Starting phenix.real_space_refine on Fri Jul 3 20:54:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7l8e_23231/07_2026/7l8e_23231.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l8e_23231/07_2026/7l8e_23231.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7l8e_23231/07_2026/7l8e_23231.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l8e_23231/07_2026/7l8e_23231.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7l8e_23231/07_2026/7l8e_23231.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l8e_23231/07_2026/7l8e_23231.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7l8e_23231/07_2026/7l8e_23231.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7l8e_23231/07_2026/7l8e_23231.cif" } resolution = 4.2 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 102 5.16 5 C 9840 2.51 5 N 2662 2.21 5 O 3223 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 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: 15827 Number of models: 1 Model: "" Number of chains: 35 Chain: "C" Number of atoms: 3506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3506 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 20, 'TRANS': 423} Chain breaks: 3 Chain: "D" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 997 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "E" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3486 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 20, 'TRANS': 420} Chain breaks: 3 Chain: "F" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1003 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "A" Number of atoms: 3514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3514 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 20, 'TRANS': 424} Chain breaks: 3 Chain: "B" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 968 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "H" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 555 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'TRANS': 110} Unresolved non-hydrogen bonds: 222 Unresolved non-hydrogen angles: 333 Unresolved non-hydrogen dihedrals: 111 Planarities with less than four sites: {'UNK:plan-1': 111} Unresolved non-hydrogen planarities: 111 Chain: "L" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 495 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'TRANS': 98} Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 297 Unresolved non-hydrogen dihedrals: 99 Planarities with less than four sites: {'UNK:plan-1': 99} Unresolved non-hydrogen planarities: 99 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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: 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: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen chiralities: 13 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 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 Time building chain proxies: 2.70, per 1000 atoms: 0.17 Number of scatterers: 15827 At special positions: 0 Unit cell: (133.9, 127.72, 142.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 102 16.00 O 3223 8.00 N 2662 7.00 C 9840 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 73 " distance=2.04 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.09 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.05 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.08 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=2.09 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.05 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.05 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 73 " distance=2.02 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.05 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.06 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.05 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.04 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.02 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA G 3 " - " MAN G 4 " " BMA Q 3 " - " MAN Q 4 " " BMA X 3 " - " MAN X 4 " ALPHA1-6 " BMA G 3 " - " MAN G 5 " " BMA Q 3 " - " MAN Q 5 " " BMA X 3 " - " MAN X 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " NAG-ASN " NAG A 701 " - " ASN A 160 " " NAG A 702 " - " ASN A 276 " " NAG A 703 " - " ASN A 295 " " NAG A 704 " - " ASN A 386 " " NAG A 705 " - " ASN A 363 " " NAG A 706 " - " ASN A 234 " " NAG A 707 " - " ASN A 133 " " NAG A 708 " - " ASN A 241 " " NAG A 709 " - " ASN A 289 " " NAG A 710 " - " ASN A 339 " " NAG A 711 " - " ASN A 355 " " NAG A 712 " - " ASN A 392 " " NAG B 701 " - " ASN B 637 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 611 " " NAG C 701 " - " ASN C 160 " " NAG C 702 " - " ASN C 276 " " NAG C 703 " - " ASN C 386 " " NAG C 704 " - " ASN C 363 " " NAG C 705 " - " ASN C 133 " " NAG C 706 " - " ASN C 88 " " NAG C 707 " - " ASN C 241 " " NAG C 708 " - " ASN C 289 " " NAG C 709 " - " ASN C 339 " " NAG C 710 " - " ASN C 355 " " NAG C 711 " - " ASN C 392 " " NAG D 701 " - " ASN D 637 " " NAG D 702 " - " ASN D 611 " " NAG E 701 " - " ASN E 160 " " NAG E 702 " - " ASN E 276 " " NAG E 703 " - " ASN E 386 " " NAG E 704 " - " ASN E 363 " " NAG E 705 " - " ASN E 234 " " NAG E 706 " - " ASN E 133 " " NAG E 707 " - " ASN E 301 " " NAG E 708 " - " ASN E 88 " " NAG E 709 " - " ASN E 289 " " NAG E 710 " - " ASN E 339 " " NAG E 711 " - " ASN E 355 " " NAG E 712 " - " ASN E 392 " " NAG E 713 " - " ASN E 137 " " NAG F 701 " - " ASN F 637 " " NAG F 702 " - " ASN F 618 " " NAG F 703 " - " ASN F 611 " " NAG G 1 " - " ASN C 262 " " NAG I 1 " - " ASN C 448 " " NAG J 1 " - " ASN C 295 " " NAG K 1 " - " ASN C 234 " " NAG M 1 " - " ASN C 197 " " NAG N 1 " - " ASN C 156 " " NAG O 1 " - " ASN C 301 " " NAG P 1 " - " ASN C 332 " " NAG Q 1 " - " ASN E 262 " " NAG R 1 " - " ASN E 448 " " NAG S 1 " - " ASN E 295 " " NAG T 1 " - " ASN E 197 " " NAG U 1 " - " ASN E 156 " " NAG V 1 " - " ASN E 241 " " NAG W 1 " - " ASN E 332 " " NAG X 1 " - " ASN A 262 " " NAG Y 1 " - " ASN A 448 " " NAG Z 1 " - " ASN A 197 " " NAG a 1 " - " ASN A 301 " " NAG b 1 " - " ASN A 88 " " NAG c 1 " - " ASN A 332 " Time building additional restraints: 1.39 Conformation dependent library (CDL) restraints added in 510.9 milliseconds 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3604 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 49 sheets defined 29.6% alpha, 71.