Starting phenix.real_space_refine on Thu Mar 5 11:02:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t9b_25755/03_2026/7t9b_25755.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t9b_25755/03_2026/7t9b_25755.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7t9b_25755/03_2026/7t9b_25755.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t9b_25755/03_2026/7t9b_25755.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7t9b_25755/03_2026/7t9b_25755.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t9b_25755/03_2026/7t9b_25755.map" } resolution = 3.72 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= 0.002 sd= 0.039 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 13523 2.51 5 N 3572 2.21 5 O 4366 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 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: 21592 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 3433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3433 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 23, 'TRANS': 411} 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: 3425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3425 Classifications: {'peptide': 434} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 23, 'TRANS': 410} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 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: 3387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3387 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 23, 'TRANS': 405} 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: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1051 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: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 809 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 98} 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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "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: 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: "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: "j" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "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: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 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: 5.66, per 1000 atoms: 0.26 Number of scatterers: 21592 At special positions: 0 Unit cell: (124.2, 127.65, 188.6, 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 4366 8.00 N 3572 7.00 C 13523 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.05 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.05 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 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=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.00 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 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=2.03 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 54 " - pdb=" SG CYS E 74 " distance=2.10 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.04 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.02 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.06 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 E 501 " - pdb=" SG CYS F 605 " distance=2.02 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 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=2.15 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 2 " - " BMA S 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG b 1 " - " NAG b 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 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG j 1 " - " NAG j 2 " BETA1-6 " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " FUC T 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG U 1 " - " FUC U 3 " " NAG a 1 " - " FUC a 2 " " NAG b 1 " - " FUC b 3 " " NAG i 1 " - " FUC i 2 " " NAG j 1 " - " FUC j 3 " 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 637 " " NAG D 702 " - " ASN D 625 " " 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 133 " " NAG F 701 " - " ASN F 625 " " NAG F 702 " - " ASN F 637 " " 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 197 " " NAG g 1 " - " ASN E 156 " " NAG h 1 " - " ASN E 160 " " NAG i 1 " - " ASN F 618 " " NAG j 1 " - " ASN F 611 " Time building additional restraints: 1.76 Conformation dependent library (CDL) restraints added in 903.5 milliseconds 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4758 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 38 sheets defined 18.7% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 99 through 115 Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.515A pdb=" N THR A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.525A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 526 removed outlier: 4.355A 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 627 through 635 Processing helix chain 'B' and resid 638 through 662 removed outlier: 3.600A pdb=" N ILE B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) removed outlier: 4.141A 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 117 removed outlier: 3.610A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) 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: 3.519A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 526 removed outlier: 4.278A 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: 3.671A pdb=" N LEU D 576 " --> pdb=" O GLY D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 623 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 661 removed outlier: 3.715A pdb=" N ILE D 642 " --> pdb=" O TYR D 638 " (cutoff:3.500A) 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 116 removed outlier: 3.755A pdb=" N LEU E 116 " --> pdb=" O TRP E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 151 Processing helix chain 'E' and resid 335 through 350 Processing helix chain 'E' and resid 368 through 373 removed outlier: 3.581A pdb=" N THR E 373 " --> pdb=" O LEU E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 484 removed outlier: 3.846A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 521 through 526 removed outlier: 4.403A pdb=" N GLY F 525 " --> pdb=" O GLY F 522 " (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 635 Processing helix chain 'F' and resid 636 through 638 No H-bonds generated for 'chain 'F' and resid 636 through 638' Processing helix chain 'F' and resid 639 through 662 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 Processing helix chain 'H' and resid 61 through 64 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: 5.381A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.123A 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 Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.489A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, 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: 3.988A pdb=" N ASN A 301 " --> pdb=" O ILE A 323A" (cutoff:3.500A) removed outlier: 5.974A pdb=" N LYS A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N THR A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ILE A 309 " --> pdb=" O ALA A 316 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ALA A 316 " --> 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=AA8, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AA9, 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=AB1, 