Starting phenix.real_space_refine on Fri Jul 3 17:52:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7l7t_23218/07_2026/7l7t_23218.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l7t_23218/07_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_23218/07_2026/7l7t_23218.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l7t_23218/07_2026/7l7t_23218.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7l7t_23218/07_2026/7l7t_23218.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7l7t_23218/07_2026/7l7t_23218.cif" model { file = "/net/cci-nas-00/data/ceres_data/7l7t_23218/07_2026/7l7t_23218.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l7t_23218/07_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-6108/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 3 Time building chain proxies: 3.57, per 1000 atoms: 0.23 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: 1.44 Conformation dependent library (CDL) restraints added in 606.5 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: 0.41 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: 2.75 Time building geometry restraints manager: 1.79 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 - 16.09: 8268 16.09 - 32.18: 282 32.18 - 48.27: 63 48.27 - 64.36: 39 64.36 - 80.45: 18 Dihedral angle restraints: 8670 sinusoidal: 3552 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 8667 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: 0.04 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: 0.560 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: 0.190 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.700 Find NCS groups from input model: 0.440 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 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 : 10.293 80.452 5244 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/Z covalent geometry : bond 0.02336 / 1.25 (15705) covalent geometry : angle 1.69417 / 1.10 (21318) SS BOND : bond 0.01068 / 0.62 ( 36) SS BOND : angle 2.80030 / 1.85 ( 72) hydrogen bonds : bond 0.16174 / 10.75 ( 624) hydrogen bonds : angle 7.47223 / 5.24 ( 1707) link_ALPHA1-3 : bond 0.08978 / 4.50 ( 3) link_ALPHA1-3 : angle 4.42527 / 3.03 ( 9) link_ALPHA1-6 : bond 0.05873 / 2.94 ( 3) link_ALPHA1-6 : angle 3.60750 / 2.46 ( 9) link_BETA1-4 : bond 0.06714 / 4.00 ( 30) link_BETA1-4 : angle 4.43404 / 3.06 ( 90) link_NAG-ASN : bond 0.07726 / 4.87 ( 66) link_NAG-ASN : angle 2.96498 / 2.07 ( 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 : 0.585 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: 0.1440 time to fit residues: 51.9810 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 : 0.580 ------------------------------------------------------------------------------- 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... B 562 GLN B 575 GLN B 577 GLN B 625 ASN C 130 GLN D 562 GLN D 570 HIS D 577 GLN F 562 GLN F 575 GLN 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 = 0.071464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.053686 restraints weight = 46655.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.056009 restraints weight = 25978.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.057564 restraints weight = 18354.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.058629 restraints weight = 14780.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.059335 restraints weight = 12799.747| |-----------------------------------------------------------------------------| r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 15843 Z= 0.243 Angle : 0.771 9.861 21696 Z= 0.383 Chirality : 0.048 0.192 2703 Planarity : 0.004 0.026 2583 Dihedral : 4.945 17.629 1875 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.33 % Allowed : 4.29 % 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: 1.29 (0.20), residues: 1740 helix: 1.78 (0.24), residues: 471 sheet: 0.85 (0.23), residues: 411 loop : 0.46 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 557 TYR 0.022 0.002 TYR A 39 PHE 0.013 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/Z covalent geometry : bond 0.00548 / 0.24 (15705) covalent geometry : angle 0.70380 / 0.37 (21318) SS BOND : bond 0.00281 / 0.18 ( 36) SS BOND : angle 0.98614 / 0.69 ( 72) hydrogen bonds : bond 0.05828 / 3.92 ( 624) hydrogen bonds : angle 5.81432 / 4.06 ( 1707) link_ALPHA1-3 : bond 0.00186 / 0.09 ( 3) link_ALPHA1-3 : angle 1.89909 / 1.18 ( 9) link_ALPHA1-6 : bond 0.00547 / 0.27 ( 3) link_ALPHA1-6 : angle 1.50565 / 0.99 ( 9) link_BETA1-4 : bond 0.00160 / 0.09 ( 30) link_BETA1-4 : angle 2.38242 / 1.66 ( 90) link_NAG-ASN : bond 0.00445 / 0.28 ( 66) link_NAG-ASN : angle 2.94727 / 2.09 ( 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 181 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 160 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASN cc_start: 0.8317 (t0) cc_final: 0.8061 (t0) REVERT: B 