Starting phenix.real_space_refine on Sun May 18 14:43:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9axi_43967/05_2025/9axi_43967.cif Found real_map, /net/cci-nas-00/data/ceres_data/9axi_43967/05_2025/9axi_43967.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9axi_43967/05_2025/9axi_43967.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9axi_43967/05_2025/9axi_43967.map" model { file = "/net/cci-nas-00/data/ceres_data/9axi_43967/05_2025/9axi_43967.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9axi_43967/05_2025/9axi_43967.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 102 5.16 5 C 10599 2.51 5 N 2920 2.21 5 O 3410 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 17031 Number of models: 1 Model: "" Number of chains: 37 Chain: "M" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1075 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 1, 'TRANS': 134} Chain breaks: 1 Chain: "D" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1043 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 1, 'TRANS': 128} Chain breaks: 1 Chain: "I" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1067 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 1, 'TRANS': 132} Chain breaks: 1 Chain: "F" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 550 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'TRANS': 109} Unresolved non-hydrogen bonds: 220 Unresolved non-hydrogen angles: 330 Unresolved non-hydrogen dihedrals: 110 Planarities with less than four sites: {'UNK:plan-1': 110} Unresolved non-hydrogen planarities: 110 Chain: "H" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 595 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 119} Link IDs: {'TRANS': 118} Unresolved non-hydrogen bonds: 238 Unresolved non-hydrogen angles: 357 Unresolved non-hydrogen dihedrals: 119 Planarities with less than four sites: {'UNK:plan-1': 119} Unresolved non-hydrogen planarities: 119 Chain: "A" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 610 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 122} Link IDs: {'TRANS': 121} Unresolved non-hydrogen bonds: 244 Unresolved non-hydrogen angles: 366 Unresolved non-hydrogen dihedrals: 122 Planarities with less than four sites: {'UNK:plan-1': 122} Unresolved non-hydrogen planarities: 122 Chain: "B" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 545 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 109} Link IDs: {'TRANS': 108} Unresolved non-hydrogen bonds: 218 Unresolved non-hydrogen angles: 327 Unresolved non-hydrogen dihedrals: 109 Planarities with less than four sites: {'UNK:plan-1': 109} Unresolved non-hydrogen planarities: 109 Chain: "K" Number of atoms: 3496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3496 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 23, 'TRANS': 415} Chain breaks: 3 Chain: "L" Number of atoms: 3425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3425 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 23, 'TRANS': 405} Chain breaks: 4 Chain: "J" Number of atoms: 3476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3476 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 23, 'TRANS': 412} Chain breaks: 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: "E" 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 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: "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: 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} 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: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "K" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "L" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 109 Unusual residues: {'MAN': 1, 'NAG': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "J" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 10.69, per 1000 atoms: 0.63 Number of scatterers: 17031 At special positions: 0 Unit cell: (139.461, 126.637, 147.476, 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 102 16.00 O 3410 8.00 N 2920 7.00 C 10599 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=28, symmetry=0 Simple disulfide: pdb=" SG CYS M 563 " - pdb=" SG CYS K 74 " distance=2.03 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 73 " distance=2.02 Simple disulfide: pdb=" SG CYS K 119 " - pdb=" SG CYS K 209 " distance=2.03 Simple disulfide: pdb=" SG CYS K 126 " - pdb=" SG CYS K 200 " distance=2.03 Simple disulfide: pdb=" SG CYS K 131 " - pdb=" SG CYS K 157 " distance=2.03 Simple disulfide: pdb=" SG CYS K 222 " - pdb=" SG CYS K 251 " distance=2.03 Simple disulfide: pdb=" SG CYS K 232 " - pdb=" SG CYS K 243 " distance=2.03 Simple disulfide: pdb=" SG CYS K 300 " - pdb=" SG CYS K 334 " distance=2.03 Simple disulfide: pdb=" SG CYS K 380 " - pdb=" SG CYS K 447 " distance=2.04 Simple disulfide: pdb=" SG CYS K 387 " - pdb=" SG CYS K 420 " distance=2.03 Simple disulfide: pdb=" SG CYS L 54 " - pdb=" SG CYS L 73 " distance=2.03 Simple disulfide: pdb=" SG CYS L 119 " - pdb=" SG CYS L 209 " distance=2.04 Simple disulfide: pdb=" SG CYS L 126 " - pdb=" SG CYS L 200 " distance=2.03 Simple disulfide: pdb=" SG CYS L 131 " - pdb=" SG CYS L 157 " distance=2.03 Simple disulfide: pdb=" SG CYS L 222 " - pdb=" SG CYS L 251 " distance=2.03 Simple disulfide: pdb=" SG CYS L 232 " - pdb=" SG CYS L 243 " distance=2.03 Simple disulfide: pdb=" SG CYS L 300 " - pdb=" SG CYS L 334 " distance=2.04 Simple disulfide: pdb=" SG CYS L 380 " - pdb=" SG CYS L 447 " distance=2.04 Simple disulfide: pdb=" SG CYS L 387 " - pdb=" SG CYS L 420 " distance=2.03 Simple disulfide: pdb=" SG CYS J 54 " - pdb=" SG CYS J 73 " distance=2.03 Simple disulfide: pdb=" SG CYS J 119 " - pdb=" SG CYS J 209 " distance=2.03 Simple disulfide: pdb=" SG CYS J 126 " - pdb=" SG CYS J 200 " distance=2.03 Simple disulfide: pdb=" SG CYS J 131 " - pdb=" SG CYS J 157 " distance=2.03 Simple disulfide: pdb=" SG CYS J 222 " - pdb=" SG CYS J 251 " distance=2.03 Simple disulfide: pdb=" SG CYS J 232 " - pdb=" SG CYS J 243 " distance=2.04 Simple disulfide: pdb=" SG CYS J 300 " - pdb=" SG CYS J 334 " distance=2.03 Simple disulfide: pdb=" SG CYS J 380 " - pdb=" SG CYS J 447 " distance=2.04 Simple disulfide: pdb=" SG CYS J 387 " - pdb=" SG CYS J 420 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA G 3 " - " MAN G 4 " " BMA W 3 " - " MAN W 4 " " BMA b 3 " - " MAN b 4 " ALPHA1-6 " BMA G 3 " - " MAN G 5 " " BMA b 3 " - " MAN b 5 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG E 1 " - " NAG E 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " BETA1-6 " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG C 1 " - " ASN K 201 " " NAG D 701 " - " ASN D 612 " " NAG E 1 " - " ASN K 245 " " NAG G 1 " - " ASN K 266 " " NAG I 701 " - " ASN I 613 " " NAG I 702 " - " ASN I 627 " " NAG I 703 " - " ASN I 618 " " NAG J 601 " - " ASN J 234 " " NAG J 602 " - " ASN J 238 " " NAG J 603 " - " ASN J 280 " " NAG J 604 " - " ASN J 305 " " NAG J 605 " - " ASN J 394 " " NAG J 606 " - " ASN J 444 " " NAG J 607 " - " ASN J 450 " " NAG J 608 " - " ASN J 160 " " NAG J 609 " - " ASN J 362 " " NAG K 601 " - " ASN K 156 " " NAG K 602 " - " ASN K 160 " " NAG K 603 " - " ASN K 234 " " NAG K 604 " - " ASN K 238 " " NAG K 605 " - " ASN K 280 " " NAG K 606 " - " ASN K 305 " " NAG K 607 " - " ASN K 444 " " NAG K 608 " - " ASN K 362 " " NAG K 609 " - " ASN K 88 " " NAG L 601 " - " ASN L 160 " " NAG L 602 " - " ASN L 280 " " NAG L 603 " - " ASN L 394 " " NAG L 604 " - " ASN L 444 " " NAG L 605 " - " ASN L 450 " " NAG L 606 " - " ASN L 305 " " NAG L 608 " - " ASN L 362 " " NAG M 701 " - " ASN M 627 " " NAG M 702 " - " ASN M 613 " " NAG M 703 " - " ASN M 618 " " NAG M 704 " - " ASN M 639 " " NAG N 1 " - " ASN K 293 " " NAG O 1 " - " ASN K 388 " " NAG P 1 " - " ASN K 394 " " NAG Q 1 " - " ASN K 450 " " NAG R 1 " - " ASN L 156 " " NAG S 1 " - " ASN L 201 " " NAG T 1 " - " ASN L 234 " " NAG U 1 " - " ASN L 238 " " NAG V 1 " - " ASN L 245 " " NAG W 1 " - " ASN L 266 " " NAG X 1 " - " ASN L 293 " " NAG Y 1 " - " ASN L 388 " " NAG Z 1 " - " ASN J 201 " " NAG a 1 " - " ASN J 245 " " NAG b 1 " - " ASN J 266 " " NAG c 1 " - " ASN J 293 " " NAG d 1 " - " ASN J 388 " " NAG e 1 " - " ASN J 156 " Time building additional restraints: 4.84 Conformation dependent library (CDL) restraints added in 1.6 seconds 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4112 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 30 sheets defined 31.3% alpha, 28.