Starting phenix.real_space_refine on Sun Jun 15 08:27:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9axi_43967/06_2025/9axi_43967.cif Found real_map, /net/cci-nas-00/data/ceres_data/9axi_43967/06_2025/9axi_43967.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9axi_43967/06_2025/9axi_43967.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9axi_43967/06_2025/9axi_43967.map" model { file = "/net/cci-nas-00/data/ceres_data/9axi_43967/06_2025/9axi_43967.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9axi_43967/06_2025/9axi_43967.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 102 5.16 5 C 10599 2.51 5 N 2920 2.21 5 O 3410 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 17031 Number of models: 1 Model: "" Number of chains: 37 Chain: "M" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1075 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 1, 'TRANS': 134} Chain breaks: 1 Chain: "D" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1043 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 1, 'TRANS': 128} Chain breaks: 1 Chain: "I" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1067 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 1, 'TRANS': 132} Chain breaks: 1 Chain: "F" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 550 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'TRANS': 109} Unresolved non-hydrogen bonds: 220 Unresolved non-hydrogen angles: 330 Unresolved non-hydrogen dihedrals: 110 Planarities with less than four sites: {'UNK:plan-1': 110} Unresolved non-hydrogen planarities: 110 Chain: "H" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 595 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 119} Link IDs: {'TRANS': 118} Unresolved non-hydrogen bonds: 238 Unresolved non-hydrogen angles: 357 Unresolved non-hydrogen dihedrals: 119 Planarities with less than four sites: {'UNK:plan-1': 119} Unresolved non-hydrogen planarities: 119 Chain: "A" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 610 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 122} Link IDs: {'TRANS': 121} Unresolved non-hydrogen bonds: 244 Unresolved non-hydrogen angles: 366 Unresolved non-hydrogen dihedrals: 122 Planarities with less than four sites: {'UNK:plan-1': 122} Unresolved non-hydrogen planarities: 122 Chain: "B" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 545 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 109} Link IDs: {'TRANS': 108} Unresolved non-hydrogen bonds: 218 Unresolved non-hydrogen angles: 327 Unresolved non-hydrogen dihedrals: 109 Planarities with less than four sites: {'UNK:plan-1': 109} Unresolved non-hydrogen planarities: 109 Chain: "K" Number of atoms: 3496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3496 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 23, 'TRANS': 415} Chain breaks: 3 Chain: "L" Number of atoms: 3425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3425 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 23, 'TRANS': 405} Chain breaks: 4 Chain: "J" Number of atoms: 3476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3476 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 23, 'TRANS': 412} Chain breaks: 3 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "L" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 109 Unusual residues: {'MAN': 1, 'NAG': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "J" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 12.13, per 1000 atoms: 0.71 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: 5.00 Conformation dependent library (CDL) restraints added in 1.8 seconds 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4112 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 30 sheets defined 31.3% alpha, 28.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.89 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: 5.58 Time building geometry restraints manager: 5.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5409 1.34 - 1.46: 4254 1.46 - 1.59: 7516 1.59 - 1.72: 0 1.72 - 1.84: 132 Bond restraints: 17311 Sorted by residual: bond pdb=" C1 MAN G 5 " pdb=" O5 MAN G 5 " ideal model delta sigma weight residual 1.399 1.481 -0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" C1 MAN G 5 " pdb=" C2 MAN G 5 " ideal model delta sigma weight residual 1.526 1.590 -0.064 2.00e-02 2.50e+03 1.01e+01 bond pdb=" N ILE J 469 " pdb=" CA ILE J 469 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.20e-02 6.94e+03 8.07e+00 bond pdb=" N SER J 56 " pdb=" CA SER J 56 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.18e-02 7.18e+03 7.87e+00 bond pdb=" C3 BMA G 3 " pdb=" C4 BMA G 3 " ideal model delta sigma weight residual 1.541 1.486 0.055 2.00e-02 2.50e+03 7.61e+00 ... (remaining 17306 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 22371 2.17 - 4.34: 1085 4.34 - 6.50: 107 6.50 - 8.67: 12 8.67 - 10.84: 3 Bond angle restraints: 23578 Sorted by residual: angle pdb=" N MET J 477 " pdb=" CA MET J 477 " pdb=" C MET J 477 " ideal model delta sigma weight residual 113.18 102.34 10.84 1.21e+00 6.83e-01 8.03e+01 angle pdb=" N ASN J 479 " pdb=" CA ASN J 479 " pdb=" C ASN J 479 " ideal model delta sigma weight residual 113.38 103.34 10.04 1.23e+00 6.61e-01 6.66e+01 angle pdb=" N VAL J 68 " pdb=" CA VAL J 68 " pdb=" C VAL J 68 " ideal model delta sigma weight residual 108.53 101.62 6.91 1.22e+00 6.72e-01 3.21e+01 angle pdb=" C ASN J 479 " pdb=" CA ASN J 479 " pdb=" CB ASN J 479 " ideal model delta sigma weight residual 109.65 118.02 -8.37 1.74e+00 3.30e-01 2.31e+01 angle pdb=" N HIS J 72 " pdb=" CA HIS J 72 " pdb=" C HIS J 72 " ideal model delta sigma weight residual 110.36 103.26 7.10 1.55e+00 4.16e-01 2.10e+01 ... (remaining 23573 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.20: 11158 22.20 - 44.39: 239 44.39 - 66.59: 65 66.59 - 88.79: 34 88.79 - 110.99: 12 Dihedral angle restraints: 11508 sinusoidal: 5201 harmonic: 6307 Sorted by residual: dihedral pdb=" CB CYS K 380 " pdb=" SG CYS K 380 " pdb=" SG CYS K 447 " pdb=" CB CYS K 447 " ideal