Starting phenix.real_space_refine on Fri Jul 3 21:19:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7l8z_23242/07_2026/7l8z_23242.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l8z_23242/07_2026/7l8z_23242.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7l8z_23242/07_2026/7l8z_23242.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l8z_23242/07_2026/7l8z_23242.map" model { file = "/net/cci-nas-00/data/ceres_data/7l8z_23242/07_2026/7l8z_23242.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l8z_23242/07_2026/7l8z_23242.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7l8z_23242/07_2026/7l8z_23242.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7l8z_23242/07_2026/7l8z_23242.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 104 5.16 5 C 9951 2.51 5 N 2696 2.21 5 O 3238 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 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: 15989 Number of models: 1 Model: "" Number of chains: 36 Chain: "H" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 545 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 109} Link IDs: {'TRANS': 108} Unresolved non-hydrogen bonds: 218 Unresolved non-hydrogen angles: 327 Unresolved non-hydrogen dihedrals: 109 Planarities with less than four sites: {'UNK:plan-1': 109} Unresolved non-hydrogen planarities: 109 Chain: "L" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 425 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'TRANS': 84} Unresolved non-hydrogen bonds: 170 Unresolved non-hydrogen angles: 255 Unresolved non-hydrogen dihedrals: 85 Planarities with less than four sites: {'UNK:plan-1': 85} Unresolved non-hydrogen planarities: 85 Chain: "A" Number of atoms: 3516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3516 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 20, 'TRANS': 424} Chain breaks: 2 Chain: "B" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1086 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 1, 'TRANS': 134} Chain breaks: 1 Chain: "C" Number of atoms: 3521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3521 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 20, 'TRANS': 425} Chain breaks: 2 Chain: "E" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1068 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 1, 'TRANS': 132} Chain breaks: 1 Chain: "D" Number of atoms: 3443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3443 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 20, 'TRANS': 415} Chain breaks: 4 Chain: "F" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1091 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 1, 'TRANS': 135} Chain breaks: 1 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: "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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 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: 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: "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: 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: "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: 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: "Z" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 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: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 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: "D" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.37, per 1000 atoms: 0.21 Number of scatterers: 15989 At special positions: 0 Unit cell: (125.66, 126.69, 155.53, 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 104 16.00 O 3238 8.00 N 2696 7.00 C 9951 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.43 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS B 561 " distance=2.02 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.02 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 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=2.02 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=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 73 " distance=2.04 Simple disulfide: pdb=" SG CYS C 74 " - pdb=" SG CYS E 561 " distance=2.07 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.02 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.14 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.01 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.01 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 73 " distance=2.77 Simple disulfide: pdb=" SG CYS D 74 " - pdb=" SG CYS F 561 " distance=2.03 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.02 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.02 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.03 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.02 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.02 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.02 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN K 4 " - " MAN K 5 " " MAN Z 4 " - " MAN Z 5 " ALPHA1-3 " BMA K 3 " - " MAN K 4 " " BMA T 3 " - " MAN T 4 " " BMA Z 3 " - " MAN Z 4 " ALPHA1-6 " BMA K 3 " - " MAN K 6 " " BMA T 3 " - " MAN T 5 " " BMA Z 3 " - " MAN Z 6 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " 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 Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " 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 Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " NAG-ASN " NAG A 601 " - " ASN A 234 " " NAG A 602 " - " ASN A 241 " " NAG A 603 " - " ASN A 276 " " NAG A 604 " - " ASN A 392 " " NAG A 605 " - " ASN A 339 " " NAG A 606 " - " ASN A 448 " " NAG A 607 " - " ASN A 301 " " NAG A 608 " - " ASN A 133 " " NAG A 609 " - " ASN A 289 " " NAG A 610 " - " ASN A 137 " " NAG A 611 " - " ASN A 363 " " NAG B 701 " - " ASN B 618 " " NAG B 702 " - " ASN B 637 " " NAG B 703 " - " ASN B 611 " " NAG C 601 " - " ASN C 234 " " NAG C 602 " - " ASN C 241 " " NAG C 603 " - " ASN C 276 " " NAG C 604 " - " ASN C 392 " " NAG C 605 " - " ASN C 339 " " NAG C 606 " - " ASN C 295 " " NAG C 607 " - " ASN C 301 " " NAG C 608 " - " ASN C 160 " " NAG C 609 " - " ASN C 133 " " NAG C 610 " - " ASN C 355 " " NAG C 611 " - " ASN C 363 " " NAG D 601 " - " ASN D 241 " " NAG D 602 " - " ASN D 276 " " NAG D 603 " - " ASN D 392 " " NAG D 604 " - " ASN D 339 " " NAG D 605 " - " ASN D 332 " " NAG D 606 " - " ASN D 295 " " NAG D 607 " - " ASN D 301 " " NAG D 608 " - " ASN D 133 " " NAG D 609 " - " ASN D 355 " " NAG D 610 " - " ASN D 289 " " NAG D 611 " - " ASN D 137 " " NAG E 701 " - " ASN E 637 " " NAG E 702 " - " ASN E 611 " " NAG F 701 " - " ASN F 611 " " NAG G 1 " - " ASN A 386 " " NAG I 1 " - " ASN A 332 " " NAG J 1 " - " ASN A 295 " " NAG K 1 " - " ASN A 262 " " NAG M 1 " - " ASN A 156 " " NAG N 1 " - " ASN A 160 " " NAG O 1 " - " ASN A 197 " " NAG P 1 " - " ASN C 88 " " NAG Q 1 " - " ASN C 386 " " NAG R 1 " - " ASN C 332 " " NAG S 1 " - " ASN C 448 " " NAG T 1 " - " ASN C 262 " " NAG U 1 " - " ASN C 156 " " NAG V 1 " - " ASN C 197 " " NAG W 1 " - " ASN D 234 " " NAG X 1 " - " ASN D 386 " " NAG Y 1 " - " ASN D 448 " " NAG Z 1 " - " ASN D 262 " " NAG a 1 " - " ASN D 156 " " NAG b 1 " - " ASN D 160 " " NAG c 1 " - " ASN D 197 " " NAG d 1 " - " ASN D 363 " Time building additional restraints: 1.52 Conformation dependent library (CDL) restraints added in 583.8 milliseconds 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3634 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 31 sheets defined 31.0% alpha, 34.