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=AB1 Processing sheet with id=AB2, first strand: chain 'K' and resid 19 through 24 Processing sheet with id=AB3, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.376A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AB6, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB7, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AB8, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.490A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB9, 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: 6.663A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 6.596A 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=AC1, first strand: chain 'M' and resid 3 through 6 Processing sheet with id=AC2, 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=AC3, 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=AC3 Processing sheet with id=AC4, first strand: chain 'N' and resid 19 through 24 Processing sheet with id=AC5, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.414A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.515A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 75 through 76 Processing sheet with id=AC8, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AC9, first strand: chain 'E' and resid 130 through 133 Processing sheet with id=AD1, first strand: chain 'E' and resid 181 through 182 Processing sheet with id=AD2, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.457A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AD3, 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: 6.722A pdb=" N ASN E 301 " --> pdb=" O ILE E 323 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ILE E 323 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N GLN E 315 " --> 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=AD4, first strand: chain 'O' and resid 3 through 6 Processing sheet with id=AD5, 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 45 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=AD6, 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=AD6 Processing sheet with id=AD7, first strand: chain 'P' and resid 19 through 24 Processing sheet with id=AD8, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AD9, first strand: chain 'H' and resid 34 through 39 removed outlier: 6.966A pdb=" N MET H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ARG H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.768A 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=AE1, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AE2, first strand: chain 'L' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 10 through 12 current: chain 'L' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 53 through 54 current: chain 'L' and resid 96 through 98 555 hydrogen bonds defined for protein. 1455 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: 3.85 Time building geometry restraints manager: 2.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4674 1.32 - 1.46: 7079 1.46 - 1.59: 10059 1.59 - 1.73: 46 1.73 - 1.87: 175 Bond restraints: 22033 Sorted by residual: bond pdb=" NE ARG E 503 " pdb=" CZ ARG E 503 " ideal model delta sigma weight residual 1.326 1.396 -0.070 1.10e-02 8.26e+03 4.00e+01 bond pdb=" CB ASP N 27B" pdb=" CG ASP N 27B" ideal model delta sigma weight residual 1.516 1.361 0.155 2.50e-02 1.60e+03 3.84e+01 bond pdb=" NE ARG C 503 " pdb=" CZ ARG C 503 " ideal model delta sigma weight residual 1.326 1.393 -0.067 1.10e-02 8.26e+03 3.75e+01 bond pdb=" NE ARG A 503 " pdb=" CZ ARG A 503 " ideal model delta sigma weight residual 1.326 1.392 -0.066 1.10e-02 8.26e+03 3.61e+01 bond pdb=" CB LEU N 107 " pdb=" CG LEU N 107 " ideal model delta sigma weight residual 1.530 1.649 -0.119 2.00e-02 2.50e+03 3.56e+01 ... (remaining 22028 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.60: 29874 7.60 - 15.21: 43 15.21 - 22.81: 0 22.81 - 30.42: 0 30.42 - 38.02: 3 Bond angle restraints: 29920 Sorted by residual: angle pdb=" C2 NAG d 1 " pdb=" N2 NAG d 1 " pdb=" C7 NAG d 1 " ideal model delta sigma weight residual 124.56 162.58 -38.02 3.00e+00 1.11e-01 1.61e+02 angle pdb=" C2 NAG I 1 " pdb=" N2 NAG I 1 " pdb=" C7 NAG I 1 " ideal model delta sigma weight residual 124.56 161.38 -36.82 3.00e+00 1.11e-01 1.51e+02 angle pdb=" C2 NAG X 1 " pdb=" N2 NAG X 1 " pdb=" C7 NAG X 1 " ideal model delta sigma weight residual 124.56 160.89 -36.33 3.00e+00 1.11e-01 1.47e+02 angle pdb=" N HIS C 85 " pdb=" CA HIS C 85 " pdb=" C HIS C 85 " ideal model delta sigma weight residual 111.82 120.98 -9.16 1.16e+00 7.43e-01 6.23e+01 angle pdb=" N GLU C 83 " pdb=" CA GLU C 83 " pdb=" C GLU C 83 " ideal model delta sigma weight residual 109.96 121.71 -11.75 1.50e+00 4.44e-01 6.14e+01 ... (remaining 29915 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.78: 13871 21.78 - 43.56: 327 43.56 - 65.34: 102 65.34 - 87.12: 59 87.12 - 108.90: 24 Dihedral angle restraints: 14383 sinusoidal: 6957 harmonic: 7426 Sorted by residual: dihedral pdb=" CA ASN C 197 " pdb=" C ASN C 197 " pdb=" N THR C 198 " pdb=" CA THR C 198 " ideal model delta harmonic sigma weight residual 180.00 147.63 32.37 0 5.00e+00 4.00e-02 4.19e+01 dihedral pdb=" CA VAL C 68 " pdb=" C VAL C 68 " pdb=" N TRP C 69 " pdb=" CA TRP C 69 " ideal model delta harmonic sigma weight residual -180.00 -151.99 -28.01 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA THR A 198 " pdb=" C THR A 198 " pdb=" N SER A 199 " pdb=" CA SER A 199 " ideal model delta harmonic sigma weight residual -180.00 -153.18 -26.82 0 5.00e+00 4.00e-02 2.88e+01 ... (remaining 14380 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.218: 3289 0.218 - 0.435: 316 0.435 - 0.653: 24 0.653 - 0.871: 0 0.871 - 1.088: 1 Chirality restraints: 3630 Sorted by residual: chirality pdb=" C1 FUC i 2 " pdb=" O6 NAG i 1 " pdb=" C2 FUC i 2 " pdb=" O5 FUC i 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.31 -1.09 2.00e-02 2.50e+03 2.96e+03 chirality pdb=" C1 NAG S 2 " pdb=" O6 NAG S 1 " pdb=" C2 NAG S 2 " pdb=" O5 NAG S 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.89 -0.51 2.00e-02 2.50e+03 6.46e+02 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 1.93 0.47 2.00e-02 2.50e+03 5.41e+02 ... (remaining 3627 not shown) Planarity restraints: 3736 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG S 2 " 0.348 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" C7 NAG S 2 " -0.089 2.00e-02 2.50e+03 pdb=" C8 NAG S 2 " 0.184 2.00e-02 2.50e+03 pdb=" N2 NAG S 2 " -0.513 2.00e-02 2.50e+03 pdb=" O7 NAG S 2 " 0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG j 2 " 0.318 2.00e-02 2.50e+03 2.78e-01 9.64e+02 pdb=" C7 NAG j 2 " -0.069 2.00e-02 2.50e+03 pdb=" C8 NAG j 2 " 0.103 2.00e-02 2.50e+03 pdb=" N2 NAG j 2 " -0.498 2.00e-02 2.50e+03 pdb=" O7 NAG j 2 " 0.145 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 701 " -0.324 2.00e-02 2.50e+03 2.75e-01 9.47e+02 pdb=" C7 NAG F 701 " 0.083 2.00e-02 2.50e+03 pdb=" C8 NAG F 701 " -0.183 2.00e-02 2.50e+03 pdb=" N2 NAG F 701 " 0.480 2.00e-02 2.50e+03 pdb=" O7 NAG F 701 " -0.055 2.00e-02 2.50e+03 ... (remaining 3733 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 5451 2.81 - 3.33: 19130 3.33 - 3.86: 36326 3.86 - 4.38: 43973 4.38 - 4.90: 70120 Nonbonded interactions: 175000 Sorted by model distance: nonbonded pdb=" O5 NAG j 1 " pdb=" O6 NAG j 1 " model vdw 2.289 2.432 nonbonded pdb=" N ASP J 84 " pdb=" OD1 ASP J 84 " model vdw 2.370 3.120 nonbonded pdb=" N ASP O 84 " pdb=" OD1 ASP O 84 " model vdw 2.370 3.120 nonbonded pdb=" N ASP M 84 " pdb=" OD1 ASP M 84 " model vdw 2.370 3.120 nonbonded pdb=" OD1 ASP A 107 " pdb=" NZ LYS B 574 " model vdw 2.411 3.120 ... (remaining 174995 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 72 through 611)) selection = (chain 'C' and (resid 33 through 57 or resid 72 through 611)) selection = chain 'E' } 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 '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 'c' and resid 1) selection = (chain 'd' and resid 1) selection = (chain 'f' and resid 1) selection = (chain 'g' 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' } ncs_group { reference = (chain 'R' and resid 1 through 2) selection = (chain 'U' and resid 1 through 2) selection = (chain 'b' and resid 1 through 2) selection = (chain 'h' and resid 1 through 2) selection = (chain 'j' and resid 1 through 2) } 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: 2.290 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: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.270 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 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 : 0.021 0.155 22174 Z= 1.146 Angle : 1.797 38.021 30303 Z= 1.146 Chirality : 0.133 1.088 3630 Planarity : 0.015 0.294 3673 Dihedral : 12.572 108.899 9505 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 0.99 Ramachandran Plot: Outliers : 0.67 % Allowed : 3.71 % Favored : 95.62 % Rotamer: Outliers : 0.98 % Allowed : 0.76 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % 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: 0.40 (0.16), residues: 2535 helix: -0.34 (0.24), residues: 385 sheet: 0.93 (0.18), residues: 817 loop : 0.13 (0.17), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG J 71 TYR 0.070 0.007 TYR L 87 PHE 0.044 0.006 PHE L 98 TRP 0.063 0.008 TRP A 96 HIS 0.009 0.002 HIS J 82A Details of bonding type rmsd covalent geometry : bond 0.02105 (22033) covalent geometry : angle 1.77494 (29920) SS BOND : bond 0.02375 ( 40) SS BOND : angle 2.43405 ( 80) hydrogen bonds : bond 0.16830 ( 555) hydrogen bonds : angle 6.86540 ( 1455) link_ALPHA1-3 : bond 0.06139 ( 5) link_ALPHA1-3 : angle 3.43561 ( 15) link_ALPHA1-6 : bond 0.00449 ( 2) link_ALPHA1-6 : angle 2.71457 ( 6) link_BETA1-4 : bond 0.05873 ( 24) link_BETA1-4 : angle 4.02949 ( 72) link_BETA1-6 : bond 0.02558 ( 7) link_BETA1-6 : angle 4.60429 ( 21) link_NAG-ASN : bond 0.06922 ( 63) link_NAG-ASN : angle 2.62635 ( 189) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 395 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 TYR cc_start: 0.8555 (m-80) cc_final: 0.8237 (m-10) REVERT: A 475 MET cc_start: 0.8713 (mmm) cc_final: 0.8353 (mmm) REVERT: A 482 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7969 (mm-30) REVERT: J 2 VAL cc_start: 0.9262 (t) cc_final: 0.8702 (t) REVERT: K 11 VAL cc_start: 0.8529 (t) cc_final: 0.8194 (p) REVERT: K 47 MET cc_start: 0.8336 (mmm) cc_final: 0.8056 (mmt) REVERT: K 94 ARG cc_start: 0.6115 (mpt180) cc_final: 0.5237 (mmt180) REVERT: K 104 LEU cc_start: 0.8447 (tp) cc_final: 0.7759 (tt) REVERT: C 72 HIS cc_start: 0.6914 (OUTLIER) cc_final: 0.6650 (p90) REVERT: C 107 ASP cc_start: 0.8076 (m-30) cc_final: 0.7734 (t0) REVERT: C 153 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8298 (tt0) REVERT: C 449 ILE cc_start: 0.9419 (mt) cc_final: 0.9217 (mm) REVERT: D 616 ASN cc_start: 0.9247 (p0) cc_final: 0.8814 (p0) REVERT: D 624 ASP cc_start: 0.8310 (p0) cc_final: 0.7721 (p0) REVERT: D 626 MET cc_start: 0.8826 (ttm) cc_final: 0.8613 (ttm) REVERT: M 78 LEU cc_start: 0.9138 (tp) cc_final: 0.8922 (tp) REVERT: N 47 MET cc_start: 0.8484 (mmm) cc_final: 0.8238 (mmp) REVERT: N 58 VAL cc_start: 0.8613 (m) cc_final: 0.8390 (p) REVERT: N 94 ARG cc_start: 0.6713 (mpt180) cc_final: 0.6141 (tpt170) REVERT: N 102 THR cc_start: 0.8431 (m) cc_final: 0.8120 (p) REVERT: E 104 MET cc_start: 0.8272 (ttm) cc_final: 0.8010 (ttt) REVERT: F 571 TRP cc_start: 0.5920 (t-100) cc_final: 0.5585 (p-90) REVERT: F 581 LEU cc_start: 0.8928 (pp) cc_final: 0.8712 (tp) REVERT: O 52 ASN cc_start: 0.8951 (t0) cc_final: 0.8700 (t0) REVERT: P 42 LYS cc_start: 0.8307 (mmtt) cc_final: 0.8034 (ttpt) REVERT: P 94 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.7679 (tpt170) REVERT: H 27 PHE cc_start: 0.5955 (t80) cc_final: 0.5594 (t80) REVERT: H 80 LEU cc_start: 0.7504 (tp) cc_final: 0.7066 (tp) REVERT: H 98 THR cc_start: 0.8274 (OUTLIER) cc_final: 0.8063 (p) REVERT: L 42 GLN cc_start: 0.8577 (mm-40) cc_final: 0.8155 (mp10) REVERT: L 71 PHE cc_start: 0.4742 (m-80) cc_final: 0.3278 (m-80) REVERT: L 75 ILE cc_start: 0.7447 (mt) cc_final: 0.6937 (mt) REVERT: L 77 ARG cc_start: 0.7874 (mmt-90) cc_final: 0.7515 (tmm-80) REVERT: L 89 GLN cc_start: 0.8572 (tt0) cc_final: 0.8090 (tm-30) outliers start: 22 outliers final: 2 residues processed: 412 average time/residue: 0.1772 time to fit residues: 106.7072 Evaluate side-chains 195 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 190 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain P residue 94 ARG Chi-restraints excluded: chain H residue 98 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 247 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN A 302 ASN A 425 ASN ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 52 ASN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 ASN D 653 GLN E 130 GLN E 195 ASN E 246 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.083548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.063951 restraints weight = 62125.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.066277 restraints weight = 33442.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.067767 restraints weight = 22764.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.068712 restraints weight = 17766.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.069327 restraints weight = 15116.700| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 22174 Z= 0.193 Angle : 0.778 16.405 30303 Z= 0.380 Chirality : 0.047 0.328 3630 Planarity : 0.004 0.060 3673 Dihedral : 9.125 75.499 4866 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.71 % Favored : 96.09 % Rotamer: Outliers : 1.43 % Allowed : 5.98 % Favored : 92.