model delta sinusoidal sigma weight residual -86.00 -133.32 47.32 1 1.00e+01 1.00e-02 3.09e+01 dihedral pdb=" CB CYS J 380 " pdb=" SG CYS J 380 " pdb=" SG CYS J 447 " pdb=" CB CYS J 447 " ideal model delta sinusoidal sigma weight residual -86.00 -132.56 46.56 1 1.00e+01 1.00e-02 3.00e+01 dihedral pdb=" CB CYS L 380 " pdb=" SG CYS L 380 " pdb=" SG CYS L 447 " pdb=" CB CYS L 447 " ideal model delta sinusoidal sigma weight residual -86.00 -131.20 45.20 1 1.00e+01 1.00e-02 2.84e+01 ... (remaining 11505 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2304 0.064 - 0.128: 571 0.128 - 0.191: 91 0.191 - 0.255: 6 0.255 - 0.319: 7 Chirality restraints: 2979 Sorted by residual: chirality pdb=" C1 NAG I 703 " pdb=" ND2 ASN I 618 " pdb=" C2 NAG I 703 " pdb=" O5 NAG I 703 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" C1 NAG D 701 " pdb=" ND2 ASN D 612 " pdb=" C2 NAG D 701 " pdb=" O5 NAG D 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.06e+00 ... (remaining 2976 not shown) Planarity restraints: 2995 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG K 478 " -0.021 2.00e-02 2.50e+03 4.22e-02 1.78e+01 pdb=" C ARG K 478 " 0.073 2.00e-02 2.50e+03 pdb=" O ARG K 478 " -0.027 2.00e-02 2.50e+03 pdb=" N ASN K 479 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER I 638 " -0.020 2.00e-02 2.50e+03 3.93e-02 1.54e+01 pdb=" C SER I 638 " 0.068 2.00e-02 2.50e+03 pdb=" O SER I 638 " -0.025 2.00e-02 2.50e+03 pdb=" N ASN I 639 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN I 579 " 0.018 2.00e-02 2.50e+03 3.69e-02 1.36e+01 pdb=" C GLN I 579 " -0.064 2.00e-02 2.50e+03 pdb=" O GLN I 579 " 0.024 2.00e-02 2.50e+03 pdb=" N THR I 580 " 0.021 2.00e-02 2.50e+03 ... (remaining 2992 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2320 2.76 - 3.29: 15998 3.29 - 3.83: 26514 3.83 - 4.36: 31365 4.36 - 4.90: 54024 Nonbonded interactions: 130221 Sorted by model distance: nonbonded pdb=" NH2 ARG D 544 " pdb=" OE1 GLU I 656 " model vdw 2.219 3.120 nonbonded pdb=" O ASN K 480 " pdb=" OG SER K 483 " model vdw 2.289 3.040 nonbonded pdb=" OD1 ASN L 362 " pdb=" OG1 THR L 396 " model vdw 2.292 3.040 nonbonded pdb=" O ASN L 480 " pdb=" OG SER L 483 " model vdw 2.330 3.040 nonbonded pdb=" OG SER L 260 " pdb=" O LEU L 263 " model vdw 2.336 3.040 ... (remaining 130216 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 15 through 123) selection = chain 'B' selection = (chain 'F' and resid 2 through 110) selection = (chain 'H' and resid 11 through 119) } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'c' selection = chain 'd' selection = chain 'e' } ncs_group { reference = chain 'D' selection = (chain 'I' and (resid 521 through 663 or resid 701)) selection = (chain 'M' and (resid 521 through 548 or resid 562 through 663 or resid 701)) } ncs_group { reference = chain 'G' selection = chain 'b' } ncs_group { reference = (chain 'J' and (resid 34 through 58 or resid 66 through 135 or resid 153 through \ 460 or resid 466 through 506 or resid 601 through 606 or resid 608)) selection = (chain 'K' and (resid 34 through 58 or resid 66 through 135 or resid 153 through \ 397 or resid 414 through 460 or resid 466 through 506 or resid 601 through 606 \ or resid 608)) selection = (chain 'L' and (resid 34 through 397 or resid 414 through 506 or resid 601 throu \ gh 606 or resid 608)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.720 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 41.430 Find NCS groups from input model: 1.100 Set up NCS constraints: 0.110 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 17422 Z= 0.332 Angle : 1.079 16.786 23883 Z= 0.574 Chirality : 0.057 0.319 2979 Planarity : 0.007 0.076 2941 Dihedral : 11.482 110.987 7312 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.19), residues: 1666 helix: 0.46 (0.23), residues: 417 sheet: 0.69 (0.24), residues: 422 loop : 0.44 (0.20), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP L 481 HIS 0.011 0.002 HIS I 566 PHE 0.024 0.003 PHE L 53 TYR 0.052 0.003 TYR L 195 ARG 0.007 0.001 ARG I 635 Details of bonding type rmsd link_NAG-ASN : bond 0.00414 ( 54) link_NAG-ASN : angle 2.48761 ( 162) link_ALPHA1-6 : bond 0.01811 ( 2) link_ALPHA1-6 : angle 2.52477 ( 6) link_BETA1-4 : bond 0.00713 ( 23) link_BETA1-4 : angle 3.99149 ( 69) link_ALPHA1-3 : bond 0.00451 ( 3) link_ALPHA1-3 : angle 2.16691 ( 9) hydrogen bonds : bond 0.13727 ( 567) hydrogen bonds : angle 7.11742 ( 1509) link_BETA1-6 : bond 0.00599 ( 1) link_BETA1-6 : angle 0.87499 ( 3) SS BOND : bond 0.00404 ( 28) SS BOND : angle 2.53442 ( 56) covalent geometry : bond 0.00698 (17311) covalent geometry : angle 1.03518 (23578) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 367 time to evaluate : 1.781 Fit side-chains revert: symmetry clash REVERT: M 577 GLN cc_start: 0.8367 (mt0) cc_final: 0.7983 (tt0) REVERT: I 570 ASP cc_start: 0.7734 (t0) cc_final: 0.7480 (t0) REVERT: I 620 SER cc_start: 0.8221 (t) cc_final: 0.7857 (p) REVERT: I 649 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7605 (mt-10) REVERT: I 650 ASP cc_start: 0.8174 (m-30) cc_final: 0.7935 (m-30) REVERT: I 651 SER cc_start: 0.8392 (t) cc_final: 0.8020 (p) REVERT: K 306 ASN cc_start: 0.8273 (m-40) cc_final: 0.8059 (m110) REVERT: K 359 ARG cc_start: 0.7417 (mmt-90) cc_final: 0.7201 (mmt90) REVERT: K 481 TRP cc_start: 0.8560 (m-10) cc_final: 0.7417 (m-10) REVERT: L 250 GLN cc_start: 0.7930 (mt0) cc_final: 0.7485 (tp40) REVERT: L 502 ARG cc_start: 0.6381 (ptt90) cc_final: 0.5981 (mpt180) REVERT: J 111 LEU cc_start: 0.8951 (mt) cc_final: 0.8748 (mp) REVERT: J 115 SER cc_start: 0.9320 (t) cc_final: 0.9068 (p) REVERT: J 195 TYR cc_start: 0.8790 (m-80) cc_final: 0.8552 (m-80) REVERT: J 215 ASP cc_start: 0.8192 (m-30) cc_final: 0.7759 (p0) REVERT: J 502 ARG cc_start: 0.7525 (mtt-85) cc_final: 0.7047 (ptt90) outliers start: 0 outliers final: 0 residues processed: 367 average time/residue: 0.3339 time to fit residues: 174.6209 Evaluate side-chains 187 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 1.