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'H' and resid 37 through 41 removed outlier: 3.693A pdb=" N UNK H 40 " --> pdb=" O UNK H 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 63 Processing helix chain 'A' and resid 67 through 73 Processing helix chain 'A' and resid 98 through 117 removed outlier: 3.549A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (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 350 removed outlier: 4.746A pdb=" N GLU A 340 " --> pdb=" O ALA A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 476 through 484 removed outlier: 3.707A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 535 Processing helix chain 'B' and resid 536 through 542 Processing helix chain 'B' and resid 545 through 550 Processing helix chain 'B' and resid 563 through 567 Processing helix chain 'B' and resid 568 through 596 Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 628 through 636 Processing helix chain 'B' and resid 638 through 662 Processing helix chain 'C' and resid 59 through 64 Processing helix chain 'C' and resid 67 through 72 removed outlier: 3.847A pdb=" N HIS C 72 " --> pdb=" O VAL C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 117 removed outlier: 4.158A 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 195 through 198 Processing helix chain 'C' and resid 334 through 350 Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 391 Processing helix chain 'C' and resid 476 through 484 removed outlier: 4.569A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 528 removed outlier: 4.331A pdb=" N GLY E 527 " --> pdb=" O GLY E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 531 through 535 Processing helix chain 'E' and resid 536 through 542 Processing helix chain 'E' and resid 542 through 547 Processing helix chain 'E' and resid 548 through 550 No H-bonds generated for 'chain 'E' and resid 548 through 550' Processing helix chain 'E' and resid 563 through 567 Processing helix chain 'E' and resid 568 through 596 Processing helix chain 'E' and resid 618 through 622 Processing helix chain 'E' and resid 627 through 636 Processing helix chain 'E' and resid 638 through 659 Processing helix chain 'E' and resid 660 through 663 Processing helix chain 'D' and resid 67 through 73 removed outlier: 3.643A pdb=" N CYS D 73 " --> pdb=" O TRP D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 117 removed outlier: 4.085A pdb=" N GLU D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 334 through 351 removed outlier: 3.566A pdb=" N LYS D 351 " --> pdb=" O LYS D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 387 through 391 Processing helix chain 'D' and resid 476 through 484 removed outlier: 4.591A pdb=" N GLU D 482 " --> pdb=" O ASN D 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 528 removed outlier: 4.143A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 532 through 535 Processing helix chain 'F' and resid 536 through 543 Processing helix chain 'F' and resid 544 through 546 No H-bonds generated for 'chain 'F' and resid 544 through 546' Processing helix chain 'F' and resid 564 through 567 Processing helix chain 'F' and resid 568 through 596 Processing helix chain 'F' and resid 611 through 615 Processing helix chain 'F' and resid 618 through 622 Processing helix chain 'F' and resid 627 through 636 removed outlier: 6.251A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 661 Processing sheet with id=AA1, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 54 through 56 removed outlier: 3.790A pdb=" N UNK H 54 " --> pdb=" O UNK H 50 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N UNK H 31 " --> pdb=" O UNK H 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 41 through 42 Processing sheet with id=AA4, first strand: chain 'L' and resid 58 through 59 removed outlier: 3.558A pdb=" N UNK L 62 " --> pdb=" O UNK L 59 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.403A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA7, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA8, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA9, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AB1, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.344A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.724A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 10.368A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 11.457A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 9.980A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.394A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.583A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.393A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.395A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.049A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 271 through 274 removed outlier: 6.834A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.049A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.395A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.393A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.583A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.394A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.980A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.457A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.368A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.528A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 494 through 499 Processing sheet with id=AB6, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.865A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 75 through 76 Processing sheet with id=AB8, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB9, first strand: chain 'C' and resid 169 through 177 removed outlier: 3.613A pdb=" N THR C 132 " --> pdb=" O ASN C 156 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.773A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.772A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLY C 451 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.803A pdb=" N GLU C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 12.008A pdb=" N ILE C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 12.141A pdb=" N LEU C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 10.939A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 10.830A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 271 through 273 removed outlier: 10.830A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.939A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 12.141A pdb=" N LEU C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 12.008A pdb=" N ILE C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 10.803A pdb=" N GLU C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLY C 451 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.583A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 494 through 499 removed outlier: 4.583A pdb=" N VAL D 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 45 through 47 Processing sheet with id=AC7, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC8, first strand: chain 'D' and resid 91 through 94 Processing sheet with id=AC9, first strand: chain 'D' and resid 169 through 177 Processing sheet with id=AD1, first strand: chain 'D' and resid 200 through 203 removed outlier: 6.367A pdb=" N ALA D 200 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N TYR D 435 " --> pdb=" O ALA D 200 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N THR D 202 " --> pdb=" O TYR D 435 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 259 through 261 removed outlier: 