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'C' and resid 67 through 73 Processing helix chain 'C' and resid 94 through 97 Processing helix chain 'C' and resid 98 through 116 removed outlier: 3.630A 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 335 through 354 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 391 Processing helix chain 'C' and resid 425 through 429 Processing helix chain 'C' and resid 475 through 483 removed outlier: 3.790A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 528 removed outlier: 4.319A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 535 Processing helix chain 'D' and resid 536 through 543 removed outlier: 3.726A pdb=" N ASN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 596 Processing helix chain 'D' and resid 618 through 623 Processing helix chain 'D' and resid 627 through 634 Processing helix chain 'D' and resid 638 through 661 Processing helix chain 'E' and resid 67 through 73 Processing helix chain 'E' and resid 96 through 98 No H-bonds generated for 'chain 'E' and resid 96 through 98' Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 335 through 354 removed outlier: 4.025A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 391 Processing helix chain 'E' and resid 427 through 429 No H-bonds generated for 'chain 'E' and resid 427 through 429' Processing helix chain 'E' and resid 475 through 483 removed outlier: 3.817A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 528 removed outlier: 4.197A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 535 Processing helix chain 'F' and resid 536 through 543 Processing helix chain 'F' and resid 569 through 596 Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 664 Processing helix chain 'A' and resid 67 through 73 Processing helix chain 'A' and resid 98 through 117 Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 334 through 354 removed outlier: 4.090A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 425 through 429 Processing helix chain 'A' and resid 475 through 483 removed outlier: 3.967A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 3.541A 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 543 removed outlier: 3.591A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 596 Processing helix chain 'B' and resid 618 through 623 Processing helix chain 'B' and resid 627 through 634 Processing helix chain 'B' and resid 638 through 661 Processing helix chain 'L' and resid 25 through 31 Processing sheet with id=AA1, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.117A pdb=" N VAL C 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.864A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AA4, first strand: chain 'C' and resid 91 through 92 Processing sheet with id=AA5, first strand: chain 'C' and resid 169 through 177 removed outlier: 3.762A pdb=" N LYS C 189 " --> pdb=" O CYS C 131 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.604A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.738A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 10.426A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 11.170A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.270A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.851A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.796A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.828A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.546A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.385A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 271 through 273 removed outlier: 7.791A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 305 through 308 Processing sheet with id=AB1, first strand: chain 'C' and resid 394 through 395 Processing sheet with id=AB2, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.270A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AB4, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AB5, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AB6, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AB7, first strand: chain 'E' and resid 200 through 203 removed outlier: 6.214A pdb=" N ALA E 200 " --> pdb=" O ALA E 433 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N TYR E 435 " --> pdb=" O ALA E 200 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 259 through 261 removed outlier: 3.682A pdb=" N GLY E 451 " --> pdb=" O LEU E 260 " (cutoff:3.500A) removed outlier: 10.368A pdb=" N VAL E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 10.903A pdb=" N CYS E 296 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 9.904A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.491A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.443A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.116A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.384A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.049A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 259 through 261 removed outlier: 3.682A pdb=" N GLY E 451 " --> pdb=" O LEU E 260 " (cutoff:3.500A) removed outlier: 10.368A pdb=" N VAL E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 10.903A pdb=" N CYS E 296 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 9.904A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.491A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.443A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.116A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.384A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.049A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ASN E 301 " --> pdb=" O ILE E 323A" (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 259 through 261 removed outlier: 3.682A pdb=" N GLY E 451 " --> pdb=" O LEU E 260 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 259 through 261 removed outlier: 3.682A pdb=" N GLY E 451 " --> pdb=" O LEU E 260 " (cutoff:3.500A) removed outlier: 10.368A pdb=" N VAL E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 10.903A pdb=" N CYS E 296 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 9.904A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.491A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.443A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.116A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.384A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.049A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 271 through 273 removed outlier: 6.687A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.049A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.384A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.116A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.443A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.491A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.904A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 10.903A pdb=" N CYS E 296 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 10.368A pdb=" N VAL E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY E 451 " --> pdb=" O LEU E 260 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 271 through 273 removed outlier: 7.680A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 271 through 273 removed outlier: 6.687A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.049A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.384A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.116A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.443A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.491A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.904A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 10.903A pdb=" N CYS E 296 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 10.368A pdb=" N VAL E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 323 through 323A