Starting phenix.real_space_refine on Wed Mar 4 18:07:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7l7t_23218/03_2026/7l7t_23218.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l7t_23218/03_2026/7l7t_23218.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7l7t_23218/03_2026/7l7t_23218.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l7t_23218/03_2026/7l7t_23218.map" model { file = "/net/cci-nas-00/data/ceres_data/7l7t_23218/03_2026/7l7t_23218.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l7t_23218/03_2026/7l7t_23218.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.006 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 105 5.16 5 C 9603 2.51 5 N 2565 2.21 5 O 3150 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15423 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 3514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3514 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 20, 'TRANS': 424} Chain breaks: 3 Chain: "B" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1160 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 2, 'TRANS': 142} Chain: "C" Number of atoms: 3514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3514 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 20, 'TRANS': 424} Chain breaks: 3 Chain: "D" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1160 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 2, 'TRANS': 142} Chain: "E" Number of atoms: 3514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3514 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 20, 'TRANS': 424} Chain breaks: 3 Chain: "F" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1160 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 2, 'TRANS': 142} 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: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" 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: "K" 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: "L" 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: 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: "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: 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 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: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" 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: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "D" 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: "E" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "F" 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 Time building chain proxies: 3.92, per 1000 atoms: 0.25 Number of scatterers: 15423 At special positions: 0 Unit cell: (129.95, 125.35, 123.05, 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 105 16.00 O 3150 8.00 N 2565 7.00 C 9603 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.02 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS B 561 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.06 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.05 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 73 " distance=2.02 Simple disulfide: pdb=" SG CYS C 74 " - pdb=" SG CYS D 561 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.06 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.02 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.05 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 73 " distance=2.02 Simple disulfide: pdb=" SG CYS E 74 " - pdb=" SG CYS F 561 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.06 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.02 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.05 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 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 P 3 " - " MAN P 4 " " BMA Y 3 " - " MAN Y 4 " ALPHA1-6 " BMA G 3 " - " MAN G 5 " " BMA P 3 " - " MAN P 5 " " BMA Y 3 " - " MAN Y 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 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 X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " NAG-ASN " NAG A 601 " - " ASN A 276 " " NAG A 602 " - " ASN A 386 " " NAG A 603 " - " ASN A 363 " " NAG A 604 " - " ASN A 234 " " NAG A 605 " - " ASN A 133 " " NAG A 606 " - " ASN A 88 " " NAG A 607 " - " ASN A 289 " " NAG A 608 " - " ASN A 339 " " NAG A 609 " - " ASN A 355 " " NAG A 610 " - " ASN A 392 " " NAG B 701 " - " ASN B 637 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 611 " " NAG C 601 " - " ASN C 276 " " NAG C 602 " - " ASN C 386 " " NAG C 603 " - " ASN C 363 " " NAG C 604 " - " ASN C 234 " " NAG C 605 " - " ASN C 133 " " NAG C 606 " - " ASN C 88 " " NAG C 607 " - " ASN C 289 " " NAG C 608 " - " ASN C 339 " " NAG C 609 " - " ASN C 355 " " NAG C 610 " - " ASN C 392 " " NAG D 701 " - " ASN D 637 " " NAG D 702 " - " ASN D 618 " " NAG D 703 " - " ASN D 611 " " NAG E 601 " - " ASN E 276 " " NAG E 602 " - " ASN E 386 " " NAG E 603 " - " ASN E 363 " " NAG E 604 " - " ASN E 234 " " NAG E 605 " - " ASN E 133 " " NAG E 606 " - " ASN E 88 " " NAG E 607 " - " ASN E 289 " " NAG E 608 " - " ASN E 339 " " NAG E 609 " - " ASN E 355 " " NAG E 610 " - " ASN E 392 " " NAG F 701 " - " ASN F 637 " " NAG F 702 " - " ASN F 618 " " NAG F 703 " - " ASN F 611 " " NAG G 1 " - " ASN A 262 " " NAG H 1 " - " ASN A 448 " " NAG I 1 " - " ASN A 295 " " NAG J 1 " - " ASN A 197 " " NAG K 1 " - " ASN A 156 " " NAG L 1 " - " ASN A 301 " " NAG M 1 " - " ASN A 241 " " NAG N 1 " - " ASN A 332 " " NAG O 1 " - " ASN A 160 " " NAG P 1 " - " ASN C 262 " " NAG Q 1 " - " ASN C 448 " " NAG R 1 " - " ASN C 295 " " NAG S 1 " - " ASN C 197 " " NAG T 1 " - " ASN C 156 " " NAG U 1 " - " ASN C 301 " " NAG V 1 " - " ASN C 241 " " NAG W 1 " - " ASN C 332 " " NAG X 1 " - " ASN C 160 " " NAG Y 1 " - " ASN E 262 " " NAG Z 1 " - " ASN E 448 " " NAG a 1 " - " ASN E 295 " " NAG b 1 " - " ASN E 197 " " NAG c 1 " - " ASN E 156 " " NAG d 1 " - " ASN E 301 " " NAG e 1 " - " ASN E 241 " " NAG f 1 " - " ASN E 332 " " NAG g 1 " - " ASN E 160 " Time building additional restraints: 1.67 Conformation dependent library (CDL) restraints added in 614.6 milliseconds 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3318 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 30 sheets defined 31.9% alpha, 36.