Starting phenix.real_space_refine on Thu Sep 18 13:30:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9axi_43967/09_2025/9axi_43967.cif Found real_map, /net/cci-nas-00/data/ceres_data/9axi_43967/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9axi_43967/09_2025/9axi_43967.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9axi_43967/09_2025/9axi_43967.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9axi_43967/09_2025/9axi_43967.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9axi_43967/09_2025/9axi_43967.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 4.00, per 1000 atoms: 0.23 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: 1.80 Conformation dependent library (CDL) restraints added in 591.7 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.61 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: 2.77 Time building geometry restraints manager: 2.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 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 701) selection = (chain 'M' and (resid 521 through 548 or resid 562 through 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 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 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: 7.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.120 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.650 ------------------------------------------------------------------------------- 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 : 2.00 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.007 0.001 ARG I 635 TYR 0.052 0.003 TYR L 195 PHE 0.024 0.003 PHE L 53 TRP 0.038 0.003 TRP L 481 HIS 0.011 0.002 HIS I 566 Details of bonding type rmsd covalent geometry : bond 0.00698 (17311) covalent geometry : angle 1.03518 (23578) SS BOND : bond 0.00404 ( 28) SS BOND : angle 2.53442 ( 56) hydrogen bonds : bond 0.13727 ( 567) hydrogen bonds : angle 7.11742 ( 1509) link_ALPHA1-3 : bond 0.00451 ( 3) link_ALPHA1-3 : angle 2.16691 ( 9) 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_BETA1-6 : bond 0.00599 ( 1) link_BETA1-6 : angle 0.87499 ( 3) link_NAG-ASN : bond 0.00414 ( 54) link_NAG-ASN : angle 2.48761 ( 162) *********************** 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 : 0.617 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: 0.7474 (t0) REVERT: I 620 SER cc_start: 0.8221 (t) cc_final: 0.7856 (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: 0.8019 (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: 0.7416 (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: 0.5967 (mpt180) REVERT: J 111 LEU cc_start: 0.8951 (mt) cc_final: 0.8747 (mp) REVERT: J 115 SER cc_start: 0.9320 (t) cc_final: 0.9069 (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: 0.7760 (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: 0.1576 time to fit residues: 82.8346 Evaluate side-chains 188 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.0050 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.5980 chunk 200 optimal weight: 0.9980 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- 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 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 632 GLN ** I 655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 191 ASN L 379 ASN L 430 GLN J 220 HIS J 291 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.138350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.116004 restraints weight = 26194.038| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.45 r_work: 0.3244 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17422 Z= 0.130 Angle : 0.639 9.796 23883 Z= 0.304 Chirality : 0.044 0.284 2979 Planarity : 0.003 0.033 2941 Dihedral : 8.395 79.020 4025 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 1.25 % Allowed : 6.85 % Favored : 91.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.20), residues: 1666 helix: 2.36 (0.26), residues: 406 sheet: 0.71 (0.24), residues: 440 loop : 0.45 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 277 TYR 0.016 0.001 TYR L 195 PHE 0.020 0.002 PHE J 53 TRP 0.020 0.001 TRP L 481 HIS 0.008 0.001 HIS I 566 Details of bonding type rmsd covalent geometry : bond 0.00285 (17311) covalent geometry : angle 0.59730 (23578) SS BOND : bond 0.00263 ( 28) SS BOND : angle 1.29639 ( 56) hydrogen bonds : bond 0.04412 ( 567) hydrogen bonds : angle 5.11239 ( 1509) link_ALPHA1-3 : bond 0.00830 ( 3) link_ALPHA1-3 : angle 2.60905 ( 9) link_ALPHA1-6 : bond 0.02437 ( 2) link_ALPHA1-6 : angle 3.22987 ( 6) link_BETA1-4 : bond 0.00543 ( 23) link_BETA1-4 : angle 2.45238 ( 69) link_BETA1-6 : bond 0.00436 ( 1) link_BETA1-6 : angle 1.01153 ( 3) link_NAG-ASN : bond 0.00469 ( 54) link_NAG-ASN : angle 2.07813 ( 162) *********************** 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 234 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 215 time to evaluate : 0.445 Fit side-chains REVERT: M 577 GLN cc_start: 0.8695 (mt0) cc_final: 0.8277 (tt0) REVERT: I 566 HIS cc_start: 0.6642 (t70) cc_final: 0.6360 (t-90) REVERT: I 570 ASP cc_start: 0.7883 (t0) cc_final: 0.7489 (t0) REVERT: I 620 SER cc_start: 0.8473 (t) cc_final: 0.8102 (p) REVERT: K 211 LYS cc_start: 0.8419 (mttt) cc_final: 0.7770 (tptp) REVERT: K 306 ASN cc_start: 0.8296 (m-40) cc_final: 0.8056 (m110) REVERT: K 359 ARG cc_start: 0.7533 (mmt-90) cc_final: 0.7189 (mmt90) REVERT: K 477 MET cc_start: 0.8349 (tpp) cc_final: 0.8147 (mmt) REVERT: K 481 TRP cc_start: 0.8673 (m-10) cc_final: 0.7468 (m-10) REVERT: L 133 GLN cc_start: 0.7989 (mm-40) cc_final: 0.6817 (mp10) REVERT: L 250 GLN cc_start: 0.7903 (mt0) cc_final: 0.7380 (tp40) REVERT: L 502 ARG cc_start: 0.6535 (ptt90) cc_final: 0.6077 (mpt180) REVERT: J 111 LEU cc_start: 0.9021 (mt) cc_final: 0.8653 (mp) REVERT: J 195 TYR cc_start: 0.8902 (m-80) cc_final: 0.8624 (m-80) REVERT: J 215 ASP cc_start: 0.8400 (m-30) cc_final: 0.7796 (p0) outliers start: 19 outliers final: 16 residues processed: 224 average time/residue: 0.1325 time to fit residues: 44.7695 Evaluate side-chains 195 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 179 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 565 HIS Chi-restraints excluded: chain D residue 603 LEU Chi-restraints excluded: chain I 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 9 optimal weight: 2.9990 chunk 42 optimal weight: 9.9990 chunk 4 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 166 optimal weight: 0.9990 chunk 55 optimal weight: 9.9990 chunk 136 optimal weight: 4.9990 chunk 163 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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** ** J 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 427 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.132152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.108689 restraints weight = 26334.058| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.58 r_work: 0.3130 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17422 Z= 0.173 Angle : 0.626 9.753 23883 Z= 0.296 Chirality : 0.044 0.264 2979 Planarity : 0.003 0.045 2941 Dihedral : 7.555 72.692 4025 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.71 % Allowed : 7.25 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.20), residues: 1666 helix: 2.30 (0.26), residues: 419 sheet: 0.59 (0.24), residues: 428 loop : 0.09 (0.21), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG K 482 TYR 0.013 0.001 TYR L 195 PHE 0.017 0.002 PHE K 53 TRP 0.017 0.002 TRP K 481 HIS 0.006 0.002 HIS M 621 Details of bonding type rmsd covalent geometry : bond 0.00402 (17311) covalent geometry : angle 0.59072 (23578) SS BOND : bond 0.00521 ( 28) SS BOND : angle 1.20162 ( 56) hydrogen bonds : bond 0.04345 ( 567) hydrogen bonds : angle 4.69116 ( 1509) link_ALPHA1-3 : bond 0.00830 ( 3) link_ALPHA1-3 : angle 1.72666 ( 9) link_ALPHA1-6 : bond 0.01923 ( 2) link_ALPHA1-6 : angle 2.94462 ( 6) link_BETA1-4 : bond 0.00544 ( 23) link_BETA1-4 : angle 2.41806 ( 69) link_BETA1-6 : bond 0.00624 ( 1) link_BETA1-6 : angle 0.82623 ( 3) link_NAG-ASN : bond 0.00341 ( 54) link_NAG-ASN : angle 1.87836 ( 162) *********************** 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 202 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 176 time to evaluate : 0.616 Fit side-chains revert: symmetry clash REVERT: M 577 GLN cc_start: 0.8725 (mt0) cc_final: 0.8277 (tt0) REVERT: D 603 LEU cc_start: 0.9432 (OUTLIER) cc_final: 0.9139 (mp) REVERT: D 661 LEU cc_start: 0.8909 (mp) cc_final: 0.8663 (mp) REVERT: I 570 ASP cc_start: 0.7763 (t0) cc_final: 0.7486 (t0) REVERT: I 620 SER cc_start: 0.8410 (t) cc_final: 0.7970 (p) REVERT: I 646 ARG cc_start: 0.8315 (tpp80) cc_final: 0.8104 (mmt-90) REVERT: K 211 LYS cc_start: 0.8683 (mttt) cc_final: 0.7707 (tptp) REVERT: K 359 ARG cc_start: 0.7520 (mmt-90) cc_final: 0.7048 (mmt90) REVERT: K 466 GLU cc_start: 0.6856 (mt-10) cc_final: 0.6556 (mm-30) REVERT: K 477 MET cc_start: 0.8367 (tpp) cc_final: 0.7623 (mmt) REVERT: K 481 TRP cc_start: 0.8670 (m-10) cc_final: 0.6881 (m-10) REVERT: L 250 GLN cc_start: 0.7866 (mt0) cc_final: 0.7381 (tt0) REVERT: L 502 ARG cc_start: 0.6521 (ptt90) cc_final: 0.5964 (mpt180) REVERT: J 111 LEU cc_start: 0.9051 (mt) cc_final: 0.8721 (mp) REVERT: J 133 GLN cc_start: 0.7470 (pp30) cc_final: 0.7166 (pp30) REVERT: J 215 ASP cc_start: 0.8436 (m-30) cc_final: 0.7715 (p0) REVERT: J 436 MET cc_start: 0.9334 (ttp) cc_final: 0.9128 (ttt) outliers start: 26 outliers final: 16 residues processed: 194 average time/residue: 0.1381 time to fit residues: 39.5854 Evaluate side-chains 176 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 159 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 638 SER 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 D residue 614 SER Chi-restraints excluded: chain K residue 373 ILE Chi-restraints excluded: chain K residue 395 SER 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 336 ILE Chi-restraints excluded: chain L residue 418 ILE Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 427 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 48 optimal weight: 10.0000 chunk 151 optimal weight: 0.9990 chunk 113 optimal weight: 0.0070 chunk 104 optimal weight: 1.9990 chunk 129 optimal weight: 8.9990 chunk 88 optimal weight: 0.5980 chunk 71 optimal weight: 4.9990 chunk 199 optimal weight: 3.9990 chunk 76 optimal weight: 8.9990 chunk 204 optimal weight: 5.9990 chunk 94 optimal weight: 0.7980 overall best weight: 0.8802 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.133474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.110211 restraints weight = 26194.424| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.58 r_work: 0.3145 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17422 Z= 0.121 Angle : 0.559 9.746 23883 Z= 0.264 Chirality : 0.043 0.270 2979 Planarity : 0.003 0.038 2941 Dihedral : 7.090 67.325 4025 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.52 % Allowed : 7.51 % Favored : 90.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.20), residues: 1666 helix: 2.43 (0.26), residues: 415 sheet: 0.57 (0.24), residues: 426 loop : 0.02 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 166 TYR 0.008 0.001 TYR K 195 PHE 0.016 0.001 PHE I 522 TRP 0.014 0.001 TRP L 96 HIS 0.005 0.001 HIS M 566 Details of bonding type rmsd covalent geometry : bond 0.00272 (17311) covalent geometry : angle 0.52362 (23578) SS BOND : bond 0.00334 ( 28) SS BOND : angle 1.18010 ( 56) hydrogen bonds : bond 0.03747 ( 567) hydrogen bonds : angle 4.48818 ( 1509) link_ALPHA1-3 : bond 0.00945 ( 3) link_ALPHA1-3 : angle 1.83080 ( 9) link_ALPHA1-6 : bond 0.02014 ( 2) link_ALPHA1-6 : angle 3.17706 ( 6) link_BETA1-4 : bond 0.00495 ( 23) link_BETA1-4 : angle 2.23831 ( 69) link_BETA1-6 : bond 0.00496 ( 1) link_BETA1-6 : angle 0.80613 ( 3) link_NAG-ASN : bond 0.00307 ( 54) link_NAG-ASN : angle 1.70714 ( 162) *********************** 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 205 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 182 time to evaluate : 0.528 Fit side-chains REVERT: M 577 GLN cc_start: 0.8713 (mt0) cc_final: 0.8244 (tt0) REVERT: M 660 LYS cc_start: 0.5925 (tttt) cc_final: 0.4113 (tttm) REVERT: D 603 LEU cc_start: 0.9452 (OUTLIER) cc_final: 0.9169 (mp) REVERT: I 570 ASP cc_start: 0.7726 (t0) cc_final: 0.7381 (t0) REVERT: I 620 SER cc_start: 0.8406 (t) cc_final: 0.7980 (p) REVERT: I 646 ARG cc_start: 0.8363 (tpp80) cc_final: 0.8128 (mmt-90) REVERT: K 211 LYS cc_start: 0.8694 (mttt) cc_final: 0.7543 (tptp) REVERT: K 359 ARG cc_start: 0.7556 (mmt-90) cc_final: 0.7142 (mmt90) REVERT: K 477 MET cc_start: 0.8313 (tpp) cc_final: 0.7729 (mmt) REVERT: K 481 TRP cc_start: 0.8626 (m-10) cc_final: 0.7053 (m-10) REVERT: L 133 GLN cc_start: 0.7743 (mm-40) cc_final: 0.6562 (mp10) REVERT: L 250 GLN cc_start: 0.7807 (mt0) cc_final: 0.7322 (tt0) REVERT: L 502 ARG cc_start: 0.6500 (ptt90) cc_final: 0.5952 (mpt180) REVERT: J 111 LEU cc_start: 0.9038 (mt) cc_final: 0.8715 (mp) REVERT: J 133 GLN cc_start: 0.7517 (pp30) cc_final: 0.7243 (pp30) REVERT: J 195 TYR cc_start: 0.8890 (m-80) cc_final: 0.8571 (m-80) REVERT: J 215 ASP cc_start: 0.8389 (m-30) cc_final: 0.7646 (p0) REVERT: J 448 LYS cc_start: 0.8661 (tttt) cc_final: 0.8364 (tttm) outliers start: 23 outliers final: 14 residues processed: 195 average time/residue: 0.1299 time to fit residues: 38.0390 Evaluate side-chains 183 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 168 time to evaluate : 0.636 ------------------------------------------------------------------------------- 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 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 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 428 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 10 optimal weight: 0.6980 chunk 196 optimal weight: 2.9990 chunk 131 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 161 optimal weight: 2.9990 chunk 209 optimal weight: 0.9980 chunk 72 optimal weight: 8.9990 chunk 132 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 57 optimal weight: 10.