removed outlier: 4.074A pdb=" N ASN E 301 " --> pdb=" O ILE E 323A" (cutoff:3.500A) removed outlier: 6.687A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.049A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.384A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.116A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.443A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.491A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.904A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 10.903A pdb=" N CYS E 296 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 10.368A pdb=" N VAL E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY E 451 " --> pdb=" O LEU E 260 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 323 through 323A removed outlier: 4.074A pdb=" N ASN E 301 " --> pdb=" O ILE E 323A" (cutoff:3.500A) removed outlier: 7.680A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 323 through 323A removed outlier: 4.074A pdb=" N ASN E 301 " --> pdb=" O ILE E 323A" (cutoff:3.500A) removed outlier: 6.687A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.049A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.384A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.116A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.443A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.491A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.904A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 10.903A pdb=" N CYS E 296 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 10.368A pdb=" N VAL E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 374 through 378 removed outlier: 3.951A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 374 through 378 removed outlier: 3.951A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ASN E 301 " --> pdb=" O ILE E 323A" (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 374 through 378 removed outlier: 3.951A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.049A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.384A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.116A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.443A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.491A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.904A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 10.903A pdb=" N CYS E 296 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 10.368A pdb=" N VAL E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY E 451 " --> pdb=" O LEU E 260 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 374 through 378 removed outlier: 3.951A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.049A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.384A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.116A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.443A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.491A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.904A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 10.903A pdb=" N CYS E 296 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 10.368A pdb=" N VAL E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 394 through 395 removed outlier: 6.013A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY E 451 " --> pdb=" O LEU E 260 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 394 through 395 removed outlier: 6.013A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 10.368A pdb=" N VAL E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 10.903A pdb=" N CYS E 296 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 9.904A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.491A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.443A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.116A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.384A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.049A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 394 through 395 removed outlier: 6.013A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 10.368A pdb=" N VAL E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 10.903A pdb=" N CYS E 296 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 9.904A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.491A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.443A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.116A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.384A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.049A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ASN E 301 " --> pdb=" O ILE E 323A" (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 394 through 395 removed outlier: 6.013A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 10.368A pdb=" N VAL E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 10.903A pdb=" N CYS E 296 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 9.904A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.491A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.443A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.116A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.384A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.049A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 305 through 312 removed outlier: 6.590A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 494 through 499 removed outlier: 4.561A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AE2, first strand: chain 'A' and resid 75 through 76 removed outlier: 4.427A pdb=" N VAL A 75 " --> pdb=" O CYS A 54 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 91 through 92 Processing sheet with id=AE4, first strand: chain 'A' and resid 130 through 133 Processing sheet with id=AE5, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AE6, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.544A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.623A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 10.025A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.543A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.675A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.506A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.601A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.347A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.641A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.347A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.601A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.506A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.675A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.543A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 10.025A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'A' and resid 301 through 312 removed outlier: 7.130A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 49 through 50 Processing sheet with id=AF2, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AF3, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AF4, first strand: chain 'L' and resid 34 through 38 removed outlier: 6.006A pdb=" N UNK L 84 " --> pdb=" O UNK L 99 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N UNK L 99 " --> pdb=" O UNK L 84 " (cutoff:3.500A) 836 hydrogen bonds defined for protein. 