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.131A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 334 through 354 removed outlier: 3.926A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 390 Processing helix chain 'A' and resid 425 through 429 Processing helix chain 'A' and resid 476 through 484 removed outlier: 4.710A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 542 Processing helix chain 'B' and resid 542 through 557 Processing helix chain 'B' and resid 558 through 568 removed outlier: 3.513A pdb=" N LEU B 566 " --> pdb=" O GLN B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 596 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 664 Processing helix chain 'C' and resid 98 through 117 removed outlier: 4.131A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 139 through 151 Processing helix chain 'C' and resid 334 through 354 removed outlier: 3.927A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 390 Processing helix chain 'C' and resid 425 through 429 Processing helix chain 'C' and resid 476 through 484 removed outlier: 4.710A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 542 Processing helix chain 'D' and resid 542 through 557 Processing helix chain 'D' and resid 558 through 568 removed outlier: 3.514A pdb=" N LEU D 566 " --> pdb=" O GLN D 562 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 596 Processing helix chain 'D' and resid 618 through 625 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 664 Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.131A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 139 through 151 Processing helix chain 'E' and resid 334 through 354 removed outlier: 3.927A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 390 Processing helix chain 'E' and resid 425 through 429 Processing helix chain 'E' and resid 476 through 484 removed outlier: 4.710A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 542 Processing helix chain 'F' and resid 542 through 557 Processing helix chain 'F' and resid 558 through 568 removed outlier: 3.514A pdb=" N LEU F 566 " --> pdb=" O GLN F 562 " (cutoff:3.500A) Processing helix chain 'F' and resid 568 through 596 Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 664 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.482A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.552A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 393 through 395 removed outlier: 6.434A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 10.153A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 10.908A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 9.870A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.540A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.507A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.240A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.266A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.107A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.562A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 271 through 274 Processing sheet with id=AB1, first strand: chain 'A' and resid 316 through 323A removed outlier: 5.463A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N THR A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N LYS A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASN A 301 " --> pdb=" O ILE A 323A" (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.482A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AB4, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=AB5, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB6, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AB7, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.552A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 393 through 395 removed outlier: 6.434A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N GLY C 451 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.260A pdb=" N GLU C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 11.747A pdb=" N ILE C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 11.758A pdb=" N LEU C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 10.720A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 10.721A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.562A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 271 through 274 Processing sheet with id=AC2, first strand: chain 'C' and resid 316 through 323A removed outlier: 5.463A pdb=" N TYR C 318 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ILE C 307 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N THR C 320 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N LYS C 305 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASN C 301 " --> pdb=" O ILE C 323A" (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.482A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AC5, first strand: chain 'E' and resid 53 through 56 Processing sheet with id=AC6, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AC7, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AC8, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.553A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 393 through 395 removed outlier: 6.435A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.260A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.747A pdb=" N ILE E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 11.759A pdb=" N LEU E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 10.721A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.721A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.562A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 271 through 274 Processing sheet with id=AD3, first strand: chain 'E' and resid 316 through 323A removed outlier: 5.463A pdb=" N TYR E 318 " --> pdb=" O ILE E 307 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ILE E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N THR E 320 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N LYS E 305 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASN E 301 " --> pdb=" O ILE E 323A" (cutoff:3.500A) 624 hydrogen bonds defined for protein. 1707 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.91 Time building geometry restraints manager: 2.