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 379 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.133564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.110380 restraints weight = 25954.913| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.56 r_work: 0.3158 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 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 : 0.003 0.037 17422 Z= 0.115 Angle : 0.546 9.731 23883 Z= 0.257 Chirality : 0.043 0.312 2979 Planarity : 0.003 0.035 2941 Dihedral : 6.712 64.427 4025 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.25 % Allowed : 8.63 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.20), residues: 1666 helix: 2.46 (0.26), residues: 419 sheet: 0.52 (0.24), residues: 429 loop : -0.03 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 166 TYR 0.012 0.001 TYR K 486 PHE 0.020 0.001 PHE I 522 TRP 0.013 0.001 TRP L 96 HIS 0.004 0.001 HIS M 566 Details of bonding type rmsd covalent geometry : bond 0.00260 (17311) covalent geometry : angle 0.51129 (23578) SS BOND : bond 0.00303 ( 28) SS BOND : angle 1.14258 ( 56) hydrogen bonds : bond 0.03554 ( 567) hydrogen bonds : angle 4.36606 ( 1509) link_ALPHA1-3 : bond 0.00919 ( 3) link_ALPHA1-3 : angle 1.77080 ( 9) link_ALPHA1-6 : bond 0.01910 ( 2) link_ALPHA1-6 : angle 3.21137 ( 6) link_BETA1-4 : bond 0.00493 ( 23) link_BETA1-4 : angle 2.15685 ( 69) link_BETA1-6 : bond 0.00479 ( 1) link_BETA1-6 : angle 0.82945 ( 3) link_NAG-ASN : bond 0.00300 ( 54) link_NAG-ASN : angle 1.72238 ( 162) *********************** 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 206 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 187 time to evaluate : 0.451 Fit side-chains REVERT: M 577 GLN cc_start: 0.8700 (mt0) cc_final: 0.8241 (tt0) REVERT: M 660 LYS cc_start: 0.5885 (tttt) cc_final: 0.4357 (tttm) REVERT: D 564 GLN cc_start: 0.7818 (tm-30) cc_final: 0.7618 (tt0) REVERT: I 570 ASP cc_start: 0.7680 (t0) cc_final: 0.7428 (t0) REVERT: I 620 SER cc_start: 0.8387 (t) cc_final: 0.7964 (p) REVERT: I 646 ARG cc_start: 0.8345 (tpp80) cc_final: 0.8111 (mmt-90) REVERT: K 211 LYS cc_start: 0.8724 (mttt) cc_final: 0.7691 (tptp) REVERT: K 282 THR cc_start: 0.8779 (m) cc_final: 0.8545 (p) REVERT: K 359 ARG cc_start: 0.7536 (mmt-90) cc_final: 0.7111 (mmt90) REVERT: K 477 MET cc_start: 0.8235 (tpp) cc_final: 0.7605 (mmt) REVERT: K 481 TRP cc_start: 0.8601 (m-10) cc_final: 0.6975 (m-10) REVERT: L 250 GLN cc_start: 0.7800 (mt0) cc_final: 0.7461 (tt0) REVERT: L 502 ARG cc_start: 0.6459 (ptt90) cc_final: 0.5925 (mpt180) REVERT: J 111 LEU cc_start: 0.8997 (mt) cc_final: 0.8669 (mp) REVERT: J 133 GLN cc_start: 0.7532 (pp30) cc_final: 0.7287 (pp30) REVERT: J 215 ASP cc_start: 0.8358 (m-30) cc_final: 0.7612 (p0) REVERT: J 448 LYS cc_start: 0.8657 (tttt) cc_final: 0.8407 (ttmm) outliers start: 19 outliers final: 15 residues processed: 201 average time/residue: 0.1369 time to fit residues: 40.8587 Evaluate side-chains 189 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 174 time to evaluate : 0.585 ------------------------------------------------------------------------------- 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 616 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 146 optimal weight: 3.9990 chunk 183 optimal weight: 0.6980 chunk 78 optimal weight: 6.9990 chunk 70 optimal weight: 8.9990 chunk 126 optimal weight: 5.9990 chunk 76 optimal weight: 7.9990 chunk 140 optimal weight: 0.6980 chunk 50 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 62 optimal weight: 9.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 244 ASN ** J 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.128731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.105555 restraints weight = 26187.964| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.54 r_work: 0.3084 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 17422 Z= 0.232 Angle : 0.683 11.316 23883 Z= 0.320 Chirality : 0.046 0.269 2979 Planarity : 0.004 0.041 2941 Dihedral : 7.042 64.833 4025 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.52 % Allowed : 9.55 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.20), residues: 1666 helix: 2.18 (0.26), residues: 418 sheet: 0.13 (0.23), residues: 455 