2202 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: 2.76 Time building geometry restraints manager: 1.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3760 1.32 - 1.46: 4949 1.46 - 1.60: 7232 1.60 - 1.74: 25 1.74 - 1.88: 132 Bond restraints: 16098 Sorted by residual: bond pdb=" CB TYR C 319 " pdb=" CG TYR C 319 " ideal model delta sigma weight residual 1.512 1.348 0.164 2.20e-02 2.07e+03 5.59e+01 bond pdb=" CB HIS E 374 " pdb=" CG HIS E 374 " ideal model delta sigma weight residual 1.497 1.406 0.091 1.40e-02 5.10e+03 4.21e+01 bond pdb=" CB TYR E 484 " pdb=" CG TYR E 484 " ideal model delta sigma weight residual 1.512 1.371 0.141 2.20e-02 2.07e+03 4.11e+01 bond pdb=" CB HIS A 374 " pdb=" CG HIS A 374 " ideal model delta sigma weight residual 1.497 1.408 0.089 1.40e-02 5.10e+03 4.03e+01 bond pdb=" NE1 TRP D 628 " pdb=" CE2 TRP D 628 " ideal model delta sigma weight residual 1.370 1.311 0.059 1.10e-02 8.26e+03 2.89e+01 ... (remaining 16093 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.13: 20261 3.13 - 6.26: 1529 6.26 - 9.40: 98 9.40 - 12.53: 5 12.53 - 15.66: 1 Bond angle restraints: 21894 Sorted by residual: angle pdb=" C VAL C 75 " pdb=" N PRO C 76 " pdb=" CA PRO C 76 " ideal model delta sigma weight residual 119.56 128.63 -9.07 1.02e+00 9.61e-01 7.91e+01 angle pdb=" C GLU C 492 " pdb=" N PRO C 493 " pdb=" CA PRO C 493 " ideal model delta sigma weight residual 119.56 128.61 -9.05 1.02e+00 9.61e-01 7.86e+01 angle pdb=" N PRO A 437 " pdb=" CA PRO A 437 " pdb=" C PRO A 437 " ideal model delta sigma weight residual 110.47 101.99 8.48 9.60e-01 1.09e+00 7.80e+01 angle pdb=" C GLY A 237 " pdb=" N PRO A 238 " pdb=" CA PRO A 238 " ideal model delta sigma weight residual 119.78 128.60 -8.82 1.03e+00 9.43e-01 7.34e+01 angle pdb=" C GLU E 492 " pdb=" N PRO E 493 " pdb=" CA PRO E 493 " ideal model delta sigma weight residual 119.56 128.19 -8.63 1.02e+00 9.61e-01 7.16e+01 ... (remaining 21889 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 8593 17.93 - 35.86: 228 35.86 - 53.79: 75 53.79 - 71.72: 19 71.72 - 89.65: 11 Dihedral angle restraints: 8926 sinusoidal: 3385 harmonic: 5541 Sorted by residual: dihedral pdb=" CB CYS E 378 " pdb=" SG CYS E 378 " pdb=" SG CYS E 445 " pdb=" CB CYS E 445 " ideal model delta sinusoidal sigma weight residual -86.00 -131.82 45.82 1 1.00e+01 1.00e-02 2.91e+01 dihedral pdb=" C ASN D 637 " pdb=" N ASN D 637 " pdb=" CA ASN D 637 " pdb=" CB ASN D 637 " ideal model delta harmonic sigma weight residual -122.60 -110.19 -12.41 0 2.50e+00 1.60e-01 2.47e+01 dihedral pdb=" CB CYS C 119 " pdb=" SG CYS C 119 " pdb=" SG CYS C 205 " pdb=" CB CYS C 205 " ideal model delta sinusoidal sigma weight residual -86.00 -126.96 40.96 1 1.00e+01 1.00e-02 2.35e+01 ... (remaining 8923 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 1779 0.101 - 0.202: 613 0.202 - 0.303: 226 0.303 - 0.404: 106 0.404 - 0.505: 69 Chirality restraints: 2793 Sorted by residual: chirality pdb=" C1 NAG S 2 " pdb=" O4 NAG S 1 " pdb=" C2 NAG S 2 " pdb=" O5 NAG S 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.46e+02 chirality pdb=" C1 NAG X 2 " pdb=" O4 NAG X 1 " pdb=" C2 NAG X 2 " pdb=" O5 NAG X 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-02 2.50e+03 1.43e+02 chirality pdb=" C1 NAG b 2 " pdb=" O4 NAG b 1 " pdb=" C2 NAG b 2 " pdb=" O5 NAG b 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.41e+02 ... (remaining 2790 not shown) Planarity restraints: 2745 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG Z 2 " -0.344 2.00e-02 2.50e+03 2.95e-01 1.09e+03 pdb=" C7 NAG Z 2 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG Z 2 " -0.153 2.00e-02 2.50e+03 pdb=" N2 NAG Z 2 " 0.523 2.00e-02 2.50e+03 pdb=" O7 NAG Z 2 " -0.112 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG X 2 " 0.341 2.00e-02 2.50e+03 2.91e-01 1.06e+03 pdb=" C7 NAG X 2 " -0.087 2.00e-02 2.50e+03 pdb=" C8 NAG X 2 " 0.171 2.00e-02 2.50e+03 pdb=" N2 NAG X 2 " -0.512 2.00e-02 2.50e+03 pdb=" O7 NAG X 2 " 0.088 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 702 " -0.333 2.00e-02 2.50e+03 2.84e-01 1.01e+03 pdb=" C7 NAG B 702 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG B 702 " -0.169 2.00e-02 2.50e+03 pdb=" N2 NAG B 702 " 0.500 2.00e-02 2.50e+03 pdb=" O7 NAG B 702 " -0.083 2.00e-02 2.50e+03 ... (remaining 2742 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3198 2.78 - 3.31: 15129 3.31 - 3.84: 25697 3.84 - 4.37: 31272 4.37 - 4.90: 48739 Nonbonded interactions: 124035 Sorted by model distance: nonbonded pdb=" O3 NAG X 1 " pdb=" O7 NAG X 1 " model vdw 2.253 3.040 nonbonded pdb=" O ASP A 325 " pdb=" OD1 ASP A 325 " model vdw 2.362 3.040 nonbonded pdb=" O3 NAG C 702 " pdb=" O7 NAG C 702 " model vdw 2.376 3.040 nonbonded pdb=" N TYR D 638 " pdb=" N THR D 639 " model vdw 2.386 2.560 nonbonded pdb=" NZ LYS E 46 " pdb=" OD2 ASP F 632 " model vdw 2.396 3.120 ... (remaining 124030 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 66 through 397 or resid 411 through \ 505 or resid 702 through 712)) selection = (chain 'C' and (resid 33 through 56 or resid 66 through 505 or resid 701 through \ 711)) selection = (chain 'E' and (resid 33 through 56 or resid 66 through 505 or resid 702 through \ 712)) } ncs_group { reference = (chain 'B' and (resid 520 through 661 or resid 702 through 703)) selection = (chain 'D' and (resid 520 through 546 or resid 568 through 661 or resid 701 thro \ ugh 702)) selection = (chain 'F' and (resid 520 through 546 or resid 568 through 661 or resid 702 thro \ ugh 703)) } ncs_group { reference = chain 'G' selection = chain 'Q' selection = chain 'X' } ncs_group { reference = (chain 'H' and resid 14 through 112) selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' } 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: 2.210 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: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 12.990 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 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 : 0.023 0.164 16226 Z= 1.206 Angle : 1.768 15.659 22245 Z= 1.118 Chirality : 0.145 0.505 2793 Planarity : 0.018 0.295 2680 Dihedral : 10.043 89.651 5223 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % 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: 1.11 (0.19), residues: 1666 helix: 0.42 (0.23), residues: 418 sheet: 1.17 (0.24), residues: 402 loop : 0.87 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 327 TYR 0.052 0.009 TYR C 40 PHE 0.035 0.006 PHE C 233 TRP 0.070 0.010 TRP E 35 HIS 0.011 0.002 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.02203 / 1.18 (16098) covalent geometry : angle 1.73873 / 1.12 (21894) SS BOND : bond 0.01971 / 1.12 ( 33) SS BOND : angle 2.91255 / 2.08 ( 66) hydrogen bonds : bond 0.16830 / 11.36 ( 591) hydrogen bonds : angle 7.85416 / 5.47 ( 2202) link_ALPHA1-3 : bond 0.07060 / 3.57 ( 3) link_ALPHA1-3 : angle 3.78367 / 2.82 ( 