557 ARG cc_start: 0.8504 (tmm160) cc_final: 0.8174 (tmm160) REVERT: B 634 GLU cc_start: 0.9071 (mm-30) cc_final: 0.8781 (tp30) REVERT: B 647 GLU cc_start: 0.8642 (tt0) cc_final: 0.8430 (tt0) REVERT: B 655 LYS cc_start: 0.9228 (tptp) cc_final: 0.8801 (pttp) REVERT: C 80 ASN cc_start: 0.8174 (t0) cc_final: 0.7875 (t0) REVERT: D 566 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.8829 (pp) REVERT: D 567 LYS cc_start: 0.8568 (pttt) cc_final: 0.8221 (pttm) REVERT: D 570 HIS cc_start: 0.7174 (m-70) cc_final: 0.6709 (m-70) REVERT: D 621 GLU cc_start: 0.8547 (tt0) cc_final: 0.7973 (tp30) REVERT: D 626 MET cc_start: 0.7812 (ttt) cc_final: 0.7550 (ttm) REVERT: F 542 ARG cc_start: 0.9061 (ttm110) cc_final: 0.8755 (ttp80) REVERT: F 566 LEU cc_start: 0.8864 (mp) cc_final: 0.8523 (pp) REVERT: F 626 MET cc_start: 0.7428 (ttt) cc_final: 0.6927 (ttt) REVERT: F 634 GLU cc_start: 0.9198 (OUTLIER) cc_final: 0.8849 (tt0) REVERT: F 655 LYS cc_start: 0.9254 (tptp) cc_final: 0.8767 (pttp) outliers start: 21 outliers final: 14 residues processed: 171 average time/residue: 0.1257 time to fit residues: 32.2240 Evaluate side-chains 152 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 0.567 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 167 optimal weight: 0.5980 chunk 173 optimal weight: 10.0000 chunk 52 optimal weight: 8.9990 chunk 24 optimal weight: 3.9990 chunk 104 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 169 optimal weight: 9.9990 chunk 107 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 162 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 170 GLN B 543 ASN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.070095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.052432 restraints weight = 47385.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.054718 restraints weight = 26105.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.056262 restraints weight = 18379.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.057298 restraints weight = 14747.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.057983 restraints weight = 12782.051| |-----------------------------------------------------------------------------| r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 15843 Z= 0.227 Angle : 0.649 6.666 21696 Z= 0.330 Chirality : 0.044 0.202 2703 Planarity : 0.003 0.026 2583 Dihedral : 4.649 18.260 1875 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.45 % Allowed : 6.06 % Favored : 92.49 % 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 (0.20), residues: 1740 helix: 2.06 (0.24), residues: 471 sheet: 0.72 (0.23), residues: 417 loop : 0.35 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 480 TYR 0.020 0.002 TYR F 643 PHE 0.013 0.002 PHE C 176 TRP 0.015 0.002 TRP E 112 HIS 0.005 0.001 HIS D 564 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.23 (15705) covalent geometry : angle 0.61074 / 0.32 (21318) SS BOND : bond 0.00202 / 0.14 ( 36) SS BOND : angle 0.72960 / 0.51 ( 72) hydrogen bonds : bond 0.04956 / 3.29 ( 624) hydrogen bonds : angle 5.42815 / 3.80 ( 1707) link_ALPHA1-3 : bond 0.00343 / 0.17 ( 3) link_ALPHA1-3 : angle 1.52750 / 0.95 ( 9) link_ALPHA1-6 : bond 0.00572 / 0.29 ( 3) link_ALPHA1-6 : angle 1.32774 / 0.91 ( 9) link_BETA1-4 : bond 0.00320 / 0.20 ( 30) link_BETA1-4 : angle 1.54593 / 1.09 ( 90) link_NAG-ASN : bond 0.00246 / 0.15 ( 66) link_NAG-ASN : angle 2.13920 / 1.51 ( 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 160 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 567 LYS cc_start: 0.8239 (pttp) cc_final: 0.7792 (pttm) REVERT: B 654 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8455 (tm-30) REVERT: C 80 ASN cc_start: 0.8262 (t0) cc_final: 0.7987 (t0) REVERT: D 566 LEU cc_start: 0.9297 (OUTLIER) cc_final: 0.8942 (pp) REVERT: D 570 HIS cc_start: 0.7067 (m-70) cc_final: 0.6625 (m-70) REVERT: D 603 ILE cc_start: 0.9506 (mt) cc_final: 0.8997 (mp) REVERT: F 530 MET cc_start: 0.8779 (mtm) cc_final: 0.8312 (mtp) REVERT: F 566 LEU cc_start: 0.8930 (mp) cc_final: 0.8429 (pp) REVERT: F 567 LYS cc_start: 0.8367 (pttp) cc_final: 0.7947 (pttm) REVERT: F 626 MET cc_start: 0.7730 (ttt) cc_final: 0.7309 (ttm) REVERT: F 634 GLU cc_start: 0.9213 (mm-30) cc_final: 0.8942 (mt-10) REVERT: F 654 GLU cc_start: 0.8691 (tt0) cc_final: 0.8301 (tm-30) outliers start: 23 outliers final: 15 residues processed: 150 average time/residue: 0.1246 time to fit residues: 27.9887 Evaluate side-chains 140 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 543 ASN 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 624 ASP Chi-restraints excluded: chain B residue 654 GLU 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 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 576 LEU 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: 8.9990 chunk 55 optimal weight: 8.9990 chunk 90 optimal weight: 6.9990 chunk 162 optimal weight: 4.9990 chunk 129 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 76 optimal weight: 3.9990 chunk 147 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 478 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.069702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.052198 restraints weight = 48735.