.273 Chirality : 0.044 0.276 3601 Planarity : 0.003 0.049 3673 Dihedral : 5.467 52.206 4758 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.29 % Favored : 95.55 % Rotamer: Outliers : 1.12 % Allowed : 9.55 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % 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: 0.02 (0.17), residues: 2538 helix: 2.14 (0.28), residues: 365 sheet: 0.49 (0.19), residues: 794 loop : -0.88 (0.16), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 77 TYR 0.009 0.001 TYR J 100G PHE 0.013 0.001 PHE C 53 TRP 0.017 0.001 TRP L 35 HIS 0.004 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00317 (21952) covalent geometry : angle 0.53815 (29806) SS BOND : bond 0.00231 ( 38) SS BOND : angle 0.85389 ( 76) hydrogen bonds : bond 0.03805 ( 566) hydrogen bonds : angle 4.36173 ( 1494) link_ALPHA1-3 : bond 0.01122 ( 5) link_ALPHA1-3 : angle 1.51200 ( 15) link_ALPHA1-6 : bond 0.01111 ( 2) link_ALPHA1-6 : angle 1.39951 ( 6) link_BETA1-4 : bond 0.00334 ( 20) link_BETA1-4 : angle 1.45076 ( 60) link_BETA1-6 : bond 0.00311 ( 6) link_BETA1-6 : angle 2.00402 ( 18) link_NAG-ASN : bond 0.00190 ( 63) link_NAG-ASN : angle 1.53392 ( 189) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 154 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.9019 (mtp) cc_final: 0.8779 (mtp) REVERT: A 475 MET cc_start: 0.8918 (tpp) cc_final: 0.8683 (tpp) REVERT: J 87 THR cc_start: 0.8377 (m) cc_final: 0.8072 (p) REVERT: K 94 ARG cc_start: 0.5583 (mpt180) cc_final: 0.5266 (tpt170) REVERT: D 632 ASP cc_start: 0.8619 (t70) cc_final: 0.8296 (t0) REVERT: M 11 LEU cc_start: 0.7772 (tp) cc_final: 0.7235 (mp) REVERT: M 105 GLN cc_start: 0.8168 (mp10) cc_final: 0.7868 (mt0) REVERT: N 94 ARG cc_start: 0.5726 (mpt180) cc_final: 0.3391 (mmt180) REVERT: E 95 MET cc_start: 0.8809 (ptm) cc_final: 0.8500 (ptm) REVERT: O 3 GLN cc_start: 0.7687 (OUTLIER) cc_final: 0.7367 (mm110) REVERT: P 94 ARG cc_start: 0.5226 (mpt180) cc_final: 0.3373 (tpp-160) REVERT: P 107 LEU cc_start: 0.6427 (mp) cc_final: 0.5739 (mt) REVERT: H 34 MET cc_start: 0.4819 (mtm) cc_final: 0.4589 (mtt) REVERT: H 38 ARG cc_start: 0.8498 (ptt180) cc_final: 0.7830 (ptm160) REVERT: H 43 LYS cc_start: 0.6410 (pptt) cc_final: 0.5869 (pptt) REVERT: H 67 PHE cc_start: 0.5954 (m-10) cc_final: 0.5480 (m-10) REVERT: H 82 LEU cc_start: 0.7237 (pp) cc_final: 0.6081 (mp) REVERT: L 35 TRP cc_start: 0.7164 (m100) cc_final: 0.6325 (m100) REVERT: L 79 GLU cc_start: 0.8300 (mm-30) cc_final: 0.7851 (mm-30) REVERT: L 90 GLN cc_start: 0.8409 (pp30) cc_final: 0.7317 (pm20) REVERT: L 91 TYR cc_start: 0.6370 (t80) cc_final: 0.6007 (t80) outliers start: 25 outliers final: 18 residues processed: 175 average time/residue: 0.1648 time to fit residues: 44.6397 Evaluate side-chains 159 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 140 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain D residue 543 LEU Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain N residue 81 ASP Chi-restraints excluded: chain N residue 106 VAL Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain F residue 526 SER Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain O residue 3 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 34 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 156 optimal weight: 4.9990 chunk 72 optimal weight: 7.9990 chunk 251 optimal weight: 40.0000 chunk 100 optimal weight: 5.9990 chunk 226 optimal weight: 7.9990 chunk 123 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 chunk 73 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 570 HIS J 39 GLN ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 GLN ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.075197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.056141 restraints weight = 68169.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.057872 restraints weight = 39928.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.059014 restraints weight = 28958.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.059783 restraints weight = 23740.