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 3943 1.33 - 1.46: 4744 1.46 - 1.60: 6871 1.60 - 1.74: 15 1.74 - 1.88: 132 Bond restraints: 15705 Sorted by residual: bond pdb=" CG GLN D 540 " pdb=" CD GLN D 540 " ideal model delta sigma weight residual 1.516 1.388 0.128 2.50e-02 1.60e+03 2.61e+01 bond pdb=" CG GLN B 540 " pdb=" CD GLN B 540 " ideal model delta sigma weight residual 1.516 1.388 0.128 2.50e-02 1.60e+03 2.61e+01 bond pdb=" CG GLN F 540 " pdb=" CD GLN F 540 " ideal model delta sigma weight residual 1.516 1.388 0.128 2.50e-02 1.60e+03 2.60e+01 bond pdb=" CB HIS A 374 " pdb=" CG HIS A 374 " ideal model delta sigma weight residual 1.497 1.428 0.069 1.40e-02 5.10e+03 2.42e+01 bond pdb=" CB HIS E 374 " pdb=" CG HIS E 374 " ideal model delta sigma weight residual 1.497 1.428 0.069 1.40e-02 5.10e+03 2.41e+01 ... (remaining 15700 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 16106 1.76 - 3.53: 4175 3.53 - 5.29: 814 5.29 - 7.06: 199 7.06 - 8.82: 24 Bond angle restraints: 21318 Sorted by residual: angle pdb=" C ARG A 298 " pdb=" N PRO A 299 " pdb=" CA PRO A 299 " ideal model delta sigma weight residual 119.56 128.38 -8.82 1.01e+00 9.80e-01 7.63e+01 angle pdb=" C ARG E 298 " pdb=" N PRO E 299 " pdb=" CA PRO E 299 " ideal model delta sigma weight residual 119.56 128.37 -8.81 1.01e+00 9.80e-01 7.61e+01 angle pdb=" C ARG C 298 " pdb=" N PRO C 299 " pdb=" CA PRO C 299 " ideal model delta sigma weight residual 119.87 128.37 -8.50 1.04e+00 9.25e-01 6.67e+01 angle pdb=" C ALA B 558 " pdb=" N PRO B 559 " pdb=" CA PRO B 559 " ideal model delta sigma weight residual 119.32 126.46 -7.14 1.14e+00 7.69e-01 3.92e+01 angle pdb=" C ALA D 558 " pdb=" N PRO D 559 " pdb=" CA PRO D 559 " ideal model delta sigma weight residual 119.32 126.46 -7.14 1.14e+00 7.69e-01 3.92e+01 ... (remaining 21313 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.14: 10488 21.14 - 42.29: 198 42.29 - 63.43: 54 63.43 - 84.58: 36 84.58 - 105.72: 18 Dihedral angle restraints: 10794 sinusoidal: 5676 harmonic: 5118 Sorted by residual: dihedral pdb=" CB CYS C 119 " pdb=" SG CYS C 119 " pdb=" SG CYS C 205 " pdb=" CB CYS C 205 " ideal model delta sinusoidal sigma weight residual -86.00 -126.83 40.83 1 1.00e+01 1.00e-02 2.34e+01 dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual -86.00 -126.81 40.81 1 1.00e+01 1.00e-02 2.33e+01 dihedral pdb=" CB CYS E 119 " pdb=" SG CYS E 119 " pdb=" SG CYS E 205 " pdb=" CB CYS E 205 " ideal model delta sinusoidal sigma weight residual -86.00 -126.80 40.80 1 1.00e+01 1.00e-02 2.33e+01 ... (remaining 10791 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 1621 0.098 - 0.196: 573 0.196 - 0.294: 269 0.294 - 0.392: 159 0.392 - 0.490: 81 Chirality restraints: 2703 Sorted by residual: chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.14e+02 chirality pdb=" C1 NAG c 2 " pdb=" O4 NAG c 1 " pdb=" C2 NAG c 2 " pdb=" O5 NAG c 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.12e+02 chirality pdb=" C1 NAG T 2 " pdb=" O4 NAG T 1 " pdb=" C2 NAG T 2 " pdb=" O5 NAG T 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.11e+02 ... (remaining 2700 not shown) Planarity restraints: 2649 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG O 1 " 0.218 2.00e-02 2.50e+03 1.82e-01 4.15e+02 pdb=" C7 NAG O 1 " -0.057 2.00e-02 2.50e+03 pdb=" C8 NAG O 1 " 0.153 2.00e-02 2.50e+03 pdb=" N2 NAG O 1 " -0.303 2.00e-02 2.50e+03 pdb=" O7 NAG O 1 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG X 1 " -0.218 2.00e-02 2.50e+03 1.82e-01 4.14e+02 pdb=" C7 NAG X 1 " 0.057 2.00e-02 2.50e+03 pdb=" C8 NAG X 1 " -0.153 2.00e-02 2.50e+03 pdb=" N2 NAG X 1 " 0.303 2.00e-02 2.50e+03 pdb=" O7 NAG X 1 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG g 1 " -0.218 2.00e-02 2.50e+03 1.82e-01 4.14e+02 pdb=" C7 NAG g 1 " 0.057 2.00e-02 2.50e+03 pdb=" C8 NAG g 1 " -0.153 2.00e-02 2.50e+03 pdb=" N2 NAG g 1 " 0.302 2.00e-02 2.50e+03 pdb=" O7 NAG g 1 " 0.011 2.00e-02 2.50e+03 ... (remaining 2646 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.91: 6533 2.91 - 3.41: 14158 3.41 - 3.91: 26517 3.91 - 4.40: 30440 4.40 - 4.90: 45822 Nonbonded interactions: 123470 Sorted by model distance: nonbonded pdb=" N ILE C 213 " pdb=" O ILE C 213 " model vdw 2.419 2.496 nonbonded pdb=" N ILE A 213 " pdb=" O ILE A 213 " model vdw 2.419 2.496 nonbonded pdb=" N ILE E 213 " pdb=" O ILE E 213 " model vdw 2.419 2.496 nonbonded pdb=" NZ LYS A 232 " pdb=" OE1 GLU A 268 " model vdw 2.435 3.120 nonbonded pdb=" NZ LYS C 232 " pdb=" OE1 GLU C 268 " model vdw 2.435 3.120 ... (remaining 123465 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'P' selection = chain 'Y' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.900 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 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 : 0.024 0.128 15843 Z= 1.281 Angle : 1.738 8.821 21696 Z= 1.099 Chirality : 0.156 0.490 2703 Planarity : 0.011 0.182 2583 Dihedral : 11.041 105.720 7368 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 0.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.19), residues: 1740 helix: 0.27 (0.22), residues: 513 sheet: 0.97 (0.22), residues: 426 loop : 0.98 (0.21), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 192 TYR 0.038 0.006 TYR C 40 PHE 0.023 0.006 PHE A 53 TRP 0.062 0.013 TRP E 35 HIS 0.012 0.003 HIS D 564 Details of bonding type rmsd covalent geometry : bond 0.02336 (15705) covalent geometry : angle 1.69417 (21318) SS BOND : bond 0.01068 ( 36) SS BOND : angle 2.80030 ( 72) hydrogen bonds : bond 0.16174 ( 624) hydrogen bonds : angle 7.47223 ( 1707) link_ALPHA1-3 : bond 0.08978 ( 3) link_ALPHA1-3 : angle 4.42527 ( 9) link_ALPHA1-6 : bond 0.05873 ( 3) link_ALPHA1-6 : angle 3.60750 ( 9) link_BETA1-4 : bond 0.06714 ( 30) link_BETA1-4 : angle 4.43404 ( 90) link_NAG-ASN : bond 0.07726 ( 66) link_NAG-ASN : angle 2.96498 ( 198) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 0.560 Fit side-chains revert: symmetry clash REVERT: A 80 ASN cc_start: 0.8135 (t0) cc_final: 0.7890 (t0) REVERT: A 426 MET cc_start: 0.7657 (mtp) cc_final: 0.6695 (mtp) REVERT: B 647 GLU cc_start: 0.8043 (tt0) cc_final: 0.7423 (tt0) REVERT: B 655 LYS cc_start: 0.9143 (tptp) cc_final: 0.8850 (pttp) REVERT: C 80 ASN cc_start: 0.7960 (t0) cc_final: 0.7730 (t0) REVERT: C 426 MET cc_start: 0.7631 (mtp) cc_final: 0.6890 (mtp) REVERT: D 603 ILE cc_start: 0.9409 (mt) cc_final: 0.9094 (mt) REVERT: D 621 GLU cc_start: 0.8096 (tt0) cc_final: 0.7893 (tm-30) REVERT: D 655 LYS cc_start: 0.9078 (tptp) cc_final: 0.8813 (pttp) REVERT: E 80 ASN cc_start: 0.8177 (t0) cc_final: 0.7922 (t0) REVERT: E 426 MET cc_start: 0.7197 (mtp) cc_final: 0.6267 (mtp) REVERT: F 570 HIS cc_start: 0.7968 (m170) cc_final: 0.7645 (m-70) REVERT: F 603 ILE cc_start: 0.9436 (mt) cc_final: 0.9137 (mt) REVERT: F 655 LYS cc_start: 0.9182 (tptp) cc_final: 0.8844 (pttp) outliers start: 0 outliers final: 0 residues processed: 254 average time/residue: 0.1551 time to fit residues: 55.6226 Evaluate side-chains 139 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 575 GLN B 577 GLN B 625 ASN D 562 GLN D 570 HIS D 577 GLN F 562 GLN F 575 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.071368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.053681 restraints weight = 46506.