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.054535 restraints weight = 25936.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.056104 restraints weight = 17937.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.057150 restraints weight = 14284.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.057750 restraints weight = 12328.100| |-----------------------------------------------------------------------------| r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 15843 Z= 0.276 Angle : 0.674 8.151 21696 Z= 0.338 Chirality : 0.044 0.171 2703 Planarity : 0.004 0.026 2583 Dihedral : 4.663 18.571 1875 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.64 % Allowed : 6.19 % Favored : 92.17 % 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: 1.15 (0.20), residues: 1740 helix: 2.15 (0.24), residues: 471 sheet: 0.55 (0.24), residues: 423 loop : 0.17 (0.22), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 617 TYR 0.011 0.002 TYR A 177 PHE 0.020 0.002 PHE B 522 TRP 0.012 0.001 TRP C 112 HIS 0.006 0.002 HIS B 564 Details of bonding type rmsd/Z covalent geometry : bond 0.00623 / 0.28 (15705) covalent geometry : angle 0.63872 / 0.33 (21318) SS BOND : bond 0.00264 / 0.18 ( 36) SS BOND : angle 0.68600 / 0.48 ( 72) hydrogen bonds : bond 0.04811 / 3.21 ( 624) hydrogen bonds : angle 5.28918 / 3.70 ( 1707) link_ALPHA1-3 : bond 0.00141 / 0.07 ( 3) link_ALPHA1-3 : angle 1.75143 / 1.12 ( 9) link_ALPHA1-6 : bond 0.00475 / 0.24 ( 3) link_ALPHA1-6 : angle 1.36002 / 0.91 ( 9) link_BETA1-4 : bond 0.00233 / 0.15 ( 30) link_BETA1-4 : angle 1.57067 / 1.12 ( 90) link_NAG-ASN : bond 0.00357 / 0.22 ( 66) link_NAG-ASN : angle 2.08973 / 1.47 ( 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: 26 poor density : 133 time to evaluate : 0.589 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: B 567 LYS cc_start: 0.8368 (pttp) cc_final: 0.8011 (pttp) REVERT: B 662 GLU cc_start: 0.7364 (tp30) cc_final: 0.7091 (tp30) REVERT: D 566 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8926 (pp) REVERT: D 567 LYS cc_start: 0.8468 (pttp) cc_final: 0.8149 (pttm) REVERT: D 570 HIS cc_start: 0.7109 (m-70) cc_final: 0.6660 (m-70) REVERT: D 574 LYS cc_start: 0.8852 (mmmm) cc_final: 0.8648 (mmmm) REVERT: D 603 ILE cc_start: 0.9450 (mt) cc_final: 0.9229 (mt) REVERT: D 634 GLU cc_start: 0.9211 (tt0) cc_final: 0.8771 (mt-10) REVERT: D 654 GLU cc_start: 0.8526 (tt0) cc_final: 0.8039 (tm-30) REVERT: E 434 MET cc_start: 0.8855 (ttp) cc_final: 0.8569 (ttp) REVERT: F 566 LEU cc_start: 0.8995 (mp) cc_final: 0.8497 (pp) REVERT: F 567 LYS cc_start: 0.8360 (pttp) cc_final: 0.7977 (pttp) REVERT: F 634 GLU cc_start: 0.9233 (OUTLIER) cc_final: 0.8980 (tt0) REVERT: F 654 GLU cc_start: 0.8662 (tt0) cc_final: 0.8356 (tm-30) outliers start: 26 outliers final: 16 residues processed: 148 average time/residue: 0.1323 time to fit residues: 28.7907 Evaluate side-chains 134 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 54 optimal weight: 9.9990 chunk 160 optimal weight: 6.9990 chunk 128 optimal weight: 9.9990 chunk 106 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 169 optimal weight: 7.9990 chunk 44 optimal weight: 0.9980 chunk 124 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 625 ASN ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 585 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.070179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.052686 restraints weight = 48203.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.055044 restraints weight = 25497.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.056623 restraints weight = 17575.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.057685 restraints weight = 13957.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.058331 restraints weight = 12012.530| |-----------------------------------------------------------------------------| r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 15843 Z= 0.204 Angle : 0.603 7.952 21696 Z= 0.305 Chirality : 0.043 0.166 2703 Planarity : 0.003 0.025 2583 Dihedral : 4.548 18.356 1875 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.58 % Allowed : 7.07 % Favored : 91.35 % 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: 1.13 (0.20), residues: 1740 helix: 2.23 (0.24), residues: 471 sheet: 0.57 (0.24), residues: 429 loop : 0.06 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 617 TYR 0.012 0.001 TYR C 217 PHE 0.015 0.002 PHE D 522 TRP 0.012 0.001 TRP C 112 HIS 0.006 0.001 HIS B 564 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.20 (15705) covalent geometry : angle 0.57321 / 0.30 (21318) SS BOND : bond 0.00205 / 0.14 ( 36) SS BOND : angle 0.59840 / 0.41 ( 72) hydrogen bonds : bond 0.04450 / 2.96 ( 624) hydrogen bonds : angle 5.14614 / 3.60 ( 1707) link_ALPHA1-3 : bond 0.00224 / 0.11 ( 3) link_ALPHA1-3 : angle 1.62117 / 1.05 ( 9) link_ALPHA1-6 : bond 0.00435 / 0.22 ( 3) link_ALPHA1-6 : angle 1.40038 / 0.93 ( 9) link_BETA1-4 : bond 0.00284 / 0.17 ( 30) link_BETA1-4 : angle 1.34556 / 0.96 ( 90) link_NAG-ASN : bond 0.00255 / 0.15 ( 66) link_NAG-ASN : angle 1.82871 / 1.28 ( 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 156 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 MET cc_start: 0.7968 (pmm) cc_final: 0.7581 (pmm) REVERT: B 567 LYS cc_start: 0.8323 (pttp) cc_final: 0.7902 (pttp) REVERT: B 621 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7617 (tp30) REVERT: D 566 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8897 (pp) REVERT: D 567 LYS cc_start: 0.8614 (pttp) cc_final: 0.8224 (pttm) REVERT: D 570 HIS cc_start: 0.7007 (m-70) cc_final: 0.6714 (m-70) REVERT: D 654 GLU cc_start: 0.8484 (tt0) cc_final: 0.8236 (tp30) REVERT: F 530 MET cc_start: 0.8590 (mtt) cc_final: 0.8200 (mtt) REVERT: F 566 LEU cc_start: 0.8952 (mp) cc_final: 0.8480 (pp) REVERT: F 567 LYS cc_start: 0.8437 (pttp) cc_final: 0.7989 (pttp) REVERT: F 634 GLU cc_start: 0.9229 (OUTLIER) cc_final: 0.8988 (tt0) REVERT: F 654 GLU cc_start: 0.8625 (tt0) cc_final: 0.8276 (tm-30) outliers start: 25 outliers final: 16 residues processed: 144 average time/residue: 0.1208 time to fit residues: 25.9545 Evaluate side-chains 134 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 131 optimal weight: 7.9990 chunk 99 optimal weight: 7.9990 chunk 86 optimal weight: 7.9990 chunk 113 optimal weight: 10.0000 chunk 37 optimal weight: 0.7980 chunk 151 optimal weight: 9.9990 chunk 82 optimal weight: 6.9990 chunk 162 optimal weight: 10.0000 chunk 157 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 137 optimal weight: 6.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 625 ASN ** 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 = 0.3229 r_free = 0.3229 target = 0.068877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.051783 restraints weight = 48853.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.054028 restraints weight = 26081.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.055542 restraints weight = 18052.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.056554 restraints weight = 14369.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.057210 restraints weight = 12389.191| |-----------------------------------------------------------------------------| r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.4113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 15843 Z= 0.254 Angle : 0.649 9.161 21696 Z= 0.326 Chirality : 0.043 0.179 2703 Planarity : 0.004 0.028 2583 Dihedral : 4.589 18.710 1875 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.52 % Allowed : 7.64 % Favored : 90.85 % 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 (0.20), residues: 1740 helix: 2.08 (0.24), residues: 471 sheet: 0.41 (0.23), residues: 459 loop : 0.02 (0.23), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 151 TYR 0.013 0.002 TYR C 217 PHE 0.010 0.002 PHE C 176 TRP 0.014 0.002 TRP E 112 HIS 0.006 0.002 HIS B 564 Details of bonding type rmsd/Z covalent geometry : bond 0.00577 / 0.25 (15705) covalent geometry : angle 0.61925 / 0.32 (21318) SS BOND : bond 0.00248 / 0.17 ( 36) SS BOND : angle 0.63435 / 0.43 ( 72) hydrogen bonds : bond 0.04557 / 3.03 ( 624) hydrogen bonds : angle 5.19392 / 3.63 ( 1707) link_ALPHA1-3 : bond 0.00131 / 0.07 ( 3) link_ALPHA1-3 : angle 1.73627 / 1.13 ( 9) link_ALPHA1-6 : bond 0.00364 / 0.18 ( 3) link_ALPHA1-6 : angle 1.40866 / 0.93 ( 9) link_BETA1-4 : bond 0.00217 / 0.13 ( 30) link_BETA1-4 : angle 1.46261 / 1.04 ( 90) link_NAG-ASN : bond 0.00388 / 0.24 ( 66) link_NAG-ASN : angle 1.86927 / 1.32 ( 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 153 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.9289 (mmm) cc_final: 0.9070 (mmm) REVERT: B 567 LYS cc_start: 0.8448 (pttp) cc_final: 0.7970 (pttp) REVERT: B 584 GLU cc_start: 0.8740 (tt0) cc_final: 0.8413 (tt0) REVERT: B 654 GLU cc_start: 0.8868 (tm-30) cc_final: 0.8629 (tm-30) REVERT: B 657 GLU cc_start: 0.8971 (tt0) cc_final: 0.8500 (tm-30) REVERT: C 104 MET cc_start: 0.9166 (ttm) cc_final: 0.8760 (tpp) REVERT: D 566 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8863 (pp) REVERT: D 567 LYS cc_start: 0.8516 (pttp) cc_final: 0.7904 (pttm) REVERT: D 570 HIS cc_start: 0.7094 (m-70) cc_final: 0.6781 (m90) REVERT: D 622 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.8456 (mm) REVERT: D 634 GLU cc_start: 0.9289 (tt0) cc_final: 0.8533 (mt-10) REVERT: F 530 MET cc_start: 0.8810 (mtt) cc_final: 0.8554 (mtt) REVERT: F 566 LEU cc_start: 0.8925 (mp) cc_final: 