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.060180 restraints weight = 20831.932| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 22086 Z= 0.275 Angle : 0.666 10.671 30170 Z= 0.325 Chirality : 0.047 0.289 3601 Planarity : 0.004 0.048 3673 Dihedral : 5.865 49.852 4758 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.36 % Favored : 94.48 % Rotamer: Outliers : 1.34 % Allowed : 9.42 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.29 (0.17), residues: 2538 helix: 1.80 (0.28), residues: 365 sheet: 0.28 (0.19), residues: 790 loop : -1.05 (0.16), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 77 TYR 0.013 0.002 TYR J 27 PHE 0.017 0.002 PHE E 53 TRP 0.017 0.002 TRP L 35 HIS 0.007 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00650 (21952) covalent geometry : angle 0.64589 (29806) SS BOND : bond 0.00370 ( 38) SS BOND : angle 1.09748 ( 76) hydrogen bonds : bond 0.04643 ( 566) hydrogen bonds : angle 4.73560 ( 1494) link_ALPHA1-3 : bond 0.01093 ( 5) link_ALPHA1-3 : angle 1.58327 ( 15) link_ALPHA1-6 : bond 0.00996 ( 2) link_ALPHA1-6 : angle 1.49180 ( 6) link_BETA1-4 : bond 0.00331 ( 20) link_BETA1-4 : angle 1.67323 ( 60) link_BETA1-6 : bond 0.00339 ( 6) link_BETA1-6 : angle 2.12718 ( 18) link_NAG-ASN : bond 0.00327 ( 63) link_NAG-ASN : angle 1.73692 ( 189) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 140 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.8976 (tpp) cc_final: 0.8707 (tpp) REVERT: J 82 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.8525 (mtm) REVERT: J 87 THR cc_start: 0.8416 (m) cc_final: 0.8086 (p) REVERT: K 94 ARG cc_start: 0.5724 (mpt180) cc_final: 0.5356 (tpt170) REVERT: M 105 GLN cc_start: 0.8259 (mp10) cc_final: 0.7899 (mt0) REVERT: N 94 ARG cc_start: 0.5856 (mpt180) cc_final: 0.3438 (mmt180) REVERT: P 94 ARG cc_start: 0.5316 (mpt180) cc_final: 0.3696 (tpp-160) REVERT: P 107 LEU cc_start: 0.6586 (mp) cc_final: 0.5926 (mt) REVERT: H 38 ARG cc_start: 0.8526 (ptt180) cc_final: 0.7824 (ptm160) REVERT: H 43 LYS cc_start: 0.6605 (pptt) cc_final: 0.6137 (pptt) REVERT: H 67 PHE cc_start: 0.6213 (m-10) cc_final: 0.5644 (m-10) REVERT: H 82 LEU cc_start: 0.7234 (pp) cc_final: 0.6210 (mp) REVERT: L 35 TRP cc_start: 0.7289 (m100) cc_final: 0.6536 (m100) REVERT: L 79 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7665 (mm-30) REVERT: L 90 GLN cc_start: 0.8006 (pp30) cc_final: 0.7604 (pp30) outliers start: 30 outliers final: 23 residues processed: 163 average time/residue: 0.1719 time to fit residues: 43.0822 Evaluate side-chains 158 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain J residue 82 MET Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain D residue 543 LEU Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain N residue 42 LYS Chi-restraints excluded: chain N residue 81 ASP Chi-restraints excluded: chain N residue 106 VAL Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain E residue 72 HIS Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain F residue 526 SER Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 82 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 169 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 166 optimal weight: 5.9990 chunk 24 optimal weight: 0.4980 chunk 146 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 chunk 180 optimal weight: 0.6980 chunk 210 optimal weight: 8.9990 chunk 77 optimal weight: 0.6980 chunk 2 optimal weight: 5.9990 chunk 147 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN F 538 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.077322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.058379 restraints weight = 67170.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.060293 restraints weight = 38160.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.061503 restraints weight = 27105.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.062238 restraints weight = 21898.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.062750 restraints weight = 19214.988| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 22086 Z= 0.102 Angle : 0.547 10.263 30170 Z= 0.268 Chirality : 0.043 0.271 3601 Planarity : 0.003 0.048 3673 Dihedral : 5.360 54.172 4758 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.02 % Favored : 95.86 % Rotamer: Outliers : 1.03 % Allowed : 9.68 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % 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: -0.06 (0.17), residues: 2538 helix: 2.24 (0.28), residues: 365 sheet: 0.49 (0.19), residues: 803 loop : -1.02 (0.16), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 77 TYR 0.009 0.001 TYR