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.87 Creating SS restraints... Processing helix chain 'M' and resid 521 through 525 Processing helix chain 'M' and resid 531 through 549 removed outlier: 3.643A pdb=" N VAL M 541 " --> pdb=" O ILE M 537 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ARG M 544 " --> pdb=" O THR M 540 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N GLN M 545 " --> pdb=" O VAL M 541 " (cutoff:3.500A) Processing helix chain 'M' and resid 563 through 567 Processing helix chain 'M' and resid 572 through 598 Processing helix chain 'M' and resid 620 through 626 Processing helix chain 'M' and resid 629 through 637 Processing helix chain 'M' and resid 640 through 662 Processing helix chain 'D' and resid 521 through 528 Processing helix chain 'D' and resid 532 through 548 removed outlier: 3.795A pdb=" N VAL D 541 " --> pdb=" O ILE D 537 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ARG D 544 " --> pdb=" O THR D 540 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLN D 545 " --> pdb=" O VAL D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 564 through 569 Processing helix chain 'D' and resid 571 through 597 Processing helix chain 'D' and resid 619 through 624 Processing helix chain 'D' and resid 628 through 636 Processing helix chain 'D' and resid 639 through 662 removed outlier: 3.581A pdb=" N LEU D 662 " --> pdb=" O GLU D 658 " (cutoff:3.500A) Processing helix chain 'I' and resid 521 through 525 Processing helix chain 'I' and resid 526 through 530 removed outlier: 3.871A pdb=" N GLY I 529 " --> pdb=" O GLY I 526 " (cutoff:3.500A) Processing helix chain 'I' and resid 531 through 537 Processing helix chain 'I' and resid 542 through 548 Processing helix chain 'I' and resid 563 through 568 removed outlier: 3.538A pdb=" N LEU I 567 " --> pdb=" O CYS I 563 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU I 568 " --> pdb=" O GLN I 564 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 563 through 568' Processing helix chain 'I' and resid 572 through 598 removed outlier: 3.515A pdb=" N LEU I 578 " --> pdb=" O GLY I 574 " (cutoff:3.500A) Processing helix chain 'I' and resid 620 through 628 removed outlier: 3.638A pdb=" N MET I 628 " --> pdb=" O ILE I 624 " (cutoff:3.500A) Processing helix chain 'I' and resid 629 through 637 Processing helix chain 'I' and resid 640 through 661 Processing helix chain 'H' and resid 27 through 31 removed outlier: 3.739A pdb=" N UNK H 31 " --> pdb=" O UNK H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 89 Processing helix chain 'A' and resid 62 through 65 Processing helix chain 'B' and resid 28 through 32 Processing helix chain 'B' and resid 79 through 83 Processing helix chain 'B' and resid 93 through 96 removed outlier: 3.562A pdb=" N UNK B 96 " --> pdb=" O UNK B 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 93 through 96' Processing helix chain 'K' and resid 67 through 72 Processing helix chain 'K' and resid 98 through 116 removed outlier: 3.851A pdb=" N GLU K 102 " --> pdb=" O ASN K 98 " (cutoff:3.500A) Processing helix chain 'K' and resid 122 through 126 Processing helix chain 'K' and resid 338 through 356 Processing helix chain 'K' and resid 370 through 375 Processing helix chain 'K' and resid 389 through 392 Processing helix chain 'K' and resid 429 through 431 No H-bonds generated for 'chain 'K' and resid 429 through 431' Processing helix chain 'K' and resid 463 through 465 No H-bonds generated for 'chain 'K' and resid 463 through 465' Processing helix chain 'K' and resid 477 through 486 removed outlier: 3.849A pdb=" N GLU K 484 " --> pdb=" O ASN K 480 " (cutoff:3.500A) Processing helix chain 'L' and resid 67 through 72 Processing helix chain 'L' and resid 98 through 117 removed outlier: 3.750A pdb=" N GLU L 102 " --> pdb=" O ASN L 98 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 126 Processing helix chain 'L' and resid 338 through 356 Processing helix chain 'L' and resid 370 through 375 Processing helix chain 'L' and resid 427 through 431 removed outlier: 4.478A pdb=" N GLN L 430 " --> pdb=" O ASN L 427 " (cutoff:3.500A) Processing helix chain 'L' and resid 477 through 486 removed outlier: 3.812A pdb=" N GLU L 484 " --> pdb=" O ASN L 480 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 117 removed outlier: 3.760A pdb=" N GLU J 102 " --> pdb=" O ASN J 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 126 Processing helix chain 'J' and resid 338 through 356 removed outlier: 3.667A pdb=" N HIS J 355 " --> pdb=" O LYS J 351 " (cutoff:3.500A) Processing helix chain 'J' and resid 370 through 375 Processing helix chain 'J' and resid 389 through 392 Processing helix chain 'J' and resid 427 through 431 removed outlier: 4.129A pdb=" N GLN J 430 " --> pdb=" O ASN J 427 " (cutoff:3.500A) Processing helix chain 'J' and resid 476 through 480 removed outlier: 3.687A pdb=" N ASN J 479 " --> pdb=" O ASP J 476 " (cutoff:3.500A) Processing helix chain 'J' and resid 481 through 486 Processing sheet with id=AA1, first strand: chain 'M' and resid 605 through 611 removed outlier: 8.057A pdb=" N CYS M 606 " --> pdb=" O TYR K 40 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N TYR K 40 " --> pdb=" O CYS M 606 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N THR M 608 " --> pdb=" O VAL K 38 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N VAL K 38 " --> pdb=" O THR M 608 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N VAL M 610 " --> pdb=" O VAL K 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 604 through 610 removed outlier: 5.002A pdb=" N VAL L 36 " --> pdb=" O THR D 607 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 605 through 611 removed outlier: 5.082A pdb=" N VAL J 36 " --> pdb=" O THR I 608 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 11 through 12 removed outlier: 6.532A pdb=" N UNK F 11 " --> pdb=" O UNK F 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'F' and resid 17 through 20 Processing sheet with id=AA6, first strand: chain 'F' and resid 43 through 46 removed outlier: 6.498A pdb=" N UNK F 33 " --> pdb=" O UNK F 45 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 4 through 6 removed outlier: 6.669A pdb=" N UNK H 76 " --> pdb=" O UNK H 72 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 32 through 38 removed outlier: 5.781A pdb=" N UNK H 37 " --> pdb=" O UNK H 46 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N UNK H 46 " --> pdb=" O UNK H 37 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 44 through 50 current: chain 'H' and resid 110 through 111 Processing sheet with id=AA9, first strand: chain 'A' and resid 4 through 8 removed outlier: 6.845A pdb=" N UNK A 77 " --> pdb=" O UNK A 73 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 58 through 60 removed outlier: 6.842A pdb=" N UNK A 36 " --> pdb=" O UNK A 48 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N UNK A 50 " --> pdb=" O UNK A 34 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N UNK A 34 " --> pdb=" O UNK A 50 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N UNK A 94 " --> pdb=" O UNK A 113 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N UNK A 113 " --> pdb=" O UNK A 94 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N UNK A 96 " --> pdb=" O UNK A 111 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N UNK A 111 " --> pdb=" O UNK A 96 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N UNK A 98 " --> pdb=" O UNK A 109 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 18 through 23 removed outlier: 4.232A pdb=" N UNK B 18 " --> pdb=" O UNK B 75 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 46 through 49 removed outlier: 6.568A pdb=" N UNK B 36 " --> pdb=" O UNK B 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 45 through 47 removed outlier: 4.639A pdb=" N VAL K 246 " --> pdb=" O LEU K 86 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 75 through 76 removed outlier: 4.221A pdb=" N VAL K 75 " --> pdb=" O CYS K 54 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 91 through 94 Processing sheet with id=AB7, first strand: chain 'K' and resid 169 through 177 Processing sheet with id=AB8, first strand: chain 'K' and resid 205 through 207 removed outlier: 