9) link_ALPHA1-6 : bond 0.04692 / 2.37 ( 3) link_ALPHA1-6 : angle 2.75848 / 2.07 ( 9) link_BETA1-4 : bond 0.07056 / 4.12 ( 24) link_BETA1-4 : angle 4.30042 / 2.94 ( 72) link_NAG-ASN : bond 0.07413 / 4.74 ( 65) link_NAG-ASN : angle 2.56469 / 1.73 ( 195) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 473 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 125 LEU cc_start: 0.9469 (mt) cc_final: 0.9232 (mt) REVERT: C 195 ASN cc_start: 0.8890 (p0) cc_final: 0.8688 (p0) REVERT: C 338 TRP cc_start: 0.9142 (t-100) cc_final: 0.8681 (t-100) REVERT: C 390 LEU cc_start: 0.9577 (mt) cc_final: 0.8959 (mt) REVERT: C 486 TYR cc_start: 0.8927 (m-80) cc_final: 0.8395 (m-80) REVERT: D 574 LYS cc_start: 0.9264 (mttt) cc_final: 0.8960 (mttp) REVERT: D 634 GLU cc_start: 0.8900 (mm-30) cc_final: 0.8579 (mm-30) REVERT: D 639 THR cc_start: 0.9074 (m) cc_final: 0.8122 (p) REVERT: D 645 LEU cc_start: 0.9087 (mt) cc_final: 0.8151 (mt) REVERT: D 663 LEU cc_start: 0.7999 (tp) cc_final: 0.7724 (tt) REVERT: E 103 GLN cc_start: 0.8707 (tt0) cc_final: 0.8299 (tp40) REVERT: E 107 ASP cc_start: 0.9068 (m-30) cc_final: 0.8845 (m-30) REVERT: E 180 ASP cc_start: 0.9157 (m-30) cc_final: 0.8723 (m-30) REVERT: E 390 LEU cc_start: 0.9637 (mt) cc_final: 0.9206 (mt) REVERT: E 426 MET cc_start: 0.8489 (mtp) cc_final: 0.8232 (mtp) REVERT: E 434 MET cc_start: 0.9490 (ttp) cc_final: 0.9258 (ttp) REVERT: F 543 ASN cc_start: 0.8449 (m-40) cc_final: 0.8140 (m110) REVERT: F 571 TRP cc_start: 0.8890 (t60) cc_final: 0.8686 (t60) REVERT: F 577 GLN cc_start: 0.9069 (mt0) cc_final: 0.8775 (mt0) REVERT: F 639 THR cc_start: 0.8258 (m) cc_final: 0.6267 (p) REVERT: A 180 ASP cc_start: 0.8591 (m-30) cc_final: 0.8353 (m-30) REVERT: A 284 ILE cc_start: 0.9606 (mt) cc_final: 0.9328 (pt) REVERT: A 430 ILE cc_start: 0.8933 (mm) cc_final: 0.8715 (tp) REVERT: B 545 LEU cc_start: 0.8793 (mt) cc_final: 0.8195 (mm) REVERT: B 586 TYR cc_start: 0.9318 (t80) cc_final: 0.8730 (t80) outliers start: 0 outliers final: 0 residues processed: 473 average time/residue: 0.1265 time to fit residues: 86.9404 Evaluate side-chains 233 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 0.562 ------------------------------------------------------------------------------- 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: 2.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 330 HIS ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 ASN D 625 ASN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN F 585 HIS F 651 ASN A 103 GLN A 137 ASN A 195 ASN A 328 GLN A 425 ASN A 462 ASN B 540 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.076289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.061784 restraints weight = 65494.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.063290 restraints weight = 40318.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.064339 restraints weight = 29282.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.064863 restraints weight = 23581.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.065394 restraints weight = 20876.353| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 16226 Z= 0.226 Angle : 0.870 19.026 22245 Z= 0.426 Chirality : 0.050 0.279 2793 Planarity : 0.005 0.062 2680 Dihedral : 5.136 28.821 2009 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.33 % Allowed : 2.43 % Favored : 97.24 % 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: 0.88 (0.20), residues: 1666 helix: 1.47 (0.26), residues: 409 sheet: 0.83 (0.24), residues: 419 loop : 0.10 (0.20), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 542 TYR 0.027 0.003 TYR C 217 PHE 0.026 0.003 PHE C 383 TRP 0.035 0.002 TRP D 631 HIS 0.008 0.001 HIS F 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.23 (16098) covalent geometry : angle 0.80689 / 0.41 (21894) SS BOND : bond 0.00760 / 0.53 ( 33) SS BOND : angle 1.21849 / 0.92 ( 66) hydrogen bonds : bond 0.06567 / 4.41 ( 591) hydrogen bonds : angle 5.32004 / 3.73 ( 2202) link_ALPHA1-3 : bond 0.00597 / 0.30 ( 3) link_ALPHA1-3 : angle 1.58962 / 0.89 ( 9) link_ALPHA1-6 : bond 0.00581 / 0.29 ( 3) link_ALPHA1-6 : angle 1.53360 / 0.95 ( 9) link_BETA1-4 : bond 0.00733 / 0.46 ( 24) link_BETA1-4 : angle 2.29170 / 1.63 ( 72) link_NAG-ASN : bond 0.00627 / 0.44 ( 65) link_NAG-ASN : angle 3.26601 / 2.45 ( 195) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 301 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 195 ASN cc_start: 0.8834 (p0) cc_final: 0.8566 (p0) REVERT: C 201 ILE cc_start: 0.8873 (tt) cc_final: 0.8615 (tt) REVERT: C 384 TYR cc_start: 0.8659 (m-80) cc_final: 0.8451 (m-80) REVERT: C 486 TYR cc_start: 0.8635 (m-80) cc_final: 0.8225 (m-80) REVERT: D 574 LYS cc_start: 0.9336 (mttt) cc_final: 0.8849 (mttp) REVERT: D 641 ILE cc_start: 0.8301 (mp) cc_final: 0.7856 (tt) REVERT: D 643 TYR cc_start: 0.8345 (m-10) cc_final: 0.8134 (m-80) REVERT: E 69 TRP cc_start: 0.8599 (m100) cc_final: 0.8396 (m100) REVERT: E 103 GLN cc_start: 0.8825 (tt0) cc_final: 0.7975 (tp40) REVERT: E 107 ASP cc_start: 0.8848 (m-30) cc_final: 0.8295 (m-30) REVERT: E 217 TYR cc_start: 0.8043 (m-80) cc_final: 0.7159 (m-80) REVERT: E 338 TRP cc_start: 0.8883 (t-100) cc_final: 0.8393 (t-100) REVERT: E 390 LEU cc_start: 0.9570 (mt) cc_final: 0.9132 (mt) REVERT: E 426 MET cc_start: 0.8267 (mtp) cc_final: 0.7812 (mtp) REVERT: F 543 ASN cc_start: 0.8376 (m110) cc_final: 0.8109 (m110) REVERT: F 630 GLN cc_start: 0.8908 (mt0) cc_final: 0.8377 (mt0) REVERT: A 180 ASP cc_start: 0.8448 (m-30) cc_final: 0.7882 (m-30) REVERT: B 523 LEU cc_start: 0.8473 (mt) cc_final: 0.8150 (mt) REVERT: B 586 TYR cc_start: 0.8841 (t80) cc_final: 0.8511 (t80) REVERT: B 657 GLU cc_start: 0.9089 (tp30) cc_final: 0.8768 (tp30) REVERT: B 661 LEU cc_start: 0.5720 (mt) cc_final: 0.4801 (mt) outliers start: 5 outliers final: 2 residues processed: 303 average time/residue: 0.1225 time to fit residues: 54.5202 Evaluate side-chains 188 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 186 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 118 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 chunk 122 optimal weight: 4.9990 chunk 134 optimal weight: 0.5980 chunk 177 optimal weight: 20.0000 chunk 87 optimal weight: 6.9990 chunk 120 optimal weight: 0.7980 chunk 74 optimal weight: 20.0000 chunk 113 optimal weight: 7.9990 chunk 147 optimal weight: 6.9990 chunk 4 optimal weight: 0.0020 overall best weight: 2.2792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 66 HIS C 330 HIS ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 625 ASN ** D 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 540 GLN A 103 GLN ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 616 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.075337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.060767 restraints weight = 66598.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.062227 restraints weight = 41361.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.063225 restraints weight = 30341.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.063877 restraints weight = 24659.