0.8334 (pp) REVERT: F 567 LYS cc_start: 0.8468 (pttp) cc_final: 0.7935 (pttp) REVERT: F 634 GLU cc_start: 0.9243 (OUTLIER) cc_final: 0.8963 (tt0) REVERT: F 654 GLU cc_start: 0.8638 (tt0) cc_final: 0.8429 (tm-30) REVERT: F 657 GLU cc_start: 0.8937 (tt0) cc_final: 0.8417 (tm-30) outliers start: 24 outliers final: 17 residues processed: 143 average time/residue: 0.1197 time to fit residues: 25.6411 Evaluate side-chains 134 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.536 ------------------------------------------------------------------------------- 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 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 576 LEU Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 622 ILE 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 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: 5.9990 chunk 19 optimal weight: 5.9990 chunk 103 optimal weight: 0.0770 chunk 78 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 129 optimal weight: 7.9990 chunk 70 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 chunk 80 optimal weight: 0.8980 chunk 110 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 overall best weight: 2.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 ASN B 625 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.070325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.053097 restraints weight = 47905.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.055428 restraints weight = 25420.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.057006 restraints weight = 17494.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.058063 restraints weight = 13853.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.058756 restraints weight = 11893.987| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15843 Z= 0.155 Angle : 0.574 9.475 21696 Z= 0.294 Chirality : 0.042 0.186 2703 Planarity : 0.003 0.031 2583 Dihedral : 4.405 18.372 1875 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.52 % Allowed : 8.21 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.21), residues: 1740 helix: 2.20 (0.25), residues: 471 sheet: 0.76 (0.26), residues: 390 loop : -0.03 (0.21), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 557 TYR 0.017 0.001 TYR C 217 PHE 0.009 0.001 PHE C 176 TRP 0.010 0.001 TRP A 96 HIS 0.004 0.001 HIS B 564 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 (15705) covalent geometry : angle 0.54861 / 0.29 (21318) SS BOND : bond 0.00171 / 0.12 ( 36) SS BOND : angle 0.51248 / 0.35 ( 72) hydrogen bonds : bond 0.04249 / 2.84 ( 624) hydrogen bonds : angle 5.05464 / 3.53 ( 1707) link_ALPHA1-3 : bond 0.00288 / 0.14 ( 3) link_ALPHA1-3 : angle 1.57378 / 1.04 ( 9) link_ALPHA1-6 : bond 0.00347 / 0.17 ( 3) link_ALPHA1-6 : angle 1.43001 / 0.94 ( 9) link_BETA1-4 : bond 0.00276 / 0.16 ( 30) link_BETA1-4 : angle 1.23764 / 0.89 ( 90) link_NAG-ASN : bond 0.00195 / 0.12 ( 66) link_NAG-ASN : angle 1.63344 / 1.15 ( 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 149 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.663 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: 0.8305 (t0) cc_final: 0.8039 (p0) REVERT: B 567 LYS cc_start: 0.8428 (pttp) cc_final: 0.7947 (pttp) REVERT: B 654 GLU cc_start: 0.8864 (tm-30) cc_final: 0.8523 (tm-30) REVERT: C 161 MET cc_start: 0.8803 (tpp) cc_final: 0.8274 (tpt) REVERT: D 566 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8837 (pp) REVERT: D 567 LYS cc_start: 0.8547 (pttp) cc_final: 0.7928 (pttm) REVERT: D 622 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8356 (mm) REVERT: F 530 MET cc_start: 0.8736 (mtt) cc_final: 0.8484 (mtt) REVERT: F 567 LYS cc_start: 0.8505 (pttp) cc_final: 0.7996 (pttp) REVERT: F 584 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8371 (mt-10) REVERT: F 654 GLU cc_start: 0.8561 (tt0) cc_final: 0.8359 (tm-30) REVERT: F 655 LYS cc_start: 0.9442 (tptp) cc_final: 0.8860 (pttp) REVERT: F 657 GLU cc_start: 0.8939 (tt0) cc_final: 0.8398 (tm-30) outliers start: 24 outliers final: 13 residues processed: 141 average time/residue: 0.1232 time to fit residues: 25.8453 Evaluate side-chains 129 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.554 ------------------------------------------------------------------------------- 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 561 CYS Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 616 ASN 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 D residue 622 ILE Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 561 CYS Chi-restraints excluded: chain F residue 616 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 150 optimal weight: 8.9990 chunk 169 optimal weight: 7.9990 chunk 137 optimal weight: 6.9990 chunk 46 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 129 optimal weight: 9.9990 chunk 128 optimal weight: 8.9990 chunk 139 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 478 ASN ** 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 = 0.3227 r_free = 0.3227 target = 0.068766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.051707 restraints weight = 49360.