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % 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: 0.43 (0.17), residues: 2535 helix: 1.60 (0.27), residues: 375 sheet: 0.72 (0.18), residues: 787 loop : -0.30 (0.17), residues: 1373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 588 TYR 0.016 0.001 TYR C 173 PHE 0.025 0.002 PHE H 29 TRP 0.027 0.001 TRP E 479 HIS 0.006 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00427 (22033) covalent geometry : angle 0.73956 (29920) SS BOND : bond 0.00278 ( 40) SS BOND : angle 0.85924 ( 80) hydrogen bonds : bond 0.05751 ( 555) hydrogen bonds : angle 5.35500 ( 1455) link_ALPHA1-3 : bond 0.01294 ( 5) link_ALPHA1-3 : angle 1.91850 ( 15) link_ALPHA1-6 : bond 0.01021 ( 2) link_ALPHA1-6 : angle 1.52820 ( 6) link_BETA1-4 : bond 0.00622 ( 24) link_BETA1-4 : angle 2.67185 ( 72) link_BETA1-6 : bond 0.01489 ( 7) link_BETA1-6 : angle 2.51063 ( 21) link_NAG-ASN : bond 0.00460 ( 63) link_NAG-ASN : angle 2.53548 ( 189) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 221 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 VAL cc_start: 0.8767 (t) cc_final: 0.8560 (p) REVERT: A 217 TYR cc_start: 0.8225 (m-80) cc_final: 0.7582 (m-80) REVERT: A 475 MET cc_start: 0.8489 (mmm) cc_final: 0.8249 (mmm) REVERT: B 648 GLU cc_start: 0.8177 (tp30) cc_final: 0.7871 (tm-30) REVERT: K 27 ASP cc_start: 0.8883 (t70) cc_final: 0.8605 (t70) REVERT: K 47 MET cc_start: 0.7988 (mmm) cc_final: 0.7755 (mmt) REVERT: K 94 ARG cc_start: 0.5407 (mpt180) cc_final: 0.4748 (mmt180) REVERT: D 616 ASN cc_start: 0.9014 (p0) cc_final: 0.8733 (p0) REVERT: M 86 ASP cc_start: 0.8369 (m-30) cc_final: 0.8085 (m-30) REVERT: N 94 ARG cc_start: 0.5991 (mpt180) cc_final: 0.5753 (tpt170) REVERT: N 95 THR cc_start: 0.8810 (p) cc_final: 0.8608 (p) REVERT: E 104 MET cc_start: 0.7885 (ttm) cc_final: 0.7648 (ttt) REVERT: F 657 GLU cc_start: 0.8375 (tp30) cc_final: 0.8141 (tp30) REVERT: O 52 ASN cc_start: 0.8899 (t0) cc_final: 0.8595 (t0) REVERT: P 94 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.7586 (tpt170) REVERT: H 27 PHE cc_start: 0.5657 (t80) cc_final: 0.5253 (t80) REVERT: H 38 ARG cc_start: 0.7536 (ptt180) cc_final: 0.7278 (ptp-170) REVERT: H 101 ASP cc_start: 0.8150 (t0) cc_final: 0.7504 (t0) REVERT: L 46 LEU cc_start: 0.9130 (tt) cc_final: 0.8792 (mt) REVERT: L 104 VAL cc_start: 0.7912 (t) cc_final: 0.7699 (p) outliers start: 32 outliers final: 16 residues processed: 248 average time/residue: 0.1565 time to fit residues: 59.3187 Evaluate side-chains 190 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 173 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain D residue 653 GLN Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 94 ARG Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 27 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 114 optimal weight: 0.8980 chunk 180 optimal weight: 9.9990 chunk 151 optimal weight: 10.0000 chunk 176 optimal weight: 1.9990 chunk 250 optimal weight: 20.0000 chunk 57 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 152 optimal weight: 4.9990 chunk 150 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN A 195 ASN B 607 ASN J 52 ASN C 195 ASN E 99 ASN ** L 42 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 = 0.3329 r_free = 0.3329 target = 0.074570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.055151 restraints weight = 63355.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.056911 restraints weight = 37644.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.058064 restraints weight = 26933.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.058840 restraints weight = 21789.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.059326 restraints weight = 18908.245| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 22174 Z= 0.155 Angle : 0.684 17.111 30303 Z= 0.326 Chirality : 0.044 0.302 3630 Planarity : 0.004 0.042 3673 Dihedral : 7.671 65.677 4861 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.75 % Favored : 96.13 % Rotamer: Outliers : 1.38 % Allowed : 7.01 % Favored : 91.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % 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: 0.37 (0.17), residues: 2535 helix: 1.60 (0.27), residues: 384 sheet: 0.72 (0.18), residues: 772 loop : -0.39 (0.17), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 360 TYR 0.017 0.001 TYR F 586 PHE 0.014 0.002 PHE L 83 TRP 0.018 0.001 TRP E 479 HIS 0.006 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00348 (22033) covalent geometry : angle 0.64757 (29920) SS BOND : bond 0.00358 ( 40) SS BOND : angle 0.74271 ( 80) hydrogen bonds : bond 0.04586 ( 555) hydrogen bonds : angle 4.89944 ( 1455) link_ALPHA1-3 : bond 0.01064 ( 5) link_ALPHA1-3 : angle 1.48062 ( 15) link_ALPHA1-6 : bond 0.00814 ( 2) link_ALPHA1-6 : angle 1.42093 ( 6) link_BETA1-4 : bond 0.00497 ( 24) link_BETA1-4 : angle 2.12349 ( 72) link_BETA1-6 : bond 0.00809 ( 7) link_BETA1-6 : angle 2.31539 ( 21) link_NAG-ASN : bond 0.00465 ( 63) link_NAG-ASN : angle 2.43053 ( 189) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 192 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 HIS cc_start: 0.6836 (OUTLIER) cc_final: 0.6534 (t-90) REVERT: A 89 VAL cc_start: 0.8780 (t) cc_final: 0.8542 (p) REVERT: A 217 TYR cc_start: 0.8213 (m-80) cc_final: 0.7489 (m-80) REVERT: A 475 MET cc_start: 0.8479 (mmm) cc_final: 0.8101 (mmm) REVERT: K 27 ASP cc_start: 0.8923 (OUTLIER) cc_final: 0.8625 (t70) REVERT: K 47 MET cc_start: 0.8034 (mmm) cc_final: 0.7802 (mmt) REVERT: K 94 ARG cc_start: 0.5501 (mpt180) cc_final: 0.4643 (mmt180) REVERT: C 434 MET cc_start: 0.8257 (OUTLIER) cc_final: 0.7932 (tpp) REVERT: D 616 ASN cc_start: 0.9051 (p0) cc_final: 0.8783 (p0) REVERT: N 94 ARG cc_start: 0.6012 (mpt180) cc_final: 0.5603 (tpt170) REVERT: E 104 MET cc_start: 0.8073 (ttm) cc_final: 0.7812 (ttt) REVERT: E 475 MET cc_start: 0.8237 (mmp) cc_final: 0.7829 (mmm) REVERT: P 94 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.7599 (tpt170) REVERT: H 27 PHE cc_start: 0.5123 (t80) cc_final: 0.4795 (t80) REVERT: H 38 ARG cc_start: 0.7660 (ptt180) cc_final: 0.6943 (ptm160) REVERT: H 101 ASP cc_start: 0.8213 (t0) cc_final: 0.7621 (t0) outliers start: 31 outliers final: 17 residues processed: 218 average time/residue: 0.1559 time to fit residues: 52.4093 Evaluate side-chains 186 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 165 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain K residue 27 ASP Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain N residue 56 SER Chi-restraints excluded: chain P residue 27 ASP Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 94 ARG Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain L residue 13 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 5 optimal weight: 3.9990 chunk 218 optimal weight: 4.9990 chunk 137 optimal weight: 4.9990 chunk 231 optimal weight: 10.0000 chunk 172 optimal weight: 10.0000 chunk 171 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 chunk 246 optimal weight: 20.0000 chunk 62 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 chunk 183 optimal weight: 0.6980 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN D 653 GLN F 570 HIS L 37 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.071385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.051972 restraints weight = 64765.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.053577 restraints weight = 38768.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.054675 restraints weight = 28200.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.055394 restraints weight = 22958.