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.056006 restraints weight = 25793.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.057589 restraints weight = 18154.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.058620 restraints weight = 14558.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.059326 restraints weight = 12621.402| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 15843 Z= 0.247 Angle : 0.780 10.335 21696 Z= 0.388 Chirality : 0.048 0.181 2703 Planarity : 0.004 0.027 2583 Dihedral : 8.110 82.854 3999 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.26 % Allowed : 4.36 % Favored : 94.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.20), residues: 1740 helix: 1.92 (0.24), residues: 471 sheet: 0.88 (0.23), residues: 411 loop : 0.49 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 557 TYR 0.021 0.002 TYR A 39 PHE 0.014 0.002 PHE C 176 TRP 0.022 0.002 TRP A 112 HIS 0.005 0.002 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00553 (15705) covalent geometry : angle 0.70132 (21318) SS BOND : bond 0.00332 ( 36) SS BOND : angle 0.99488 ( 72) hydrogen bonds : bond 0.06100 ( 624) hydrogen bonds : angle 5.84444 ( 1707) link_ALPHA1-3 : bond 0.00891 ( 3) link_ALPHA1-3 : angle 2.42144 ( 9) link_ALPHA1-6 : bond 0.00659 ( 3) link_ALPHA1-6 : angle 1.42249 ( 9) link_BETA1-4 : bond 0.00269 ( 30) link_BETA1-4 : angle 2.59244 ( 90) link_NAG-ASN : bond 0.00343 ( 66) link_NAG-ASN : angle 3.15956 ( 198) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 159 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASN cc_start: 0.8247 (t0) cc_final: 0.7996 (t0) REVERT: B 557 ARG cc_start: 0.8476 (tmm160) cc_final: 0.8066 (tmm160) REVERT: B 634 GLU cc_start: 0.9048 (mm-30) cc_final: 0.8773 (tp30) REVERT: B 647 GLU cc_start: 0.8606 (tt0) cc_final: 0.8374 (tt0) REVERT: B 655 LYS cc_start: 0.9211 (tptp) cc_final: 0.8798 (pttp) REVERT: C 80 ASN cc_start: 0.8157 (t0) cc_final: 0.7867 (t0) REVERT: D 566 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8835 (pp) REVERT: D 621 GLU cc_start: 0.8511 (tt0) cc_final: 0.7923 (tp30) REVERT: D 626 MET cc_start: 0.7753 (ttt) cc_final: 0.7486 (ttm) REVERT: F 626 MET cc_start: 0.7479 (ttt) cc_final: 0.7007 (ttt) REVERT: F 634 GLU cc_start: 0.9165 (OUTLIER) cc_final: 0.8742 (tt0) outliers start: 20 outliers final: 14 residues processed: 170 average time/residue: 0.1252 time to fit residues: 32.1084 Evaluate side-chains 142 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 561 CYS Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 561 CYS Chi-restraints excluded: chain F residue 576 LEU Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 634 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 167 optimal weight: 2.9990 chunk 173 optimal weight: 10.0000 chunk 52 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 104 optimal weight: 9.9990 chunk 77 optimal weight: 1.9990 chunk 169 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 162 optimal weight: 9.9990 chunk 7 optimal weight: 4.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 170 GLN B 543 ASN B 562 GLN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 GLN C 170 GLN C 478 ASN D 575 GLN ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 170 GLN E 478 ASN F 543 ASN F 577 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.071274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.053545 restraints weight = 47052.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.055893 restraints weight = 25961.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.057474 restraints weight = 18239.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.058543 restraints weight = 14638.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.059252 restraints weight = 12653.765| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 15843 Z= 0.181 Angle : 0.629 7.101 21696 Z= 0.318 Chirality : 0.044 0.197 2703 Planarity : 0.003 0.023 2583 Dihedral : 7.151 73.812 3999 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.45 % Allowed : 5.81 % Favored : 92.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.20), residues: 1740 helix: 2.11 (0.24), residues: 471 sheet: 0.86 (0.23), residues: 411 loop : 0.33 (0.22), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 480 TYR 0.020 0.002 TYR F 643 PHE 0.013 0.002 PHE C 176 TRP 0.016 0.002 TRP A 112 HIS 0.005 0.001 HIS D 564 Details of bonding type rmsd covalent geometry : bond 0.00403 (15705) covalent geometry : angle 0.58213 (21318) SS BOND : bond 0.00156 ( 36) SS BOND : angle 0.75497 ( 72) hydrogen bonds : bond 0.04808 ( 624) hydrogen bonds : angle 5.37433 ( 1707) link_ALPHA1-3 : bond 0.01111 ( 3) link_ALPHA1-3 : angle 2.02017 ( 9) link_ALPHA1-6 : bond 0.00932 ( 3) link_ALPHA1-6 : angle 1.58796 ( 9) link_BETA1-4 : bond 0.00386 ( 30) link_BETA1-4 : angle 1.73833 ( 90) link_NAG-ASN : bond 0.00188 ( 66) link_NAG-ASN : angle 2.23233 ( 198) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASN cc_start: 0.8537 (t0) cc_final: 0.8333 (t0) REVERT: C 80 ASN cc_start: 0.8271 (t0) cc_final: 0.7960 (t0) REVERT: D 566 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8916 (pp) REVERT: D 603 ILE cc_start: 0.9497 (mt) cc_final: 0.8946 (mp) REVERT: D 621 GLU cc_start: 0.8464 (tt0) cc_final: 0.7857 (tm-30) REVERT: F 530 MET cc_start: 0.8765 (mtm) cc_final: 0.8267 (mtp) REVERT: F 567 LYS cc_start: 0.8589 (pttt) cc_final: 0.8290 (pttp) REVERT: F 634 GLU cc_start: 0.9222 (mm-30) cc_final: 0.8967 (tt0) outliers start: 23 outliers final: 12 residues processed: 158 average time/residue: 0.1270 time to fit residues: 30.0093 Evaluate side-chains 142 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 129 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 561 CYS Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 543 ASN Chi-restraints excluded: chain F residue 561 CYS Chi-restraints excluded: chain F residue 616 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 3 optimal weight: 6.9990 chunk 55 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 162 optimal weight: 0.9980 chunk 129 optimal weight: 9.9990 chunk 11 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 chunk 76 optimal weight: 8.9990 chunk 147 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 570 HIS D 625 ASN ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 478 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.070111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.052420 restraints weight = 47409.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.054713 restraints weight = 26172.