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 178 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 54 optimal weight: 9.9990 chunk 107 optimal weight: 0.9980 chunk 85 optimal weight: 8.9990 chunk 165 optimal weight: 6.9990 chunk 63 optimal weight: 9.9990 chunk 100 optimal weight: 0.9990 chunk 123 optimal weight: 7.9990 chunk 191 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 621 HIS M 632 GLN M 654 GLN I 632 GLN ** I 655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 191 ASN L 379 ASN L 430 GLN J 220 HIS J 291 HIS J 427 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.136600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.114176 restraints weight = 26330.216| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.44 r_work: 0.3219 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17422 Z= 0.156 Angle : 0.664 9.784 23883 Z= 0.315 Chirality : 0.045 0.286 2979 Planarity : 0.003 0.032 2941 Dihedral : 8.433 79.266 4025 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 1.38 % Allowed : 6.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.20), residues: 1666 helix: 2.28 (0.26), residues: 406 sheet: 0.68 (0.24), residues: 434 loop : 0.39 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP L 481 HIS 0.012 0.001 HIS I 566 PHE 0.019 0.002 PHE J 53 TYR 0.018 0.001 TYR L 195 ARG 0.005 0.001 ARG J 277 Details of bonding type rmsd link_NAG-ASN : bond 0.00448 ( 54) link_NAG-ASN : angle 2.12578 ( 162) link_ALPHA1-6 : bond 0.02218 ( 2) link_ALPHA1-6 : angle 3.05794 ( 6) link_BETA1-4 : bond 0.00487 ( 23) link_BETA1-4 : angle 2.50778 ( 69) link_ALPHA1-3 : bond 0.00773 ( 3) link_ALPHA1-3 : angle 2.65693 ( 9) hydrogen bonds : bond 0.04587 ( 567) hydrogen bonds : angle 5.11122 ( 1509) link_BETA1-6 : bond 0.00499 ( 1) link_BETA1-6 : angle 0.98562 ( 3) SS BOND : bond 0.00377 ( 28) SS BOND : angle 1.46283 ( 56) covalent geometry : bond 0.00355 (17311) covalent geometry : angle 0.62168 (23578) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 207 time to evaluate : 1.717 Fit side-chains REVERT: M 577 GLN cc_start: 0.8704 (mt0) cc_final: 0.8299 (tt0) REVERT: I 570 ASP cc_start: 0.7960 (t0) cc_final: 0.7574 (t0) REVERT: I 620 SER cc_start: 0.8507 (t) cc_final: 0.8134 (p) REVERT: K 336 ILE cc_start: 0.9114 (mt) cc_final: 0.8910 (tt) REVERT: K 359 ARG cc_start: 0.7546 (mmt-90) cc_final: 0.7189 (mmt90) REVERT: K 477 MET cc_start: 0.8390 (tpp) cc_final: 0.8149 (mmt) REVERT: K 481 TRP cc_start: 0.8699 (m-10) cc_final: 0.7419 (m-10) REVERT: L 133 GLN cc_start: 0.8016 (mm-40) cc_final: 0.6828 (mp10) REVERT: L 250 GLN cc_start: 0.7970 (mt0) cc_final: 0.7441 (tp40) REVERT: L 502 ARG cc_start: 0.6490 (ptt90) cc_final: 0.6053 (mpt180) REVERT: J 111 LEU cc_start: 0.9048 (mt) cc_final: 0.8668 (mp) REVERT: J 215 ASP cc_start: 0.8390 (m-30) cc_final: 0.7816 (p0) outliers start: 21 outliers final: 18 residues processed: 219 average time/residue: 0.3156 time to fit residues: 102.8807 Evaluate side-chains 198 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 180 time to evaluate : 1.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 638 SER Chi-restraints excluded: chain D residue 565 HIS Chi-restraints excluded: chain D residue 603 LEU Chi-restraints excluded: chain D residue 614 SER Chi-restraints excluded: chain K residue 395 SER Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain L residue 294 GLU Chi-restraints excluded: chain L residue 328 ASN Chi-restraints excluded: chain L residue 336 ILE Chi-restraints excluded: chain L residue 390 SER Chi-restraints excluded: chain L residue 418 ILE Chi-restraints excluded: chain L residue 428 MET Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain J residue 96 TRP Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 427 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 107 optimal weight: 0.8980 chunk 48 optimal weight: 10.0000 chunk 144 optimal weight: 3.9990 chunk 141 optimal weight: 6.9990 chunk 204 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 78 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 138 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 306 ASN ** 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 = 0.3549 r_free = 0.3549 target = 0.131561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.108040 restraints weight = 25988.505| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.57 r_work: 0.3121 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17422 Z= 0.187 Angle : 0.637 9.932 23883 Z= 0.301 Chirality : 0.045 0.272 2979 Planarity : 0.003 0.046 2941 Dihedral : 7.775 74.001 4025 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.58 % Allowed : 7.91 % Favored : 90.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.20), residues: 1666 helix: 2.24 (0.26), residues: 419 sheet: 0.51 (0.24), residues: 429 loop : 0.06 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP L 481 HIS 0.006 0.002 HIS M 621 PHE 0.018 0.002 PHE I 522 TYR 0.012 0.001 TYR L 195 ARG 0.003 0.001 ARG J 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00329 ( 54) link_NAG-ASN : angle 1.92512 ( 162) link_ALPHA1-6 : bond 0.02188 ( 2) link_ALPHA1-6 : angle 2.98513 ( 6) link_BETA1-4 : bond 0.00474 ( 23) link_BETA1-4 : angle 2.48175 ( 69) link_ALPHA1-3 : bond 0.00839 ( 3) link_ALPHA1-3 : angle 1.73483 ( 9) hydrogen bonds : bond 0.04498 ( 567) hydrogen bonds : angle 4.75997 ( 1509) link_BETA1-6 : bond 0.00491 ( 1) link_BETA1-6 : angle 0.81841 ( 3) SS BOND : bond 0.00367 ( 28) SS BOND : angle 1.16756 ( 56) covalent geometry : bond 0.00440 (17311) covalent geometry : angle 0.60080 (23578) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 176 time to evaluate : 1.790 Fit side-chains REVERT: M 577 GLN cc_start: 0.8717 (mt0) cc_final: 0.8276 (tt0) REVERT: D 564 GLN cc_start: 0.7796 (tm-30) cc_final: 0.7567 (tt0) REVERT: D 603 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9144 (mp) REVERT: D 617 ASN cc_start: 0.7734 (p0) cc_final: 0.7484 (t0) REVERT: D 661 LEU cc_start: 0.8936 (mp) cc_final: 0.8686 (mp) REVERT: I 565 GLN cc_start: 0.6704 (mm-40) cc_final: 0.6467 (pp30) REVERT: I 570 