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.053950 restraints weight = 26156.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.055476 restraints weight = 18041.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.056478 restraints weight = 14326.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.057125 restraints weight = 12349.618| |-----------------------------------------------------------------------------| r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.4365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 15843 Z= 0.276 Angle : 0.651 9.584 21696 Z= 0.327 Chirality : 0.043 0.185 2703 Planarity : 0.004 0.048 2583 Dihedral : 4.509 18.273 1875 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.45 % Allowed : 8.08 % 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: 1.02 (0.21), residues: 1740 helix: 2.02 (0.24), residues: 471 sheet: 0.70 (0.25), residues: 414 loop : -0.03 (0.22), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 557 TYR 0.017 0.001 TYR A 217 PHE 0.010 0.002 PHE C 176 TRP 0.011 0.001 TRP C 479 HIS 0.005 0.001 HIS B 564 Details of bonding type rmsd/Z covalent geometry : bond 0.00628 / 0.28 (15705) covalent geometry : angle 0.62423 / 0.32 (21318) SS BOND : bond 0.00275 / 0.18 ( 36) SS BOND : angle 0.61344 / 0.42 ( 72) hydrogen bonds : bond 0.04463 / 2.96 ( 624) hydrogen bonds : angle 5.14063 / 3.59 ( 1707) link_ALPHA1-3 : bond 0.00128 / 0.06 ( 3) link_ALPHA1-3 : angle 1.73242 / 1.12 ( 9) link_ALPHA1-6 : bond 0.00344 / 0.17 ( 3) link_ALPHA1-6 : angle 1.42203 / 0.93 ( 9) link_BETA1-4 : bond 0.00235 / 0.14 ( 30) link_BETA1-4 : angle 1.40915 / 1.00 ( 90) link_NAG-ASN : bond 0.00376 / 0.24 ( 66) link_NAG-ASN : angle 1.78337 / 1.26 ( 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 139 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8858 (tpp) cc_final: 0.8541 (tpt) REVERT: B 567 LYS cc_start: 0.8457 (pttp) cc_final: 0.7956 (pttp) REVERT: B 648 GLU cc_start: 0.8338 (pp20) cc_final: 0.8110 (pp20) REVERT: B 654 GLU cc_start: 0.8892 (tm-30) cc_final: 0.8465 (tm-30) REVERT: B 657 GLU cc_start: 0.8963 (tt0) cc_final: 0.8437 (tm-30) REVERT: D 566 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8804 (pp) REVERT: D 567 LYS cc_start: 0.8558 (pttp) cc_final: 0.8018 (pttm) REVERT: D 601 LYS cc_start: 0.8567 (mppt) cc_final: 0.7823 (mppt) REVERT: D 622 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8425 (mm) REVERT: D 634 GLU cc_start: 0.9268 (tt0) cc_final: 0.8762 (mt-10) REVERT: D 648 GLU cc_start: 0.8210 (pp20) cc_final: 0.7974 (pp20) REVERT: D 654 GLU cc_start: 0.8965 (tp30) cc_final: 0.8605 (tm-30) REVERT: D 655 LYS cc_start: 0.9464 (tptp) cc_final: 0.8831 (pttp) REVERT: E 434 MET cc_start: 0.8379 (ttp) cc_final: 0.8144 (ttm) REVERT: F 530 MET cc_start: 0.8822 (mtt) cc_final: 0.8334 (mtp) REVERT: F 566 LEU cc_start: 0.8963 (mp) cc_final: 0.8672 (pp) REVERT: F 567 LYS cc_start: 0.8500 (pttp) cc_final: 0.7961 (pttp) REVERT: F 626 MET cc_start: 0.8214 (ttm) cc_final: 0.7962 (ttm) outliers start: 23 outliers final: 19 residues processed: 131 average time/residue: 0.1232 time to fit residues: 24.1369 Evaluate side-chains 133 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 355 ASN 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 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 576 LEU Chi-restraints excluded: chain D residue 584 GLU Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain E residue 184 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 71 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 97 optimal weight: 10.0000 chunk 169 optimal weight: 0.8980 chunk 172 optimal weight: 0.9990 chunk 138 optimal weight: 0.9990 chunk 145 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.069697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.052473 restraints weight = 47291.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.054670 restraints weight = 25970.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.056173 restraints weight = 18207.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.057167 restraints weight = 14618.