loop : -0.24 (0.21), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 166 TYR 0.018 0.002 TYR L 221 PHE 0.021 0.002 PHE K 53 TRP 0.016 0.001 TRP L 96 HIS 0.007 0.002 HIS M 621 Details of bonding type rmsd covalent geometry : bond 0.00554 (17311) covalent geometry : angle 0.64704 (23578) SS BOND : bond 0.00865 ( 28) SS BOND : angle 1.36993 ( 56) hydrogen bonds : bond 0.04530 ( 567) hydrogen bonds : angle 4.70409 ( 1509) link_ALPHA1-3 : bond 0.00785 ( 3) link_ALPHA1-3 : angle 2.18000 ( 9) link_ALPHA1-6 : bond 0.01768 ( 2) link_ALPHA1-6 : angle 3.20376 ( 6) link_BETA1-4 : bond 0.00478 ( 23) link_BETA1-4 : angle 2.43542 ( 69) link_BETA1-6 : bond 0.00582 ( 1) link_BETA1-6 : angle 0.82683 ( 3) link_NAG-ASN : bond 0.00330 ( 54) link_NAG-ASN : angle 1.97842 ( 162) *********************** 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 192 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 169 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 577 GLN cc_start: 0.8704 (mt0) cc_final: 0.8266 (tt0) REVERT: M 601 SER cc_start: 0.9374 (t) cc_final: 0.9130 (m) REVERT: D 603 LEU cc_start: 0.9471 (OUTLIER) cc_final: 0.9202 (mp) REVERT: D 661 LEU cc_start: 0.8926 (mp) cc_final: 0.8650 (mp) REVERT: I 548 SER cc_start: 0.7408 (t) cc_final: 0.7181 (m) REVERT: I 570 ASP cc_start: 0.7795 (t0) cc_final: 0.7502 (t0) REVERT: I 601 SER cc_start: 0.9228 (t) cc_final: 0.8901 (p) REVERT: I 620 SER cc_start: 0.8425 (t) cc_final: 0.7948 (p) REVERT: I 655 GLN cc_start: 0.8067 (mt0) cc_final: 0.7641 (tt0) REVERT: K 211 LYS cc_start: 0.8744 (mttt) cc_final: 0.7722 (tptp) REVERT: K 359 ARG cc_start: 0.7622 (mmt-90) cc_final: 0.7216 (mmt90) REVERT: K 466 GLU cc_start: 0.6886 (mt-10) cc_final: 0.6631 (mm-30) REVERT: K 477 MET cc_start: 0.8427 (tpp) cc_final: 0.7628 (mmt) REVERT: K 481 TRP cc_start: 0.8679 (m-10) cc_final: 0.6893 (m-10) REVERT: L 250 GLN cc_start: 0.7799 (mt0) cc_final: 0.7521 (tt0) REVERT: L 502 ARG cc_start: 0.6254 (ptt90) cc_final: 0.5775 (mpt180) REVERT: J 111 LEU cc_start: 0.9084 (mt) cc_final: 0.8763 (mp) REVERT: J 133 GLN cc_start: 0.7666 (pp30) cc_final: 0.7380 (pp30) outliers start: 23 outliers final: 18 residues processed: 186 average time/residue: 0.1450 time to fit residues: 40.2122 Evaluate side-chains 183 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 164 time to evaluate : 0.542 ------------------------------------------------------------------------------- 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 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 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 106 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 165 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 123 optimal weight: 0.0980 chunk 192 optimal weight: 0.5980 chunk 51 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 198 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.3557 r_free = 0.3557 target = 0.131934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.108996 restraints weight = 26017.634| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.54 r_work: 0.3138 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 17422 Z= 0.114 Angle : 0.561 10.554 23883 Z= 0.266 Chirality : 0.042 0.267 2979 Planarity : 0.003 0.034 2941 Dihedral : 6.503 59.890 4025 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.25 % Allowed : 10.34 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.20), residues: 1666 helix: 2.37 (0.26), residues: 419 sheet: 0.25 (0.24), residues: 432 loop : -0.27 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 166 TYR 0.011 0.001 TYR K 486 PHE 0.014 0.001 PHE I 522 TRP 0.014 0.001 TRP L 96 HIS 0.004 0.001 HIS M 566 Details of bonding type rmsd covalent geometry : bond 0.00259 (17311) covalent geometry : angle 0.52798 (23578) SS BOND : bond 0.00573 ( 28) SS BOND : angle 1.27273 ( 56) hydrogen bonds : bond 0.03576 ( 567) hydrogen bonds : angle 4.39628 ( 1509) link_ALPHA1-3 : bond 0.00930 ( 3) link_ALPHA1-3 : angle 1.71175 ( 9) link_ALPHA1-6 : bond 0.01893 ( 2) link_ALPHA1-6 : angle 3.27810 ( 6) link_BETA1-4 : bond 0.00500 ( 23) link_BETA1-4 : angle 2.13709 ( 69) link_BETA1-6 : bond 0.00477 ( 1) link_BETA1-6 : angle 0.76984 ( 3) link_NAG-ASN : bond 0.00280 ( 54) link_NAG-ASN : angle 1.66864 ( 162) *********************** 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: 19 poor density : 182 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 577 GLN cc_start: 0.8678 (mt0) cc_final: 0.8229 (tt0) REVERT: M 601 SER cc_start: 0.9324 (t) cc_final: 0.9102 (m) REVERT: M 660 LYS cc_start: 0.5914 (tttt) cc_final: 