6.469A pdb=" N THR K 206 " --> pdb=" O TYR K 437 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 263 through 265 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 263 through 265 current: chain 'K' and resid 317 through 325 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 317 through 325 current: chain 'K' and resid 383 through 387 removed outlier: 4.099A pdb=" N PHE K 384 " --> pdb=" O LYS K 423 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 415 through 423 current: chain 'K' and resid 467 through 472 Processing sheet with id=AC1, first strand: chain 'L' and resid 45 through 47 removed outlier: 4.684A pdb=" N VAL L 246 " --> pdb=" O LEU L 86 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 75 through 76 removed outlier: 3.990A pdb=" N VAL L 75 " --> pdb=" O CYS L 54 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 91 through 93 Processing sheet with id=AC4, first strand: chain 'L' and resid 169 through 177 Processing sheet with id=AC5, first strand: chain 'L' and resid 205 through 207 removed outlier: 6.516A pdb=" N THR L 206 " --> pdb=" O TYR L 437 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 263 through 264 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 263 through 264 current: chain 'L' and resid 288 through 314 removed outlier: 6.827A pdb=" N ASN L 305 " --> pdb=" O ILE L 325 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ILE L 325 " --> pdb=" O ASN L 305 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR L 307 " --> pdb=" O GLY L 323 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N GLN L 317 " --> pdb=" O ILE L 313 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 317 through 325 current: chain 'L' and resid 383 through 387 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 383 through 387 current: chain 'L' and resid 467 through 472 Processing sheet with id=AC7, first strand: chain 'J' and resid 45 through 47 removed outlier: 4.647A pdb=" N VAL J 246 " --> pdb=" O LEU J 86 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 53 through 55 Processing sheet with id=AC9, first strand: chain 'J' and resid 91 through 94 Processing sheet with id=AD1, first strand: chain 'J' and resid 169 through 177 Processing sheet with id=AD2, first strand: chain 'J' and resid 205 through 207 removed outlier: 6.464A pdb=" N THR J 206 " --> pdb=" O TYR J 437 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 263 through 265 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 263 through 265 current: chain 'J' and resid 288 through 314 removed outlier: 6.893A pdb=" N ASN J 305 " --> pdb=" O ILE J 325 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ILE J 325 " --> pdb=" O ASN J 305 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR J 307 " --> pdb=" O GLY J 323 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N GLN J 317 " --> pdb=" O ILE J 313 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 317 through 326 current: chain 'J' and resid 383 through 387 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 383 through 387 current: chain 'J' and resid 467 through 472 567 hydrogen bonds defined for protein. 1509 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: 4.93 Time building geometry restraints manager: 5.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5409 1.34 - 1.46: 4254 1.46 - 1.59: 7516 1.59 - 1.72: 0 1.72 - 1.84: 132 Bond restraints: 17311 Sorted by residual: bond pdb=" C1 MAN G 5 " pdb=" O5 MAN G 5 " ideal model delta sigma weight residual 1.399 1.481 -0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" C1 MAN G 5 " pdb=" C2 MAN G 5 " ideal model delta sigma weight residual 1.526 1.590 -0.064 2.00e-02 2.50e+03 1.01e+01 bond pdb=" N ILE J 469 " pdb=" CA ILE J 469 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.20e-02 6.94e+03 8.07e+00 bond pdb=" N SER J 56 " pdb=" CA SER J 56 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.18e-02 7.18e+03 7.87e+00 bond pdb=" C3 BMA G 3 " pdb=" C4 BMA G 3 " ideal model delta sigma weight residual 1.541 1.486 0.055 2.00e-02 2.50e+03 7.61e+00 ... (remaining 17306 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 22371 2.17 - 4.34: 1085 4.34 - 6.50: 107 6.50 - 8.67: 12 8.67 - 10.84: 3 Bond angle restraints: 23578 Sorted by residual: angle pdb=" N MET J 477 " pdb=" CA MET J 477 " pdb=" C MET J 477 " ideal model delta sigma weight residual 113.18 102.34 10.84 1.21e+00 6.83e-01 8.03e+01 angle pdb=" N ASN J 479 " pdb=" CA ASN J 479 " pdb=" C ASN J 479 " ideal model delta sigma weight residual 113.38 103.34 10.04 1.23e+00 6.61e-01 6.66e+01 angle pdb=" N VAL J 68 " pdb=" CA VAL J 68 " pdb=" C VAL J 68 " ideal model delta sigma weight residual 108.53 101.62 6.91 1.22e+00 6.72e-01 3.21e+01 angle pdb=" C ASN J 479 " pdb=" CA ASN J 479 " pdb=" CB ASN J 479 " ideal model delta sigma weight residual 109.65 118.02 -8.37 1.74e+00 3.30e-01 2.31e+01 angle pdb=" N HIS J 72 " pdb=" CA HIS J 72 " pdb=" C HIS J 72 " ideal model delta sigma weight residual 110.36 103.26 7.10 1.55e+00 4.16e-01 2.10e+01 ... (remaining 23573 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.20: 11158 22.20 - 44.39: 239 44.39 - 66.59: 65 66.59 - 88.79: 34 88.79 - 110.99: 12 Dihedral angle restraints: 11508 sinusoidal: 5201 harmonic: 6307 Sorted by residual: dihedral pdb=" CB CYS K 380 " pdb=" SG CYS K 380 " pdb=" SG CYS K 447 " pdb=" CB CYS K 447 " ideal model delta sinusoidal sigma weight residual -86.00 -133.32 47.32 1 1.00e+01 1.00e-02 3.09e+01 dihedral pdb=" CB CYS J 380 " pdb=" SG CYS J 380 " pdb=" SG CYS J 447 " pdb=" CB CYS J 447 " ideal model delta sinusoidal sigma weight residual -86.00 -132.56 46.56 1 1.00e+01 1.00e-02 3.00e+01 dihedral pdb=" CB CYS L 380 " pdb=" SG CYS L 380 " pdb=" SG CYS L 447 " pdb=" CB CYS L 447 " ideal model delta sinusoidal sigma weight residual -86.00 -131.20 45.20 1 1.00e+01 1.00e-02 2.84e+01 ... (remaining 11505 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2304 0.064 - 0.128: 571 0.128 - 0.191: 91 0.191 - 0.255: 6 0.255 - 0.319: 7 Chirality restraints: 2979 Sorted by residual: chirality pdb=" C1 NAG I 703 " pdb=" ND2 ASN I 618 " pdb=" C2 NAG I 703 " pdb=" O5 NAG I 703 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" C1 NAG D 701 " pdb=" ND2 ASN D 612 " pdb=" C2 NAG D 701 " pdb=" O5 NAG D 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.06e+00 ... (remaining 2976 not shown) Planarity restraints: 2995 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG K 478 " -0.021 2.00e-02 2.50e+03 4.22e-02 1.78e+01 pdb=" C ARG K 478 " 0.073 2.00e-02 2.50e+03 pdb=" O ARG K 478 " -0.027 2.00e-02 2.50e+03 pdb=" N ASN K 479 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER I 638 " -0.020 2.00e-02 2.50e+03 3.93e-02 1.54e+01 pdb=" C SER I 638 " 0.068 2.00e-02 2.50e+03 pdb=" O SER I 638 " -0.025 2.00e-02 2.50e+03 pdb=" N ASN I 639 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN I 579 " 0.018 2.00e-02 2.50e+03 3.69e-02 1.36e+01 pdb=" C GLN I 579 " -0.064 2.00e-02 2.50e+03 pdb=" O GLN I 579 " 0.024 2.00e-02 2.50e+03 pdb=" N THR I 580 " 0.021 2.00e-02 2.50e+03 ... (remaining 2992 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2320 2.76 - 3.29: 15998 3.29 - 3.83: 26514 3.83 - 4.36: 31365 4.36 - 4.90: 54024 Nonbonded interactions: 130221 Sorted by model distance: nonbonded pdb=" NH2 ARG D 544 " pdb=" OE1 GLU I 656 " model vdw 2.219 3.120 nonbonded pdb=" O ASN K 480 " pdb=" OG SER K 483 " model vdw 2.289 3.040 nonbonded pdb=" OD1 ASN L 362 " pdb=" OG1 THR L 396 " model vdw 2.292 3.040 nonbonded pdb=" O ASN L 480 " pdb=" OG SER L 483 " model vdw 2.330 3.040 nonbonded pdb=" OG SER L 260 " pdb=" O LEU L 263 " model vdw 2.336 3.040 ... (remaining 130216 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 15 through 123) selection = chain 'B' selection = (chain 'F' and resid 2 through 110) selection = (chain 'H' and resid 11 through 119) } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'c' selection = chain 'd' selection = chain 'e' } ncs_group { reference = chain 'D' selection = (chain 'I' and (resid 521 through 663 or resid 701)) selection = (chain 'M' and (resid 521 through 548 or resid 562 through 663 or resid 701)) } ncs_group { reference = chain 'G' selection = chain 'b' } ncs_group { reference = (chain 'J' and (resid 34 through 58 or resid 66 through 135 or resid 153 through \ 460 or resid 466 through 