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.056246 restraints weight = 18413.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.057226 restraints weight = 14793.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.057932 restraints weight = 12895.869| |-----------------------------------------------------------------------------| r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15843 Z= 0.217 Angle : 0.640 8.517 21696 Z= 0.319 Chirality : 0.044 0.209 2703 Planarity : 0.003 0.023 2583 Dihedral : 6.752 69.088 3999 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.45 % Allowed : 6.25 % Favored : 92.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.20), residues: 1740 helix: 2.32 (0.24), residues: 471 sheet: 0.69 (0.23), residues: 429 loop : 0.28 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 617 TYR 0.010 0.001 TYR F 643 PHE 0.016 0.002 PHE D 522 TRP 0.013 0.001 TRP D 628 HIS 0.005 0.001 HIS B 564 Details of bonding type rmsd covalent geometry : bond 0.00489 (15705) covalent geometry : angle 0.59724 (21318) SS BOND : bond 0.00207 ( 36) SS BOND : angle 0.61796 ( 72) hydrogen bonds : bond 0.04613 ( 624) hydrogen bonds : angle 5.22330 ( 1707) link_ALPHA1-3 : bond 0.00927 ( 3) link_ALPHA1-3 : angle 2.49872 ( 9) link_ALPHA1-6 : bond 0.00849 ( 3) link_ALPHA1-6 : angle 1.71247 ( 9) link_BETA1-4 : bond 0.00270 ( 30) link_BETA1-4 : angle 1.71773 ( 90) link_NAG-ASN : bond 0.00266 ( 66) link_NAG-ASN : angle 2.14828 ( 198) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 136 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 548 ILE cc_start: 0.7869 (mt) cc_final: 0.7541 (tt) REVERT: B 567 LYS cc_start: 0.8286 (pttp) cc_final: 0.7931 (pttp) REVERT: D 621 GLU cc_start: 0.8561 (tt0) cc_final: 0.8193 (tm-30) REVERT: D 654 GLU cc_start: 0.8510 (tt0) cc_final: 0.8016 (tm-30) REVERT: E 434 MET cc_start: 0.8696 (ttp) cc_final: 0.8407 (ttp) REVERT: F 567 LYS cc_start: 0.8442 (pttt) cc_final: 0.8116 (pttp) REVERT: F 584 GLU cc_start: 0.8730 (mt-10) cc_final: 0.8417 (mt-10) REVERT: F 634 GLU cc_start: 0.9207 (OUTLIER) cc_final: 0.8949 (tt0) REVERT: F 654 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8232 (tm-30) outliers start: 23 outliers final: 17 residues processed: 147 average time/residue: 0.1247 time to fit residues: 26.9727 Evaluate side-chains 139 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 548 ILE Chi-restraints excluded: chain D residue 561 CYS Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 561 CYS Chi-restraints excluded: chain F residue 576 LEU Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 634 GLU Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain F residue 654 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 54 optimal weight: 1.9990 chunk 160 optimal weight: 9.9990 chunk 128 optimal weight: 10.0000 chunk 106 optimal weight: 9.9990 chunk 81 optimal weight: 9.9990 chunk 50 optimal weight: 0.9990 chunk 169 optimal weight: 8.9990 chunk 44 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 570 HIS ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 478 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.071202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.053707 restraints weight = 47874.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.056089 restraints weight = 25249.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.057712 restraints weight = 17310.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.058793 restraints weight = 13682.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.059446 restraints weight = 11742.631| |-----------------------------------------------------------------------------| r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15843 Z= 0.167 Angle : 0.588 7.747 21696 Z= 0.296 Chirality : 0.043 0.219 2703 Planarity : 0.003 0.026 2583 Dihedral : 6.245 61.562 3999 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.64 % Allowed : 6.50 % Favored : 91.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.21), residues: 1740 helix: 2.44 (0.25), residues: 471 sheet: 0.60 (0.23), residues: 441 loop : 0.18 (0.23), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 151 TYR 0.009 0.001 TYR C 191 PHE 0.010 0.002 PHE C 176 TRP 0.015 0.001 TRP C 112 HIS 0.005 0.001 HIS B 564 Details of bonding type rmsd covalent geometry : bond 0.00375 (15705) covalent geometry : angle 0.55092 (21318) SS BOND : bond 0.00158 ( 36) SS BOND : angle 0.56465 ( 72) hydrogen bonds : bond 0.04272 ( 624) hydrogen bonds : angle 5.09137 ( 1707) link_ALPHA1-3 : bond 0.00851 ( 3) link_ALPHA1-3 : angle 2.28580 ( 9) link_ALPHA1-6 : bond 0.00938 ( 3) link_ALPHA1-6 : angle 1.75851 ( 9) link_BETA1-4 : bond 0.00310 ( 30) link_BETA1-4 : angle 1.47913 ( 90) link_NAG-ASN : bond 0.00256 ( 66) link_NAG-ASN : angle 1.91264 ( 198) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8982 (ttm) cc_final: 0.8761 (tpp) REVERT: B 548 ILE cc_start: 0.7900 (mt) cc_final: 0.7699 (tt) REVERT: B 567 LYS cc_start: 0.8264 (pttp) cc_final: 0.7864 (pttp) REVERT: B 621 GLU cc_start: 0.7843 (tm-30) cc_final: 0.7595 (tp30) REVERT: D 621 GLU cc_start: 0.8636 (tt0) cc_final: 0.8229 (tm-30) REVERT: D 634 GLU cc_start: 0.9339 (tt0) cc_final: 0.8861 (mt-10) REVERT: D 654 GLU cc_start: 0.8516 (tt0) cc_final: 0.8227 (tp30) REVERT: E 434 MET cc_start: 0.8700 (ttp) cc_final: 0.8412 (ttp) REVERT: F 530 MET cc_start: 0.8665 (mtt) cc_final: 0.8346 (mtt) REVERT: F 567 LYS cc_start: 0.8484 (pttt) cc_final: 0.8238 (pttp) REVERT: F 634 GLU cc_start: 0.9241 (OUTLIER) cc_final: 0.8986 (tt0) REVERT: F 654 GLU cc_start: 0.8604 (tt0) cc_final: 0.8372 (tm-30) REVERT: F 657 GLU cc_start: 0.8945 (tt0) cc_final: 0.8475 (tm-30) outliers start: 26 outliers final: 16 residues processed: 150 average time/residue: 0.1282 time to fit residues: 28.6235 Evaluate side-chains 139 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 548 ILE Chi-restraints excluded: chain D residue 561 CYS Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 561 CYS Chi-restraints excluded: chain F residue 576 LEU Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 634 GLU Chi-restraints excluded: chain F residue 641 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 131 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 86 optimal weight: 5.9990 chunk 113 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 151 optimal weight: 9.9990 chunk 82 optimal weight: 9.9990 chunk 162 optimal weight: 10.0000 chunk 157 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 chunk 137 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN D 570 HIS ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 585 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.070090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.052575 restraints weight = 47207.