ASP cc_start: 0.7956 (t0) cc_final: 0.7664 (t0) REVERT: I 620 SER cc_start: 0.8436 (t) cc_final: 0.7980 (p) REVERT: K 359 ARG cc_start: 0.7562 (mmt-90) cc_final: 0.7198 (mmt90) REVERT: K 477 MET cc_start: 0.8459 (tpp) cc_final: 0.7790 (mmt) REVERT: K 481 TRP cc_start: 0.8673 (m-10) cc_final: 0.6920 (m-10) REVERT: L 250 GLN cc_start: 0.7962 (mt0) cc_final: 0.7442 (tt0) REVERT: L 502 ARG cc_start: 0.6518 (ptt90) cc_final: 0.5955 (mpt180) REVERT: J 111 LEU cc_start: 0.9080 (mt) cc_final: 0.8764 (mp) REVERT: J 133 GLN cc_start: 0.7513 (pp30) cc_final: 0.7173 (pp30) REVERT: J 215 ASP cc_start: 0.8396 (m-30) cc_final: 0.7694 (p0) REVERT: J 448 LYS cc_start: 0.8646 (tttt) cc_final: 0.8243 (tttm) outliers start: 24 outliers final: 17 residues processed: 191 average time/residue: 0.3072 time to fit residues: 87.5884 Evaluate side-chains 180 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 162 time to evaluate : 1.820 ------------------------------------------------------------------------------- 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 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 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 336 ILE Chi-restraints excluded: chain L residue 383 GLU Chi-restraints excluded: chain L residue 418 ILE Chi-restraints excluded: chain L residue 428 MET Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 269 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 197 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 195 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 114 optimal weight: 0.9980 chunk 75 optimal weight: 10.0000 chunk 64 optimal weight: 8.9990 chunk 58 optimal weight: 10.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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** J 427 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.129986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.106674 restraints weight = 26025.409| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.55 r_work: 0.3100 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 17422 Z= 0.202 Angle : 0.647 9.913 23883 Z= 0.304 Chirality : 0.045 0.281 2979 Planarity : 0.003 0.043 2941 Dihedral : 7.436 68.313 4025 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.91 % Allowed : 7.51 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.20), residues: 1666 helix: 2.12 (0.26), residues: 420 sheet: 0.24 (0.24), residues: 418 loop : -0.22 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 481 HIS 0.006 0.001 HIS M 621 PHE 0.017 0.002 PHE K 53 TYR 0.009 0.001 TYR K 40 ARG 0.003 0.000 ARG K 482 Details of bonding type rmsd link_NAG-ASN : bond 0.00306 ( 54) link_NAG-ASN : angle 1.92182 ( 162) link_ALPHA1-6 : bond 0.01934 ( 2) link_ALPHA1-6 : angle 3.02694 ( 6) link_BETA1-4 : bond 0.00484 ( 23) link_BETA1-4 : angle 2.44036 ( 69) link_ALPHA1-3 : bond 0.00875 ( 3) link_ALPHA1-3 : angle 2.12726 ( 9) hydrogen bonds : bond 0.04369 ( 567) hydrogen bonds : angle 4.69230 ( 1509) link_BETA1-6 : bond 0.00562 ( 1) link_BETA1-6 : angle 0.82042 ( 3) SS BOND : bond 0.00364 ( 28) SS BOND : angle 1.34376 ( 56) covalent geometry : bond 0.00481 (17311) covalent geometry : angle 0.61077 (23578) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 170 time to evaluate : 1.949 Fit side-chains REVERT: M 577 GLN cc_start: 0.8717 (mt0) cc_final: 0.8272 (tt0) REVERT: M 601 SER cc_start: 0.9397 (t) cc_final: 0.9143 (m) REVERT: I 565 GLN cc_start: 0.6874 (mm-40) cc_final: 0.6554 (pp30) REVERT: I 570 ASP cc_start: 0.7948 (t0) cc_final: 0.7627 (t0) REVERT: I 620 SER cc_start: 0.8408 (t) cc_final: 0.7929 (p) REVERT: I 655 GLN cc_start: 0.8081 (mt0) cc_final: 0.7637 (tt0) REVERT: K 211 LYS cc_start: 0.8707 (mttt) cc_final: 0.7705 (tptp) REVERT: K 359 ARG cc_start: 0.7641 (mmt-90) cc_final: 0.7017 (mmt-90) REVERT: K 477 MET cc_start: 0.8449 (tpp) cc_final: 0.7784 (mmt) REVERT: K 481 TRP cc_start: 0.8665 (m-10) cc_final: 0.6892 (m-10) REVERT: L 250 GLN cc_start: 0.7958 (mt0) cc_final: 0.7444 (tt0) REVERT: L 383 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8340 (mt-10) REVERT: L 502 ARG cc_start: 0.6327 (ptt90) cc_final: 0.5801 (mpt180) REVERT: J 111 LEU cc_start: 0.9107 (mt) cc_final: 0.8791 (mp) REVERT: J 133 GLN cc_start: 0.7621 (pp30) cc_final: 0.7303 (pp30) REVERT: J 215 ASP cc_start: 0.8329 (m-30) cc_final: 0.7639 (p0) REVERT: J 448 LYS cc_start: 0.8698 (tttt) cc_final: 0.8434 (ttmm) outliers start: 29 outliers final: 20 residues processed: 191 average time/residue: 0.3032 time to fit residues: 87.3573 Evaluate side-chains 179 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 158 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 616 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 336 ILE Chi-restraints excluded: chain L residue 383 GLU Chi-restraints excluded: chain L residue 418 ILE Chi-restraints excluded: chain L residue 490 VAL 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 177 optimal weight: 2.9990 chunk 158 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 147 optimal weight: 0.0020 chunk 136 optimal weight: 2.9990 chunk 205 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 7 optimal weight: 0.7980 chunk 39 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 overall best weight: 1.1590 ------------------------------------------------------------------------------- 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 = 0.3541 r_free = 0.3541 target = 0.130871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.107705 restraints weight = 26237.234| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.56 r_work: 0.3117 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17422 Z= 0.137 Angle : 0.586 9.798 23883 Z= 0.274 Chirality : 0.043 0.329 2979 Planarity : 0.003 0.037 2941 Dihedral : 7.080 65.108 4025 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.52 % Allowed : 8.83 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.20), residues: 1666 helix: 2.24 (0.26), residues: 420 sheet: 0.27 (0.24), residues: 425 loop : -0.28 (0.21), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 96 HIS 0.005 0.001 HIS M 566 PHE 0.017 0.001 PHE I 522 TYR 0.013 0.001 TYR K 486 ARG 0.005 0.000 ARG J 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00298 ( 54) link_NAG-ASN : angle 1.82973 ( 162) link_ALPHA1-6 : bond 0.01949 ( 2) link_ALPHA1-6 : angle 3.10834 ( 6) link_BETA1-4 : bond 0.00497 ( 23) link_BETA1-4 : angle 2.27193 ( 69) link_ALPHA1-3 : bond 0.00922 ( 3) link_ALPHA1-3 : angle 1.79028 ( 9) hydrogen bonds : bond 0.03897 ( 567) hydrogen bonds : angle 4.53383 ( 1509) link_BETA1-6 : bond 0.00508 ( 1) link_BETA1-6 : angle 0.78743 ( 3) SS BOND : bond 0.00428 ( 28) SS BOND : angle 1.26966 ( 56) covalent geometry : bond 0.00316 (17311) covalent geometry : angle 0.55008 (23578) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 174 time to evaluate : 1.689 Fit side-chains REVERT: M 577 GLN cc_start: 0.8694 (mt0) cc_final: 0.8235 (tt0) REVERT: M 601 SER cc_start: 0.9357 (t) cc_final: 0.9120 (m) REVERT: M 660 LYS cc_start: 0.5908 (tttt) cc_final: 0.4131 (tttm) REVERT: D 564 GLN cc_start: 0.7967 (tm-30) cc_final: 0.7698 (tt0) REVERT: D 603 LEU cc_start: 0.9475 (OUTLIER) cc_final: 0.9196 (mp) REVERT: I 565 GLN cc_start: 0.6892 (mm-40) cc_final: 0.6568 (pp30) REVERT: I 570 ASP cc_start: 0.7747 (t0) cc_final: 0.7363 (t0) REVERT: I 620 SER cc_start: 0.8419 (t) cc_final: 0.7957 (p) REVERT: I 655 GLN cc_start: 0.8087 (mt0) cc_final: 0.7773 (tt0) REVERT: K 211 LYS cc_start: 0.8726 (mttt) cc_final: 0.7706 (tptp) REVERT: K 359 ARG cc_start: 0.7669 (mmt-90) cc_final: 0.6962 (mmt-90) REVERT: K 477 MET cc_start: 0.8376 (tpp) cc_final: 0.7650 (mmt) REVERT: K 481 TRP cc_start: 0.8631 (m-10) cc_final: 0.6942 (m-10) REVERT: L 250 GLN cc_start: 0.7888 (mt0) cc_final: 0.7365 (tt0) REVERT: L 502 ARG cc_start: 0.6292 (ptt90) cc_final: 0.5778 (mpt180) REVERT: J 111 LEU cc_start: 0.9076 (mt) cc_final: 0.8746 (mp) REVERT: J 133 GLN cc_start: 0.7637 (pp30) cc_final: 0.7320 (pp30) REVERT: J 448 LYS cc_start: 0.8711 (tttt) cc_final: 0.8324 (tttm) outliers start: 23 outliers final: 14 residues processed: 189 average time/residue: 0.3046 time to fit residues: 85.9577 Evaluate side-chains 181 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 166 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 603 LEU Chi-restraints excluded: chain D residue 606 CYS Chi-restraints excluded: chain D residue 614 SER Chi-restraints excluded: chain I residue 597 ILE Chi-restraints excluded: chain K residue 291 HIS Chi-restraints excluded: chain K residue 373 ILE Chi-restraints excluded: chain L residue 74 CYS Chi-restraints excluded: chain L residue 126 CYS Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain L residue 294 GLU Chi-restraints excluded: chain L residue 328 ASN Chi-restraints excluded: chain L residue 418 ILE Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain J residue 126 CYS Chi-restraints excluded: chain J residue 269 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 145 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 166 optimal weight: 0.6980 chunk 130 optimal weight: 10.0000 chunk 185 optimal weight: 0.8980 chunk 55 optimal weight: 10.0000 chunk 132 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 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** L 191 ASN ** L 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.129928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.106756 restraints weight = 26240.731| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.56 r_work: 0.3099 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17422 Z= 0.165 Angle : 0.600 9.821 23883 Z= 0.281 Chirality : 0.044 0.275 2979 Planarity : 0.003 0.039 2941 Dihedral : 6.899 63.164 4025 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.52 % Allowed : 9.75 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.20), residues: 1666 helix: 2.26 (0.26), residues: 418 sheet: 0.25 (0.24), residues: 423 loop : -0.38 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 96 HIS 0.005 0.001 HIS M 566 PHE 0.015 0.002 PHE K 53 TYR 0.012 0.001 TYR K 486 ARG 0.006 0.000 ARG J 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00283 ( 54) link_NAG-ASN : angle 1.82848 ( 162) link_ALPHA1-6 : bond 0.01942 ( 2) link_ALPHA1-6 : angle 3.12105 ( 6) link_BETA1-4 : bond 0.00478 ( 23) link_BETA1-4 : angle 2.27952 ( 69) link_ALPHA1-3 : bond 0.00859 ( 3) link_ALPHA1-3 : angle 1.97072 ( 9) hydrogen bonds : bond 0.03989 ( 567) hydrogen bonds : angle 4.50434 ( 1509) link_BETA1-6 : bond 0.00532 ( 1) link_BETA1-6 : angle 0.79545 ( 3) SS BOND : bond 0.00391 ( 28) SS BOND : angle 1.19173 ( 56) covalent geometry : bond 0.00388 (17311) covalent geometry : angle 0.56485 (23578) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 171 time to evaluate : 1.671 Fit side-chains revert: symmetry clash REVERT: M 577 GLN cc_start: 0.8699 (mt0) cc_final: 0.8244 (tt0) REVERT: M 601 SER cc_start: 0.9350 (t) cc_final: 0.9131 (m) REVERT: M 660 LYS cc_start: 0.5912 (tttt) cc_final: 0.4181 (tttm) REVERT: D 661 LEU cc_start: 0.8905 (mp) cc_final: 0.8637 (mp) REVERT: I 565 GLN cc_start: 0.6938 (mm-40) cc_final: 0.6594 (pp30) REVERT: I 570 ASP cc_start: 0.7725 (t0) cc_final: 0.7446 (t0) REVERT: I 601 SER cc_start: 0.9229 (t) cc_final: 0.8882 (p) REVERT: I 620 SER cc_start: 0.8409 (t) cc_final: 0.7952 (p) REVERT: I 655 GLN cc_start: 0.8114 (mt0) cc_final: 0.7804 (tt0) REVERT: K 211 LYS cc_start: 0.8752 (mttt) cc_final: 0.7738 (tptp) REVERT: K 282 THR cc_start: 0.8785 (m) cc_final: 0.8546 (p) REVERT: K 324 ASP cc_start: 0.8885 (t0) cc_final: 0.8675 (t0) REVERT: K 359 ARG cc_start: 0.7716 (mmt-90) cc_final: 0.6994 (mmt-90) REVERT: K 477 MET cc_start: 0.8378 (tpp) cc_final: 0.7639 (mmt) REVERT: K 481 TRP cc_start: 0.8640 (m-10) cc_final: 0.6946 (m-10) REVERT: L 250 GLN cc_start: 0.7908 (mt0) cc_final: 0.7438 (tt0) REVERT: L 502 ARG cc_start: 0.6355 (ptt90) cc_final: 0.6040 (mtt-85) REVERT: J 111 LEU cc_start: 0.9100 (mt) cc_final: 0.8766 (mp) REVERT: J 133 GLN cc_start: 0.7705 (pp30) cc_final: 0.7359 (pp30) REVERT: J 448 LYS cc_start: 