A 173 PHE 0.013 0.001 PHE C 53 TRP 0.015 0.001 TRP E 479 HIS 0.003 0.001 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00227 (21952) covalent geometry : angle 0.52903 (29806) SS BOND : bond 0.00212 ( 38) SS BOND : angle 0.77985 ( 76) hydrogen bonds : bond 0.03482 ( 566) hydrogen bonds : angle 4.30414 ( 1494) link_ALPHA1-3 : bond 0.01049 ( 5) link_ALPHA1-3 : angle 1.51144 ( 15) link_ALPHA1-6 : bond 0.01110 ( 2) link_ALPHA1-6 : angle 1.39722 ( 6) link_BETA1-4 : bond 0.00352 ( 20) link_BETA1-4 : angle 1.37647 ( 60) link_BETA1-6 : bond 0.00302 ( 6) link_BETA1-6 : angle 1.81057 ( 18) link_NAG-ASN : bond 0.00226 ( 63) link_NAG-ASN : angle 1.47295 ( 189) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 152 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.8899 (tpp) cc_final: 0.8688 (tpp) REVERT: J 87 THR cc_start: 0.8361 (m) cc_final: 0.8067 (p) REVERT: K 94 ARG cc_start: 0.5498 (mpt180) cc_final: 0.5249 (tpt170) REVERT: D 632 ASP cc_start: 0.8633 (t70) cc_final: 0.8315 (t0) REVERT: M 105 GLN cc_start: 0.8200 (mp10) cc_final: 0.7869 (mt0) REVERT: N 94 ARG cc_start: 0.5705 (mpt180) cc_final: 0.3472 (mmt180) REVERT: E 69 TRP cc_start: 0.8473 (OUTLIER) cc_final: 0.6353 (m100) REVERT: E 95 MET cc_start: 0.8714 (ptm) cc_final: 0.8392 (ptm) REVERT: P 94 ARG cc_start: 0.5073 (mpt180) cc_final: 0.3357 (tpp-160) REVERT: P 107 LEU cc_start: 0.6150 (mp) cc_final: 0.5487 (mt) REVERT: H 19 ARG cc_start: 0.6664 (ttm170) cc_final: 0.6404 (tpp80) REVERT: H 38 ARG cc_start: 0.8495 (ptt180) cc_final: 0.7786 (ptm160) REVERT: H 43 LYS cc_start: 0.6511 (pptt) cc_final: 0.5933 (pptt) REVERT: H 67 PHE cc_start: 0.6058 (m-10) cc_final: 0.5458 (m-10) REVERT: H 82 LEU cc_start: 0.7245 (pp) cc_final: 0.6177 (mp) REVERT: L 35 TRP cc_start: 0.7162 (m100) cc_final: 0.6377 (m100) REVERT: L 79 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7914 (mm-30) REVERT: L 90 GLN cc_start: 0.7793 (pp30) cc_final: 0.7420 (pp30) outliers start: 23 outliers final: 17 residues processed: 172 average time/residue: 0.1760 time to fit residues: 46.6830 Evaluate side-chains 154 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 136 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain N residue 42 LYS Chi-restraints excluded: chain N residue 81 ASP Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain F residue 526 SER Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain L residue 82 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 171 optimal weight: 1.9990 chunk 214 optimal weight: 4.9990 chunk 193 optimal weight: 7.9990 chunk 118 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 3 optimal weight: 0.0770 chunk 216 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 overall best weight: 1.3742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.076890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.057980 restraints weight = 67502.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.059902 restraints weight = 38599.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.061070 restraints weight = 27426.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.061834 restraints weight = 22308.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.062228 restraints weight = 19535.976| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 22086 Z= 0.133 Angle : 0.564 10.219 30170 Z= 0.275 Chirality : 0.044 0.268 3601 Planarity : 0.004 0.047 3673 Dihedral : 5.303 52.083 4758 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.33 % Favored : 95.51 % Rotamer: Outliers : 1.07 % Allowed : 9.91 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % 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: -0.00 (0.17), residues: 2538 helix: 2.44 (0.28), residues: 353 sheet: 0.41 (0.18), residues: 833 loop : -0.95 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 77 TYR 0.022 0.001 TYR N 91 PHE 0.019 0.001 PHE H 29 TRP 0.014 0.001 TRP A 479 HIS 0.004 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00311 (21952) covalent geometry : angle 0.54509 (29806) SS BOND : bond 0.00244 ( 38) SS BOND : angle 1.09614 ( 76) hydrogen bonds : bond 0.03618 ( 566) hydrogen bonds : angle 4.30272 ( 1494) link_ALPHA1-3 : bond 0.01015 ( 5) link_ALPHA1-3 : angle 1.51796 ( 15) link_ALPHA1-6 : bond 0.01041 ( 2) link_ALPHA1-6 : angle 1.38407 ( 6) link_BETA1-4 : bond 0.00329 ( 