0.4234 (tttm) REVERT: D 564 GLN cc_start: 0.7915 (tm-30) cc_final: 0.7609 (tt0) REVERT: D 661 LEU cc_start: 0.8883 (mp) cc_final: 0.8634 (mp) REVERT: I 570 ASP cc_start: 0.7621 (t0) cc_final: 0.7325 (t0) REVERT: I 601 SER cc_start: 0.9210 (t) cc_final: 0.8887 (p) REVERT: I 620 SER cc_start: 0.8393 (t) cc_final: 0.7963 (p) REVERT: I 655 GLN cc_start: 0.8089 (mt0) cc_final: 0.7748 (tt0) REVERT: K 211 LYS cc_start: 0.8722 (mttt) cc_final: 0.7689 (tptp) REVERT: K 282 THR cc_start: 0.8763 (m) cc_final: 0.8523 (p) REVERT: K 359 ARG cc_start: 0.7638 (mmt-90) cc_final: 0.7217 (mmt90) REVERT: K 448 LYS cc_start: 0.8841 (ptmm) cc_final: 0.8570 (ptmm) REVERT: K 477 MET cc_start: 0.8302 (tpp) cc_final: 0.7648 (mmt) REVERT: K 481 TRP cc_start: 0.8600 (m-10) cc_final: 0.6984 (m-10) REVERT: L 250 GLN cc_start: 0.7769 (mt0) cc_final: 0.7439 (tp40) REVERT: L 502 ARG cc_start: 0.6309 (ptt90) cc_final: 0.5848 (mpt180) REVERT: J 84 MET cc_start: 0.8052 (ttp) cc_final: 0.7647 (ttp) REVERT: J 111 LEU cc_start: 0.9009 (mt) cc_final: 0.8689 (mp) REVERT: J 133 GLN cc_start: 0.7694 (pp30) cc_final: 0.7401 (pp30) REVERT: J 448 LYS cc_start: 0.8827 (tttt) cc_final: 0.8574 (tttm) outliers start: 19 outliers final: 17 residues processed: 196 average time/residue: 0.1511 time to fit residues: 43.9217 Evaluate side-chains 191 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 174 time to evaluate : 0.594 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 190 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 chunk 64 optimal weight: 8.9990 chunk 148 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 133 GLN ** J 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.125106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.101782 restraints weight = 26656.420| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.57 r_work: 0.2994 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.118 17422 Z= 0.398 Angle : 0.865 12.862 23883 Z= 0.403 Chirality : 0.053 0.301 2979 Planarity : 0.005 0.048 2941 Dihedral : 7.734 66.314 4025 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.65 % Allowed : 10.54 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.20), residues: 1666 helix: 1.53 (0.26), residues: 426 sheet: -0.31 (0.23), residues: 445 loop : -0.64 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 482 TYR 0.016 0.002 TYR K 486 PHE 0.027 0.003 PHE K 53 TRP 0.020 0.002 TRP D 572 HIS 0.009 0.002 HIS M 621 Details of bonding type rmsd covalent geometry : bond 0.00956 (17311) covalent geometry : angle 0.82847 (23578) SS BOND : bond 0.00737 ( 28) SS BOND : angle 1.54188 ( 56) hydrogen bonds : bond 0.05455 ( 567) hydrogen bonds : angle 5.03062 ( 1509) link_ALPHA1-3 : bond 0.00594 ( 3) link_ALPHA1-3 : angle 2.35719 ( 9) link_ALPHA1-6 : bond 0.01557 ( 2) link_ALPHA1-6 : angle 3.38473 ( 6) link_BETA1-4 : bond 0.00508 ( 23) link_BETA1-4 : angle 2.75759 ( 69) link_BETA1-6 : bond 0.00667 ( 1) link_BETA1-6 : angle 0.97509 ( 3) link_NAG-ASN : bond 0.00467 ( 54) link_NAG-ASN : angle 2.34618 ( 162) *********************** 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 191 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 166 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 577 GLN cc_start: 0.8762 (mt0) cc_final: 0.8316 (tt0) REVERT: M 590 LYS cc_start: 0.9255 (tmmt) cc_final: 0.8913 (tttm) REVERT: D 603 LEU cc_start: 0.9503 (OUTLIER) cc_final: 0.9236 (mp) REVERT: I 548 SER cc_start: 0.7561 (t) cc_final: 0.7229 (m) REVERT: I 570 ASP cc_start: 0.7930 (t0) cc_final: 0.7634 (t0) REVERT: I 620 SER cc_start: 0.8497 (t) cc_final: 0.7953 (p) REVERT: K 359 ARG cc_start: 0.7726 (mmt-90) cc_final: 0.7196 (mmt90) REVERT: K 466 GLU cc_start: 0.6843 (mt-10) cc_final: 0.6497 (mm-30) REVERT: K 481 TRP cc_start: 0.8754 (m-10) cc_final: 0.6803 (m-10) REVERT: L 250 GLN cc_start: 0.8088 (mt0) cc_final: 0.7723 (tp40) REVERT: L 502 ARG cc_start: 0.6329 (ptt90) cc_final: 0.5964 (mtt-85) REVERT: J 83 GLU cc_start: 0.7989 (tt0) cc_final: 0.7690 (tm-30) REVERT: J 111 LEU cc_start: 0.9153 (mt) cc_final: 0.8631 (mp) REVERT: J 133 GLN cc_start: 0.7716 (pp30) cc_final: 0.7360 (pp30) REVERT: J 448 LYS cc_start: 0.8964 (tttt) cc_final: 0.8744 (ttmm) outliers start: 25 outliers final: 19 residues processed: 185 average time/residue: 0.1528 time to fit residues: 42.0694 Evaluate side-chains 179 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 159 time to evaluate : 0.647 ------------------------------------------------------------------------------- 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 