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.054827 restraints weight = 26058.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.056339 restraints weight = 18350.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.057344 restraints weight = 14757.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.058013 restraints weight = 12803.871| |-----------------------------------------------------------------------------| r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15843 Z= 0.172 Angle : 0.586 9.202 21696 Z= 0.296 Chirality : 0.043 0.218 2703 Planarity : 0.003 0.027 2583 Dihedral : 5.858 53.540 3999 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.52 % Allowed : 7.45 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.21), residues: 1740 helix: 2.51 (0.25), residues: 471 sheet: 0.60 (0.24), residues: 441 loop : 0.10 (0.23), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 557 TYR 0.012 0.001 TYR C 217 PHE 0.009 0.001 PHE C 176 TRP 0.012 0.001 TRP C 112 HIS 0.005 0.001 HIS B 564 Details of bonding type rmsd covalent geometry : bond 0.00388 (15705) covalent geometry : angle 0.55255 (21318) SS BOND : bond 0.00168 ( 36) SS BOND : angle 0.52880 ( 72) hydrogen bonds : bond 0.04201 ( 624) hydrogen bonds : angle 5.00007 ( 1707) link_ALPHA1-3 : bond 0.00847 ( 3) link_ALPHA1-3 : angle 2.43884 ( 9) link_ALPHA1-6 : bond 0.00871 ( 3) link_ALPHA1-6 : angle 1.67625 ( 9) link_BETA1-4 : bond 0.00286 ( 30) link_BETA1-4 : angle 1.44599 ( 90) link_NAG-ASN : bond 0.00201 ( 66) link_NAG-ASN : angle 1.81571 ( 198) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASN cc_start: 0.8342 (t0) cc_final: 0.8014 (p0) REVERT: A 104 MET cc_start: 0.9034 (ttm) cc_final: 0.8816 (tpp) REVERT: B 567 LYS cc_start: 0.8286 (pttp) cc_final: 0.7835 (pttp) REVERT: B 657 GLU cc_start: 0.8950 (tt0) cc_final: 0.8495 (tm-30) REVERT: C 161 MET cc_start: 0.8790 (tpp) cc_final: 0.8290 (tpt) REVERT: D 634 GLU cc_start: 0.9317 (tt0) cc_final: 0.8843 (mt-10) REVERT: F 530 MET cc_start: 0.8779 (mtt) cc_final: 0.8530 (mtt) REVERT: F 567 LYS cc_start: 0.8433 (pttt) cc_final: 0.8185 (pttp) REVERT: F 584 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8487 (mt-10) REVERT: F 634 GLU cc_start: 0.9265 (OUTLIER) cc_final: 0.9000 (tt0) REVERT: F 654 GLU cc_start: 0.8633 (tt0) cc_final: 0.8388 (tm-30) REVERT: F 657 GLU cc_start: 0.8940 (tt0) cc_final: 0.8422 (tm-30) outliers start: 24 outliers final: 17 residues processed: 144 average time/residue: 0.1369 time to fit residues: 29.1944 Evaluate side-chains 139 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 548 ILE Chi-restraints excluded: chain D residue 561 CYS Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 561 CYS Chi-restraints excluded: chain F residue 576 LEU Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 634 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 17 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 chunk 41 optimal weight: 6.9990 chunk 129 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 80 optimal weight: 0.0870 chunk 110 optimal weight: 7.9990 chunk 58 optimal weight: 7.9990 overall best weight: 3.3364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 ASN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 570 HIS D 625 ASN ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.069743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.052117 restraints weight = 47051.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.054353 restraints weight = 26195.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.055845 restraints weight = 18573.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.056841 restraints weight = 14981.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.057513 restraints weight = 13043.180| |-----------------------------------------------------------------------------| r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15843 Z= 0.184 Angle : 0.592 9.392 21696 Z= 0.299 Chirality : 0.043 0.179 2703 Planarity : 0.003 0.027 2583 Dihedral : 5.399 59.544 3999 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.58 % Allowed : 7.32 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.21), residues: 1740 helix: 2.43 (0.25), residues: 471 sheet: 0.55 (0.24), residues: 441 loop : 0.03 (0.23), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 557 TYR 0.017 0.001 TYR C 217 PHE 0.008 0.002 PHE C 176 TRP 0.011 0.001 TRP C 112 HIS 0.005 0.001 HIS B 564 Details of bonding type rmsd covalent geometry : bond 0.00418 (15705) covalent geometry : angle 0.56070 (21318) SS BOND : bond 0.00176 ( 36) SS BOND : angle 0.53628 ( 72) hydrogen bonds : bond 0.04216 ( 624) hydrogen bonds : angle 4.97381 ( 1707) link_ALPHA1-3 : bond 0.00804 ( 3) link_ALPHA1-3 : angle 2.45753 ( 9) link_ALPHA1-6 : bond 0.00724 ( 3) link_ALPHA1-6 : angle 1.35166 ( 9) link_BETA1-4 : bond 0.00291 ( 30) link_BETA1-4 : angle 1.42159 ( 90) link_NAG-ASN : bond 0.00243 ( 66) link_NAG-ASN : angle 1.77348 ( 198) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASN cc_start: 0.8459 (t0) cc_final: 0.8186 (p0) REVERT: B 567 LYS cc_start: 0.8337 (pttp) cc_final: 0.7870 (pttp) REVERT: C 161 MET cc_start: 0.8772 (tpp) cc_final: 0.8260 (tpt) REVERT: D 634 GLU cc_start: 0.9287 (tt0) cc_final: 0.8849 (mt-10) REVERT: D 654 GLU cc_start: 0.8541 (tt0) cc_final: 0.8270 (tm-30) REVERT: F 530 MET cc_start: 0.8754 (mtt) cc_final: 0.8510 (mtp) REVERT: F 567 LYS cc_start: 0.8480 (pttt) cc_final: 0.8225 (pttp) REVERT: F 634 GLU cc_start: 0.9262 (OUTLIER) cc_final: 0.8998 (tt0) REVERT: F 654 GLU cc_start: 0.8653 (tt0) cc_final: 0.8439 (tm-30) REVERT: F 655 LYS cc_start: 0.9404 (tptp) cc_final: 0.8820 (pttp) REVERT: F 657 GLU cc_start: 0.8917 (tt0) cc_final: 0.8386 (tm-30) outliers start: 25 outliers final: 17 residues processed: 143 average time/residue: 0.1245 time to fit residues: 26.1182 Evaluate side-chains 137 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 548 ILE Chi-restraints excluded: chain D residue 561 CYS Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 561 CYS Chi-restraints excluded: chain F residue 576 LEU Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 634 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 150 optimal weight: 9.9990 chunk 169 optimal weight: 8.9990 chunk 137 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 64 optimal weight: 8.9990 chunk 129 optimal weight: 10.0000 chunk 128 optimal weight: 10.0000 chunk 139 optimal weight: 10.