0.8802 (tttt) cc_final: 0.8569 (ttmm) outliers start: 23 outliers final: 19 residues processed: 188 average time/residue: 0.3229 time to fit residues: 90.6306 Evaluate side-chains 191 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 172 time to evaluate : 1.604 ------------------------------------------------------------------------------- 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 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 291 HIS Chi-restraints excluded: chain K residue 373 ILE Chi-restraints excluded: chain L residue 74 CYS Chi-restraints excluded: chain L residue 96 TRP Chi-restraints excluded: chain L residue 126 CYS Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain L residue 294 GLU Chi-restraints excluded: chain L residue 328 ASN Chi-restraints excluded: chain L residue 418 ILE Chi-restraints excluded: chain J residue 126 CYS Chi-restraints excluded: chain J residue 209 CYS Chi-restraints excluded: chain J residue 269 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 52 optimal weight: 20.0000 chunk 123 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 112 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 chunk 185 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 173 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 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 = 0.3510 r_free = 0.3510 target = 0.128620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.105349 restraints weight = 26150.427| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.56 r_work: 0.3071 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 17422 Z= 0.198 Angle : 0.641 9.804 23883 Z= 0.299 Chirality : 0.045 0.281 2979 Planarity : 0.003 0.040 2941 Dihedral : 6.978 62.354 4025 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.84 % Allowed : 9.95 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.20), residues: 1666 helix: 2.06 (0.26), residues: 420 sheet: 0.08 (0.24), residues: 430 loop : -0.50 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 96 HIS 0.006 0.001 HIS M 621 PHE 0.017 0.002 PHE K 53 TYR 0.013 0.001 TYR K 486 ARG 0.007 0.000 ARG J 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00300 ( 54) link_NAG-ASN : angle 1.90901 ( 162) link_ALPHA1-6 : bond 0.01911 ( 2) link_ALPHA1-6 : angle 3.18539 ( 6) link_BETA1-4 : bond 0.00484 ( 23) link_BETA1-4 : angle 2.33292 ( 69) link_ALPHA1-3 : bond 0.00839 ( 3) link_ALPHA1-3 : angle 1.97262 ( 9) hydrogen bonds : bond 0.04268 ( 567) hydrogen bonds : angle 4.56626 ( 1509) link_BETA1-6 : bond 0.00556 ( 1) link_BETA1-6 : angle 0.78673 ( 3) SS BOND : bond 0.00472 ( 28) SS BOND : angle 1.08327 ( 56) covalent geometry : bond 0.00471 (17311) covalent geometry : angle 0.60707 (23578) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 170 time to evaluate : 1.800 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 577 GLN cc_start: 0.8688 (mt0) cc_final: 0.8224 (tt0) REVERT: M 601 SER cc_start: 0.9378 (t) cc_final: 0.9169 (m) REVERT: M 660 LYS cc_start: 0.5858 (tttt) cc_final: 0.4380 (tttm) REVERT: D 564 GLN cc_start: 0.7940 (tm-30) cc_final: 0.7669 (tt0) REVERT: I 565 GLN cc_start: 0.7092 (mm-40) cc_final: 0.6628 (pp30) REVERT: I 570 ASP cc_start: 0.7647 (t0) cc_final: 0.7349 (t0) REVERT: I 620 SER cc_start: 0.8443 (t) cc_final: 0.7965 (p) REVERT: I 655 GLN cc_start: 0.8164 (mt0) cc_final: 0.7841 (tt0) REVERT: K 211 LYS cc_start: 0.8737 (mttt) cc_final: 0.7753 (tptp) REVERT: K 282 THR cc_start: 0.8764 (m) cc_final: 0.8518 (p) REVERT: K 359 ARG cc_start: 0.7743 (mmt-90) cc_final: 0.7129 (mmt-90) REVERT: K 477 MET cc_start: 0.8421 (tpp) cc_final: 0.7555 (mmt) REVERT: K 481 TRP cc_start: 0.8676 (m-10) cc_final: 0.6856 (m-10) REVERT: L 250 GLN cc_start: 0.7985 (mt0) cc_final: 0.7536 (tt0) REVERT: L 502 ARG cc_start: 0.6286 (ptt90) cc_final: 0.5936 (mtt-85) REVERT: J 111 LEU cc_start: 0.9099 (mt) cc_final: 0.8759 (mp) REVERT: J 133 GLN cc_start: 0.7719 (pp30) cc_final: 0.7374 (pp30) REVERT: J 418 ILE cc_start: 0.8806 (OUTLIER) cc_final: 0.8606 (mt) REVERT: J 448 LYS cc_start: 0.8860 (tttt) cc_final: 0.8597 (tttm) outliers start: 28 outliers final: 23 residues processed: 190 average time/residue: 0.3146 time to fit residues: 88.7371 Evaluate side-chains 190 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 166 time to evaluate : 1.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 638 SER Chi-restraints excluded: chain D residue 603 LEU Chi-restraints excluded: chain D residue 606 CYS Chi-restraints excluded: chain D residue 614 SER Chi-restraints excluded: chain D residue 619 SER Chi-restraints excluded: chain I residue 531 THR Chi-restraints excluded: chain I residue 597 ILE Chi-restraints excluded: chain K residue 187 GLU Chi-restraints excluded: chain K residue 291 HIS Chi-restraints excluded: chain K residue 373 ILE Chi-restraints excluded: chain L residue 74 CYS Chi-restraints excluded: chain L residue 96 TRP Chi-restraints excluded: chain L residue 126 CYS Chi-restraints excluded: chain L residue 209 CYS Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain L residue 294 GLU Chi-restraints excluded: chain L residue 328 ASN Chi-restraints excluded: chain L residue 418 ILE Chi-restraints excluded: chain 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 Chi-restraints excluded: chain J residue 418 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 37 optimal weight: 0.9980 chunk 137 optimal weight: 2.9990 chunk 7 optimal weight: 0.1980 chunk 206 optimal weight: 0.9980 chunk 120 optimal weight: 0.1980 chunk 178 optimal weight: 2.9990 chunk 138 optimal weight: 0.8980 chunk 39 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 139 optimal weight: 0.8980 chunk 156 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3549 r_free = 0.3549 target = 0.131659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.108603 restraints weight = 25870.955| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.54 r_work: 0.3121 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17422 Z= 0.105 Angle : 0.553 9.508 23883 Z= 