6.678A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) removed outlier: 10.420A pdb=" N VAL D 442 " --> pdb=" O CYS D 296 " (cutoff:3.500A) removed outlier: 11.310A pdb=" N CYS D 296 " --> pdb=" O VAL D 442 " (cutoff:3.500A) removed outlier: 10.153A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 11.536A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 9.779A pdb=" N VAL D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 10.661A pdb=" N VAL D 292 " --> pdb=" O VAL D 446 " (cutoff:3.500A) removed outlier: 9.279A pdb=" N ASN D 448 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 10.127A pdb=" N GLU D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N THR D 450 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ALA D 329 " --> pdb=" O CYS D 418 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N PHE D 382 " --> pdb=" O LYS D 421 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 271 through 273 removed outlier: 6.940A pdb=" N THR D 450 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 10.127A pdb=" N GLU D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 9.279A pdb=" N ASN D 448 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 10.661A pdb=" N VAL D 292 " --> pdb=" O VAL D 446 " (cutoff:3.500A) removed outlier: 9.779A pdb=" N VAL D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 11.536A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 10.153A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 11.310A pdb=" N CYS D 296 " --> pdb=" O VAL D 442 " (cutoff:3.500A) removed outlier: 10.420A pdb=" N VAL D 442 " --> pdb=" O CYS D 296 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 304 through 312 removed outlier: 6.736A pdb=" N GLN D 315 " --> pdb=" O ILE D 309 " (cutoff:3.500A) 625 hydrogen bonds defined for protein. 1629 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.77 Time building geometry restraints manager: 1.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.35: 5200 1.35 - 1.51: 6379 1.51 - 1.67: 4541 1.67 - 1.82: 118 1.82 - 1.98: 19 Bond restraints: 16257 Sorted by residual: bond pdb=" NE ARG D 503 " pdb=" CZ ARG D 503 " ideal model delta sigma weight residual 1.326 1.412 -0.086 1.10e-02 8.26e+03 6.17e+01 bond pdb=" CB LEU E 663 " pdb=" CG LEU E 663 " ideal model delta sigma weight residual 1.530 1.674 -0.144 2.00e-02 2.50e+03 5.19e+01 bond pdb=" CB HIS F 564 " pdb=" CG HIS F 564 " ideal model delta sigma weight residual 1.497 1.406 0.091 1.40e-02 5.10e+03 4.27e+01 bond pdb=" CB ASN A 67 " pdb=" CG ASN A 67 " ideal model delta sigma weight residual 1.516 1.356 0.160 2.50e-02 1.60e+03 4.09e+01 bond pdb=" NE ARG A 503 " pdb=" CZ ARG A 503 " ideal model delta sigma weight residual 1.326 1.396 -0.070 1.10e-02 8.26e+03 4.02e+01 ... (remaining 16252 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.61: 20942 3.61 - 7.23: 1098 7.23 - 10.84: 52 10.84 - 14.46: 2 14.46 - 18.07: 4 Bond angle restraints: 22098 Sorted by residual: angle pdb=" N GLN C 428 " pdb=" CA GLN C 428 " pdb=" C GLN C 428 " ideal model delta sigma weight residual 114.04 95.97 18.07 1.24e+00 6.50e-01 2.12e+02 angle pdb=" N GLN D 428 " pdb=" CA GLN D 428 " pdb=" C GLN D 428 " ideal model delta sigma weight residual 114.04 97.50 16.54 1.24e+00 6.50e-01 1.78e+02 angle pdb=" N LEU F 629 " pdb=" CA LEU F 629 " pdb=" C LEU F 629 " ideal model delta sigma weight residual 110.55 94.69 15.86 1.35e+00 5.49e-01 1.38e+02 angle pdb=" N VAL D 242 " pdb=" CA VAL D 242 " pdb=" C VAL D 242 " ideal model delta sigma weight residual 109.34 127.10 -17.76 2.08e+00 2.31e-01 7.29e+01 angle pdb=" C GLU D 492 " pdb=" N PRO D 493 " pdb=" CA PRO D 493 " ideal model delta sigma weight residual 119.56 128.06 -8.50 1.02e+00 9.61e-01 6.94e+01 ... (remaining 22093 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 8718 17.78 - 35.56: 216 35.56 - 53.34: 83 53.34 - 71.12: 29 71.12 - 88.91: 11 Dihedral angle restraints: 9057 sinusoidal: 3470 harmonic: 5587 Sorted by residual: dihedral pdb=" CB CYS D 228 " pdb=" SG CYS D 228 " pdb=" SG CYS D 239 " pdb=" CB CYS D 239 " ideal model delta sinusoidal sigma weight residual 93.00 176.67 -83.67 1 1.00e+01 1.00e-02 8.54e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 158.96 -65.96 1 1.00e+01 1.00e-02 5.69e+01 dihedral pdb=" CB CYS C 126 " pdb=" SG CYS C 126 " pdb=" SG CYS C 196 " pdb=" CB CYS C 196 " ideal model delta sinusoidal sigma weight residual 93.00 158.73 -65.73 1 1.00e+01 1.00e-02 5.65e+01 ... (remaining 9054 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.278: 2550 0.278 - 0.557: 270 0.557 - 0.835: 1 0.835 - 1.114: 0 1.114 - 1.392: 2 Chirality restraints: 2823 Sorted by residual: chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.66 0.26 2.00e-02 2.50e+03 1.63e+02 chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.25e+02 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.18e+02 ... (remaining 2820 not shown) Planarity restraints: 2760 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 601 " 0.290 2.00e-02 2.50e+03 2.42e-01 7.29e+02 pdb=" C7 NAG D 601 " -0.081 2.00e-02 2.50e+03 pdb=" C8 NAG D 601 " 0.191 2.00e-02 2.50e+03 pdb=" N2 NAG D 601 " -0.406 2.00e-02 2.50e+03 pdb=" O7 NAG D 601 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 234 " -0.155 2.00e-02 2.50e+03 1.93e-01 4.67e+02 pdb=" CG ASN D 234 " 0.062 2.00e-02 2.50e+03 pdb=" OD1 ASN D 234 " -0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN D 234 " 0.332 2.00e-02 2.50e+03 pdb=" C1 NAG W 1 " -0.220 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 137 " -0.134 2.00e-02 2.50e+03 1.89e-01 4.47e+02 pdb=" CG ASN D 137 " 0.058 2.00e-02 2.50e+03 pdb=" OD1 ASN D 137 " -0.041 2.00e-02 2.50e+03 pdb=" ND2 ASN D 137 " 0.332 2.00e-02 2.50e+03 pdb=" C1 NAG D 611 " -0.215 2.00e-02 2.50e+03 ... (remaining 2757 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 161 2.62 - 3.19: 14142 3.19 - 3.76: 22602 3.76 - 4.33: 33269 4.33 - 4.90: 51962 Nonbonded interactions: 122136 Sorted by model distance: nonbonded pdb=" O3 NAG D 601 " pdb=" O7 NAG D 601 " model vdw 2.046 3.040 nonbonded pdb=" O3 NAG W 1 " pdb=" O7 NAG W 1 " model vdw 2.052 3.040 nonbonded pdb=" N LEU F 629 " pdb=" O LEU F 629 " model vdw 2.216 2.496 nonbonded pdb=" N GLN C 428 " pdb=" N ARG C 429 " model vdw 2.327 2.560 nonbonded pdb=" N UNK L 45 " pdb=" O UNK L 49 " model vdw 2.337 3.120 ... (remaining 122131 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 56 or resid 63 through 140 or resid 151 through \ 611)) selection = (chain 'C' and (resid 33 through 56 or resid 63 through 140 or resid 151 through \ 611)) selection = chain 'D' } ncs_group { reference = (chain 'B' and (resid 521 through 550 or resid 561 through 701)) selection = (chain 'E' and (resid 521 through 550 or resid 561 through 701)) selection = (chain 'F' and (resid 521 through 550 or resid 561 through 701)) } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'b' selection = chain 'c' selection = chain 'd' } ncs_group { reference = chain 'K' selection = chain 'Z' } 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: 3.480 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: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 14.630 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 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 : 0.025 0.743 16386 Z= 1.317 Angle : 1.827 22.448 22451 Z= 1.126 Chirality : 0.153 1.392 2823 Planarity : 0.010 0.242 2699 Dihedral : 10.412 88.906 5321 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 0.