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN B 585 HIS C 99 ASN D 570 HIS E 188 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.067633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.050030 restraints weight = 49238.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.052137 restraints weight = 27792.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.053559 restraints weight = 19844.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.054482 restraints weight = 16160.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.055088 restraints weight = 14165.564| |-----------------------------------------------------------------------------| r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.4383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.099 15843 Z= 0.353 Angle : 0.742 9.892 21696 Z= 0.369 Chirality : 0.046 0.193 2703 Planarity : 0.004 0.035 2583 Dihedral : 5.072 26.624 3999 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.83 % Allowed : 7.39 % Favored : 90.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.21), residues: 1740 helix: 1.86 (0.25), residues: 480 sheet: 0.46 (0.25), residues: 432 loop : -0.08 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 480 TYR 0.020 0.002 TYR C 217 PHE 0.013 0.002 PHE E 391 TRP 0.010 0.002 TRP F 610 HIS 0.008 0.002 HIS D 564 Details of bonding type rmsd covalent geometry : bond 0.00803 (15705) covalent geometry : angle 0.70534 (21318) SS BOND : bond 0.00333 ( 36) SS BOND : angle 0.74344 ( 72) hydrogen bonds : bond 0.04867 ( 624) hydrogen bonds : angle 5.28436 ( 1707) link_ALPHA1-3 : bond 0.00425 ( 3) link_ALPHA1-3 : angle 2.82500 ( 9) link_ALPHA1-6 : bond 0.00391 ( 3) link_ALPHA1-6 : angle 2.00573 ( 9) link_BETA1-4 : bond 0.00229 ( 30) link_BETA1-4 : angle 1.79058 ( 90) link_NAG-ASN : bond 0.00537 ( 66) link_NAG-ASN : angle 2.14709 ( 198) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 120 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASN cc_start: 0.8562 (t0) cc_final: 0.8302 (p0) REVERT: A 104 MET cc_start: 0.9203 (tpp) cc_final: 0.8988 (tpp) REVERT: A 161 MET cc_start: 0.8835 (tpp) cc_final: 0.8465 (tpt) REVERT: B 567 LYS cc_start: 0.8481 (pttp) cc_final: 0.7926 (pttp) REVERT: B 655 LYS cc_start: 0.9477 (tptp) cc_final: 0.8820 (pttp) REVERT: B 657 GLU cc_start: 0.8976 (tt0) cc_final: 0.8500 (tm-30) REVERT: D 654 GLU cc_start: 0.8538 (tt0) cc_final: 0.8099 (tm-30) REVERT: F 530 MET cc_start: 0.8798 (mtt) cc_final: 0.8390 (mtp) REVERT: F 567 LYS cc_start: 0.8535 (pttt) cc_final: 0.8260 (pttp) REVERT: F 570 HIS cc_start: 0.7798 (m-70) cc_final: 0.7592 (m-70) REVERT: F 584 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8590 (mt-10) outliers start: 29 outliers final: 19 residues processed: 135 average time/residue: 0.1248 time to fit residues: 24.9883 Evaluate side-chains 130 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 548 ILE Chi-restraints excluded: chain D residue 561 CYS Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 584 GLU Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 561 CYS Chi-restraints excluded: chain F residue 576 LEU Chi-restraints excluded: chain F residue 616 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 71 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 88 optimal weight: 0.3980 chunk 53 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 169 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 chunk 138 optimal weight: 0.7980 chunk 145 optimal weight: 0.9990 chunk 38 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 GLN ** 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 = 0.3271 r_free = 0.3271 target = 0.070864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.053601 restraints weight = 47867.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.055976 restraints weight = 25069.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.057573 restraints weight = 17170.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.058616 restraints weight = 13571.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.059318 restraints weight = 11650.503| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.4482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15843 Z= 0.121 Angle : 0.573 8.778 21696 Z= 0.295 Chirality : 0.043 0.201 2703 Planarity : 0.003 0.028 2583 Dihedral : 4.542 25.258 3999 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.14 % Allowed : 8.40 % Favored : 90.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.21), residues: 1740 helix: 2.31 (0.25), residues: 471 sheet: 0.53 (0.25), residues: 408 loop : -0.02 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 557 TYR 0.015 0.001 TYR C 217 PHE 0.009 0.001 PHE C 176 TRP 0.014 0.001 TRP D 623 HIS 0.005 0.001 HIS F 564 Details of bonding type rmsd covalent geometry : bond 0.00267 (15705) covalent geometry : angle 0.54686 (21318) SS BOND : bond 0.00139 ( 36) SS BOND : angle 0.55809 ( 72) hydrogen bonds : bond 0.04216 ( 624) hydrogen bonds : angle 5.02144 ( 1707) link_ALPHA1-3 : bond 0.00947 ( 3) link_ALPHA1-3 : angle 1.84375 ( 9) link_ALPHA1-6 : bond 0.00382 ( 3) link_ALPHA1-6 : angle 1.62928 ( 9) link_BETA1-4 : bond 0.00366 ( 30) link_BETA1-4 : angle 1.20426 ( 90) link_NAG-ASN : bond 0.00198 ( 66) link_NAG-ASN : angle 1.63475 ( 198) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASN cc_start: 0.8575 (t0) cc_final: 0.8298 (p0) REVERT: A 104 MET cc_start: 0.9081 (tpp) cc_final: 0.8845 (tpp) REVERT: A 161 MET cc_start: 0.8852 (tpp) cc_final: 0.8627 (tpt) REVERT: B 567 LYS cc_start: 0.8464 (pttp) cc_final: 0.7950 (pttp) REVERT: B 634 GLU cc_start: 0.9311 (tt0) cc_final: 0.9105 (mt-10) REVERT: B 648 GLU cc_start: 0.8274 (pp20) cc_final: 0.8016 (pp20) REVERT: B 655 LYS cc_start: 0.9394 (tptp) cc_final: 0.8838 (pttp) REVERT: B 657 GLU cc_start: 0.8975 (tt0) cc_final: 0.8464 (tm-30) REVERT: C 161 MET cc_start: 0.8741 (tpp) cc_final: 0.8357 (tpt) REVERT: D 634 GLU cc_start: 0.9221 (tt0) cc_final: 0.8645 (mt-10) REVERT: D 648 GLU cc_start: 0.8134 (pp20) cc_final: 0.7861 (pp20) REVERT: D 655 LYS cc_start: 0.9290 (tptp) cc_final: 0.8674 (pttp) REVERT: E 80 ASN cc_start: 0.8485 (t0) cc_final: 0.8279 (p0) REVERT: F 530 MET cc_start: 0.8752 (mtt) cc_final: 0.8549 (mtp) REVERT: F 567 LYS cc_start: 0.8650 (pttt) cc_final: 0.8193 (pttp) REVERT: F 621 GLU cc_start: 0.8190 (tp30) cc_final: 0.7873 (tm-30) REVERT: F 648 GLU cc_start: 0.8288 (pp20) cc_final: 0.8052 (pp20) outliers start: 18 outliers final: 14 residues processed: 143 average