0.260 Chirality : 0.042 0.268 2979 Planarity : 0.003 0.053 2941 Dihedral : 6.453 59.582 4025 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.38 % Allowed : 10.47 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.21), residues: 1666 helix: 2.38 (0.27), residues: 412 sheet: 0.29 (0.24), residues: 421 loop : -0.45 (0.21), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 96 HIS 0.005 0.001 HIS M 566 PHE 0.012 0.001 PHE L 53 TYR 0.011 0.001 TYR K 486 ARG 0.015 0.000 ARG J 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00300 ( 54) link_NAG-ASN : angle 1.65671 ( 162) link_ALPHA1-6 : bond 0.01916 ( 2) link_ALPHA1-6 : angle 3.26680 ( 6) link_BETA1-4 : bond 0.00498 ( 23) link_BETA1-4 : angle 2.08827 ( 69) link_ALPHA1-3 : bond 0.00932 ( 3) link_ALPHA1-3 : angle 1.69809 ( 9) hydrogen bonds : bond 0.03479 ( 567) hydrogen bonds : angle 4.32188 ( 1509) link_BETA1-6 : bond 0.00490 ( 1) link_BETA1-6 : angle 0.74113 ( 3) SS BOND : bond 0.00379 ( 28) SS BOND : angle 0.81827 ( 56) covalent geometry : bond 0.00230 (17311) covalent geometry : angle 0.52191 (23578) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 189 time to evaluate : 1.661 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 577 GLN cc_start: 0.8636 (mt0) cc_final: 0.8169 (tt0) REVERT: M 660 LYS cc_start: 0.5765 (tttt) cc_final: 0.4272 (tttm) REVERT: D 589 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8318 (mttt) REVERT: I 565 GLN cc_start: 0.7030 (mm-40) cc_final: 0.6631 (pp30) REVERT: I 620 SER cc_start: 0.8360 (t) cc_final: 0.7926 (p) REVERT: I 646 ARG cc_start: 0.8392 (tpp80) cc_final: 0.8104 (mmt-90) REVERT: I 655 GLN cc_start: 0.8123 (mt0) cc_final: 0.7880 (tt0) REVERT: K 211 LYS cc_start: 0.8746 (mttt) cc_final: 0.7828 (tptp) REVERT: K 282 THR cc_start: 0.8721 (m) cc_final: 0.8484 (p) REVERT: K 359 ARG cc_start: 0.7632 (mmt-90) cc_final: 0.6948 (mmt-90) REVERT: K 477 MET cc_start: 0.8276 (mpp) cc_final: 0.7650 (mmt) REVERT: K 481 TRP cc_start: 0.8573 (m-10) cc_final: 0.6958 (m-10) REVERT: L 250 GLN cc_start: 0.7823 (mt0) cc_final: 0.7522 (tt0) REVERT: L 502 ARG cc_start: 0.6326 (ptt90) cc_final: 0.5825 (mpt180) REVERT: J 35 TRP cc_start: 0.9005 (m100) cc_final: 0.8740 (m100) REVERT: J 111 LEU cc_start: 0.9016 (mt) cc_final: 0.8690 (mp) REVERT: J 133 GLN cc_start: 0.7732 (pp30) cc_final: 0.7389 (pp30) REVERT: J 448 LYS cc_start: 0.8851 (tttt) cc_final: 0.8618 (tttm) outliers start: 21 outliers final: 17 residues processed: 203 average time/residue: 0.2936 time to fit residues: 88.8560 Evaluate side-chains 187 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 169 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 638 SER Chi-restraints excluded: chain D residue 589 LYS Chi-restraints excluded: chain D residue 606 CYS Chi-restraints excluded: chain D residue 614 SER Chi-restraints excluded: chain 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 291 HIS 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 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 145 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 185 optimal weight: 0.9980 chunk 49 optimal weight: 9.9990 chunk 61 optimal weight: 9.9990 chunk 210 optimal weight: 4.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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** J 250 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.129900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.106723 restraints weight = 26219.989| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.56 r_work: 0.3092 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 17422 Z= 0.166 Angle : 0.611 13.099 23883 Z= 0.288 Chirality : 0.044 0.267 2979 Planarity : 0.003 0.050 2941 Dihedral : 6.486 60.119 4025 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.38 % Allowed : 10.94 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.21), residues: 1666 helix: 2.22 (0.26), residues: 419 sheet: 0.16 (0.24), residues: 422 loop : -0.50 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP J 429 HIS 0.005 0.001 HIS M 566 PHE 0.020 0.002 PHE I 522 TYR 0.012 0.001 TYR K 486 ARG 0.016 0.000 ARG J 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00284 ( 54) link_NAG-ASN : angle 1.74562 ( 162) link_ALPHA1-6 : bond 0.01702 ( 2) link_ALPHA1-6 : angle 3.33005 ( 6) link_BETA1-4 : bond 0.00483 ( 23) link_BETA1-4 : angle 2.18192 ( 69) link_ALPHA1-3 : bond 0.00834 ( 3) link_ALPHA1-3 : angle 1.92109 ( 9) hydrogen bonds : bond 0.03883 ( 567) hydrogen bonds : angle 4.39068 ( 1509) link_BETA1-6 : bond 0.00511 ( 1) link_BETA1-6 : angle 0.77314 ( 3) SS BOND : bond 0.00528 ( 28) SS BOND : angle 1.33143 ( 56) covalent geometry : bond 0.00395 (17311) covalent geometry : angle 0.57870 (23578) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 167 time to evaluate : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 577 GLN cc_start: 0.8674 (mt0) cc_final: 0.8206 (tt0) REVERT: M 660 LYS cc_start: 0.5930 (tttt) cc_final: 0.4282 (tttm) REVERT: D 564 GLN cc_start: 0.7943 (tm-30) cc_final: 0.7604 (tt0) REVERT: D 589 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8335 (mttt) REVERT: I 565 GLN cc_start: 0.7075 (mm-40) cc_final: 0.6666 (pp30) REVERT: I 620 SER cc_start: 0.8436 (t) cc_final: 0.7973 (p) REVERT: I 655 GLN cc_start: 0.8158 (mt0) cc_final: 0.7897 (tt0) REVERT: K 211 LYS cc_start: 0.8743 (mttt) cc_final: 0.7852 (tptp) REVERT: K 282 THR cc_start: 0.8729 (m) cc_final: 0.8501 (p) REVERT: K 477 MET cc_start: 0.8329 (mpp) cc_final: 0.7520 (mmt) REVERT: K 481 TRP cc_start: 0.8632 (m-10) cc_final: 0.6826 (m-10) REVERT: L 250 GLN cc_start: 0.7708 (mt0) cc_final: 0.7475 (tt0) REVERT: L 502 ARG cc_start: 0.6357 (ptt90) cc_final: 0.6112 (mtt-85) REVERT: J 111 LEU cc_start: 0.9012 (mt) cc_final: 0.8679 (mp) REVERT: J 133 GLN cc_start: 0.7734 (pp30) cc_final: 0.7359 (pp30) REVERT: J 448 LYS cc_start: 0.8899 (tttt) cc_final: 0.8665 (ttmm) outliers start: 21 outliers final: 18 residues processed: 182 average time/residue: 0.3056 time to fit residues: 82.0021 Evaluate side-chains 184 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 165 time to evaluate : 1.