506 or resid 601 through 606 or resid 608)) selection = (chain 'K' and (resid 34 through 58 or resid 66 through 135 or resid 153 through \ 397 or resid 414 through 460 or resid 466 through 506 or resid 601 through 606 \ or resid 608)) selection = (chain 'L' and (resid 34 through 397 or resid 414 through 506 or resid 601 throu \ gh 606 or resid 608)) } 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 individual isotropic 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: 4.660 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: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 37.070 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.100 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 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 : 0.007 0.082 17422 Z= 0.332 Angle : 1.079 16.786 23883 Z= 0.574 Chirality : 0.057 0.319 2979 Planarity : 0.007 0.076 2941 Dihedral : 11.482 110.987 7312 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.19), residues: 1666 helix: 0.46 (0.23), residues: 417 sheet: 0.69 (0.24), residues: 422 loop : 0.44 (0.20), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP L 481 HIS 0.011 0.002 HIS I 566 PHE 0.024 0.003 PHE L 53 TYR 0.052 0.003 TYR L 195 ARG 0.007 0.001 ARG I 635 Details of bonding type rmsd link_NAG-ASN : bond 0.00414 ( 54) link_NAG-ASN : angle 2.48761 ( 162) link_ALPHA1-6 : bond 0.01811 ( 2) link_ALPHA1-6 : angle 2.52477 ( 6) link_BETA1-4 : bond 0.00713 ( 23) link_BETA1-4 : angle 3.99149 ( 69) link_ALPHA1-3 : bond 0.00451 ( 3) link_ALPHA1-3 : angle 2.16691 ( 9) hydrogen bonds : bond 0.13727 ( 567) hydrogen bonds : angle 7.11742 ( 1509) link_BETA1-6 : bond 0.00599 ( 1) link_BETA1-6 : angle 0.87499 ( 3) SS BOND : bond 0.00404 ( 28) SS BOND : angle 2.53442 ( 56) covalent geometry : bond 0.00698 (17311) covalent geometry : angle 1.03518 (23578) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 367 time to evaluate : 1.740 Fit side-chains revert: symmetry clash REVERT: M 577 GLN cc_start: 0.8367 (mt0) cc_final: 0.7983 (tt0) REVERT: I 570 ASP cc_start: 0.7734 (t0) cc_final: 0.7480 (t0) REVERT: I 620 SER cc_start: 0.8221 (t) cc_final: 0.7857 (p) REVERT: I 649 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7605 (mt-10) REVERT: I 650 ASP cc_start: 0.8174 (m-30) cc_final: 0.7935 (m-30) REVERT: I 651 SER cc_start: 0.8392 (t) cc_final: 0.8020 (p) REVERT: K 306 ASN cc_start: 0.8273 (m-40) cc_final: 0.8059 (m110) REVERT: K 359 ARG cc_start: 0.7417 (mmt-90) cc_final: 0.7201 (mmt90) REVERT: K 481 TRP cc_start: 0.8560 (m-10) cc_final: 0.7417 (m-10) REVERT: L 250 GLN cc_start: 0.7930 (mt0) cc_final: 0.7485 (tp40) REVERT: L 502 ARG cc_start: 0.6381 (ptt90) cc_final: 0.5981 (mpt180) REVERT: J 111 LEU cc_start: 0.8951 (mt) cc_final: 0.8748 (mp) REVERT: J 115 SER cc_start: 0.9320 (t) cc_final: 0.9068 (p) REVERT: J 195 TYR cc_start: 0.8790 (m-80) cc_final: 0.8552 (m-80) REVERT: J 215 ASP cc_start: 0.8192 (m-30) cc_final: 0.7759 (p0) REVERT: J 502 ARG cc_start: 0.7525 (mtt-85) cc_final: 0.7047 (ptt90) outliers start: 0 outliers final: 0 residues processed: 367 average time/residue: 0.3221 time to fit residues: 168.1114 Evaluate side-chains 187 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 178 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 54 optimal weight: 9.9990 chunk 107 optimal weight: 0.9980 chunk 85 optimal weight: 8.9990 chunk 165 optimal weight: 6.9990 chunk 63 optimal weight: 9.9990 chunk 100 optimal weight: 0.9990 chunk 123 optimal weight: 7.9990 chunk 191 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 621 HIS M 632 GLN M 654 GLN I 632 GLN ** I 655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 191 ASN L 379 ASN L 430 GLN J 220 HIS J 291 HIS J 427 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.136600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.114163 restraints weight = 26329.842| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.45 r_work: 0.3218 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17422 Z= 0.156 Angle : 0.664 9.784 23883 Z= 0.315 Chirality : 0.045 0.286 2979 Planarity : 0.003 0.032 2941 Dihedral : 8.433 79.265 4025 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 1.38 % Allowed : 6.65 % Favored : 91.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.20), residues: 1666 helix: 2.28 (0.26), residues: 406 sheet: 0.68 (0.24), residues: 434 loop : 0.39 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP L 481 HIS 0.012 0.001 HIS I 566 PHE 0.019 0.002 PHE J 53 TYR 0.018 0.001 TYR L 195 ARG 0.005 0.001 ARG J 277 Details of bonding type rmsd link_NAG-ASN : bond 0.00448 ( 54) link_NAG-ASN : angle 2.12581 ( 162) link_ALPHA1-6 : bond 0.02220 ( 2) link_ALPHA1-6 : angle 3.05940 ( 6) link_BETA1-4 : bond 0.00487 ( 23) link_BETA1-4 : angle 2.50771 ( 69) link_ALPHA1-3 : bond 0.00773 ( 3) link_ALPHA1-3 : angle 2.65688 ( 9) hydrogen bonds : bond 0.04587 ( 567) hydrogen bonds : angle 5.11117 ( 1509) link_BETA1-6 : bond 0.00499 ( 1) link_BETA1-6 : angle 0.98555 ( 3) SS BOND : bond 0.00377 ( 28) SS BOND : angle 1.46283 ( 56) covalent geometry : bond 0.00355 (17311) covalent geometry : angle 0.62169 (23578) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 207 time to evaluate : 1.805 Fit side-chains REVERT: M 577 GLN cc_start: 0.8705 (mt0) cc_final: 0.8300 (tt0) REVERT: I 570 ASP cc_start: 0.7961 (t0) cc_final: 0.7574 (t0) REVERT: I 620 SER cc_start: 0.8507 (t) cc_final: 0.8135 (p) REVERT: K 336 ILE cc_start: 0.9114 (mt) cc_final: 0.8910 (tt) REVERT: K 359 ARG cc_start: 0.7546 (mmt-90) cc_final: 0.7189 (mmt90) REVERT: K 477 MET cc_start: 0.8390 (tpp) cc_final: 0.8149 (mmt) REVERT: K 481 TRP cc_start: 0.8699 (m-10) cc_final: 0.7419 (m-10) REVERT: L 133 GLN cc_start: 0.8016 (mm-40) cc_final: 0.6829 (mp10) REVERT: L 250 GLN cc_start: 0.7970 (mt0) cc_final: 0.7441 (tp40) REVERT: L 502 ARG cc_start: 0.6491 (ptt90) cc_final: 0.6054 (mpt180) REVERT: J 111 LEU cc_start: 0.9047 (mt) cc_final: 0.8667 (mp) REVERT: J 215 ASP cc_start: 0.8390 (m-30) cc_final: 0.7817 (p0) outliers start: 21 outliers final: 18 residues processed: 219 average time/residue: 0.2990 time to fit residues: 97.3638 Evaluate side-chains 198 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 180 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 638 SER Chi-restraints excluded: chain D residue 565 HIS Chi-restraints excluded: chain D residue 603 LEU Chi-restraints excluded: chain D residue 614 SER Chi-restraints excluded: chain K residue 395 SER Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain L residue 294 GLU Chi-restraints excluded: chain L residue 328 ASN Chi-restraints excluded: chain L residue 336 ILE Chi-restraints excluded: chain L residue 390 SER Chi-restraints excluded: chain L residue 418 ILE Chi-restraints excluded: chain L residue 428 MET Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain J residue 96 TRP Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 427 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 107 optimal weight: 0.9990 chunk 48 optimal weight: 9.9990 chunk 144 optimal weight: 0.9990 chunk 141 optimal weight: 6.9990 chunk 204 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 78 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 306 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.133570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.110139 restraints weight = 25917.081| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.56 r_work: 0.3153 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17422 Z= 0.144 Angle : 0.590 9.691 23883 Z= 0.279 Chirality : 0.043 0.271 2979 Planarity : 0.003 0.045 2941 Dihedral : 7.674 73.970 4025 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.32 % Allowed : 7.77 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.20), residues: 1666 helix: 2.33 (0.26), residues: 419 sheet: 0.56 (0.24), residues: 438 loop : 0.19 (0.21), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP L 481 HIS 0.005 0.001 HIS M 566 PHE 0.015 0.002 PHE I 522 TYR 0.011 0.001 TYR L 195 ARG 0.004 0.000 ARG J 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00326 ( 54) link_NAG-ASN : angle 1.82986 ( 162) link_ALPHA1-6 : bond 0.02059 ( 2) link_ALPHA1-6 : angle 3.00027 ( 6) link_BETA1-4 : bond 0.00535 ( 23) link_BETA1-4 : angle 2.36915 ( 69) link_ALPHA1-3 : bond 0.00880 ( 3) link_ALPHA1-3 : angle 1.65786 ( 