time/residue: 0.1397 time to fit residues: 29.2756 Evaluate side-chains 136 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 548 ILE Chi-restraints excluded: chain D residue 561 CYS Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 561 CYS Chi-restraints excluded: chain F residue 576 LEU Chi-restraints excluded: chain F residue 616 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 163 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 146 optimal weight: 0.0070 chunk 68 optimal weight: 10.0000 chunk 78 optimal weight: 7.9990 chunk 140 optimal weight: 5.9990 chunk 131 optimal weight: 0.9990 chunk 18 optimal weight: 9.9990 chunk 123 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 overall best weight: 2.1404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 570 HIS ** E 103 GLN ** 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 = 0.3271 r_free = 0.3271 target = 0.070969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.053791 restraints weight = 48382.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.056171 restraints weight = 25175.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.057769 restraints weight = 17160.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.058826 restraints weight = 13520.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.059417 restraints weight = 11571.574| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.4571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15843 Z= 0.143 Angle : 0.591 11.267 21696 Z= 0.301 Chirality : 0.043 0.233 2703 Planarity : 0.003 0.028 2583 Dihedral : 4.366 24.209 3999 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.95 % Allowed : 8.90 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.21), residues: 1740 helix: 2.21 (0.25), residues: 471 sheet: 0.78 (0.27), residues: 372 loop : 0.02 (0.22), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 579 TYR 0.010 0.001 TYR C 191 PHE 0.013 0.001 PHE E 53 TRP 0.011 0.001 TRP D 623 HIS 0.006 0.001 HIS D 564 Details of bonding type rmsd covalent geometry : bond 0.00324 (15705) covalent geometry : angle 0.56603 (21318) SS BOND : bond 0.00159 ( 36) SS BOND : angle 0.50571 ( 72) hydrogen bonds : bond 0.04221 ( 624) hydrogen bonds : angle 5.00342 ( 1707) link_ALPHA1-3 : bond 0.00717 ( 3) link_ALPHA1-3 : angle 1.84025 ( 9) link_ALPHA1-6 : bond 0.00289 ( 3) link_ALPHA1-6 : angle 1.57679 ( 9) link_BETA1-4 : bond 0.00302 ( 30) link_BETA1-4 : angle 1.29138 ( 90) link_NAG-ASN : bond 0.00179 ( 66) link_NAG-ASN : angle 1.61217 ( 198) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASN cc_start: 0.8600 (t0) cc_final: 0.8330 (p0) REVERT: A 104 MET cc_start: 0.9118 (tpp) cc_final: 0.8904 (tpp) REVERT: A 161 MET cc_start: 0.8880 (tpp) cc_final: 0.8614 (tpt) REVERT: A 426 MET cc_start: 0.6095 (mtm) cc_final: 0.5611 (mtp) REVERT: B 567 LYS cc_start: 0.8466 (pttp) cc_final: 0.7962 (pttp) REVERT: B 648 GLU cc_start: 0.8293 (pp20) cc_final: 0.8015 (pp20) REVERT: B 657 GLU cc_start: 0.8959 (tt0) cc_final: 0.8468 (tm-30) REVERT: C 161 MET cc_start: 0.8813 (tpp) cc_final: 0.8397 (tpt) REVERT: D 584 GLU cc_start: 0.8485 (tt0) cc_final: 0.8246 (tt0) REVERT: D 601 LYS cc_start: 0.8519 (mppt) cc_final: 0.7730 (mppt) REVERT: D 634 GLU cc_start: 0.9195 (tt0) cc_final: 0.8600 (mt-10) REVERT: D 648 GLU cc_start: 0.8122 (pp20) cc_final: 0.7856 (pp20) REVERT: D 655 LYS cc_start: 0.9313 (tptp) cc_final: 0.8811 (pttp) REVERT: E 80 ASN cc_start: 0.8568 (t0) cc_final: 0.8352 (p0) REVERT: F 567 LYS cc_start: 0.8590 (pttt) cc_final: 0.8117 (pttp) REVERT: F 601 LYS cc_start: 0.8415 (mtmm) cc_final: 0.8078 (mtmm) REVERT: F 621 GLU cc_start: 0.8142 (tp30) cc_final: 0.7899 (tm-30) REVERT: F 648 GLU cc_start: 0.8264 (pp20) cc_final: 0.8015 (pp20) REVERT: F 654 GLU cc_start: 0.9074 (tp30) cc_final: 0.8857 (tm-30) outliers start: 15 outliers final: 13 residues processed: 132 average time/residue: 0.1338 time to fit residues: 26.1985 Evaluate side-chains 132 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 548 ILE Chi-restraints excluded: chain D residue 561 CYS Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 561 CYS Chi-restraints excluded: chain F residue 576 LEU Chi-restraints excluded: chain F residue 616 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 93 optimal weight: 4.9990 chunk 158 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 4 optimal weight: 0.3980 chunk 44 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 6.9990 chunk 48 optimal weight: 20.0000 chunk 163 optimal weight: 4.9990 chunk 151 optimal weight: 0.7980 chunk 115 optimal weight: 6.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 GLN ** 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 = 0.3273 r_free = 0.3273 target = 0.070975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.053859 restraints weight = 48231.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.056226 restraints weight = 25106.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.057814 restraints weight = 17132.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.058861 restraints weight = 13494.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.059548 restraints weight = 11571.478| |-----------------------------------------------------------------------------| r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.4659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15843 Z= 0.144 Angle : 0.576 8.441 21696 Z= 0.295 Chirality : 0.043 0.208 2703 Planarity : 0.003 0.027 2583 Dihedral : 4.258 23.201 3999 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.88 % Allowed : 8.52 % Favored : 90.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.21), residues: 1740 helix: 2.23 (0.25), residues: 471 sheet: 0.81 (0.27), residues: 372 loop : 0.02 (0.22), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG F 557 TYR 0.010 0.001 TYR C 191 PHE 0.012 0.001 PHE E 53 TRP 0.011 0.001 TRP D 623 HIS 0.005 0.001 HIS D 564 Details of bonding type rmsd covalent geometry : bond 0.00326 (15705) covalent geometry : angle 0.55158 (21318) SS BOND : bond 0.00162 ( 36) SS BOND : angle 0.50696 ( 72) hydrogen bonds : bond 0.04181 ( 624) hydrogen bonds : angle 4.97370 ( 1707) link_ALPHA1-3 : bond 0.00602 ( 3) link_ALPHA1-3 : angle 1.77003 ( 9) link_ALPHA1-6 : bond 0.00293 ( 3) link_ALPHA1-6 : angle 1.55235 ( 9) link_BETA1-4 : bond 0.00302 ( 30) link_BETA1-4 : angle 1.27714 ( 90) link_NAG-ASN : bond 0.00174 ( 66) link_NAG-ASN : angle 1.57412 ( 198) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2019.33 seconds wall clock time: 35 minutes 58.02 seconds (2158.02 seconds total)