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 96 TRP Chi-restraints excluded: chain L residue 126 CYS Chi-restraints excluded: chain L residue 209 CYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 193 optimal weight: 1.9990 chunk 50 optimal weight: 9.9990 chunk 175 optimal weight: 0.9980 chunk 109 optimal weight: 0.7980 chunk 76 optimal weight: 6.9990 chunk 119 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 192 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 = 0.3510 r_free = 0.3510 target = 0.128691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.105685 restraints weight = 26158.402| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.55 r_work: 0.3074 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 17422 Z= 0.170 Angle : 0.645 10.658 23883 Z= 0.302 Chirality : 0.045 0.294 2979 Planarity : 0.003 0.054 2941 Dihedral : 7.074 60.943 4025 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.05 % Allowed : 11.33 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.20), residues: 1666 helix: 1.93 (0.26), residues: 420 sheet: -0.20 (0.24), residues: 441 loop : -0.64 (0.21), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG J 166 TYR 0.011 0.001 TYR K 486 PHE 0.013 0.001 PHE K 53 TRP 0.016 0.001 TRP L 96 HIS 0.004 0.001 HIS M 566 Details of bonding type rmsd covalent geometry : bond 0.00403 (17311) covalent geometry : angle 0.61040 (23578) SS BOND : bond 0.00623 ( 28) SS BOND : angle 1.36316 ( 56) hydrogen bonds : bond 0.04175 ( 567) hydrogen bonds : angle 4.60762 ( 1509) link_ALPHA1-3 : bond 0.00926 ( 3) link_ALPHA1-3 : angle 1.81064 ( 9) link_ALPHA1-6 : bond 0.01848 ( 2) link_ALPHA1-6 : angle 3.26345 ( 6) link_BETA1-4 : bond 0.00500 ( 23) link_BETA1-4 : angle 2.28606 ( 69) link_BETA1-6 : bond 0.00520 ( 1) link_BETA1-6 : angle 0.73818 ( 3) link_NAG-ASN : bond 0.00301 ( 54) link_NAG-ASN : angle 1.91695 ( 162) *********************** 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 181 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 165 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 577 GLN cc_start: 0.8699 (mt0) cc_final: 0.8255 (tt0) REVERT: M 660 LYS cc_start: 0.5916 (tttt) cc_final: 0.4307 (tttm) REVERT: D 564 GLN cc_start: 0.7908 (tm-30) cc_final: 0.7603 (tt0) REVERT: I 566 HIS cc_start: 0.6738 (t-90) cc_final: 0.6509 (t-90) REVERT: I 570 ASP cc_start: 0.7719 (t0) cc_final: 0.7409 (t0) REVERT: I 620 SER cc_start: 0.8429 (t) cc_final: 0.7935 (p) REVERT: I 655 GLN cc_start: 0.8115 (mt0) cc_final: 0.7738 (tt0) REVERT: K 359 ARG cc_start: 0.7695 (mmt-90) cc_final: 0.7378 (mmt90) REVERT: K 477 MET cc_start: 0.8361 (tpp) cc_final: 0.7573 (mmt) REVERT: K 481 TRP cc_start: 0.8667 (m-10) cc_final: 0.6962 (m-10) REVERT: L 250 GLN cc_start: 0.7954 (mt0) cc_final: 0.7635 (tp40) REVERT: L 502 ARG cc_start: 0.6321 (ptt90) cc_final: 0.5798 (mpt180) REVERT: J 83 GLU cc_start: 0.7950 (tt0) cc_final: 0.7730 (tm-30) REVERT: J 111 LEU cc_start: 0.9064 (mt) cc_final: 0.8731 (mp) REVERT: J 133 GLN cc_start: 0.7740 (pp30) cc_final: 0.7386 (pp30) REVERT: J 448 LYS cc_start: 0.8925 (tttt) cc_final: 0.8711 (ttmm) outliers start: 16 outliers final: 15 residues processed: 180 average time/residue: 0.1514 time to fit residues: 40.0783 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 : 0.605 ------------------------------------------------------------------------------- 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 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 126 CYS Chi-restraints excluded: chain L residue 209 CYS 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 77 optimal weight: 8.9990 chunk 210 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 141 optimal weight: 0.4980 chunk 55 optimal weight: 9.9990 chunk 151 optimal weight: 3.9990 chunk 190 optimal weight: 0.3980 chunk 135 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 93 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 overall best weight: 1.3382 ------------------------------------------------------------------------------- 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 = 0.3520 r_free = 0.3520 target = 0.129460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.106523 restraints weight = 26012.610| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.53 r_work: 0.3092 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17422 Z= 0.155 Angle : 0.609 9.677 23883 Z= 0.286 Chirality : 0.044 0.278 2979 Planarity : 0.003 0.056 2941 Dihedral : 6.687 60.277 4025 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.05 % Allowed : 11.53 