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.055852 restraints weight = 20020.582| |-----------------------------------------------------------------------------| r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 22174 Z= 0.278 Angle : 0.745 16.957 30303 Z= 0.359 Chirality : 0.047 0.304 3630 Planarity : 0.004 0.048 3673 Dihedral : 6.872 57.686 4861 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.30 % Favored : 95.62 % Rotamer: Outliers : 1.83 % Allowed : 7.18 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % 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: 0.04 (0.16), residues: 2535 helix: 1.37 (0.27), residues: 390 sheet: 0.41 (0.18), residues: 770 loop : -0.56 (0.16), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 45 TYR 0.025 0.002 TYR A 484 PHE 0.019 0.002 PHE H 29 TRP 0.029 0.002 TRP L 35 HIS 0.007 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00645 (22033) covalent geometry : angle 0.71147 (29920) SS BOND : bond 0.00404 ( 40) SS BOND : angle 0.82754 ( 80) hydrogen bonds : bond 0.04950 ( 555) hydrogen bonds : angle 5.03405 ( 1455) link_ALPHA1-3 : bond 0.01011 ( 5) link_ALPHA1-3 : angle 1.81194 ( 15) link_ALPHA1-6 : bond 0.00753 ( 2) link_ALPHA1-6 : angle 1.37923 ( 6) link_BETA1-4 : bond 0.00397 ( 24) link_BETA1-4 : angle 2.14854 ( 72) link_BETA1-6 : bond 0.00689 ( 7) link_BETA1-6 : angle 2.10657 ( 21) link_NAG-ASN : bond 0.00704 ( 63) link_NAG-ASN : angle 2.43196 ( 189) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 171 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.9486 (t) cc_final: 0.9229 (m) REVERT: A 452 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.7976 (mt) REVERT: A 475 MET cc_start: 0.8603 (mmm) cc_final: 0.7898 (tmm) REVERT: K 27 ASP cc_start: 0.8905 (OUTLIER) cc_final: 0.8673 (t70) REVERT: K 94 ARG cc_start: 0.5895 (mpt180) cc_final: 0.4929 (mmt180) REVERT: D 616 ASN cc_start: 0.9094 (p0) cc_final: 0.8832 (p0) REVERT: N 94 ARG cc_start: 0.6243 (mpt180) cc_final: 0.4866 (mmt180) REVERT: E 95 MET cc_start: 0.8456 (ptm) cc_final: 0.8213 (ptp) REVERT: E 173 TYR cc_start: 0.7460 (p90) cc_final: 0.7043 (p90) REVERT: F 586 TYR cc_start: 0.9375 (t80) cc_final: 0.9102 (t80) REVERT: O 75 LYS cc_start: 0.8938 (mttm) cc_final: 0.8597 (mttp) REVERT: P 94 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.7745 (tpt170) REVERT: H 3 GLN cc_start: 0.7984 (tm-30) cc_final: 0.7490 (tm-30) REVERT: H 27 PHE cc_start: 0.5158 (t80) cc_final: 0.4796 (t80) REVERT: H 38 ARG cc_start: 0.7728 (ptt180) cc_final: 0.7379 (ptp-170) REVERT: H 75 LYS cc_start: 0.8106 (mmmt) cc_final: 0.7812 (mtmm) outliers start: 41 outliers final: 28 residues processed: 199 average time/residue: 0.1576 time to fit residues: 48.3080 Evaluate side-chains 183 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 152 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 26 THR Chi-restraints excluded: chain K residue 27 ASP Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain D residue 653 GLN Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain N residue 47 MET Chi-restraints excluded: chain N residue 56 SER Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 84 ASP Chi-restraints excluded: chain P residue 27 ASP Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 94 ARG Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 223 optimal weight: 5.9990 chunk 161 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 211 optimal weight: 0.8980 chunk 183 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 9 optimal weight: 8.9990 chunk 178 optimal weight: 6.9990 chunk 209 optimal weight: 9.9990 chunk 251 optimal weight: 20.0000 chunk 199 optimal weight: 0.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN A 302 ASN C 195 ASN D 653 GLN E 195 ASN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.071864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.052529 restraints weight = 64049.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.054138 restraints weight = 38346.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.055240 restraints weight = 27949.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.055957 restraints weight = 22660.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.056426 restraints weight = 19793.348| |-----------------------------------------------------------------------------| r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 22174 Z= 0.188 Angle : 0.656 16.341 30303 Z= 0.315 Chirality : 0.045 0.287 3630 Planarity : 0.004 0.046 3673 Dihedral : 6.439 57.559 4861 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.46 % Favored : 95.50 % Rotamer: Outliers : 1.92 % Allowed : 7.76 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % 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: 0.03 (0.17), residues: 2535 helix: 1.65 (0.28), residues: 380 sheet: 0.36 (0.18), residues: 775 loop : -0.63 (0.16), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 103 TYR 0.016 0.001 TYR B 586 PHE 0.015 0.002 PHE M 102 TRP 0.018 0.001 TRP E 479 HIS 0.005 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00429 (22033) covalent geometry : angle 0.62371 (29920) SS BOND : bond 0.00276 ( 40) SS BOND : angle 0.72358 ( 80) hydrogen bonds : bond 0.04420 ( 555) hydrogen bonds : angle 4.80239 ( 1455) link_ALPHA1-3 : bond 0.01034 ( 5) link_ALPHA1-3 : angle 1.65596 ( 15) link_ALPHA1-6 : bond 0.00866 ( 2) link_ALPHA1-6 : angle 1.35866 ( 6) link_BETA1-4 : bond 0.00354 ( 24) link_BETA1-4 : angle 1.89331 ( 72) link_BETA1-6 : bond 0.00638 ( 7) link_BETA1-6 : angle 2.05356 ( 21) link_NAG-ASN : bond 0.00480 ( 63) link_NAG-ASN : angle 2.26842 ( 189) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 162 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.9465 (t) cc_final: 0.9194 (m) REVERT: A 475 MET cc_start: 0.8557 (mmm) cc_final: 0.7948 (tmm) REVERT: B 653 GLN cc_start: 0.8886 (OUTLIER) cc_final: 0.8628 (tt0) REVERT: K 94 ARG cc_start: 0.5901 (mpt180) cc_final: 0.4805 (mmt180) REVERT: C 72 HIS cc_start: 0.7670 (OUTLIER) cc_final: 0.7416 (p90) REVERT: D 616 ASN cc_start: 0.9112 (p0) cc_final: 0.8893 (p0) REVERT: D 653 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.8278 (tt0) REVERT: N 94 ARG cc_start: 0.6052 (mpt180) cc_final: 0.4743 (mmt180) REVERT: F 586 TYR cc_start: 0.9326 (t80) cc_final: 0.9062 (t80) REVERT: P 94 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.7748 (tpt170) REVERT: H 3 GLN cc_start: 0.8103 (tm-30) cc_final: 0.7575 (tm-30) REVERT: H 27 PHE cc_start: 0.4910 (t80) cc_final: 0.4545 (t80) REVERT: H 38 ARG cc_start: 0.7689 (ptt180) cc_final: 0.7357 (ptp-170) REVERT: L 70 ASP cc_start: 0.7211 (p0) cc_final: 0.6900 (m-30) REVERT: L 77 ARG cc_start: 0.8114 (tmm-80) cc_final: 0.7842 (ttp80) outliers start: 43 outliers final: 25 residues processed: 195 average time/residue: 0.1592 time to fit residues: 48.0322 Evaluate side-chains 182 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain K residue 26 THR Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain D residue 653 GLN Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain N residue 47 MET Chi-restraints excluded: chain N residue 56 SER Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 84 ASP Chi-restraints excluded: chain P residue 27 ASP Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 94 ARG Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 236 optimal weight: 8.9990 chunk 174 optimal weight: 8.9990 chunk 187 optimal weight: 6.9990 chunk 193 optimal weight: 4.9990 chunk 209 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 110 optimal weight: 7.9990 chunk 149 optimal weight: 8.9990 chunk 196 optimal weight: 0.8980 chunk 238 optimal weight: 30.0000 chunk 11 optimal weight: 7.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN C 195 ASN P 39 HIS ** 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 = 0.3224 r_free = 0.3224 target = 0.069715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.050186 restraints weight = 65558.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.051830 restraints weight = 38788.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.052918 restraints weight = 27886.