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 638 SER Chi-restraints excluded: chain D residue 589 LYS Chi-restraints excluded: chain D residue 606 CYS Chi-restraints excluded: chain D residue 614 SER Chi-restraints excluded: chain 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 291 HIS Chi-restraints excluded: chain K residue 373 ILE Chi-restraints excluded: chain L residue 74 CYS Chi-restraints excluded: chain L residue 95 MET 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 J residue 126 CYS Chi-restraints excluded: chain J residue 209 CYS Chi-restraints excluded: chain J residue 269 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 55 optimal weight: 9.9990 chunk 63 optimal weight: 10.0000 chunk 120 optimal weight: 0.0770 chunk 202 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 144 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 112 optimal weight: 0.9990 chunk 86 optimal weight: 0.1980 overall best weight: 0.4938 ------------------------------------------------------------------------------- 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 = 0.3565 r_free = 0.3565 target = 0.132977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.110024 restraints weight = 25990.487| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.55 r_work: 0.3145 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.073 17422 Z= 0.102 Angle : 0.543 10.005 23883 Z= 0.258 Chirality : 0.042 0.258 2979 Planarity : 0.003 0.051 2941 Dihedral : 5.958 57.476 4025 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.05 % Allowed : 11.07 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.21), residues: 1666 helix: 2.42 (0.27), residues: 418 sheet: 0.33 (0.25), residues: 423 loop : -0.39 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP J 429 HIS 0.005 0.001 HIS M 566 PHE 0.011 0.001 PHE I 522 TYR 0.009 0.001 TYR K 486 ARG 0.017 0.000 ARG J 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00289 ( 54) link_NAG-ASN : angle 1.54194 ( 162) link_ALPHA1-6 : bond 0.01674 ( 2) link_ALPHA1-6 : angle 3.04537 ( 6) link_BETA1-4 : bond 0.00490 ( 23) link_BETA1-4 : angle 1.98369 ( 69) link_ALPHA1-3 : bond 0.00908 ( 3) link_ALPHA1-3 : angle 1.60615 ( 9) hydrogen bonds : bond 0.03249 ( 567) hydrogen bonds : angle 4.20784 ( 1509) link_BETA1-6 : bond 0.00456 ( 1) link_BETA1-6 : angle 0.82622 ( 3) SS BOND : bond 0.00581 ( 28) SS BOND : angle 1.30218 ( 56) covalent geometry : bond 0.00230 (17311) covalent geometry : angle 0.51268 (23578) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 192 time to evaluate : 1.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 577 GLN cc_start: 0.8610 (mt0) cc_final: 0.8135 (tt0) REVERT: M 660 LYS cc_start: 0.5817 (tttt) cc_final: 0.4200 (tttm) REVERT: D 564 GLN cc_start: 0.8009 (tm-30) cc_final: 0.7645 (tt0) REVERT: I 565 GLN cc_start: 0.7070 (mm-40) cc_final: 0.6673 (pp30) REVERT: I 620 SER cc_start: 0.8314 (t) cc_final: 0.7911 (p) REVERT: I 646 ARG cc_start: 0.8392 (tpp80) cc_final: 0.8094 (mmt-90) REVERT: K 211 LYS cc_start: 0.8775 (mttt) cc_final: 0.7774 (tptp) REVERT: K 282 THR cc_start: 0.8683 (m) cc_final: 0.8445 (p) REVERT: K 477 MET cc_start: 0.8171 (mpp) cc_final: 0.7534 (mmt) REVERT: K 481 TRP cc_start: 0.8537 (m-10) cc_final: 0.6889 (m-10) REVERT: J 35 TRP cc_start: 0.9007 (m100) cc_final: 0.8747 (m100) REVERT: J 111 LEU cc_start: 0.8965 (mt) cc_final: 0.8651 (mp) REVERT: J 133 GLN cc_start: 0.7741 (pp30) cc_final: 0.7371 (pp30) outliers start: 16 outliers final: 14 residues processed: 203 average time/residue: 0.2947 time to fit residues: 89.4652 Evaluate side-chains 187 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 173 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 606 CYS Chi-restraints excluded: chain I residue 597 ILE Chi-restraints excluded: chain K residue 291 HIS 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 J residue 66 ARG Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 126 CYS Chi-restraints excluded: chain J residue 209 CYS Chi-restraints excluded: chain J residue 269 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 195 optimal weight: 7.9990 chunk 102 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 169 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 43 optimal weight: 9.9990 chunk 18 optimal weight: 0.5980 chunk 26 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 572 HIS ** J 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 250 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.127153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.103811 restraints weight = 26323.638| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.57 r_work: 0.3021 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 17422 Z= 0.283 Angle : 0.734 11.629 23883 Z= 0.344 Chirality : 0.047 0.270 2979 Planarity : 0.004 0.053 2941 Dihedral : 6.734 61.757 4025 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.19 % Allowed : 11.53 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.21), residues: 1666 helix: 2.00 (0.26), residues: 419 sheet: -0.04 (0.24), residues: 438 loop : -0.62 (0.21), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 572 HIS 0.010 0.002 HIS M 621 PHE 0.021 0.002 PHE K 53 TYR 0.022 0.002 TYR K 486 ARG 0.019 0.001 ARG J 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00363 ( 54) link_NAG-ASN : angle 1.99723 ( 162) link_ALPHA1-6 : bond 0.01230 ( 2) link_ALPHA1-6 : angle 3.63426 ( 6) link_BETA1-4 : bond 0.00486 ( 23) link_BETA1-4 : angle 2.40799 ( 69) link_ALPHA1-3 : bond 0.00786 ( 3) link_ALPHA1-3 : angle 2.19571 ( 9) hydrogen bonds : bond 0.04665 ( 567) hydrogen bonds : angle 4.69063 ( 1509) link_BETA1-6 : bond 0.00619 ( 1) link_BETA1-6 : angle 0.83395 ( 3) SS BOND : bond 0.00628 ( 28) SS BOND : angle 1.44469 ( 56) covalent geometry : bond 0.00674 (17311) covalent geometry : angle 0.70079 (23578) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8894.24 seconds wall clock time: 152 minutes 58.29 seconds (9178.29 seconds total)