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.06 % 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: 0.76 (0.20), residues: 1700 helix: -0.10 (0.24), residues: 420 sheet: 0.85 (0.22), residues: 464 loop : 0.86 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 429 TYR 0.051 0.008 TYR D 40 PHE 0.030 0.006 PHE D 383 TRP 0.074 0.009 TRP E 610 HIS 0.015 0.003 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.02335 / 1.25 (16257) covalent geometry : angle 1.75417 / 1.12 (22098) SS BOND : bond 0.14622 / 7.39 ( 34) SS BOND : angle 4.08742 / 2.11 ( 68) hydrogen bonds : bond 0.18330 / 10.25 ( 607) hydrogen bonds : angle 7.47904 / 4.03 ( 1629) link_ALPHA1-2 : bond 0.08015 / 4.03 ( 2) link_ALPHA1-2 : angle 4.31461 / 1.98 ( 6) link_ALPHA1-3 : bond 0.08409 / 4.21 ( 3) link_ALPHA1-3 : angle 4.04938 / 1.97 ( 9) link_ALPHA1-6 : bond 0.05647 / 2.82 ( 3) link_ALPHA1-6 : angle 4.16944 / 1.97 ( 9) link_BETA1-4 : bond 0.06917 / 3.81 ( 26) link_BETA1-4 : angle 4.66144 / 2.32 ( 78) link_NAG-ASN : bond 0.07790 / 4.29 ( 61) link_NAG-ASN : angle 4.48897 / 2.29 ( 183) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 420 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8667 (mttm) cc_final: 0.7927 (mtpt) REVERT: A 80 ASN cc_start: 0.8414 (m-40) cc_final: 0.8062 (m-40) REVERT: A 115 SER cc_start: 0.9169 (m) cc_final: 0.8766 (t) REVERT: A 163 THR cc_start: 0.9297 (p) cc_final: 0.9041 (t) REVERT: B 607 ASN cc_start: 0.8279 (m-40) cc_final: 0.8007 (m-40) REVERT: B 613 THR cc_start: 0.9177 (p) cc_final: 0.8732 (t) REVERT: B 639 THR cc_start: 0.8895 (m) cc_final: 0.8541 (p) REVERT: C 80 ASN cc_start: 0.8489 (m-40) cc_final: 0.8278 (m-40) REVERT: C 217 TYR cc_start: 0.9206 (m-80) cc_final: 0.9000 (m-80) REVERT: C 264 SER cc_start: 0.8465 (m) cc_final: 0.8254 (m) REVERT: C 426 MET cc_start: 0.8227 (tpp) cc_final: 0.7985 (tpp) REVERT: C 427 TRP cc_start: 0.8339 (t-100) cc_final: 0.7908 (t-100) REVERT: E 585 ARG cc_start: 0.8801 (mtt-85) cc_final: 0.8278 (mtm180) REVERT: D 128 THR cc_start: 0.9236 (m) cc_final: 0.8996 (p) REVERT: F 545 LEU cc_start: 0.8840 (tp) cc_final: 0.8610 (tp) REVERT: F 637 ASN cc_start: 0.7671 (p0) cc_final: 0.6929 (t0) outliers start: 0 outliers final: 0 residues processed: 420 average time/residue: 0.1274 time to fit residues: 77.2060 Evaluate side-chains 208 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 203 GLN ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 616 ASN B 653 GLN C 72 HIS E 564 HIS E 577 GLN D 440 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.125245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.104172 restraints weight = 28157.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.107102 restraints weight = 16526.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.109049 restraints weight = 11754.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.110295 restraints weight = 9368.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.111197 restraints weight = 8049.479| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16386 Z= 0.189 Angle : 0.839 18.211 22451 Z= 0.409 Chirality : 0.049 0.322 2823 Planarity : 0.004 0.042 2699 Dihedral : 5.266 37.792 2028 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.59 % Allowed : 9.14 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.20), residues: 1700 helix: 0.99 (0.26), residues: 429 sheet: 0.67 (0.22), residues: 468 loop : 0.41 (0.22), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 273 TYR 0.019 0.002 TYR F 643 PHE 0.020 0.003 PHE A 383 TRP 0.031 0.002 TRP C 427 HIS 0.006 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.19 (16257) covalent geometry : angle 0.75947 / 0.39 (22098) SS BOND : bond 0.00349 / 0.19 ( 34) SS BOND : angle 1.30275 / 0.67 ( 68) hydrogen bonds : bond 0.05961 / 3.31 ( 607) hydrogen bonds : angle 5.69762 / 3.16 ( 1629) link_ALPHA1-2 : bond 0.01086 / 0.56 ( 2) link_ALPHA1-2 : angle 1.60934 / 0.81 ( 6) link_ALPHA1-3 : bond 0.01242 / 0.61 ( 3) link_ALPHA1-3 : angle 1.41963 / 0.82 ( 9) link_ALPHA1-6 : bond 0.01035 / 0.52 ( 3) link_ALPHA1-6 : angle 1.24614 / 0.66 ( 9) link_BETA1-4 : bond 0.00728 / 0.42 ( 26) link_BETA1-4 : angle 2.54672 / 1.26 ( 78) link_NAG-ASN : bond 0.00526 / 0.28 ( 61) link_NAG-ASN : angle 3.61213 / 1.84 ( 183) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 255 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 SER cc_start: 0.8925 (m) cc_final: 0.8573 (t) REVERT: A 199 SER cc_start: 0.9137 (p) cc_final: 0.8823 (t) REVERT: A 231 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7866 (ptmt) REVERT: B 543 ASN cc_start: 0.8312 (t0) cc_final: 0.8017 (t0) REVERT: B 586 TYR cc_start: 0.9144 (t80) cc_final: 0.8903 (t80) REVERT: B 613 THR cc_start: 0.9123 (p) cc_final: 0.8784 (t) REVERT: B 654 GLU cc_start: 0.7886 (tp30) cc_final: 0.7654 (tp30) REVERT: C 51 THR cc_start: 0.9322 (m) cc_final: 0.9086 (p) REVERT: C 103 GLN cc_start: 0.8132 (tp40) cc_final: 0.7576 (tp-100) REVERT: C 215 ILE cc_start: 0.9159 (mm) cc_final: 0.8883 (tt) REVERT: C 426 MET cc_start: 0.8090 (tpp) cc_final: 0.7743 (tpp) REVERT: E 542 ARG cc_start: 0.7649 (ttm110) cc_final: 0.7364 (ttm110) REVERT: D 125 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9127 (tp) REVERT: F 628 TRP cc_start: 0.6682 (m100) cc_final: 0.6329 (m100) REVERT: F 637 ASN cc_start: 0.7411 (p0) cc_final: 0.6939 (t0) outliers start: 40 outliers final: 24 residues processed: 276 average time/residue: 0.1067 time to fit residues: 44.9413 Evaluate side-chains 224 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 198 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain E residue 599 SER Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 646 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 55 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 133 optimal weight: 6.9990 chunk 23 optimal weight: 0.0570 chunk 185 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 119 optimal weight: 5.9990 chunk 184 optimal weight: 4.9990 overall best weight: 1.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 478 ASN ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 616 ASN ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 GLN E 564 HIS ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 658 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.122453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.101016 restraints weight = 28883.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.103994 restraints weight = 16749.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.105966 restraints weight = 11837.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.107148 restraints weight = 9409.