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.057826 restraints weight = 12668.877| |-----------------------------------------------------------------------------| r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.4498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15843 Z= 0.134 Angle : 0.559 10.392 21696 Z= 0.289 Chirality : 0.042 0.178 2703 Planarity : 0.003 0.028 2583 Dihedral : 4.309 18.185 1875 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.39 % Allowed : 8.14 % 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: 2.20 (0.25), residues: 471 sheet: 0.73 (0.26), residues: 390 loop : -0.04 (0.22), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 557 TYR 0.019 0.001 TYR A 217 PHE 0.010 0.001 PHE E 53 TRP 0.015 0.001 TRP C 427 HIS 0.005 0.001 HIS B 564 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (15705) covalent geometry : angle 0.53693 / 0.29 (21318) SS BOND : bond 0.00162 / 0.11 ( 36) SS BOND : angle 0.53383 / 0.37 ( 72) hydrogen bonds : bond 0.04127 / 2.76 ( 624) hydrogen bonds : angle 5.00402 / 3.50 ( 1707) link_ALPHA1-3 : bond 0.00331 / 0.17 ( 3) link_ALPHA1-3 : angle 1.51744 / 1.01 ( 9) link_ALPHA1-6 : bond 0.00343 / 0.17 ( 3) link_ALPHA1-6 : angle 1.44000 / 0.94 ( 9) link_BETA1-4 : bond 0.00308 / 0.19 ( 30) link_BETA1-4 : angle 1.15448 / 0.83 ( 90) link_NAG-ASN : bond 0.00175 / 0.11 ( 66) link_NAG-ASN : angle 1.50392 / 1.05 ( 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 154 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASN cc_start: 0.8396 (t0) cc_final: 0.8194 (p0) REVERT: A 215 ILE cc_start: 0.8526 (mm) cc_final: 0.8320 (mm) REVERT: B 567 LYS cc_start: 0.8452 (pttp) cc_final: 0.7943 (pttp) REVERT: B 584 GLU cc_start: 0.8914 (tp30) cc_final: 0.8618 (mm-30) REVERT: B 603 ILE cc_start: 0.9170 (mt) cc_final: 0.8902 (tt) REVERT: B 634 GLU cc_start: 0.9311 (tt0) cc_final: 0.9103 (mt-10) REVERT: B 654 GLU cc_start: 0.8884 (tm-30) cc_final: 0.8468 (tm-30) REVERT: B 655 LYS cc_start: 0.9468 (tptp) cc_final: 0.8791 (pttp) REVERT: B 657 GLU cc_start: 0.8974 (tt0) cc_final: 0.8469 (tm-30) REVERT: C 161 MET cc_start: 0.8805 (tpp) cc_final: 0.8244 (tpt) REVERT: D 566 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8662 (pp) REVERT: D 567 LYS cc_start: 0.8522 (pttp) cc_final: 0.7959 (pttm) REVERT: D 621 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7438 (tm-30) REVERT: D 622 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.8186 (mm) REVERT: D 634 GLU cc_start: 0.9234 (tt0) cc_final: 0.8706 (mt-10) REVERT: D 648 GLU cc_start: 0.8121 (pp20) cc_final: 0.7864 (pp20) REVERT: D 654 GLU cc_start: 0.8835 (tp30) cc_final: 0.8573 (tm-30) REVERT: D 655 LYS cc_start: 0.9474 (tptp) cc_final: 0.8831 (pttp) REVERT: E 80 ASN cc_start: 0.8472 (t0) cc_final: 0.8265 (p0) REVERT: F 530 MET cc_start: 0.8738 (mtt) cc_final: 0.8506 (mtp) REVERT: F 566 LEU cc_start: 0.8908 (mp) cc_final: 0.8633 (pp) REVERT: F 567 LYS cc_start: 0.8436 (pttp) cc_final: 0.7874 (pttp) REVERT: F 621 GLU cc_start: 0.8096 (tp30) cc_final: 0.7837 (tm-30) REVERT: F 648 GLU cc_start: 0.8260 (pp20) cc_final: 0.8011 (pp20) REVERT: F 657 GLU cc_start: 0.8952 (tt0) cc_final: 0.8401 (tm-30) outliers start: 22 outliers final: 13 residues processed: 146 average time/residue: 0.1260 time to fit residues: 27.6530 Evaluate side-chains 140 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.592 ------------------------------------------------------------------------------- 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 561 CYS Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain C residue 184 ILE 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 D residue 622 ILE Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 561 CYS Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 626 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 163 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 146 optimal weight: 0.9980 chunk 68 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 140 optimal weight: 10.0000 chunk 131 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 chunk 66 optimal weight: 0.3980 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 585 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 = 0.3250 r_free = 0.3250 target = 0.069804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.052617 restraints weight = 48502.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.054944 restraints weight = 25496.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.056521 restraints weight = 17504.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.057515 restraints weight = 13845.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.058232 restraints weight = 11957.024| |-----------------------------------------------------------------------------| r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.4587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15843 Z= 0.176 Angle : 0.586 10.495 21696 Z= 0.299 Chirality : 0.042 0.179 2703 Planarity : 0.003 0.037 2583 Dihedral : 4.312 18.356 1875 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.26 % Allowed : 8.52 % Favored : 90.21 % 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: 1.12 (0.21), residues: 1740 helix: 2.18 (0.25), residues: 471 sheet: 0.81 (0.27), residues: 372 loop : -0.02 (0.21), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 557 TYR 0.009 0.001 TYR A 217 PHE 0.012 0.001 PHE E 53 TRP 0.013 0.001 TRP C 112 HIS 0.005 0.001 HIS