9) hydrogen bonds : bond 0.04171 ( 567) hydrogen bonds : angle 4.69564 ( 1509) link_BETA1-6 : bond 0.00564 ( 1) link_BETA1-6 : angle 0.88277 ( 3) SS BOND : bond 0.00662 ( 28) SS BOND : angle 1.19359 ( 56) covalent geometry : bond 0.00331 (17311) covalent geometry : angle 0.55350 (23578) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 185 time to evaluate : 1.768 Fit side-chains REVERT: M 577 GLN cc_start: 0.8709 (mt0) cc_final: 0.8256 (tt0) REVERT: D 564 GLN cc_start: 0.7796 (tm-30) cc_final: 0.7590 (tt0) REVERT: D 603 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.9126 (mp) REVERT: I 565 GLN cc_start: 0.6713 (mm-40) cc_final: 0.6501 (pp30) REVERT: I 570 ASP cc_start: 0.7822 (t0) cc_final: 0.7471 (t0) REVERT: I 620 SER cc_start: 0.8406 (t) cc_final: 0.7960 (p) REVERT: K 359 ARG cc_start: 0.7507 (mmt-90) cc_final: 0.7115 (mmt90) REVERT: K 477 MET cc_start: 0.8378 (tpp) cc_final: 0.7817 (mmt) REVERT: K 481 TRP cc_start: 0.8647 (m-10) cc_final: 0.7095 (m-10) REVERT: L 250 GLN cc_start: 0.7866 (mt0) cc_final: 0.7374 (tp40) REVERT: L 502 ARG cc_start: 0.6646 (ptt90) cc_final: 0.6050 (mpt180) REVERT: J 111 LEU cc_start: 0.9042 (mt) cc_final: 0.8726 (mp) REVERT: J 133 GLN cc_start: 0.7552 (pp30) cc_final: 0.7240 (pp30) REVERT: J 195 TYR cc_start: 0.8936 (m-80) cc_final: 0.8526 (m-80) REVERT: J 215 ASP cc_start: 0.8409 (m-30) cc_final: 0.7695 (p0) REVERT: J 448 LYS cc_start: 0.8628 (tttt) cc_final: 0.8289 (tttm) outliers start: 20 outliers final: 11 residues processed: 194 average time/residue: 0.3114 time to fit residues: 89.6608 Evaluate side-chains 177 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 165 time to evaluate : 1.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 545 GLN Chi-restraints excluded: chain D residue 603 LEU Chi-restraints excluded: chain D residue 606 CYS Chi-restraints excluded: chain K residue 395 SER Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain L residue 294 GLU Chi-restraints excluded: chain L residue 328 ASN Chi-restraints excluded: chain L residue 336 ILE Chi-restraints excluded: chain L residue 383 GLU Chi-restraints excluded: chain L residue 418 ILE Chi-restraints excluded: chain L residue 428 MET Chi-restraints excluded: chain J residue 269 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 197 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 195 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 87 optimal weight: 10.0000 chunk 114 optimal weight: 0.7980 chunk 75 optimal weight: 9.9990 chunk 64 optimal weight: 8.9990 chunk 58 optimal weight: 10.0000 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 72 HIS ** 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 = 0.3508 r_free = 0.3508 target = 0.128432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.105165 restraints weight = 26085.042| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.54 r_work: 0.3078 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 17422 Z= 0.247 Angle : 0.713 9.891 23883 Z= 0.335 Chirality : 0.047 0.278 2979 Planarity : 0.004 0.047 2941 Dihedral : 7.667 69.507 4025 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.91 % Allowed : 7.64 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.20), residues: 1666 helix: 2.00 (0.26), residues: 420 sheet: 0.23 (0.24), residues: 416 loop : -0.27 (0.20), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 481 HIS 0.008 0.002 HIS M 621 PHE 0.025 0.002 PHE I 522 TYR 0.011 0.002 TYR K 40 ARG 0.005 0.001 ARG K 482 Details of bonding type rmsd link_NAG-ASN : bond 0.00343 ( 54) link_NAG-ASN : angle 2.06328 ( 162) link_ALPHA1-6 : bond 0.01891 ( 2) link_ALPHA1-6 : angle 2.86525 ( 6) link_BETA1-4 : bond 0.00478 ( 23) link_BETA1-4 : angle 2.58251 ( 69) link_ALPHA1-3 : bond 0.00812 ( 3) link_ALPHA1-3 : angle 2.31270 ( 9) hydrogen bonds : bond 0.04817 ( 567) hydrogen bonds : angle 4.86164 ( 1509) link_BETA1-6 : bond 0.00631 ( 1) link_BETA1-6 : angle 0.83904 ( 3) SS BOND : bond 0.00509 ( 28) SS BOND : angle 1.49493 ( 56) covalent geometry : bond 0.00590 (17311) covalent geometry : angle 0.67599 (23578) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 160 time to evaluate : 1.812 Fit side-chains REVERT: M 577 GLN cc_start: 0.8708 (mt0) cc_final: 0.8272 (tt0) REVERT: M 601 SER cc_start: 0.9400 (t) cc_final: 0.9159 (m) REVERT: I 565 GLN cc_start: 0.6941 (mm-40) cc_final: 0.6593 (pp30) REVERT: I 570 ASP cc_start: 0.7981 (t0) cc_final: 0.7759 (t0) REVERT: I 620 SER cc_start: 0.8425 (t) cc_final: 0.7926 (p) REVERT: I 655 GLN cc_start: 0.8102 (mt0) cc_final: 0.7751 (mt0) REVERT: K 359 ARG cc_start: 0.7604 (mmt-90) cc_final: 0.7198 (mmt90) REVERT: K 466 GLU cc_start: 0.6877 (mt-10) cc_final: 0.6672 (mm-30) REVERT: K 481 TRP cc_start: 0.8707 (m-10) cc_final: 0.6819 (m-10) REVERT: L 250 GLN cc_start: 0.8031 (mt0) cc_final: 0.7491 (tt0) REVERT: L 502 ARG cc_start: 0.6266 (ptt90) cc_final: 0.5795 (mpp-170) REVERT: J 133 GLN cc_start: 0.7616 (pp30) cc_final: 0.7281 (pp30) REVERT: J 215 ASP cc_start: 0.8337 (m-30) cc_final: 0.7641 (p0) REVERT: J 448 LYS cc_start: 0.8731 (tttt) cc_final: 0.8400 (tttm) outliers start: 29 outliers final: 18 residues processed: 180 average time/residue: 0.2936 time to fit residues: 78.4259 Evaluate side-chains 173 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 155 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 638 SER Chi-restraints excluded: chain D residue 565 HIS Chi-restraints excluded: chain D residue 603 LEU Chi-restraints excluded: chain D residue 606 CYS Chi-restraints excluded: chain D residue 614 SER Chi-restraints excluded: chain I residue 597 ILE Chi-restraints excluded: chain K residue 373 ILE Chi-restraints excluded: chain L residue 74 CYS Chi-restraints excluded: chain L residue 96 TRP Chi-restraints excluded: chain L residue 126 CYS Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain L residue 294 GLU Chi-restraints excluded: chain L residue 328 ASN Chi-restraints excluded: chain L residue 418 ILE Chi-restraints excluded: chain L residue 490 VAL Chi-restraints excluded: chain J residue 126 CYS Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 269 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 177 optimal weight: 0.0170 chunk 158 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 147 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 205 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 chunk 7 optimal weight: 0.9980 chunk 39 optimal weight: 10.0000 chunk 73 optimal weight: 9.9990 chunk 57 optimal weight: 9.9990 overall best weight: 1.0020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 579 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 = 0.3545 r_free = 0.3545 target = 0.131215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.108074 restraints weight = 26187.323| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.56 r_work: 0.3121 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17422 Z= 0.129 Angle : 0.580 9.814 23883 Z= 0.272 Chirality : 0.043 0.280 2979 Planarity : 0.003 0.038 2941 Dihedral : 7.067 64.413 4025 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.32 % Allowed : 9.29 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.20), residues: 1666 helix: 2.23 (0.26), residues: 420 sheet: 0.34 (0.24), residues: 420 loop : -0.31 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 96 HIS 0.005 0.001 HIS M 566 PHE 0.021 0.001 PHE I 522 TYR 0.011 0.001 TYR K 486 ARG 0.005 0.000 ARG J 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00300 ( 54) link_NAG-ASN : angle 1.78180 ( 162) link_ALPHA1-6 : bond 0.02020 ( 2) link_ALPHA1-6 : angle 3.16332 ( 6) link_BETA1-4 : bond 0.00500 ( 23) link_BETA1-4 : angle 2.25623 ( 69) link_ALPHA1-3 : bond 0.00958 ( 3) link_ALPHA1-3 : angle 1.72313 ( 9) hydrogen bonds : bond 0.03852 ( 567) hydrogen bonds : angle 4.52905 ( 1509) link_BETA1-6 : bond 0.00499 ( 1) link_BETA1-6 : angle 0.77169 ( 3) SS BOND : bond 0.00490 ( 28) SS BOND : angle 1.42736 ( 56) covalent geometry : bond 0.00298 (17311) covalent geometry : angle 0.54342 (23578) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 170 time to evaluate : 1.601 Fit side-chains REVERT: M 577 GLN cc_start: 0.8680 (mt0) cc_final: 0.8230 (tt0) REVERT: M 601 SER cc_start: 0.9335 (t) cc_final: 0.9118 (m) REVERT: M 660 LYS cc_start: 0.5891 (tttt) cc_final: 0.4315 (tttm) REVERT: D 564 GLN cc_start: 