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.064267 restraints weight = 21510.343| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 16226 Z= 0.188 Angle : 0.741 16.932 22245 Z= 0.363 Chirality : 0.047 0.430 2793 Planarity : 0.004 0.042 2680 Dihedral : 4.914 27.470 2009 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.13 % Allowed : 2.96 % Favored : 96.91 % 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: 0.65 (0.20), residues: 1666 helix: 1.40 (0.25), residues: 419 sheet: 0.66 (0.24), residues: 428 loop : -0.13 (0.20), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 500 TYR 0.016 0.002 TYR E 217 PHE 0.022 0.002 PHE D 522 TRP 0.030 0.002 TRP D 631 HIS 0.005 0.001 HIS C 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.19 (16098) covalent geometry : angle 0.68708 / 0.35 (21894) SS BOND : bond 0.00329 / 0.20 ( 33) SS BOND : angle 0.92170 / 0.70 ( 66) hydrogen bonds : bond 0.05396 / 3.65 ( 591) hydrogen bonds : angle 4.89525 / 3.45 ( 2202) link_ALPHA1-3 : bond 0.00636 / 0.33 ( 3) link_ALPHA1-3 : angle 1.56803 / 1.01 ( 9) link_ALPHA1-6 : bond 0.00539 / 0.27 ( 3) link_ALPHA1-6 : angle 1.47167 / 1.03 ( 9) link_BETA1-4 : bond 0.00484 / 0.27 ( 24) link_BETA1-4 : angle 1.68741 / 1.17 ( 72) link_NAG-ASN : bond 0.00574 / 0.36 ( 65) link_NAG-ASN : angle 2.83142 / 2.13 ( 195) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 261 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 195 ASN cc_start: 0.8812 (p0) cc_final: 0.8489 (p0) REVERT: C 201 ILE cc_start: 0.8826 (tt) cc_final: 0.8590 (tt) REVERT: C 390 LEU cc_start: 0.9359 (mt) cc_final: 0.9113 (mt) REVERT: C 486 TYR cc_start: 0.8743 (m-80) cc_final: 0.8315 (m-80) REVERT: D 577 GLN cc_start: 0.8518 (tm-30) cc_final: 0.8074 (tm-30) REVERT: D 639 THR cc_start: 0.8452 (m) cc_final: 0.7427 (p) REVERT: D 645 LEU cc_start: 0.8543 (mp) cc_final: 0.8217 (mt) REVERT: D 656 ASN cc_start: 0.8984 (m-40) cc_final: 0.8689 (m110) REVERT: E 104 MET cc_start: 0.8447 (tpp) cc_final: 0.7552 (tpp) REVERT: E 109 ILE cc_start: 0.9114 (mm) cc_final: 0.8830 (mm) REVERT: E 217 TYR cc_start: 0.7825 (m-80) cc_final: 0.7220 (m-80) REVERT: E 338 TRP cc_start: 0.8994 (t-100) cc_final: 0.8128 (t-100) REVERT: E 390 LEU cc_start: 0.9571 (mt) cc_final: 0.8969 (mt) REVERT: E 426 MET cc_start: 0.8220 (mtp) cc_final: 0.7978 (mtp) REVERT: F 543 ASN cc_start: 0.8475 (m110) cc_final: 0.8200 (m110) REVERT: F 571 TRP cc_start: 0.7687 (t60) cc_final: 0.7445 (t60) REVERT: F 626 MET cc_start: 0.8033 (tpp) cc_final: 0.7466 (tpp) REVERT: A 131 CYS cc_start: 0.6209 (m) cc_final: 0.5776 (m) REVERT: A 180 ASP cc_start: 0.8457 (m-30) cc_final: 0.7894 (m-30) REVERT: B 542 ARG cc_start: 0.8779 (ptm160) cc_final: 0.8408 (ttp-110) REVERT: B 661 LEU cc_start: 0.5636 (mt) cc_final: 0.4632 (mt) outliers start: 2 outliers final: 0 residues processed: 261 average time/residue: 0.1187 time to fit residues: 45.9281 Evaluate side-chains 183 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 130 optimal weight: 9.9990 chunk 123 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 180 optimal weight: 50.0000 chunk 128 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 185 optimal weight: 10.0000 chunk 155 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 83 optimal weight: 0.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 246 GLN ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 625 ASN ** D 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.074713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.059997 restraints weight = 67066.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.061472 restraints weight = 40824.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.062484 restraints weight = 29666.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.063154 restraints weight = 23944.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.063489 restraints weight = 20847.563| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.4370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16226 Z= 0.183 Angle : 0.703 14.916 22245 Z= 0.344 Chirality : 0.046 0.343 2793 Planarity : 0.004 0.054 2680 Dihedral : 4.821 27.092 2009 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.07 % Allowed : 2.50 % Favored : 97.44 % 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: 0.51 (0.20), residues: 1666 helix: 1.48 (0.26), residues: 418 sheet: 0.53 (0.24), residues: 412 loop : -0.29 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 503 TYR 0.031 0.002 TYR D 643 PHE 0.018 0.002 PHE E 53 TRP 0.023 0.002 TRP E 395 HIS 0.009 0.001 HIS F 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.18 (16098) covalent geometry : angle 0.65557 / 0.33 (21894) SS BOND : bond 0.00413 / 0.26 ( 33) SS BOND : angle 0.83592 / 0.65 ( 66) hydrogen bonds : bond 0.04931 / 3.36 ( 591) hydrogen bonds : angle 4.73828 / 3.35 ( 2202) link_ALPHA1-3 : bond 0.00537 / 0.28 ( 3) link_ALPHA1-3 : angle 1.63285 / 1.03 ( 9) link_ALPHA1-6 : bond 0.00470 / 0.24 ( 3) link_ALPHA1-6 : angle 1.53720 / 1.09 ( 9) link_BETA1-4 : bond 0.00408 / 0.23 ( 24) link_BETA1-4 : angle 1.47827 / 1.02 ( 72) link_NAG-ASN : bond 0.00631 / 0.33 ( 65) link_NAG-ASN : angle 2.62099 / 1.98 ( 195) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 241 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 195 ASN cc_start: 0.8804 (p0) cc_final: 0.8463 (p0) REVERT: C 201 ILE cc_start: 0.8946 (tt) cc_final: 0.8687 (tt) REVERT: C 317 PHE cc_start: 0.8972 (t80) cc_final: 0.8739 (t80) REVERT: C 486 TYR cc_start: 0.8733 (m-80) cc_final: 0.8402 (m-80) REVERT: D 577 GLN cc_start: 0.8608 (tm-30) cc_final: 0.8265 (tm-30) REVERT: D 639 THR cc_start: 0.8549 (m) cc_final: 0.7875 (p) REVERT: D 643 TYR cc_start: 0.8467 (m-80) cc_final: 0.8256 (m-80) REVERT: D 645 LEU cc_start: 0.8680 (mp) cc_final: 0.8184 (mp) REVERT: E 95 MET cc_start: 0.8365 (ttp) cc_final: 0.8155 (ttp) REVERT: E 109 ILE cc_start: 0.9132 (mm) cc_final: 0.8852 (mm) REVERT: E 217 TYR cc_start: 0.7939 (m-80) cc_final: 0.7376 (m-80) REVERT: E 338 TRP cc_start: 0.8966 (t-100) cc_final: 0.8121 (t-100) REVERT: E 390 LEU cc_start: 0.9585 (mt) cc_final: 0.8997 (mt) REVERT: E 434 MET cc_start: 0.8768 (mtp) cc_final: 0.8427 (mtp) REVERT: F 543 ASN cc_start: 0.8428 (m110) cc_final: 0.8136 (m110) REVERT: F 571 TRP cc_start: 0.7627 (t60) cc_final: 0.7408 (t60) REVERT: F 626 MET cc_start: 0.8150 (tpp) cc_final: 0.7949 (tpp) REVERT: A 131 CYS cc_start: 0.6231 (m) cc_final: 0.5611 (m) REVERT: A 180 ASP cc_start: 0.8511 (m-30) cc_final: 0.7967 (m-30) REVERT: B 542 ARG cc_start: 0.8785 (ptm160) cc_final: 0.8249 (ttp-110) REVERT: B 601 LYS cc_start: 0.8511 (pttp) cc_final: 0.8301 (pttt) REVERT: B 643 TYR cc_start: 0.8745 (m-10) cc_final: 0.8519 (m-80) outliers start: 1 outliers final: 0 residues processed: 242 average time/residue: 0.1169 time to fit residues: 42.1435 Evaluate side-chains 182 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 7 optimal weight: 5.9990 chunk 135 optimal weight: 9.9990 chunk 103 optimal weight: 1.9990 chunk 64 optimal weight: 0.0970 chunk 96 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 chunk 136 optimal weight: 8.9990 chunk 120 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 112 optimal weight: 10.0000 chunk 167 optimal weight: 5.