B 564 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.18 (15705) covalent geometry : angle 0.56322 / 0.30 (21318) SS BOND : bond 0.00198 / 0.13 ( 36) SS BOND : angle 0.55300 / 0.37 ( 72) hydrogen bonds : bond 0.04213 / 2.81 ( 624) hydrogen bonds : angle 4.98884 / 3.49 ( 1707) link_ALPHA1-3 : bond 0.00246 / 0.12 ( 3) link_ALPHA1-3 : angle 1.58948 / 1.05 ( 9) link_ALPHA1-6 : bond 0.00333 / 0.17 ( 3) link_ALPHA1-6 : angle 1.42317 / 0.93 ( 9) link_BETA1-4 : bond 0.00246 / 0.15 ( 30) link_BETA1-4 : angle 1.26621 / 0.91 ( 90) link_NAG-ASN : bond 0.00246 / 0.16 ( 66) link_NAG-ASN : angle 1.55103 / 1.09 ( 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 144 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASN cc_start: 0.8487 (t0) cc_final: 0.8276 (p0) REVERT: A 161 MET cc_start: 0.8892 (tpp) cc_final: 0.8583 (tpt) REVERT: B 567 LYS cc_start: 0.8482 (pttp) cc_final: 0.7970 (pttp) REVERT: B 584 GLU cc_start: 0.8844 (tp30) cc_final: 0.8556 (mm-30) REVERT: B 634 GLU cc_start: 0.9335 (tt0) cc_final: 0.9055 (mt-10) REVERT: B 654 GLU cc_start: 0.8927 (tm-30) cc_final: 0.8477 (tm-30) REVERT: B 655 LYS cc_start: 0.9440 (tptp) cc_final: 0.8767 (pttp) REVERT: B 657 GLU cc_start: 0.8959 (tt0) cc_final: 0.8439 (tm-30) REVERT: C 161 MET cc_start: 0.8816 (tpp) cc_final: 0.8268 (tpt) REVERT: D 566 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8630 (pp) REVERT: D 567 LYS cc_start: 0.8558 (pttp) cc_final: 0.7971 (pttm) REVERT: D 621 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7477 (tm-30) REVERT: D 622 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.8167 (mm) REVERT: D 634 GLU cc_start: 0.9250 (tt0) cc_final: 0.9000 (tt0) REVERT: D 648 GLU cc_start: 0.8174 (pp20) cc_final: 0.7918 (pp20) REVERT: D 654 GLU cc_start: 0.8865 (tp30) cc_final: 0.8633 (tm-30) REVERT: D 655 LYS cc_start: 0.9483 (tptp) cc_final: 0.8831 (pttp) REVERT: E 80 ASN cc_start: 0.8585 (t0) cc_final: 0.8375 (p0) REVERT: F 530 MET cc_start: 0.8778 (mtt) cc_final: 0.8283 (mtp) REVERT: F 566 LEU cc_start: 0.8969 (mp) cc_final: 0.8748 (pp) REVERT: F 567 LYS cc_start: 0.8428 (pttp) cc_final: 0.7863 (pttp) REVERT: F 601 LYS cc_start: 0.8668 (mtmm) cc_final: 0.8351 (mtmm) REVERT: F 621 GLU cc_start: 0.8137 (tp30) cc_final: 0.7903 (tm-30) outliers start: 20 outliers final: 16 residues processed: 138 average time/residue: 0.1209 time to fit residues: 24.7588 Evaluate side-chains 136 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 184 ILE 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 184 ILE 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 D residue 622 ILE Chi-restraints excluded: chain E residue 184 ILE 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 626 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 93 optimal weight: 5.9990 chunk 158 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 163 optimal weight: 8.9990 chunk 151 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 99 ASN ** 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 = 0.3254 r_free = 0.3254 target = 0.069992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.052918 restraints weight = 48301.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.055228 restraints weight = 25382.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.056809 restraints weight = 17389.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.057853 restraints weight = 13724.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.058451 restraints weight = 11770.298| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 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 : 0.004 0.045 15843 Z= 0.171 Angle : 0.589 10.821 21696 Z= 0.302 Chirality : 0.043 0.177 2703 Planarity : 0.004 0.103 2583 Dihedral : 4.347 18.251 1875 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.14 % Allowed : 8.59 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.21), residues: 1740 helix: 2.14 (0.25), residues: 471 sheet: 0.80 (0.27), residues: 372 loop : -0.03 (0.21), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG F 557 TYR 0.025 0.001 TYR A 217 PHE 0.011 0.001 PHE E 53 TRP 0.016 0.001 TRP C 112 HIS 0.005 0.001 HIS B 564 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (15705) covalent geometry : angle 0.56810 / 0.30 (21318) SS BOND : bond 0.00195 / 0.13 ( 36) SS BOND : angle 0.57512 / 0.38 ( 72) hydrogen bonds : bond 0.04228 / 2.81 ( 624) hydrogen bonds : angle 4.99601 / 3.49 ( 1707) link_ALPHA1-3 : bond 0.00253 / 0.13 ( 3) link_ALPHA1-3 : angle 1.58411 / 1.05 ( 9) link_ALPHA1-6 : bond 0.00340 / 0.17 ( 3) link_ALPHA1-6 : angle 1.43296 / 0.94 ( 9) link_BETA1-4 : bond 0.00264 / 0.16 ( 30) link_BETA1-4 : angle 1.23320 / 0.88 ( 90) link_NAG-ASN : bond 0.00230 / 0.15 ( 66) link_NAG-ASN : angle 1.51417 / 1.07 ( 198) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1977.40 seconds wall clock time: 35 minutes 24.72 seconds (2124.72 seconds total)