0.7912 (tm-30) cc_final: 0.7621 (tt0) REVERT: I 565 GLN cc_start: 0.6918 (mm-40) cc_final: 0.6573 (pp30) REVERT: I 570 ASP cc_start: 0.7771 (t0) cc_final: 0.7437 (t0) REVERT: I 620 SER cc_start: 0.8409 (t) cc_final: 0.7939 (p) REVERT: I 655 GLN cc_start: 0.8107 (mt0) cc_final: 0.7782 (tt0) REVERT: K 211 LYS cc_start: 0.8710 (mttt) cc_final: 0.7703 (tptp) REVERT: K 359 ARG cc_start: 0.7564 (mmt-90) cc_final: 0.7292 (mmt90) REVERT: K 477 MET cc_start: 0.8360 (tpp) cc_final: 0.7633 (mmt) REVERT: K 481 TRP cc_start: 0.8616 (m-10) cc_final: 0.6919 (m-10) REVERT: L 250 GLN cc_start: 0.7896 (mt0) cc_final: 0.7357 (tt0) REVERT: L 502 ARG cc_start: 0.6287 (ptt90) cc_final: 0.5795 (mpt180) REVERT: J 111 LEU cc_start: 0.9059 (mt) cc_final: 0.8792 (mp) REVERT: J 133 GLN cc_start: 0.7670 (pp30) cc_final: 0.7318 (pp30) outliers start: 20 outliers final: 15 residues processed: 186 average time/residue: 0.2926 time to fit residues: 81.2662 Evaluate side-chains 173 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 158 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 638 SER Chi-restraints excluded: chain D residue 606 CYS Chi-restraints excluded: chain D residue 614 SER Chi-restraints excluded: chain D residue 619 SER Chi-restraints excluded: chain I residue 597 ILE Chi-restraints excluded: chain K residue 373 ILE Chi-restraints excluded: chain L residue 74 CYS Chi-restraints excluded: chain L residue 126 CYS Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain L residue 294 GLU Chi-restraints excluded: chain L residue 328 ASN Chi-restraints excluded: chain L residue 418 ILE Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain J residue 126 CYS Chi-restraints excluded: chain J residue 269 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 145 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 166 optimal weight: 0.6980 chunk 130 optimal weight: 7.9990 chunk 185 optimal weight: 2.9990 chunk 55 optimal weight: 9.9990 chunk 132 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 72 HIS ** 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 = 0.3509 r_free = 0.3509 target = 0.128425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.105234 restraints weight = 26271.713| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.56 r_work: 0.3074 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 17422 Z= 0.216 Angle : 0.664 9.944 23883 Z= 0.309 Chirality : 0.046 0.409 2979 Planarity : 0.004 0.041 2941 Dihedral : 7.217 64.701 4025 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.65 % Allowed : 9.95 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.20), residues: 1666 helix: 2.13 (0.26), residues: 418 sheet: 0.10 (0.23), residues: 436 loop : -0.43 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 96 HIS 0.006 0.001 HIS M 621 PHE 0.018 0.002 PHE K 53 TYR 0.014 0.001 TYR K 486 ARG 0.006 0.000 ARG J 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00327 ( 54) link_NAG-ASN : angle 2.04643 ( 162) link_ALPHA1-6 : bond 0.01921 ( 2) link_ALPHA1-6 : angle 3.06547 ( 6) link_BETA1-4 : bond 0.00476 ( 23) link_BETA1-4 : angle 2.42113 ( 69) link_ALPHA1-3 : bond 0.00818 ( 3) link_ALPHA1-3 : angle 2.14206 ( 9) hydrogen bonds : bond 0.04417 ( 567) hydrogen bonds : angle 4.63324 ( 1509) link_BETA1-6 : bond 0.00554 ( 1) link_BETA1-6 : angle 0.81124 ( 3) SS BOND : bond 0.00470 ( 28) SS BOND : angle 1.36932 ( 56) covalent geometry : bond 0.00518 (17311) covalent geometry : angle 0.62602 (23578) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 165 time to evaluate : 1.694 Fit side-chains revert: symmetry clash REVERT: M 525 LEU cc_start: 0.9576 (tp) cc_final: 0.9318 (mp) REVERT: M 577 GLN cc_start: 0.8690 (mt0) cc_final: 0.8263 (tt0) REVERT: M 601 SER cc_start: 0.9361 (t) cc_final: 0.9141 (m) REVERT: D 603 LEU cc_start: 0.9454 (OUTLIER) cc_final: 0.9189 (mp) REVERT: I 548 SER cc_start: 0.7502 (t) cc_final: 0.7250 (m) REVERT: I 565 GLN cc_start: 0.7069 (mm-40) cc_final: 0.6683 (pp30) REVERT: I 570 ASP cc_start: 0.7817 (t0) cc_final: 0.7559 (t0) REVERT: I 601 SER cc_start: 0.9240 (t) cc_final: 0.8868 (p) REVERT: I 620 SER cc_start: 0.8430 (t) cc_final: 0.7935 (p) REVERT: I 655 GLN cc_start: 0.8140 (mt0) cc_final: 0.7812 (tt0) REVERT: K 211 LYS cc_start: 0.8750 (mttt) cc_final: 0.7746 (tptp) REVERT: K 359 ARG cc_start: 0.7676 (mmt-90) cc_final: 0.7253 (mmt90) REVERT: K 466 GLU cc_start: 0.6848 (mt-10) cc_final: 0.6637 (mm-30) REVERT: K 477 MET cc_start: 0.8462 (tpp) cc_final: 0.7670 (mmt) REVERT: K 481 TRP cc_start: 0.8687 (m-10) cc_final: 0.6888 (m-10) REVERT: L 250 GLN cc_start: 0.7934 (mt0) cc_final: 0.7485 (tt0) REVERT: L 502 ARG cc_start: 0.6362 (ptt90) cc_final: 0.6047 (mtt-85) REVERT: J 111 LEU cc_start: 0.9141 (mt) cc_final: 0.8844 (mp) REVERT: J 133 GLN cc_start: 0.7695 (pp30) cc_final: 0.7336 (pp30) outliers start: 25 outliers final: 19 residues processed: 183 average time/residue: 0.3054 time to fit residues: 83.6181 Evaluate side-chains 181 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 161 time to evaluate : 1.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 638 SER Chi-restraints excluded: chain D residue 565 HIS Chi-restraints excluded: chain D residue 603 LEU Chi-restraints excluded: chain D residue 606 CYS Chi-restraints excluded: chain D residue 614 SER Chi-restraints excluded: chain D residue 619 SER Chi-restraints excluded: chain I residue 597 ILE Chi-restraints excluded: chain K residue 187 GLU Chi-restraints excluded: chain K residue 373 ILE Chi-restraints excluded: chain L residue 74 CYS Chi-restraints excluded: chain L residue 96 TRP Chi-restraints excluded: chain L residue 126 CYS Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain L residue 294 GLU Chi-restraints excluded: chain L residue 328 ASN Chi-restraints excluded: chain L residue 418 ILE Chi-restraints excluded: chain J residue 126 CYS Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 209 CYS Chi-restraints excluded: chain J residue 269 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 52 optimal weight: 10.0000 chunk 123 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 61 optimal weight: 10.0000 chunk 112 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 140 optimal weight: 1.9990 chunk 185 optimal weight: 0.7980 chunk 129 optimal weight: 5.9990 chunk 173 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 191 ASN L 244 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.130582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.107645 restraints weight = 26058.653| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.54 r_work: 0.3115 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17422 Z= 0.122 Angle : 0.573 9.865 23883 Z= 0.269 Chirality : 0.043 0.277 2979 Planarity : 0.003 0.036 2941 Dihedral : 6.801 61.135 4025 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.52 % Allowed : 10.41 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.20), residues: 1666 helix: 2.26 (0.26), residues: 419 sheet: 0.24 (0.24), residues: 416 loop : -0.44 (0.21), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 96 HIS 0.005 0.001 HIS M 566 PHE 0.014 0.001 PHE I 522 TYR 0.012 0.001 TYR K 486 ARG 0.007 0.000 ARG J 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00291 ( 54) link_NAG-ASN : angle 1.77415 ( 162) link_ALPHA1-6 : bond 0.02030 ( 2) link_ALPHA1-6 : angle 3.21604 ( 6) link_BETA1-4 : bond 0.00502 ( 23) link_BETA1-4 : angle 2.19424 ( 69) link_ALPHA1-3 : bond 0.00961 ( 3) link_ALPHA1-3 : angle 1.81512 ( 9) hydrogen bonds : bond 0.03734 ( 567) hydrogen bonds : angle 4.41728 ( 1509) link_BETA1-6 : bond 0.00484 ( 1) link_BETA1-6 : angle 0.75781 ( 3) SS BOND : bond 0.00409 ( 28) SS BOND : angle 0.92716 ( 56) covalent geometry : bond 0.00280 (17311) covalent geometry : angle 0.53936 (23578) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 178 time to evaluate : 1.788 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 525 LEU cc_start: 0.9541 (tp) cc_final: 0.9290 (mp) REVERT: M 577 GLN cc_start: 0.8671 (mt0) cc_final: 0.8200 (tt0) REVERT: M 660 LYS cc_start: 0.5826 (tttt) cc_final: 0.4348 (tttm) REVERT: D 564 GLN cc_start: 0.7973 (tm-30) cc_final: 0.7712 (tt0) REVERT: D 603 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9239 (mp) REVERT: I 565 GLN cc_start: 0.7070 (mm-40) cc_final: 0.6632 (pp30) REVERT: I 570 ASP cc_start: 0.7694 (t0) cc_final: 0.7373 (t0) REVERT: I 601 SER cc_start: 0.9219 (t) cc_final: 0.8858 (p) REVERT: I 620 SER cc_start: 0.8425 (t) cc_final: 0.7953 (p) REVERT: I 655 GLN cc_start: 0.8085 (mt0) cc_final: 0.7796 (tt0) REVERT: K 211 LYS cc_start: 0.8744 (mttt) cc_final: 0.7738 (tptp) REVERT: K 282 THR cc_start: 0.8757 (m) cc_final: 0.8527 (p) REVERT: K 324 ASP cc_start: 0.8851 (t0) cc_final: 0.8640 (t0) REVERT: K 359 ARG cc_start: 0.7659 (mmt-90) cc_final: 0.7335 (mmt90) REVERT: K 477 MET cc_start: 0.8364 (tpp) cc_final: 0.7669 (mmt) REVERT: K 481 TRP cc_start: 0.8607 (m-10) cc_final: 0.6927 (m-10) REVERT: L 250 GLN cc_start: 0.7910 (mt0) cc_final: 0.7440 (tt0) REVERT: L 502 ARG cc_start: 0.6332 (ptt90) cc_final: 0.6022 (mtt-85) REVERT: J 111 LEU cc_start: 0.9080 (mt) cc_final: 0.8777 (mp) REVERT: J 133 GLN cc_start: 0.7708 (pp30) cc_final: 0.7362 (pp30) outliers start: 23 outliers final: 18 residues processed: 193 average time/residue: 0.3036 time to fit residues: 86.8786 Evaluate side-chains 190 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 171 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 638 SER Chi-restraints excluded: chain D residue 603 LEU Chi-restraints excluded: chain D residue 606 CYS Chi-restraints excluded: chain D residue 614 SER Chi-restraints excluded: chain D residue 619 SER Chi-restraints excluded: chain I residue 531 THR Chi-restraints excluded: chain I residue 597 ILE Chi-restraints excluded: chain K residue 187 GLU Chi-restraints excluded: chain K residue 373 ILE Chi-restraints excluded: chain L residue 74 CYS Chi-restraints excluded: chain L residue 126 CYS Chi-restraints excluded: chain L residue 209 CYS Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain L residue 294 GLU Chi-restraints excluded: chain L residue 328 ASN Chi-restraints excluded: chain L residue 418 ILE Chi-restraints excluded: chain J residue 126 CYS Chi-restraints excluded: chain J residue 209 CYS Chi-restraints excluded: chain J residue 269 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 37 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 206 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 178 optimal weight: 5.9990 chunk 138 optimal weight: 0.9990 chunk 39 optimal weight: 9.9990 chunk 74 optimal weight: 9.9990 chunk 139 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 72 HIS ** 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 = 0.3497 r_free = 0.3497 target = 0.127564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.104303 restraints weight = 26159.995| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.56 r_work: 0.3051 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 17422 Z= 0.246 Angle : 0.683 9.876 23883 Z= 0.317 Chirality : 0.047 0.286 2979 Planarity : 0.004 0.043 2941 Dihedral : 7.161 63.512 4025 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.65 % Allowed : 10.67 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.20), residues: 1666 helix: 1.97 (0.26), residues: 420 sheet: 0.02 (0.24), residues: 428 loop : -0.58 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 96 HIS 0.007 0.001 HIS M 621 PHE 0.019 0.002 PHE K 53 TYR 0.015 0.001 TYR K 486 ARG 0.008 0.001 ARG J 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00339 ( 54) link_NAG-ASN : angle 2.00672 ( 162) link_ALPHA1-6 : bond 0.01918 ( 2) link_ALPHA1-6 : angle 3.19434 ( 6) link_BETA1-4 : bond 0.00484 ( 23) link_BETA1-4 : angle 2.43131 ( 69) link_ALPHA1-3 : bond 0.00928 ( 3) link_ALPHA1-3 : angle 2.12550 ( 9) hydrogen bonds : bond 0.04508 ( 567) hydrogen bonds : angle 4.63825 ( 1509) link_BETA1-6 : bond 0.00619 ( 1) link_BETA1-6 : angle 0.84120 ( 3) SS BOND : bond 0.00483 ( 28) SS BOND : angle 1.03827 ( 56) covalent geometry : bond 0.00590 (17311) covalent geometry : angle 0.64873 (23578) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 167 time to evaluate : 1.854 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 577 GLN cc_start: 0.8681 (mt0) cc_final: 0.8240 (tt0) REVERT: M 590 LYS cc_start: 0.9222 (tmmt) cc_final: 0.8870 (tttm) REVERT: D 589 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8420 (mttt) REVERT: D 603 LEU cc_start: 0.9493 (OUTLIER) cc_final: 0.9224 (mp) REVERT: I 565 GLN cc_start: 0.7135 (mm-40) cc_final: 0.6717 (pp30) REVERT: I 570 ASP cc_start: 0.7689 (t0) cc_final: 0.7441 (t0) REVERT: I 620 SER cc_start: 0.8459 (t) cc_final: 0.7962 (p) REVERT: I 655 GLN cc_start: 0.8207 (mt0) cc_final: 0.7867 (tt0) REVERT: K 49 GLU cc_start: 0.8965 (tt0) cc_final: 0.8689 (pt0) REVERT: K 211 LYS cc_start: 0.8744 (mttt) cc_final: 0.7768 (tptp) REVERT: K 359 ARG cc_start: 0.7677 (mmt-90) cc_final: 0.7268 (mmt90) REVERT: K 466 GLU cc_start: 0.6821 (mt-10) cc_final: 0.6556 (mm-30) REVERT: K 477 MET cc_start: 0.8425 (tpp) cc_final: 0.7576 (mmt) REVERT: K 481 TRP cc_start: 0.8684 (m-10) cc_final: 0.6858 (m-10) REVERT: L 250 GLN cc_start: 0.7956 (mt0) cc_final: 0.7555 (tt0) REVERT: L 502 ARG cc_start: 0.6328 (ptt90) cc_final: 0.5987 (mtt-85) REVERT: J 111 LEU cc_start: 0.9070 (mt) cc_final: 0.8730 (mp) REVERT: J 133 GLN cc_start: 0.7709 (pp30) cc_final: 0.7337 (pp30) REVERT: J 418 ILE cc_start: 0.8802 (OUTLIER) cc_final: 0.8599 (mt) outliers start: 25 outliers final: 21 residues processed: 184 average time/residue: 0.3100 time to fit residues: 84.9686 Evaluate side-chains 187 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 163 time to evaluate : 1.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 638 SER Chi-restraints excluded: chain D residue 565 HIS Chi-restraints excluded: chain D residue 589 LYS Chi-restraints excluded: chain D residue 603 LEU Chi-restraints excluded: chain D residue 606 CYS Chi-restraints excluded: chain D residue 614 SER Chi-restraints excluded: chain D residue 619 SER Chi-restraints excluded: chain I residue 531 THR Chi-restraints excluded: chain I residue 597 ILE Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain K residue 187 GLU Chi-restraints excluded: chain K residue 373 ILE Chi-restraints excluded: chain L residue 74 CYS Chi-restraints excluded: chain L residue 96 TRP Chi-restraints excluded: chain L residue 126 CYS Chi-restraints excluded: chain L residue 209 CYS Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain L residue 294 GLU Chi-restraints excluded: chain L residue 328 ASN Chi-restraints excluded: chain L residue 418 ILE Chi-restraints excluded: chain J residue 126 CYS Chi-restraints excluded: chain J residue 209 CYS Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 418 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 145 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 185 optimal weight: 0.6980 chunk 49 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 chunk 210 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 72 HIS ** 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 = 0.3536 r_free = 0.3536 target = 0.130668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.107510 restraints weight = 26170.239| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.57 r_work: 0.3103 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17422 Z= 0.124 Angle : 0.569 9.625 23883 Z= 0.268 Chirality : 0.043 0.275 2979 Planarity : 0.003 0.055 2941 Dihedral : 6.621 59.848 4025 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.19 % Allowed : 11.13 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.21), residues: 1666 helix: 2.21 (0.26), residues: 420 sheet: 0.17 (0.25), residues: 416 loop : -0.55 (0.21), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP J 429 HIS 0.005 0.001 HIS M 566 PHE 0.012 0.001 PHE L 53 TYR 0.010 0.001 TYR K 486 ARG 0.015 0.000 ARG J 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00296 ( 54) link_NAG-ASN : angle 1.70936 ( 162) link_ALPHA1-6 : bond 0.01942 ( 2) link_ALPHA1-6 : angle 3.25711 ( 6) link_BETA1-4 : bond 0.00511 ( 23) link_BETA1-4 : angle 2.12714 ( 69) link_ALPHA1-3 : bond 0.00922 ( 3) link_ALPHA1-3 : angle 1.71122 ( 9) hydrogen bonds : bond 0.03635 ( 567) hydrogen bonds : angle 4.34948 ( 1509) link_BETA1-6 : bond 0.00497 ( 1) link_BETA1-6 : angle 0.70480 ( 3) SS BOND : bond 0.00390 ( 28) SS BOND : angle 0.85982 ( 56) covalent geometry : bond 0.00286 (17311) covalent geometry : angle 0.53796 (23578) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 177 time to evaluate : 1.679 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 577 