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.053616 restraints weight = 22592.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.054083 restraints weight = 19753.804| |-----------------------------------------------------------------------------| r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.4080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.063 22174 Z= 0.338 Angle : 0.777 14.726 30303 Z= 0.376 Chirality : 0.048 0.330 3630 Planarity : 0.005 0.045 3673 Dihedral : 6.733 55.147 4861 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.36 % Favored : 94.56 % Rotamer: Outliers : 2.01 % Allowed : 8.43 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % 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: -0.44 (0.16), residues: 2535 helix: 1.19 (0.27), residues: 378 sheet: 0.08 (0.18), residues: 760 loop : -0.91 (0.16), residues: 1397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG O 53 TYR 0.020 0.002 TYR A 484 PHE 0.015 0.002 PHE K 98 TRP 0.022 0.002 TRP E 479 HIS 0.008 0.002 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00785 (22033) covalent geometry : angle 0.74508 (29920) SS BOND : bond 0.00406 ( 40) SS BOND : angle 0.86998 ( 80) hydrogen bonds : bond 0.05148 ( 555) hydrogen bonds : angle 5.18554 ( 1455) link_ALPHA1-3 : bond 0.01019 ( 5) link_ALPHA1-3 : angle 1.88631 ( 15) link_ALPHA1-6 : bond 0.00868 ( 2) link_ALPHA1-6 : angle 1.41555 ( 6) link_BETA1-4 : bond 0.00416 ( 24) link_BETA1-4 : angle 1.95122 ( 72) link_BETA1-6 : bond 0.00659 ( 7) link_BETA1-6 : angle 2.04489 ( 21) link_NAG-ASN : bond 0.00650 ( 63) link_NAG-ASN : angle 2.52186 ( 189) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 153 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 452 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.7966 (mt) REVERT: A 475 MET cc_start: 0.8703 (mmm) cc_final: 0.8090 (tmm) REVERT: B 586 TYR cc_start: 0.9030 (t80) cc_final: 0.8752 (t80) REVERT: K 94 ARG cc_start: 0.6048 (mpt180) cc_final: 0.4839 (tpp-160) REVERT: C 72 HIS cc_start: 0.7949 (OUTLIER) cc_final: 0.7581 (p90) REVERT: C 195 ASN cc_start: 0.8571 (OUTLIER) cc_final: 0.8345 (t0) REVERT: D 616 ASN cc_start: 0.9183 (p0) cc_final: 0.8923 (p0) REVERT: M 52 ASN cc_start: 0.8331 (t0) cc_final: 0.7974 (p0) REVERT: N 94 ARG cc_start: 0.6379 (mpt180) cc_final: 0.4697 (mmt180) REVERT: E 104 MET cc_start: 0.8479 (tpp) cc_final: 0.8169 (tpp) REVERT: E 173 TYR cc_start: 0.7605 (p90) cc_final: 0.7127 (p90) REVERT: F 657 GLU cc_start: 0.8509 (tp30) cc_final: 0.7922 (tp30) REVERT: O 75 LYS cc_start: 0.9048 (mttm) cc_final: 0.8730 (mttp) REVERT: H 3 GLN cc_start: 0.8252 (tm-30) cc_final: 0.7726 (tm-30) REVERT: H 20 LEU cc_start: 0.6056 (mp) cc_final: 0.5753 (mm) REVERT: H 38 ARG cc_start: 0.7793 (ptt180) cc_final: 0.7274 (ptp-170) REVERT: H 75 LYS cc_start: 0.7960 (mmmt) cc_final: 0.7710 (ptpp) REVERT: L 70 ASP cc_start: 0.7426 (p0) cc_final: 0.6928 (m-30) REVERT: L 77 ARG cc_start: 0.8217 (tmm-80) cc_final: 0.7819 (ttp80) outliers start: 45 outliers final: 35 residues processed: 184 average time/residue: 0.1510 time to fit residues: 43.3905 Evaluate side-chains 183 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 145 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain J residue 27 TYR Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 26 THR Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain D residue 625 ASN Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain N residue 47 MET Chi-restraints excluded: chain N residue 56 SER Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 84 ASP Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain P residue 27 ASP Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 102 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 chunk 188 optimal weight: 0.0980 chunk 31 optimal weight: 3.9990 chunk 208 optimal weight: 7.9990 chunk 157 optimal weight: 8.9990 chunk 192 optimal weight: 1.9990 chunk 235 optimal weight: 4.9990 chunk 230 optimal weight: 10.0000 chunk 53 optimal weight: 0.8980 chunk 211 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 ASN D 653 GLN ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.071946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.052665 restraints weight = 64404.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.054297 restraints weight = 38313.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.055422 restraints weight = 27732.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.056143 restraints weight = 22388.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.056618 restraints weight = 19536.696| |-----------------------------------------------------------------------------| r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 22174 Z= 0.127 Angle : 0.624 13.930 30303 Z= 0.301 Chirality : 0.044 0.322 3630 Planarity : 0.004 0.044 3673 Dihedral : 6.103 54.537 4857 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.50 % Favored : 95.42 % Rotamer: Outliers : 1.38 % Allowed : 9.55 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % 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: -0.17 (0.17), residues: 2535 helix: 1.76 (0.28), residues: 374 sheet: 0.17 (0.18), residues: 766 loop : -0.78 (0.16), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 500 TYR 0.012 0.001 TYR O 100G PHE 0.020 0.001 PHE H 29 TRP 0.016 0.001 TRP E 479 HIS 0.004 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00281 (22033) covalent geometry : angle 0.59240 (29920) SS BOND : bond 0.00400 ( 40) SS BOND : angle 1.04771 ( 80) hydrogen bonds : bond 0.04070 ( 555) hydrogen bonds : angle 4.71437 ( 1455) link_ALPHA1-3 : bond 0.01049 ( 5) link_ALPHA1-3 : angle 1.62779 ( 15) link_ALPHA1-6 : bond 0.01002 ( 2) link_ALPHA1-6 : angle 1.27310 ( 6) link_BETA1-4 : bond 0.00353 ( 24) link_BETA1-4 : angle 1.65034 ( 72) link_BETA1-6 : bond 0.00491 ( 7) link_BETA1-6 : angle 1.99276 ( 21) link_NAG-ASN : bond 0.00515 ( 63) link_NAG-ASN : angle 2.17509 ( 189) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 158 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.8488 (mmm) cc_final: 0.8092 (tmm) REVERT: B 586 TYR cc_start: 0.8950 (t80) cc_final: 0.8618 (t80) REVERT: B 653 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8652 (tt0) REVERT: K 27 ASP cc_start: 0.8720 (t70) cc_final: 0.8508 (t0) REVERT: K 94 ARG cc_start: 0.5960 (mpt180) cc_final: 0.5121 (tpt170) REVERT: C 72 HIS cc_start: 0.7816 (OUTLIER) cc_final: 0.7455 (p90) REVERT: C 195 ASN cc_start: 0.8438 (OUTLIER) cc_final: 0.8229 (t0) REVERT: D 616 ASN cc_start: 0.9114 (p0) cc_final: 0.8865 (p0) REVERT: D 653 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.8280 (tp40) REVERT: N 94 ARG cc_start: 0.6160 (mpt180) cc_final: 0.4606 (mmt180) REVERT: E 104 MET cc_start: 0.8358 (tpp) cc_final: 0.8034 (tpp) REVERT: E 138 ILE cc_start: 0.8511 (mp) cc_final: 0.8173 (tt) REVERT: F 586 TYR cc_start: 0.9298 (t80) cc_final: 0.9041 (t80) REVERT: O 43 LYS cc_start: 0.8465 (mmtm) cc_final: 0.8161 (mmmt) REVERT: O 75 LYS cc_start: 0.8919 (mttm) cc_final: 0.8588 (mttp) REVERT: H 3 GLN cc_start: 0.8292 (tm-30) cc_final: 0.7843 (tm-30) REVERT: H 27 PHE cc_start: 0.5014 (t80) cc_final: 0.4812 (t80) REVERT: H 38 ARG cc_start: 0.7680 (ptt180) cc_final: 0.7257 (ptp-170) REVERT: L 70 ASP cc_start: 0.7327 (p0) cc_final: 0.6851 (m-30) REVERT: L 77 ARG cc_start: 0.8211 (tmm-80) cc_final: 0.7464 (ttp80) outliers start: 31 outliers final: 21 residues processed: 181 average time/residue: 0.1417 time to fit residues: 40.9416 Evaluate side-chains 174 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 149 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain D residue 625 ASN Chi-restraints excluded: chain D residue 653 GLN Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain N residue 47 MET Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain P residue 27 ASP Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 173 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 227 optimal weight: 8.9990 chunk 39 optimal weight: 0.8980 chunk 126 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 189 optimal weight: 2.9990 chunk 205 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 192 optimal weight: 7.9990 chunk 142 optimal weight: 10.