20) link_BETA1-4 : angle 1.44125 ( 60) link_BETA1-6 : bond 0.00286 ( 6) link_BETA1-6 : angle 1.79948 ( 18) link_NAG-ASN : bond 0.00191 ( 63) link_NAG-ASN : angle 1.46891 ( 189) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.8922 (tpp) cc_final: 0.8689 (tpp) REVERT: J 82 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.8532 (mtm) REVERT: J 87 THR cc_start: 0.8370 (m) cc_final: 0.8009 (p) REVERT: K 94 ARG cc_start: 0.5548 (mpt180) cc_final: 0.5273 (tpt170) REVERT: C 475 MET cc_start: 0.8092 (mmt) cc_final: 0.7720 (mmm) REVERT: M 105 GLN cc_start: 0.8204 (mp10) cc_final: 0.7858 (mt0) REVERT: N 94 ARG cc_start: 0.5901 (mpt180) cc_final: 0.3565 (mmt180) REVERT: E 95 MET cc_start: 0.8745 (ptm) cc_final: 0.8428 (ptm) REVERT: P 94 ARG cc_start: 0.5146 (mpt180) cc_final: 0.3448 (tpp-160) REVERT: P 107 LEU cc_start: 0.6287 (mp) cc_final: 0.5627 (mt) REVERT: H 19 ARG cc_start: 0.6700 (ttm170) cc_final: 0.6419 (tpp80) REVERT: H 38 ARG cc_start: 0.8516 (ptt180) cc_final: 0.7751 (ptm160) REVERT: H 43 LYS cc_start: 0.6550 (pptt) cc_final: 0.6055 (pptt) REVERT: H 67 PHE cc_start: 0.6180 (m-10) cc_final: 0.5506 (m-10) REVERT: H 78 LEU cc_start: 0.7703 (tp) cc_final: 0.7470 (tp) REVERT: H 82 LEU cc_start: 0.7165 (pp) cc_final: 0.6079 (mp) REVERT: L 35 TRP cc_start: 0.7194 (m100) cc_final: 0.6435 (m100) REVERT: L 79 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7857 (mm-30) REVERT: L 90 GLN cc_start: 0.7940 (pp30) cc_final: 0.7527 (pp30) outliers start: 24 outliers final: 19 residues processed: 159 average time/residue: 0.1600 time to fit residues: 39.6370 Evaluate side-chains 153 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain J residue 82 MET Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain N residue 42 LYS Chi-restraints excluded: chain N residue 81 ASP Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain E residue 72 HIS Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain F residue 526 SER Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain L residue 82 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 47 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 216 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 80 optimal weight: 0.1980 chunk 199 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 144 optimal weight: 0.5980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 79 GLN N 39 HIS O 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.077774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.059019 restraints weight = 67340.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.060903 restraints weight = 37752.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.062112 restraints weight = 26697.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.062861 restraints weight = 21516.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.063285 restraints weight = 18815.281| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.4246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 22086 Z= 0.107 Angle : 0.543 10.113 30170 Z= 0.266 Chirality : 0.043 0.262 3601 Planarity : 0.003 0.048 3673 Dihedral : 5.087 53.456 4758 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.02 % Favored : 95.86 % Rotamer: Outliers : 0.94 % Allowed : 10.13 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % 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: 0.05 (0.17), residues: 2538 helix: 2.39 (0.28), residues: 365 sheet: 0.46 (0.18), residues: 833 loop : -0.93 (0.17), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 77 TYR 0.015 0.001 TYR N 91 PHE 0.014 0.001 PHE H 29 TRP 0.014 0.001 TRP A 479 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00244 (21952) covalent geometry : angle 0.52579 (29806) SS BOND : bond 0.00184 ( 38) SS BOND : angle 0.95906 ( 76) hydrogen bonds : bond 0.03355 ( 566) hydrogen bonds : angle 4.16682 ( 1494) link_ALPHA1-3 : bond 0.00991 ( 5) link_ALPHA1-3 : angle 1.49007 ( 15) link_ALPHA1-6 : bond 0.01036 ( 2) link_ALPHA1-6 : angle 1.37391 ( 6) link_BETA1-4 : bond 0.00341 ( 20) link_BETA1-4 : angle 1.38358 ( 60) link_BETA1-6 : bond 0.00290 ( 6) link_BETA1-6 : angle 1.66556 ( 18) link_NAG-ASN : bond 0.00196 ( 63) link_NAG-ASN : angle 1.40766 ( 189) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3411.87 seconds wall clock time: 60 minutes 11.73 seconds (3611.73 seconds total)