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.108102 restraints weight = 8116.019| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16386 Z= 0.180 Angle : 0.722 14.659 22451 Z= 0.354 Chirality : 0.045 0.318 2823 Planarity : 0.004 0.039 2699 Dihedral : 4.973 29.095 2028 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.69 % Allowed : 10.17 % Favored : 86.13 % 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: 0.83 (0.21), residues: 1700 helix: 1.41 (0.27), residues: 415 sheet: 0.47 (0.22), residues: 491 loop : 0.28 (0.23), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 542 TYR 0.022 0.002 TYR C 61 PHE 0.019 0.002 PHE E 522 TRP 0.019 0.002 TRP F 623 HIS 0.006 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 (16257) covalent geometry : angle 0.66600 / 0.34 (22098) SS BOND : bond 0.00499 / 0.26 ( 34) SS BOND : angle 1.09407 / 0.56 ( 68) hydrogen bonds : bond 0.05224 / 2.90 ( 607) hydrogen bonds : angle 5.31591 / 2.94 ( 1629) link_ALPHA1-2 : bond 0.00940 / 0.49 ( 2) link_ALPHA1-2 : angle 1.71205 / 0.81 ( 6) link_ALPHA1-3 : bond 0.00994 / 0.49 ( 3) link_ALPHA1-3 : angle 1.20183 / 0.66 ( 9) link_ALPHA1-6 : bond 0.00598 / 0.30 ( 3) link_ALPHA1-6 : angle 1.32218 / 0.68 ( 9) link_BETA1-4 : bond 0.00620 / 0.36 ( 26) link_BETA1-4 : angle 1.82202 / 0.91 ( 78) link_NAG-ASN : bond 0.00426 / 0.23 ( 61) link_NAG-ASN : angle 2.87042 / 1.47 ( 183) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 226 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 SER cc_start: 0.9195 (p) cc_final: 0.8908 (t) REVERT: A 211 GLU cc_start: 0.8465 (tp30) cc_final: 0.8189 (tp30) REVERT: A 231 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7897 (ptmt) REVERT: B 543 ASN cc_start: 0.8485 (t0) cc_final: 0.8215 (t0) REVERT: B 586 TYR cc_start: 0.9219 (t80) cc_final: 0.8992 (t80) REVERT: B 613 THR cc_start: 0.9258 (p) cc_final: 0.9035 (t) REVERT: B 654 GLU cc_start: 0.8010 (tp30) cc_final: 0.7742 (tp30) REVERT: C 51 THR cc_start: 0.9358 (m) cc_final: 0.9064 (p) REVERT: C 103 GLN cc_start: 0.8165 (tp40) cc_final: 0.7726 (tm-30) REVERT: C 217 TYR cc_start: 0.9025 (m-80) cc_final: 0.8490 (m-80) REVERT: C 258 GLN cc_start: 0.8970 (mt0) cc_final: 0.8762 (mt0) REVERT: D 125 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.9112 (tp) REVERT: F 637 ASN cc_start: 0.7549 (p0) cc_final: 0.6893 (t0) outliers start: 57 outliers final: 40 residues processed: 258 average time/residue: 0.1075 time to fit residues: 42.2377 Evaluate side-chains 242 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 200 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 419 ARG Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain E residue 546 SER Chi-restraints excluded: chain E residue 561 CYS Chi-restraints excluded: chain E residue 564 HIS Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 659 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 13 optimal weight: 10.0000 chunk 113 optimal weight: 0.9980 chunk 99 optimal weight: 0.3980 chunk 101 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 136 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 187 optimal weight: 0.9980 chunk 9 optimal weight: 9.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 478 ASN ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 ASN ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 543 ASN E 564 HIS E 577 GLN D 249 HIS ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.122765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.101491 restraints weight = 28540.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.104477 restraints weight = 16451.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.106439 restraints weight = 11589.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.107712 restraints weight = 9214.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.108491 restraints weight = 7895.758| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16386 Z= 0.145 Angle : 0.685 21.663 22451 Z= 0.330 Chirality : 0.044 0.315 2823 Planarity : 0.003 0.037 2699 Dihedral : 4.842 29.544 2028 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.63 % Allowed : 11.02 % Favored : 85.35 % 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: 0.71 (0.21), residues: 1700 helix: 1.47 (0.27), residues: 426 sheet: 0.49 (0.23), residues: 474 loop : 0.01 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 542 TYR 0.012 0.001 TYR C 61 PHE 0.014 0.002 PHE D 383 TRP 0.013 0.001 TRP D 427 HIS 0.023 0.001 HIS E 564 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (16257) covalent geometry : angle 0.61533 / 0.31 (22098) SS BOND : bond 0.00322 / 0.17 ( 34) SS BOND : angle 1.04090 / 0.52 ( 68) hydrogen bonds : bond 0.04506 / 2.49 ( 607) hydrogen bonds : angle 5.04568 / 2.78 ( 1629) link_ALPHA1-2 : bond 0.00854 / 0.45 ( 2) link_ALPHA1-2 : angle 1.68084 / 0.78 ( 6) link_ALPHA1-3 : bond 0.00888 / 0.43 ( 3) link_ALPHA1-3 : angle 1.23208 / 0.69 ( 9) link_ALPHA1-6 : bond 0.00518 / 0.26 ( 3) link_ALPHA1-6 : angle 1.36535 / 0.70 ( 9) link_BETA1-4 : bond 0.00490 / 0.28 ( 26) link_BETA1-4 : angle 1.52393 / 0.76 ( 78) link_NAG-ASN : bond 0.00420 / 0.25 ( 61) link_NAG-ASN : angle 3.20270 / 1.65 ( 183) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 222 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASN cc_start: 0.8391 (m-40) cc_final: 0.8190 (m-40) REVERT: A 199 SER cc_start: 0.9235 (p) cc_final: 0.8952 (t) REVERT: A 231 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7969 (ptmt) REVERT: B 586 TYR cc_start: 0.9218 (t80) cc_final: 0.8923 (t80) REVERT: B 621 GLU cc_start: 0.8713 (tm-30) cc_final: 0.8446 (tm-30) REVERT: B 632 ASP cc_start: 0.8579 (t70) cc_final: 0.8369 (t70) REVERT: B 654 GLU cc_start: 0.8064 (tp30) cc_final: 0.7733 (tp30) REVERT: C 51 THR cc_start: 0.9381 (m) cc_final: 0.9141 (p) REVERT: C 103 GLN cc_start: 0.7998 (tp40) cc_final: 0.7728 (tp40) REVERT: C 217 TYR cc_start: 0.8912 (m-80) cc_final: 0.8605 (m-80) REVERT: C 258 GLN cc_start: 0.9005 (mt0) cc_final: 0.8768 (mt0) REVERT: F 640 GLN cc_start: 0.7331 (tp40) cc_final: 0.7122 (tm-30) outliers start: 56 outliers final: 37 residues processed: 255 average time/residue: 0.1160 time to fit residues: 44.8434 Evaluate side-chains 238 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 200 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 419 ARG Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 464 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain E residue 564 HIS Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain F residue 659 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 51 optimal weight: 0.7980 chunk 147 optimal weight: 3.9990 chunk 165 optimal weight: 0.9980 chunk 174 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 149 optimal weight: 0.8980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 HIS C 428 GLN E 564 HIS E 577 GLN D 80 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.121668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.100424 restraints weight = 28764.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.103356 restraints weight = 16634.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.105312 restraints weight = 11750.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.106466 restraints weight = 9360.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.107334 restraints weight = 8084.070| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 16386 Z= 0.164 Angle : 0.708 20.893 22451 Z= 0.335 Chirality : 0.048 0.775 2823 Planarity : 0.004 0.038 2699 Dihedral : 4.790 26.548 2028 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.24 % Favored : 96.71 % Rotamer: Outliers : 3.76 % Allowed : 11.67 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.69 (0.21), residues: 1700 helix: 1.56 (0.27), residues: 426 sheet: 0.53 (0.23), residues: 447 loop : -0.09 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 542 TYR 0.011 0.001 TYR C 61 PHE 0.013 0.002 PHE A 383 TRP 0.013 0.001 TRP F 631 HIS 0.006 0.001 HIS E 564 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 (16257) covalent geometry : angle 0.62652 / 0.32 (22098) SS BOND : bond 0.00389 / 0.20 ( 34) SS BOND : angle 1.12350 / 0.54 ( 68) hydrogen bonds : bond 0.04420 / 2.44 ( 607) hydrogen bonds : angle 4.98147 / 2.75 ( 1629) link_ALPHA1-2 : bond 0.00841 / 0.44 ( 2) link_ALPHA1-2 : angle 1.59505 / 0.75 ( 6) link_ALPHA1-3 : bond 0.00842 / 0.41 ( 3) link_ALPHA1-3 : angle 1.36253 / 0.77 ( 9) link_ALPHA1-6 : bond 0.00497 / 0.25 ( 3) link_ALPHA1-6 : angle 1.35092 / 0.69 ( 9) link_BETA1-4 : bond 0.00479 / 0.27 ( 26) link_BETA1-4 : angle 1.44846 / 0.70 ( 78) link_NAG-ASN : bond 0.00548 / 0.32 ( 61) link_NAG-ASN : angle 3.53970 / 1.85 ( 183) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 210 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 SER cc_start: 0.9332 (p) cc_final: 0.8997 (t) REVERT: A 231 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7965 (ptmt) REVERT: B 551 GLN cc_start: 0.6113 (OUTLIER) cc_final: 0.5020 (pm20) REVERT: B 586 TYR cc_start: 0.9245 (t80) cc_final: 0.8907 (t80) REVERT: B 654 GLU cc_start: 0.8075 (tp30) cc_final: 0.7707 (tp30) REVERT: C 51 THR cc_start: 0.9353 (m) cc_final: 0.9133 (p) REVERT: C 103 GLN cc_start: 0.8011 (tp40) cc_final: 0.7716 (tm-30) REVERT: C 217 TYR cc_start: 0.8937 (m-80) cc_final: 0.8425 (m-80) REVERT: C 258 GLN cc_start: 0.9008 (mt0) cc_final: 0.8680 (mt0) REVERT: C 340 GLU cc_start: 0.8214 (tt0) cc_final: 0.7935 (mt-10) REVERT: D 282 LYS cc_start: 0.9077 (mmtt) cc_final: 0.8807 (mttm) REVERT: D 297 THR cc_start: 0.9019 (OUTLIER) cc_final: 0.8462 (p) REVERT: F 640 GLN cc_start: 0.7311 (tp40) cc_final: 0.7103 (tm-30) outliers start: 58 outliers final: 38 residues processed: 251 average time/residue: 0.1158 time to fit residues: 44.0755 Evaluate side-chains 238 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 197 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 419 ARG Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 551 GLN Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain F residue 659 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 71 optimal weight: 2.9990 chunk 10 optimal weight: 20.0000 chunk 133 optimal weight: 4.9990 chunk 164 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 173 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 ASN A 99 ASN A 478 ASN E 563 GLN E 577 GLN D 99 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 562 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.117037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.095760 restraints weight = 29255.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.098490 restraints weight = 17331.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.100288 restraints weight = 12490.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.101476 restraints weight = 10096.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.102289 restraints weight = 8751.410| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.4329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 16386 Z= 0.272 Angle : 0.814 16.900 22451 Z= 0.390 Chirality : 0.050 0.579 2823 Planarity : 0.004 0.041 2699 Dihedral : 5.078 27.538 2028 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.12 % Favored : 95.76 % Rotamer: Outliers : 4.67 % Allowed : 11.73 % Favored : 83.60 % 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: 0.38 (0.21), residues: 1700 helix: 1.42 (0.27), residues: 418 sheet: 0.24 (0.23), residues: 445 loop : -0.26 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 617 TYR 0.022 0.002 TYR D 217 PHE 0.016 0.003 PHE C 383 TRP 0.024 0.002 TRP A 427 HIS 0.008 0.002 HIS E 564 Details of bonding type rmsd/Z covalent geometry : bond 0.00643 / 0.27 (16257) covalent geometry : angle 0.75251 / 0.38 (22098) SS BOND : bond 0.00645 / 0.40 ( 34) SS BOND : angle 1.12977 / 0.55 ( 68) hydrogen bonds : bond 0.05209 / 2.90 ( 607) hydrogen bonds : angle 5.25106 / 2.87 ( 1629) link_ALPHA1-2 : bond 0.00839 / 0.44 ( 2) link_ALPHA1-2 : angle 1.51041 / 0.75 ( 6) link_ALPHA1-3 : bond 0.01064 / 0.52 ( 3) link_ALPHA1-3 : angle 1.42184 / 0.84 ( 9) link_ALPHA1-6 : bond 0.00438 / 0.22 ( 3) link_ALPHA1-6 : angle 1.47036 / 0.72 ( 9) link_BETA1-4 : bond 0.00431 / 0.25 ( 26) link_BETA1-4 : angle 1.64543 / 0.80 ( 78) link_NAG-ASN : bond 0.00674 / 0.41 ( 61) link_NAG-ASN : angle 3.31146 / 1.71 ( 183) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 196 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLU cc_start: 0.6898 (OUTLIER) cc_final: 0.4825 (pm20) REVERT: A 199 SER cc_start: 0.9473 (p) cc_final: 0.9120 (t) REVERT: A 207 LYS cc_start: 0.8480 (pttt) cc_final: 0.8247 (ptpt) REVERT: B 551 GLN cc_start: 0.6307 (OUTLIER) cc_final: 0.5064 (pm20) REVERT: B 586 TYR cc_start: 0.9298 (t80) cc_final: 0.8960 (t80) REVERT: B 621 GLU cc_start: 0.8692 (tm-30) cc_final: 0.8033 (tm-30) REVERT: B 654 GLU cc_start: 0.8056 (tp30) cc_final: 0.7726 (tp30) REVERT: C 53 PHE cc_start: 0.9031 (p90) cc_final: 0.8594 (p90) REVERT: C 217 TYR cc_start: 0.9108 (m-80) cc_final: 0.8648 (m-80) REVERT: C 258 GLN cc_start: 0.9098 (mt0) cc_final: 0.8663 (mt0) REVERT: D 125 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9107 (tt) REVERT: D 243 SER cc_start: 0.8332 (OUTLIER) cc_final: 0.8116 (t) REVERT: D 282 LYS cc_start: 0.9179 (mmtt) cc_final: 0.8933 (mttm) REVERT: D 297 THR cc_start: 0.9100 (OUTLIER) cc_final: 0.8606 (p) REVERT: F 640 GLN cc_start: 0.7505 (tp40) cc_final: 0.7073 (tm-30) REVERT: F 647 GLU cc_start: 0.7846 (tm-30) cc_final: 0.7370 (tt0) outliers start: 72 outliers final: 48 residues processed: 245 average time/residue: 0.1149 time to fit residues: 42.3582 Evaluate side-chains 228 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 175 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 419 ARG Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 551 GLN Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 622 ILE Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 649 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 60 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 chunk 165 optimal weight: 0.7980 chunk 51 optimal weight: 0.0970 chunk 95 optimal weight: 2.9990 chunk 184 optimal weight: 8.9990 chunk 13 optimal weight: 8.9990 chunk 71 optimal weight: 3.9990 chunk 105 optimal weight: 0.6980 chunk 17 optimal weight: 10.0000 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 564 HIS D 88 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.120331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.099091 restraints weight = 28659.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.101957 restraints weight = 16763.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.103825 restraints weight = 11959.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.105013 restraints weight = 9579.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.105879 restraints weight = 8304.360| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.4463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 16386 Z= 0.138 Angle : 0.678 16.208 22451 Z= 0.326 Chirality : 0.045 0.511 2823 Planarity : 0.003 0.037 2699 Dihedral : 4.899 36.376 2028 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.29 % Favored : 96.59 % Rotamer: Outliers : 3.31 % Allowed : 13.03 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.21), residues: 1700 helix: 1.52 (0.27), residues: 429 sheet: 0.37 (0.24), residues: 427 loop : -0.21 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 617 TYR 0.015 0.001 TYR D 40 PHE 0.018 0.002 PHE F 522 TRP 0.013 0.001 TRP C 479 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (16257) covalent geometry : angle 0.61682 / 0.31 (22098) SS BOND : bond 0.00436 / 0.22 ( 34) SS BOND : angle 1.19721 / 0.62 ( 68) hydrogen bonds : bond 0.04352 / 2.40 ( 607) hydrogen bonds : angle 5.01486 / 2.74 ( 1629) link_ALPHA1-2 : bond 0.00826 / 0.43 ( 2) link_ALPHA1-2 : angle 1.67740 / 0.77 ( 6) link_ALPHA1-3 : bond 0.00894 / 0.44 ( 3) link_ALPHA1-3 : angle 1.34648 / 0.76 ( 9) link_ALPHA1-6 : bond 0.00444 / 0.23 ( 3) link_ALPHA1-6 : angle 1.44938 / 0.74 ( 9) link_BETA1-4 : bond 0.00439 / 0.25 ( 26) link_BETA1-4 : angle 1.27603 / 0.62 ( 78) link_NAG-ASN : bond 0.00489 / 0.29 ( 61) link_NAG-ASN : angle 2.98430 / 1.55 ( 183) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 203 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLU cc_start: 0.6810 (OUTLIER) cc_final: 0.4650 (pm20) REVERT: A 199 SER cc_start: 0.9442 (p) cc_final: 0.9056 (t) REVERT: A 231 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7967 (ptmt) REVERT: A 273 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7944 (mtt180) REVERT: B 551 GLN cc_start: 0.6255 (OUTLIER) cc_final: 0.5236 (pm20) REVERT: B 586 TYR cc_start: 0.9246 (t80) cc_final: 0.8886 (t80) REVERT: B 654 GLU cc_start: 0.8014 (tp30) cc_final: 0.7684 (tp30) REVERT: C 103 GLN cc_start: 0.8452 (tm-30) cc_final: 0.7922 (tm-30) REVERT: C 217 TYR cc_start: 0.9006 (m-80) cc_final: 0.8568 (m-80) REVERT: C 258 GLN cc_start: 0.9005 (mt0) cc_final: 0.8689 (mt0) REVERT: C 340 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7755 (tm-30) REVERT: D 243 SER cc_start: 0.8318 (OUTLIER) cc_final: 0.8109 (t) REVERT: D 282 LYS cc_start: 0.9141 (mmtt) cc_final: 0.8930 (mttm) REVERT: D 297 THR cc_start: 0.9115 (OUTLIER) cc_final: 0.8665 (p) REVERT: F 647 GLU cc_start: 0.7530 (tm-30) cc_final: 0.7313 (tt0) outliers start: 51 outliers final: 35 residues processed: 236 average time/residue: 0.1021 time to fit residues: 36.3464 Evaluate side-chains 229 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 187 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 419 ARG Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 551 GLN Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain E residue 599 SER Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain F residue 659 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 170 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A 94 ASN A 478 ASN ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.119444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.098069 restraints weight = 29112.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.100928 restraints weight = 17121.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.102798 restraints weight = 12244.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.103908 restraints weight = 9841.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.104711 restraints weight = 8585.890| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.4586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 16386 Z= 0.169 Angle : 0.688 15.324 22451 Z= 0.329 Chirality : 0.045 0.462 2823 Planarity : 0.003 0.036 2699 Dihedral : 4.786 26.574 2028 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.88 % Favored : 96.00 % Rotamer: Outliers : 3.89 % Allowed : 12.64 % Favored : 83.47 % 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: 0.54 (0.21), residues: 1700 helix: 1.58 (0.27), residues: 429 sheet: 0.39 (0.24), residues: 426 loop : -0.22 (0.22), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 617 TYR 0.014 0.001 TYR D 40 PHE 0.017 0.002 PHE F 522 TRP 0.011 0.001 TRP C 479 HIS 0.011 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (16257) covalent geometry : angle 0.63321 / 0.32 (22098) SS BOND : bond 0.00339 / 0.18 ( 34) SS BOND : angle 0.95158 / 0.48 ( 68) hydrogen bonds : bond 0.04370 / 2.41 ( 607) hydrogen bonds : angle 4.99239 / 2.73 ( 1629) link_ALPHA1-2 : bond 0.00915 / 0.48 ( 2) link_ALPHA1-2 : angle 1.61422 / 0.77 ( 6) link_ALPHA1-3 : bond 0.00951 / 0.46 ( 3) link_ALPHA1-3 : angle 1.32996 / 0.77 ( 9) link_ALPHA1-6 : bond 0.00419 / 0.21 ( 3) link_ALPHA1-6 : angle 1.44972 / 0.74 ( 9) link_BETA1-4 : bond 0.00423 / 0.24 ( 26) link_BETA1-4 : angle 1.32895 / 0.65 ( 78) link_NAG-ASN : bond 0.00496 / 0.30 ( 61) link_NAG-ASN : angle 2.88797 / 1.49 ( 183) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 196 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLU cc_start: 0.6844 (OUTLIER) cc_final: 0.4631 (pm20) REVERT: A 66 HIS cc_start: 0.7610 (m-70) cc_final: 0.7316 (m-70) REVERT: A 199 SER cc_start: 0.9494 (p) cc_final: 0.8983 (t) REVERT: A 207 LYS cc_start: 0.8362 (pptt) cc_final: 0.7769 (pptt) REVERT: A 208 VAL cc_start: 0.9281 (t) cc_final: 0.8909 (p) REVERT: A 231 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7974 (ptmt) REVERT: B 551 GLN cc_start: 0.6249 (OUTLIER) cc_final: 0.5259 (pm20) REVERT: B 586 TYR cc_start: 0.9268 (t80) cc_final: 0.8914 (t80) REVERT: B 654 GLU cc_start: 0.8071 (tp30) cc_final: 0.7759 (tp30) REVERT: C 53 PHE cc_start: 0.9078 (p90) cc_final: 0.8642 (p90) REVERT: C 103 GLN cc_start: 0.8553 (tm-30) cc_final: 0.8235 (tm-30) REVERT: C 217 TYR cc_start: 0.9018 (m-80) cc_final: 0.8594 (m-80) REVERT: C 258 GLN cc_start: 0.9048 (mt0) cc_final: 0.8688 (mt0) REVERT: C 340 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.8003 (mt-10) REVERT: D 243 SER cc_start: 0.8288 (OUTLIER) cc_final: 0.8068 (t) REVERT: D 282 LYS cc_start: 0.9157 (mmtt) cc_final: 0.8949 (mttm) REVERT: D 297 THR cc_start: 0.9125 (OUTLIER) cc_final: 0.8678 (p) REVERT: F 647 GLU cc_start: 0.7572 (tm-30) cc_final: 0.7359 (tt0) outliers start: 60 outliers final: 41 residues processed: 237 average time/residue: 0.1042 time to fit residues: 37.3442 Evaluate side-chains 231 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 184 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 419 ARG Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 551 GLN Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain E residue 599 SER Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 622 ILE Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain F residue 661 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 126 optimal weight: 1.9990 chunk 141 optimal weight: 0.5980 chunk 149 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 35 optimal weight: 0.0010 chunk 119 optimal weight: 2.9990 chunk 70 optimal weight: 0.0970 chunk 169 optimal weight: 1.9990 chunk 116 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 overall best weight: 0.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 GLN A 478 ASN B 562 GLN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.122477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.101641 restraints weight = 28625.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.104475 restraints weight = 17062.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.106316 restraints weight = 12220.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.107562 restraints weight = 9827.