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN C 195 ASN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.073573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.054501 restraints weight = 63884.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.056313 restraints weight = 37037.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.057523 restraints weight = 26267.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.058224 restraints weight = 20979.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.058751 restraints weight = 18328.616| |-----------------------------------------------------------------------------| r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 22174 Z= 0.134 Angle : 0.610 13.122 30303 Z= 0.294 Chirality : 0.044 0.326 3630 Planarity : 0.004 0.045 3673 Dihedral : 5.847 54.384 4857 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.50 % Favored : 95.42 % Rotamer: Outliers : 1.20 % Allowed : 9.91 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.17), residues: 2535 helix: 1.92 (0.28), residues: 371 sheet: 0.29 (0.19), residues: 755 loop : -0.82 (0.16), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 103 TYR 0.019 0.001 TYR L 49 PHE 0.029 0.001 PHE H 29 TRP 0.014 0.001 TRP E 479 HIS 0.004 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00305 (22033) covalent geometry : angle 0.57922 (29920) SS BOND : bond 0.00351 ( 40) SS BOND : angle 0.92609 ( 80) hydrogen bonds : bond 0.03939 ( 555) hydrogen bonds : angle 4.62025 ( 1455) link_ALPHA1-3 : bond 0.01002 ( 5) link_ALPHA1-3 : angle 1.57325 ( 15) link_ALPHA1-6 : bond 0.00987 ( 2) link_ALPHA1-6 : angle 1.26769 ( 6) link_BETA1-4 : bond 0.00343 ( 24) link_BETA1-4 : angle 1.61957 ( 72) link_BETA1-6 : bond 0.00506 ( 7) link_BETA1-6 : angle 1.90324 ( 21) link_NAG-ASN : bond 0.00464 ( 63) link_NAG-ASN : angle 2.12526 ( 189) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 154 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.8517 (mmm) cc_final: 0.8087 (tmm) REVERT: B 586 TYR cc_start: 0.8941 (t80) cc_final: 0.8615 (t80) REVERT: K 27 ASP cc_start: 0.8715 (t70) cc_final: 0.8479 (t0) REVERT: K 94 ARG cc_start: 0.5920 (mpt180) cc_final: 0.5049 (tpt170) REVERT: C 72 HIS cc_start: 0.7765 (OUTLIER) cc_final: 0.7362 (p90) REVERT: N 94 ARG cc_start: 0.6168 (mpt180) cc_final: 0.4611 (mmt180) REVERT: E 104 MET cc_start: 0.8375 (tpp) cc_final: 0.8038 (tpp) REVERT: E 138 ILE cc_start: 0.8502 (mp) cc_final: 0.8183 (tt) REVERT: F 586 TYR cc_start: 0.9294 (t80) cc_final: 0.9048 (t80) REVERT: O 43 LYS cc_start: 0.8488 (mmtm) cc_final: 0.8186 (mmmt) REVERT: O 75 LYS cc_start: 0.8919 (mttm) cc_final: 0.8611 (mttp) REVERT: H 3 GLN cc_start: 0.8351 (tm-30) cc_final: 0.7900 (tm-30) REVERT: H 20 LEU cc_start: 0.6183 (mp) cc_final: 0.5377 (mt) REVERT: H 27 PHE cc_start: 0.5058 (t80) cc_final: 0.4845 (t80) REVERT: H 38 ARG cc_start: 0.7741 (ptt180) cc_final: 0.7290 (ptp-170) REVERT: L 70 ASP cc_start: 0.7275 (p0) cc_final: 0.6808 (m-30) REVERT: L 77 ARG cc_start: 0.8253 (tmm-80) cc_final: 0.7836 (ttp80) outliers start: 27 outliers final: 22 residues processed: 174 average time/residue: 0.1489 time to fit residues: 41.1333 Evaluate side-chains 173 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 26 THR Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain N residue 47 MET Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain P residue 27 ASP Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 210 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 198 optimal weight: 2.9990 chunk 146 optimal weight: 6.9990 chunk 236 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 118 optimal weight: 5.9990 chunk 213 optimal weight: 0.8980 chunk 175 optimal weight: 2.9990 chunk 132 optimal weight: 9.9990 chunk 83 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN D 653 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.073023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.054065 restraints weight = 64148.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.055814 restraints weight = 37510.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.056982 restraints weight = 26791.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.057736 restraints weight = 21509.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.058168 restraints weight = 18702.270| |-----------------------------------------------------------------------------| r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.4344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 22174 Z= 0.172 Angle : 0.624 11.786 30303 Z= 0.301 Chirality : 0.044 0.327 3630 Planarity : 0.004 0.046 3673 Dihedral : 5.824 54.489 4857 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.50 % Favored : 95.42 % Rotamer: Outliers : 1.29 % Allowed : 9.86 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % 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: -0.17 (0.17), residues: 2535 helix: 1.88 (0.28), residues: 372 sheet: 0.28 (0.19), residues: 738 loop : -0.87 (0.16), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 103 TYR 0.017 0.001 TYR A 484 PHE 0.027 0.001 PHE H 29 TRP 0.015 0.001 TRP E 479 HIS 0.005 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00398 (22033) covalent geometry : angle 0.59302 (29920) SS BOND : bond 0.00374 ( 40) SS BOND : angle 0.91118 ( 80) hydrogen bonds : bond 0.04048 ( 555) hydrogen bonds : angle 4.65969 ( 1455) link_ALPHA1-3 : bond 0.00950 ( 5) link_ALPHA1-3 : angle 1.60837 ( 15) link_ALPHA1-6 : bond 0.00965 ( 2) link_ALPHA1-6 : angle 1.29191 ( 6) link_BETA1-4 : bond 0.00326 ( 24) link_BETA1-4 : angle 1.60099 ( 72) link_BETA1-6 : bond 0.00481 ( 7) link_BETA1-6 : angle 1.88672 ( 21) link_NAG-ASN : bond 0.00453 ( 63) link_NAG-ASN : angle 2.17254 ( 189) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.8547 (mmm) cc_final: 0.8149 (tmm) REVERT: B 586 TYR cc_start: 0.8974 (t80) cc_final: 0.8649 (t80) REVERT: K 27 ASP cc_start: 0.8748 (t70) cc_final: 0.8528 (t0) REVERT: K 94 ARG cc_start: 0.5889 (mpt180) cc_final: 0.4923 (tpp-160) REVERT: C 72 HIS cc_start: 0.7928 (OUTLIER) cc_final: 0.7481 (p90) REVERT: C 452 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8523 (mt) REVERT: D 653 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.8253 (tp40) REVERT: N 94 ARG cc_start: 0.6259 (mpt180) cc_final: 0.4653 (mmt180) REVERT: E 104 MET cc_start: 0.8442 (tpp) cc_final: 0.8090 (tpp) REVERT: E 138 ILE cc_start: 0.8524 (mp) cc_final: 0.8222 (tt) REVERT: F 528 MET cc_start: 0.8673 (mtt) cc_final: 0.8428 (mtt) REVERT: F 586 TYR cc_start: 0.9312 (t80) cc_final: 0.9066 (t80) REVERT: O 75 LYS cc_start: 0.8917 (mttm) cc_final: 0.8621 (mttp) REVERT: H 3 GLN cc_start: 0.8367 (tm-30) cc_final: 0.8004 (tm-30) REVERT: H 38 ARG cc_start: 0.7860 (ptt180) cc_final: 0.7372 (ptp-170) REVERT: L 70 ASP cc_start: 0.7238 (p0) cc_final: 0.6849 (m-30) REVERT: L 77 ARG cc_start: 0.8277 (tmm-80) cc_final: 0.7941 (tmm-80) outliers start: 29 outliers final: 26 residues processed: 175 average time/residue: 0.1465 time to fit residues: 40.8256 Evaluate side-chains 177 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 148 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 26 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain D residue 625 ASN Chi-restraints excluded: chain D residue 653 GLN Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain N residue 47 MET Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain P residue 27 ASP Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 180 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 chunk 213 optimal weight: 3.9990 chunk 235 optimal weight: 6.9990 chunk 231 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 154 optimal weight: 0.6980 chunk 13 optimal weight: 10.0000 chunk 101 optimal weight: 2.9990 chunk 126 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3301 r_free = 0.3301 target = 0.073009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.053972 restraints weight = 64115.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.055769 restraints weight = 37281.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.056953 restraints weight = 26438.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.057702 restraints weight = 21207.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.058214 restraints weight = 18365.609| |-----------------------------------------------------------------------------| r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.4402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 22174 Z= 0.171 Angle : 0.622 11.433 30303 Z= 0.300 Chirality : 0.044 0.322 3630 Planarity : 0.004 0.045 3673 Dihedral : 5.799 54.568 4857 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.50 % Favored : 95.42 % Rotamer: Outliers : 1.29 % Allowed : 10.00 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % 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: -0.17 (0.17), residues: 2535 helix: 1.87 (0.28), residues: 372 sheet: 0.31 (0.19), residues: 737 loop : -0.90 (0.16), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 103 TYR 0.017 0.001 TYR A 484 PHE 0.026 0.001 PHE H 29 TRP 0.015 0.001 TRP E 479 HIS 0.005 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00397 (22033) covalent geometry : angle 0.59207 (29920) SS BOND : bond 0.00369 ( 40) SS BOND : angle 0.90386 ( 80) hydrogen bonds : bond 0.04018 ( 555) hydrogen bonds : angle 4.66824 ( 1455) link_ALPHA1-3 : bond 0.00916 ( 5) link_ALPHA1-3 : angle 1.60237 ( 15) link_ALPHA1-6 : bond 0.00945 ( 2) link_ALPHA1-6 : angle 1.26369 ( 6) link_BETA1-4 : bond 0.00320 ( 24) link_BETA1-4 : angle 1.57926 ( 72) link_BETA1-6 : bond 0.00466 ( 7) link_BETA1-6 : angle 1.87704 ( 21) link_NAG-ASN : bond 0.00442 ( 63) link_NAG-ASN : angle 2.15912 ( 189) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5070 Ramachandran restraints generated. 2535 Oldfield, 0 Emsley, 2535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 149 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 586 TYR cc_start: 0.8972 (t80) cc_final: 0.8650 (t80) REVERT: B 653 GLN cc_start: 0.8901 (OUTLIER) cc_final: 0.8692 (tt0) REVERT: K 27 ASP cc_start: 0.8747 (t70) cc_final: 0.8523 (t0) REVERT: K 94 ARG cc_start: 0.5890 (mpt180) cc_final: 0.4909 (tpp-160) REVERT: C 72 HIS cc_start: 0.8005 (OUTLIER) cc_final: 0.7499 (p90) REVERT: C 452 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8495 (mt) REVERT: N 94 ARG cc_start: 0.6284 (mpt180) cc_final: 0.4696 (mmt180) REVERT: E 104 MET cc_start: 0.8451 (tpp) cc_final: 0.8097 (tpp) REVERT: E 138 ILE cc_start: 0.8520 (mp) cc_final: 0.8232 (tt) REVERT: F 586 TYR cc_start: 0.9313 (t80) cc_final: 0.9067 (t80) REVERT: F 657 GLU cc_start: 0.8422 (tp30) cc_final: 0.7898 (tp30) REVERT: O 75 LYS cc_start: 0.8926 (mttm) cc_final: 0.8624 (mttp) REVERT: H 3 GLN cc_start: 0.8413 (tm-30) cc_final: 0.8096 (tm-30) REVERT: H 38 ARG cc_start: 0.7893 (ptt180) cc_final: 0.7402 (ptp-170) REVERT: L 70 ASP cc_start: 0.7444 (p0) cc_final: 0.6997 (m-30) REVERT: L 77 ARG cc_start: 0.8228 (tmm-80) cc_final: 0.7882 (tmm-80) REVERT: L 103 LYS cc_start: 0.8645 (tppt) cc_final: 0.7896 (ttpt) outliers start: 29 outliers final: 25 residues processed: 171 average time/residue: 0.1447 time to fit residues: 39.2663 Evaluate side-chains 174 residues out of total 2242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 26 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain N residue 47 MET Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain P residue 27 ASP Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 95 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 149 optimal weight: 3.9990 chunk 197 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 201 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 57 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 1 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN D 653 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.074382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.055761 restraints weight = 63835.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.057516 restraints weight = 37631.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.058682 restraints weight = 26885.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.059356 restraints weight = 21599.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.059911 restraints weight = 18860.876| |-----------------------------------------------------------------------------| r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.4518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22174 Z= 0.112 Angle : 0.582 12.367 30303 Z= 0.280 Chirality : 0.043 0.293 3630 Planarity : 0.004 0.043 3673 Dihedral : 5.453 54.449 4857 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.46 % Favored : 95.46 % Rotamer: Outliers : 1.25 % Allowed : 9.95 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % 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: 2535 helix: 2.01 (0.28), residues: 377 sheet: 0.47 (0.19), residues: 784 loop : -0.87 (0.17), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 500 TYR 0.012 0.001 TYR O 100G PHE 0.022 0.001 PHE H 29 TRP 0.012 0.001 TRP E 479 HIS 0.004 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00252 (22033) covalent geometry : angle 0.55387 (29920) SS BOND : bond 0.00322 ( 40) SS BOND : angle 0.81777 ( 80) hydrogen bonds : bond 0.03464 ( 555) hydrogen bonds : angle 4.40738 ( 1455) link_ALPHA1-3 : bond 0.00893 ( 5) link_ALPHA1-3 : angle 1.52202 ( 15) link_ALPHA1-6 : bond 0.01031 ( 2) link_ALPHA1-6 : angle 1.22336 ( 6) link_BETA1-4 : bond 0.00364 ( 24) link_BETA1-4 : angle 1.43550 ( 72) link_BETA1-6 : bond 0.00407 ( 7) link_BETA1-6 : angle 1.74213 ( 21) link_NAG-ASN : bond 0.00451 ( 63) link_NAG-ASN : angle 2.00637 ( 189) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3155.05 seconds wall clock time: 55 minutes 31.83 seconds (3331.83 seconds total)