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 246 GLN D 540 GLN D 625 ASN E 103 GLN F 585 HIS ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.073350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.058709 restraints weight = 66732.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.060214 restraints weight = 40478.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.061221 restraints weight = 29257.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.061829 restraints weight = 23624.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.062286 restraints weight = 20715.525| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.4794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16226 Z= 0.198 Angle : 0.709 11.591 22245 Z= 0.346 Chirality : 0.047 0.421 2793 Planarity : 0.004 0.053 2680 Dihedral : 4.825 28.421 2009 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % 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: 0.32 (0.20), residues: 1666 helix: 1.48 (0.26), residues: 420 sheet: 0.21 (0.23), residues: 452 loop : -0.41 (0.21), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 419 TYR 0.022 0.002 TYR D 643 PHE 0.019 0.002 PHE E 53 TRP 0.034 0.002 TRP F 631 HIS 0.009 0.001 HIS F 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.20 (16098) covalent geometry : angle 0.66651 / 0.34 (21894) SS BOND : bond 0.00425 / 0.25 ( 33) SS BOND : angle 0.92787 / 0.67 ( 66) hydrogen bonds : bond 0.04705 / 3.19 ( 591) hydrogen bonds : angle 4.68470 / 3.32 ( 2202) link_ALPHA1-3 : bond 0.00499 / 0.26 ( 3) link_ALPHA1-3 : angle 1.69540 / 1.06 ( 9) link_ALPHA1-6 : bond 0.00429 / 0.22 ( 3) link_ALPHA1-6 : angle 1.57040 / 1.14 ( 9) link_BETA1-4 : bond 0.00369 / 0.21 ( 24) link_BETA1-4 : angle 1.41025 / 0.96 ( 72) link_NAG-ASN : bond 0.00599 / 0.33 ( 65) link_NAG-ASN : angle 2.48847 / 1.87 ( 195) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 95 MET cc_start: 0.8758 (ptp) cc_final: 0.8471 (ptp) REVERT: C 195 ASN cc_start: 0.8837 (p0) cc_final: 0.8451 (p0) REVERT: C 201 ILE cc_start: 0.9144 (tt) cc_final: 0.8909 (tt) REVERT: C 217 TYR cc_start: 0.8314 (m-80) cc_final: 0.7372 (m-80) REVERT: D 577 GLN cc_start: 0.8615 (tm-30) cc_final: 0.8314 (tm-30) REVERT: D 639 THR cc_start: 0.8731 (m) cc_final: 0.7550 (p) REVERT: D 643 TYR cc_start: 0.8521 (m-10) cc_final: 0.8244 (m-80) REVERT: D 645 LEU cc_start: 0.8607 (mp) cc_final: 0.8073 (mt) REVERT: E 95 MET cc_start: 0.8569 (ttp) cc_final: 0.7892 (tmm) REVERT: E 104 MET cc_start: 0.8707 (tpp) cc_final: 0.8224 (tpp) REVERT: E 161 MET cc_start: 0.8410 (tpp) cc_final: 0.8046 (tpp) REVERT: E 217 TYR cc_start: 0.8180 (m-80) cc_final: 0.7606 (m-80) REVERT: E 390 LEU cc_start: 0.9606 (mt) cc_final: 0.9217 (mt) REVERT: F 543 ASN cc_start: 0.8381 (m110) cc_final: 0.8086 (m110) REVERT: A 69 TRP cc_start: 0.8759 (m100) cc_final: 0.8356 (m-90) REVERT: A 100 MET cc_start: 0.8812 (mtp) cc_final: 0.8571 (mtm) REVERT: A 131 CYS cc_start: 0.6177 (m) cc_final: 0.5629 (m) REVERT: A 180 ASP cc_start: 0.8538 (m-30) cc_final: 0.7980 (m-30) REVERT: A 370 GLU cc_start: 0.7842 (tt0) cc_final: 0.7639 (tt0) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.1191 time to fit residues: 40.7109 Evaluate side-chains 167 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 171 optimal weight: 30.0000 chunk 39 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 177 optimal weight: 9.9990 chunk 136 optimal weight: 6.9990 chunk 167 optimal weight: 0.9980 chunk 150 optimal weight: 0.9990 chunk 168 optimal weight: 40.0000 chunk 93 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 246 GLN D 543 ASN D 625 ASN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.074109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.059592 restraints weight = 65106.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.061012 restraints weight = 40747.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.061975 restraints weight = 30129.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.062611 restraints weight = 24661.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.062974 restraints weight = 21656.326| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.4991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16226 Z= 0.143 Angle : 0.676 15.503 22245 Z= 0.325 Chirality : 0.050 1.173 2793 Planarity : 0.004 0.060 2680 Dihedral : 4.620 29.171 2009 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % 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: 0.30 (0.20), residues: 1666 helix: 1.53 (0.26), residues: 419 sheet: 0.27 (0.24), residues: 439 loop : -0.51 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 419 TYR 0.018 0.002 TYR B 638 PHE 0.017 0.002 PHE A 53 TRP 0.024 0.002 TRP F 631 HIS 0.005 0.001 HIS C 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (16098) covalent geometry : angle 0.63816 / 0.32 (21894) SS BOND : bond 0.00239 / 0.15 ( 33) SS BOND : angle 0.99394 / 0.71 ( 66) hydrogen bonds : bond 0.04355 / 2.98 ( 591) hydrogen bonds : angle 4.51993 / 3.20 ( 2202) link_ALPHA1-3 : bond 0.00402 / 0.20 ( 3) link_ALPHA1-3 : angle 1.50225 / 0.96 ( 9) link_ALPHA1-6 : bond 0.00463 / 0.23 ( 3) link_ALPHA1-6 : angle 1.46915 / 1.05 ( 9) link_BETA1-4 : bond 0.00570 / 0.38 ( 24) link_BETA1-4 : angle 1.30218 / 0.88 ( 72) link_NAG-ASN : bond 0.00479 / 0.36 ( 65) link_NAG-ASN : angle 2.29629 / 1.74 ( 195) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 195 ASN cc_start: 0.8850 (p0) cc_final: 0.8475 (p0) REVERT: C 217 TYR cc_start: 0.8201 (m-80) cc_final: 0.7306 (m-80) REVERT: D 577 GLN cc_start: 0.8566 (tm-30) cc_final: 0.8228 (tm-30) REVERT: D 639 THR cc_start: 0.8576 (m) cc_final: 0.7185 (p) REVERT: D 643 TYR cc_start: 0.8499 (m-10) cc_final: 0.8285 (m-80) REVERT: E 95 MET cc_start: 0.8401 (ttp) cc_final: 0.7866 (tmm) REVERT: E 104 MET cc_start: 0.8586 (tpp) cc_final: 0.7925 (tpp) REVERT: E 161 MET cc_start: 0.8355 (tpp) cc_final: 0.8097 (tpp) REVERT: E 217 TYR cc_start: 0.7917 (m-80) cc_final: 0.6983 (m-80) REVERT: E 338 TRP cc_start: 0.8915 (t-100) cc_final: 0.7947 (t-100) REVERT: E 390 LEU cc_start: 0.9570 (mt) cc_final: 0.8988 (mt) REVERT: E 434 MET cc_start: 0.8939 (mtp) cc_final: 0.8633 (mtm) REVERT: F 571 TRP cc_start: 0.8196 (t60) cc_final: 0.7676 (t60) REVERT: F 596 TRP cc_start: 0.8257 (m-10) cc_final: 0.7936 (m-10) REVERT: F 626 MET cc_start: 0.7558 (tpp) cc_final: 0.7185 (tpp) REVERT: F 646 LEU cc_start: 0.9269 (mt) cc_final: 0.8698 (mm) REVERT: A 69 TRP cc_start: 0.8575 (m100) cc_final: 0.8226 (m-90) REVERT: A 100 MET cc_start: 0.8769 (mtp) cc_final: 0.8486 (mtm) REVERT: A 131 CYS cc_start: 0.6164 (m) cc_final: 0.5591 (m) REVERT: A 180 ASP cc_start: 0.8471 (m-30) cc_final: 0.7941 (m-30) REVERT: A 217 TYR cc_start: 0.8172 (m-80) cc_final: 0.7825 (m-80) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.1195 time to fit residues: 40.8710 Evaluate side-chains 166 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 119 optimal weight: 0.9980 chunk 37 optimal weight: 0.0980 chunk 177 optimal weight: 30.0000 chunk 60 optimal weight: 20.0000 chunk 113 optimal weight: 0.3980 chunk 94 optimal weight: 1.9990 chunk 87 optimal weight: 0.4980 chunk 122 optimal weight: 4.9990 chunk 126 optimal weight: 8.9990 chunk 105 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 170 GLN C 246 GLN ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 ASN D 625 ASN A 374 HIS B 543 ASN ** B 607 ASN ** 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 = 0.3391 r_free = 0.3391 target = 0.075129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.060652 restraints weight = 64475.