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.108359 restraints weight = 8459.394| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.4736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 16386 Z= 0.112 Angle : 0.637 14.131 22451 Z= 0.308 Chirality : 0.044 0.432 2823 Planarity : 0.003 0.034 2699 Dihedral : 4.657 32.428 2028 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.12 % Favored : 96.76 % Rotamer: Outliers : 2.92 % Allowed : 13.93 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.21), residues: 1700 helix: 1.74 (0.27), residues: 429 sheet: 0.47 (0.23), residues: 445 loop : -0.22 (0.23), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 350 TYR 0.012 0.001 TYR D 40 PHE 0.018 0.001 PHE F 522 TRP 0.023 0.001 TRP F 628 HIS 0.003 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (16257) covalent geometry : angle 0.58778 / 0.30 (22098) SS BOND : bond 0.00222 / 0.11 ( 34) SS BOND : angle 0.96488 / 0.49 ( 68) hydrogen bonds : bond 0.03813 / 2.09 ( 607) hydrogen bonds : angle 4.82164 / 2.64 ( 1629) link_ALPHA1-2 : bond 0.00848 / 0.44 ( 2) link_ALPHA1-2 : angle 1.72281 / 0.78 ( 6) link_ALPHA1-3 : bond 0.00782 / 0.39 ( 3) link_ALPHA1-3 : angle 1.29216 / 0.71 ( 9) link_ALPHA1-6 : bond 0.00458 / 0.23 ( 3) link_ALPHA1-6 : angle 1.45351 / 0.76 ( 9) link_BETA1-4 : bond 0.00444 / 0.25 ( 26) link_BETA1-4 : angle 1.16575 / 0.57 ( 78) link_NAG-ASN : bond 0.00478 / 0.28 ( 61) link_NAG-ASN : angle 2.60451 / 1.35 ( 183) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 201 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLU cc_start: 0.6704 (OUTLIER) cc_final: 0.4476 (pm20) REVERT: A 46 LYS cc_start: 0.8299 (mtpt) cc_final: 0.8065 (mtpt) REVERT: A 231 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.8037 (ptmt) REVERT: B 551 GLN cc_start: 0.6208 (OUTLIER) cc_final: 0.5129 (pm20) REVERT: B 586 TYR cc_start: 0.9234 (t80) cc_final: 0.8862 (t80) REVERT: B 654 GLU cc_start: 0.8013 (tp30) cc_final: 0.7715 (tp30) REVERT: C 217 TYR cc_start: 0.8826 (m-80) cc_final: 0.8498 (m-80) REVERT: C 258 GLN cc_start: 0.8973 (mt0) cc_final: 0.8734 (mt0) REVERT: C 498 PRO cc_start: 0.8817 (Cg_exo) cc_final: 0.8469 (Cg_endo) outliers start: 45 outliers final: 33 residues processed: 230 average time/residue: 0.1085 time to fit residues: 37.7170 Evaluate side-chains 223 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 187 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 419 ARG Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 551 GLN Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain E residue 599 SER Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain F residue 661 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 75 optimal weight: 2.9990 chunk 140 optimal weight: 0.0370 chunk 173 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 92 optimal weight: 0.8980 chunk 142 optimal weight: 6.9990 chunk 165 optimal weight: 4.9990 chunk 65 optimal weight: 7.9990 chunk 139 optimal weight: 1.9990 chunk 12 optimal weight: 20.0000 overall best weight: 0.9060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.121509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.100333 restraints weight = 28828.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.103234 restraints weight = 16911.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.105123 restraints weight = 12042.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.106370 restraints weight = 9656.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.107210 restraints weight = 8305.652| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.4829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 16386 Z= 0.132 Angle : 0.647 13.275 22451 Z= 0.311 Chirality : 0.045 0.409 2823 Planarity : 0.003 0.034 2699 Dihedral : 4.611 32.688 2028 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.00 % Favored : 95.88 % Rotamer: Outliers : 2.33 % Allowed : 14.97 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.21), residues: 1700 helix: 1.73 (0.27), residues: 425 sheet: 0.33 (0.23), residues: 450 loop : -0.16 (0.23), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 350 TYR 0.012 0.001 TYR C 40 PHE 0.017 0.002 PHE F 522 TRP 0.014 0.001 TRP F 628 HIS 0.004 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (16257) covalent geometry : angle 0.60032 / 0.30 (22098) SS BOND : bond 0.00295 / 0.15 ( 34) SS BOND : angle 0.99481 / 0.49 ( 68) hydrogen bonds : bond 0.03911 / 2.15 ( 607) hydrogen bonds : angle 4.80309 / 2.64 ( 1629) link_ALPHA1-2 : bond 0.00828 / 0.43 ( 2) link_ALPHA1-2 : angle 1.60836 / 0.75 ( 6) link_ALPHA1-3 : bond 0.00820 / 0.40 ( 3) link_ALPHA1-3 : angle 1.26661 / 0.71 ( 9) link_ALPHA1-6 : bond 0.00421 / 0.21 ( 3) link_ALPHA1-6 : angle 1.43816 / 0.74 ( 9) link_BETA1-4 : bond 0.00434 / 0.25 ( 26) link_BETA1-4 : angle 1.23640 / 0.61 ( 78) link_NAG-ASN : bond 0.00460 / 0.27 ( 61) link_NAG-ASN : angle 2.55217 / 1.32 ( 183) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 190 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLU cc_start: 0.6684 (OUTLIER) cc_final: 0.4472 (pm20) REVERT: A 46 LYS cc_start: 0.8345 (mtpt) cc_final: 0.8097 (mtpt) REVERT: A 231 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.8006 (ptmt) REVERT: A 376 PHE cc_start: 0.7868 (t80) cc_final: 0.7489 (t80) REVERT: B 551 GLN cc_start: 0.6113 (OUTLIER) cc_final: 0.5150 (pm20) REVERT: B 586 TYR cc_start: 0.9247 (t80) cc_final: 0.8893 (t80) REVERT: B 621 GLU cc_start: 0.8708 (tm-30) cc_final: 0.8436 (pp20) REVERT: B 654 GLU cc_start: 0.8007 (tp30) cc_final: 0.7710 (tp30) REVERT: C 53 PHE cc_start: 0.9049 (p90) cc_final: 0.8554 (p90) REVERT: C 217 TYR cc_start: 0.8836 (m-80) cc_final: 0.8495 (m-80) REVERT: C 258 GLN cc_start: 0.8996 (mt0) cc_final: 0.8750 (mt0) REVERT: C 498 PRO cc_start: 0.8776 (Cg_exo) cc_final: 0.8465 (Cg_endo) REVERT: D 199 SER cc_start: 0.9389 (p) cc_final: 0.8972 (t) REVERT: D 282 LYS cc_start: 0.9193 (mmtt) cc_final: 0.8967 (mttm) outliers start: 36 outliers final: 29 residues processed: 215 average time/residue: 0.1049 time to fit residues: 34.0499 Evaluate side-chains 214 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 182 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 419 ARG Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 551 GLN Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain E residue 599 SER Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain D residue 80 ASN Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain F residue 661 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 156 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 182 optimal weight: 0.2980 chunk 18 optimal weight: 3.9990 chunk 146 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.122005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.100738 restraints weight = 28699.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.103581 restraints weight = 16891.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.105511 restraints weight = 12151.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.106758 restraints weight = 9692.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.107525 restraints weight = 8347.085| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.4901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16386 Z= 0.137 Angle : 0.642 12.241 22451 Z= 0.311 Chirality : 0.045 0.413 2823 Planarity : 0.003 0.034 2699 Dihedral : 4.591 32.240 2028 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.76 % Favored : 96.12 % Rotamer: Outliers : 2.53 % Allowed : 14.65 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.21), residues: 1700 helix: 1.76 (0.27), residues: 425 sheet: 0.36 (0.23), residues: 429 loop : -0.17 (0.22), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 350 TYR 0.013 0.001 TYR C 40 PHE 0.017 0.002 PHE F 522 TRP 0.011 0.001 TRP F 628 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (16257) covalent geometry : angle 0.59867 / 0.30 (22098) SS BOND : bond 0.00291 / 0.15 ( 34) SS BOND : angle 0.90430 / 0.45 ( 68) hydrogen bonds : bond 0.03911 / 2.15 ( 607) hydrogen bonds : angle 4.78293 / 2.63 ( 1629) link_ALPHA1-2 : bond 0.00846 / 0.44 ( 2) link_ALPHA1-2 : angle 1.58884 / 0.75 ( 6) link_ALPHA1-3 : bond 0.00814 / 0.40 ( 3) link_ALPHA1-3 : angle 1.28385 / 0.72 ( 9) link_ALPHA1-6 : bond 0.00412 / 0.21 ( 3) link_ALPHA1-6 : angle 1.44869 / 0.75 ( 9) link_BETA1-4 : bond 0.00421 / 0.24 ( 26) link_BETA1-4 : angle 1.23001 / 0.60 ( 78) link_NAG-ASN : bond 0.00444 / 0.26 ( 61) link_NAG-ASN : angle 2.47418 / 1.28 ( 183) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2230.84 seconds wall clock time: 39 minutes 35.21 seconds (2375.21 seconds total)