GLN cc_start: 0.8659 (mt0) cc_final: 0.8192 (tt0) REVERT: M 660 LYS cc_start: 0.5808 (tttt) cc_final: 0.4146 (tttm) REVERT: D 564 GLN cc_start: 0.7990 (tm-30) cc_final: 0.7657 (tt0) REVERT: I 565 GLN cc_start: 0.7141 (mm-40) cc_final: 0.6734 (pp30) REVERT: I 566 HIS cc_start: 0.6881 (t-90) cc_final: 0.6416 (t-90) REVERT: I 570 ASP cc_start: 0.7526 (t0) cc_final: 0.7261 (t0) REVERT: I 620 SER cc_start: 0.8411 (t) cc_final: 0.7947 (p) REVERT: I 655 GLN cc_start: 0.8160 (mt0) cc_final: 0.7876 (tt0) REVERT: K 211 LYS cc_start: 0.8736 (mttt) cc_final: 0.7764 (tptp) REVERT: K 282 THR cc_start: 0.8722 (m) cc_final: 0.8489 (p) REVERT: K 359 ARG cc_start: 0.7684 (mmt-90) cc_final: 0.7328 (mmt90) REVERT: K 477 MET cc_start: 0.8298 (mpp) cc_final: 0.7606 (mmt) REVERT: K 481 TRP cc_start: 0.8604 (m-10) cc_final: 0.6923 (m-10) REVERT: L 250 GLN cc_start: 0.7876 (mt0) cc_final: 0.7560 (tt0) REVERT: L 502 ARG cc_start: 0.6307 (ptt90) cc_final: 0.6057 (mtt-85) REVERT: J 111 LEU cc_start: 0.9007 (mt) cc_final: 0.8681 (mp) REVERT: J 133 GLN cc_start: 0.7739 (pp30) cc_final: 0.7380 (pp30) outliers start: 18 outliers final: 17 residues processed: 190 average time/residue: 0.3029 time to fit residues: 86.1146 Evaluate side-chains 184 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 167 time to evaluate : 1.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 638 SER Chi-restraints excluded: chain D residue 606 CYS Chi-restraints excluded: chain D residue 614 SER Chi-restraints excluded: chain D residue 619 SER Chi-restraints excluded: chain I residue 531 THR Chi-restraints excluded: chain I residue 597 ILE Chi-restraints excluded: chain K residue 373 ILE Chi-restraints excluded: chain L residue 74 CYS Chi-restraints excluded: chain L residue 126 CYS Chi-restraints excluded: chain L residue 209 CYS Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain L residue 294 GLU Chi-restraints excluded: chain L residue 328 ASN Chi-restraints excluded: chain L residue 418 ILE Chi-restraints excluded: chain J residue 126 CYS Chi-restraints excluded: chain J residue 209 CYS Chi-restraints excluded: chain J residue 269 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 55 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 120 optimal weight: 3.9990 chunk 202 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 144 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 112 optimal weight: 1.9990 chunk 86 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: ** I 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 72 HIS ** 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 = 0.3509 r_free = 0.3509 target = 0.128502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.105337 restraints weight = 26211.118| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.55 r_work: 0.3075 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.125 17422 Z= 0.212 Angle : 0.653 13.964 23883 Z= 0.305 Chirality : 0.045 0.277 2979 Planarity : 0.004 0.051 2941 Dihedral : 6.793 61.431 4025 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.25 % Allowed : 11.66 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.21), residues: 1666 helix: 2.09 (0.26), residues: 419 sheet: -0.03 (0.24), residues: 434 loop : -0.60 (0.21), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP L 96 HIS 0.006 0.001 HIS M 621 PHE 0.016 0.002 PHE K 53 TYR 0.013 0.001 TYR J 195 ARG 0.018 0.001 ARG J 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00304 ( 54) link_NAG-ASN : angle 1.86325 ( 162) link_ALPHA1-6 : bond 0.01828 ( 2) link_ALPHA1-6 : angle 3.35518 ( 6) link_BETA1-4 : bond 0.00478 ( 23) link_BETA1-4 : angle 2.27294 ( 69) link_ALPHA1-3 : bond 0.00813 ( 3) link_ALPHA1-3 : angle 1.97979 ( 9) hydrogen bonds : bond 0.04187 ( 567) hydrogen bonds : angle 4.49007 ( 1509) link_BETA1-6 : bond 0.00527 ( 1) link_BETA1-6 : angle 0.75563 ( 3) SS BOND : bond 0.00543 ( 28) SS BOND : angle 1.49013 ( 56) covalent geometry : bond 0.00511 (17311) covalent geometry : angle 0.61867 (23578) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 170 time to evaluate : 1.930 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 577 GLN cc_start: 0.8691 (mt0) cc_final: 0.8223 (tt0) REVERT: M 660 LYS cc_start: 0.5925 (tttt) cc_final: 0.4301 (tttm) REVERT: D 564 GLN cc_start: 0.8016 (tm-30) cc_final: 0.7628 (tt0) REVERT: D 589 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8348 (mttt) REVERT: D 661 LEU cc_start: 0.8892 (mp) cc_final: 0.8621 (mp) REVERT: I 565 GLN cc_start: 0.7136 (mm-40) cc_final: 0.6719 (pp30) REVERT: I 570 ASP cc_start: 0.7612 (t0) cc_final: 0.7346 (t0) REVERT: I 620 SER cc_start: 0.8454 (t) cc_final: 0.7943 (p) REVERT: I 655 GLN cc_start: 0.8172 (mt0) cc_final: 0.7864 (tt0) REVERT: K 49 GLU cc_start: 0.8943 (tt0) cc_final: 0.8692 (pt0) REVERT: K 211 LYS cc_start: 0.8775 (mttt) cc_final: 0.7823 (tptp) REVERT: K 282 THR cc_start: 0.8745 (m) cc_final: 0.8518 (p) REVERT: K 359 ARG cc_start: 0.7705 (mmt-90) cc_final: 0.7356 (mmt90) REVERT: K 477 MET cc_start: 0.8364 (mpp) cc_final: 0.7513 (mmt) REVERT: K 481 TRP cc_start: 0.8652 (m-10) cc_final: 0.6891 (m-10) REVERT: L 250 GLN cc_start: 0.7766 (mt0) cc_final: 0.7539 (tt0) REVERT: L 502 ARG cc_start: 0.6218 (ptt90) cc_final: 0.5994 (mtt-85) REVERT: J 111 LEU cc_start: 0.9062 (mt) cc_final: 0.8729 (mp) REVERT: J 133 GLN cc_start: 0.7735 (pp30) cc_final: 0.7366 (pp30) outliers start: 19 outliers final: 17 residues processed: 183 average time/residue: 0.3203 time to fit residues: 87.7249 Evaluate side-chains 187 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 169 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 638 SER Chi-restraints excluded: chain D residue 589 LYS Chi-restraints excluded: chain D residue 606 CYS Chi-restraints excluded: chain D residue 614 SER Chi-restraints excluded: chain D residue 619 SER Chi-restraints excluded: chain I residue 531 THR Chi-restraints excluded: chain I residue 597 ILE Chi-restraints excluded: chain K residue 373 ILE Chi-restraints excluded: chain L residue 74 CYS Chi-restraints excluded: chain L residue 126 CYS Chi-restraints excluded: chain L residue 209 CYS Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain L residue 294 GLU Chi-restraints excluded: chain L residue 328 ASN Chi-restraints excluded: chain L residue 418 ILE Chi-restraints excluded: chain J residue 126 CYS Chi-restraints excluded: chain J residue 209 CYS Chi-restraints excluded: chain J residue 269 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 195 optimal weight: 5.9990 chunk 102 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 43 optimal weight: 8.9990 chunk 18 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 40 optimal weight: 10.0000 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 72 HIS ** 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 = 0.3517 r_free = 0.3517 target = 0.129156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.106047 restraints weight = 26169.071| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.55 r_work: 0.3078 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 17422 Z= 0.172 Angle : 0.621 10.887 23883 Z= 0.291 Chirality : 0.044 0.275 2979 Planarity : 0.003 0.052 2941 Dihedral : 6.695 60.082 4025 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.38 % Allowed : 11.33 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.21), residues: 1666 helix: 2.11 (0.26), residues: 419 sheet: -0.03 (0.24), residues: 432 loop : -0.63 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J 429 HIS 0.005 0.001 HIS M 566 PHE 0.014 0.001 PHE K 53 TYR 0.016 0.001 TYR J 195 ARG 0.019 0.000 ARG J 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00288 ( 54) link_NAG-ASN : angle 1.80964 ( 162) link_ALPHA1-6 : bond 0.01719 ( 2) link_ALPHA1-6 : angle 3.32526 ( 6) link_BETA1-4 : bond 0.00484 ( 23) link_BETA1-4 : angle 2.20328 ( 69) link_ALPHA1-3 : bond 0.00859 ( 3) link_ALPHA1-3 : angle 1.84011 ( 9) hydrogen bonds : bond 0.03989 ( 567) hydrogen bonds : angle 4.45110 ( 1509) link_BETA1-6 : bond 0.00563 ( 1) link_BETA1-6 : angle 0.73306 ( 3) SS BOND : bond 0.00587 ( 28) SS BOND : angle 1.36191 ( 56) covalent geometry : bond 0.00409 (17311) covalent geometry : angle 0.58773 (23578) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8353.76 seconds wall clock time: 145 minutes 44.79 seconds (8744.79 seconds total)