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.20), residues: 1666 helix: 2.10 (0.26), residues: 419 sheet: -0.01 (0.24), residues: 427 loop : -0.66 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG J 166 TYR 0.011 0.001 TYR K 486 PHE 0.012 0.001 PHE K 53 TRP 0.014 0.001 TRP L 96 HIS 0.004 0.001 HIS M 566 Details of bonding type rmsd covalent geometry : bond 0.00367 (17311) covalent geometry : angle 0.57570 (23578) SS BOND : bond 0.00541 ( 28) SS BOND : angle 1.26014 ( 56) hydrogen bonds : bond 0.03930 ( 567) hydrogen bonds : angle 4.43930 ( 1509) link_ALPHA1-3 : bond 0.00847 ( 3) link_ALPHA1-3 : angle 1.85597 ( 9) link_ALPHA1-6 : bond 0.01676 ( 2) link_ALPHA1-6 : angle 3.34307 ( 6) link_BETA1-4 : bond 0.00486 ( 23) link_BETA1-4 : angle 2.20372 ( 69) link_BETA1-6 : bond 0.00500 ( 1) link_BETA1-6 : angle 0.70764 ( 3) link_NAG-ASN : bond 0.00291 ( 54) link_NAG-ASN : angle 1.79696 ( 162) ********************** 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 184 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 168 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 577 GLN cc_start: 0.8682 (mt0) cc_final: 0.8220 (tt0) REVERT: M 660 LYS cc_start: 0.5907 (tttt) cc_final: 0.4295 (tttm) REVERT: D 564 GLN cc_start: 0.8055 (tm-30) cc_final: 0.7696 (tt0) REVERT: I 566 HIS cc_start: 0.6752 (t-90) cc_final: 0.6487 (t-90) REVERT: I 570 ASP cc_start: 0.7591 (t0) cc_final: 0.7339 (t0) REVERT: I 620 SER cc_start: 0.8431 (t) cc_final: 0.7956 (p) REVERT: I 655 GLN cc_start: 0.8139 (mt0) cc_final: 0.7783 (tt0) REVERT: K 282 THR cc_start: 0.8723 (m) cc_final: 0.8489 (p) REVERT: K 359 ARG cc_start: 0.7725 (mmt-90) cc_final: 0.7366 (mmt90) REVERT: K 477 MET cc_start: 0.8339 (tpp) cc_final: 0.7562 (mmt) REVERT: K 481 TRP cc_start: 0.8637 (m-10) cc_final: 0.6888 (m-10) REVERT: L 250 GLN cc_start: 0.7971 (mt0) cc_final: 0.7648 (tp40) REVERT: L 502 ARG cc_start: 0.6282 (ptt90) cc_final: 0.6039 (mtt-85) REVERT: J 35 TRP cc_start: 0.9024 (m100) cc_final: 0.8759 (m100) REVERT: J 111 LEU cc_start: 0.9047 (mt) cc_final: 0.8701 (mp) REVERT: J 133 GLN cc_start: 0.7746 (pp30) cc_final: 0.7373 (pp30) REVERT: J 448 LYS cc_start: 0.8926 (tttt) cc_final: 0.8684 (ttmm) outliers start: 16 outliers final: 16 residues processed: 181 average time/residue: 0.1533 time to fit residues: 40.8916 Evaluate side-chains 181 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 165 time to evaluate : 0.545 ------------------------------------------------------------------------------- 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 I residue 597 ILE Chi-restraints excluded: chain K residue 49 GLU 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 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 41 optimal weight: 7.9990 chunk 97 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 chunk 142 optimal weight: 0.7980 chunk 117 optimal weight: 5.9990 chunk 161 optimal weight: 3.9990 chunk 150 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 chunk 159 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 579 GLN ** J 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.130157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.107132 restraints weight = 26164.062| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.56 r_work: 0.3101 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17422 Z= 0.144 Angle : 0.590 9.275 23883 Z= 0.278 Chirality : 0.043 0.268 2979 Planarity : 0.003 0.052 2941 Dihedral : 6.431 59.454 4025 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.12 % Allowed : 11.26 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.21), residues: 1666 helix: 2.19 (0.27), residues: 419 sheet: -0.07 (0.24), residues: 438 loop : -0.59 (0.21), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG J 166 TYR 0.011 0.001 TYR K 486 PHE 0.019 0.001 PHE I 522 TRP 0.014 0.001 TRP L 96 HIS 0.004 0.001 HIS M 566 Details of bonding type rmsd covalent geometry : bond 0.00339 (17311) covalent geometry : angle 0.55780 (23578) SS BOND : bond 0.00523 ( 28) SS BOND : angle 1.19353 ( 56) hydrogen bonds : bond 0.03785 ( 567) hydrogen bonds : angle 4.35921 ( 1509) link_ALPHA1-3 : bond 0.00865 ( 3) link_ALPHA1-3 : angle 1.77006 ( 9) link_ALPHA1-6 : bond 0.01561 ( 2) link_ALPHA1-6 : angle 3.27340 ( 6) link_BETA1-4 : bond 0.00500 ( 23) link_BETA1-4 : angle 2.15030 ( 69) link_BETA1-6 : bond 0.00512 ( 1) link_BETA1-6 : angle 0.71451 ( 3) link_NAG-ASN : bond 0.00292 ( 54) link_NAG-ASN : angle 1.74127 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4176.33 seconds wall clock time: 72 minutes 14.97 seconds (4334.97 seconds total)