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.062102 restraints weight = 40382.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.063056 restraints weight = 29688.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.063703 restraints weight = 24352.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.064016 restraints weight = 21314.417| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.5146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16226 Z= 0.113 Angle : 0.637 13.988 22245 Z= 0.304 Chirality : 0.046 0.605 2793 Planarity : 0.004 0.046 2680 Dihedral : 4.473 32.322 2009 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.20), residues: 1666 helix: 1.65 (0.26), residues: 418 sheet: 0.27 (0.24), residues: 433 loop : -0.46 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 542 TYR 0.017 0.002 TYR B 586 PHE 0.020 0.001 PHE E 53 TRP 0.020 0.001 TRP C 45 HIS 0.006 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (16098) covalent geometry : angle 0.58623 / 0.29 (21894) SS BOND : bond 0.00196 / 0.12 ( 33) SS BOND : angle 0.86912 / 0.63 ( 66) hydrogen bonds : bond 0.04115 / 2.79 ( 591) hydrogen bonds : angle 4.41912 / 3.16 ( 2202) link_ALPHA1-3 : bond 0.00534 / 0.27 ( 3) link_ALPHA1-3 : angle 1.50042 / 0.97 ( 9) link_ALPHA1-6 : bond 0.00480 / 0.24 ( 3) link_ALPHA1-6 : angle 1.41003 / 0.99 ( 9) link_BETA1-4 : bond 0.00425 / 0.25 ( 24) link_BETA1-4 : angle 1.23499 / 0.82 ( 72) link_NAG-ASN : bond 0.00601 / 0.41 ( 65) link_NAG-ASN : angle 2.59298 / 1.91 ( 195) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 0.547 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: C 104 MET cc_start: 0.8596 (ttm) cc_final: 0.7865 (tpp) REVERT: C 161 MET cc_start: 0.8265 (tpp) cc_final: 0.8053 (tmm) REVERT: C 195 ASN cc_start: 0.8844 (p0) cc_final: 0.8450 (p0) REVERT: C 201 ILE cc_start: 0.9143 (tt) cc_final: 0.8939 (tt) REVERT: C 217 TYR cc_start: 0.8244 (m-80) cc_final: 0.6957 (m-80) REVERT: D 577 GLN cc_start: 0.8529 (tm-30) cc_final: 0.8201 (tm-30) REVERT: D 591 GLN cc_start: 0.9044 (tt0) cc_final: 0.8448 (tt0) REVERT: D 639 THR cc_start: 0.8485 (m) cc_final: 0.7316 (p) REVERT: D 645 LEU cc_start: 0.8446 (mt) cc_final: 0.8120 (mt) REVERT: D 652 GLN cc_start: 0.8818 (tp-100) cc_final: 0.8299 (tp-100) REVERT: E 49 GLU cc_start: 0.8598 (pm20) cc_final: 0.8349 (pt0) REVERT: E 95 MET cc_start: 0.8360 (ttp) cc_final: 0.7801 (tmm) REVERT: E 104 MET cc_start: 0.8589 (tpp) cc_final: 0.7927 (tpp) REVERT: E 161 MET cc_start: 0.8391 (tpp) cc_final: 0.8077 (tpp) REVERT: E 217 TYR cc_start: 0.7925 (m-80) cc_final: 0.6958 (m-80) REVERT: E 390 LEU cc_start: 0.9561 (mt) cc_final: 0.9206 (mt) REVERT: F 571 TRP cc_start: 0.8207 (t60) cc_final: 0.7699 (t60) REVERT: F 596 TRP cc_start: 0.8110 (m-10) cc_final: 0.7881 (m-10) REVERT: F 626 MET cc_start: 0.7736 (tpp) cc_final: 0.7422 (tpp) REVERT: F 646 LEU cc_start: 0.9169 (mt) cc_final: 0.8585 (mm) REVERT: A 69 TRP cc_start: 0.8548 (m100) cc_final: 0.8217 (m-90) REVERT: A 100 MET cc_start: 0.8732 (mtp) cc_final: 0.8445 (mtm) REVERT: A 131 CYS cc_start: 0.6028 (m) cc_final: 0.5505 (m) REVERT: A 180 ASP cc_start: 0.8478 (m-30) cc_final: 0.7919 (m-30) REVERT: A 217 TYR cc_start: 0.8065 (m-80) cc_final: 0.7843 (m-80) outliers start: 0 outliers final: 0 residues processed: 235 average time/residue: 0.1103 time to fit residues: 39.8409 Evaluate side-chains 172 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 57 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 109 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 187 optimal weight: 20.0000 chunk 169 optimal weight: 40.0000 chunk 66 optimal weight: 0.6980 chunk 61 optimal weight: 9.9990 chunk 128 optimal weight: 0.9990 chunk 39 optimal weight: 0.1980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 ASN D 625 ASN F 585 HIS ** B 607 ASN ** 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 = 0.3403 r_free = 0.3403 target = 0.075885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.061420 restraints weight = 64680.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.062882 restraints weight = 40335.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.063890 restraints weight = 29586.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.064459 restraints weight = 24054.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.064930 restraints weight = 21276.958| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.5325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 16226 Z= 0.121 Angle : 0.658 16.038 22245 Z= 0.318 Chirality : 0.046 0.687 2793 Planarity : 0.004 0.047 2680 Dihedral : 4.481 24.827 2009 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.21), residues: 1666 helix: 1.57 (0.26), residues: 418 sheet: 0.32 (0.25), residues: 427 loop : -0.50 (0.21), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 542 TYR 0.018 0.002 TYR D 643 PHE 0.026 0.002 PHE B 522 TRP 0.019 0.001 TRP C 45 HIS 0.011 0.001 HIS F 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (16098) covalent geometry : angle 0.61122 / 0.31 (21894) SS BOND : bond 0.00180 / 0.11 ( 33) SS BOND : angle 1.44646 / 0.95 ( 66) hydrogen bonds : bond 0.04076 / 2.78 ( 591) hydrogen bonds : angle 4.40862 / 3.15 ( 2202) link_ALPHA1-3 : bond 0.00511 / 0.26 ( 3) link_ALPHA1-3 : angle 1.45656 / 0.95 ( 9) link_ALPHA1-6 : bond 0.00479 / 0.24 ( 3) link_ALPHA1-6 : angle 1.40195 / 0.98 ( 9) link_BETA1-4 : bond 0.00432 / 0.26 ( 24) link_BETA1-4 : angle 1.19400 / 0.80 ( 72) link_NAG-ASN : bond 0.00473 / 0.35 ( 65) link_NAG-ASN : angle 2.45963 / 1.81 ( 195) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 195 ASN cc_start: 0.8871 (p0) cc_final: 0.8496 (p0) REVERT: C 317 PHE cc_start: 0.8975 (t80) cc_final: 0.8668 (t80) REVERT: D 577 GLN cc_start: 0.8557 (tm-30) cc_final: 0.8221 (tm-30) REVERT: D 591 GLN cc_start: 0.9038 (tt0) cc_final: 0.8336 (tt0) REVERT: D 645 LEU cc_start: 0.8590 (mt) cc_final: 0.8348 (mt) REVERT: D 652 GLN cc_start: 0.8806 (tp-100) cc_final: 0.8292 (tp-100) REVERT: E 104 MET cc_start: 0.8540 (tpp) cc_final: 0.7801 (tpp) REVERT: E 161 MET cc_start: 0.8340 (tpp) cc_final: 0.8105 (tpp) REVERT: E 217 TYR cc_start: 0.7844 (m-80) cc_final: 0.6854 (m-80) REVERT: E 390 LEU cc_start: 0.9536 (mt) cc_final: 0.9178 (mt) REVERT: E 452 LEU cc_start: 0.9364 (mm) cc_final: 0.9108 (mp) REVERT: F 571 TRP cc_start: 0.8220 (t60) cc_final: 0.7682 (t60) REVERT: F 626 MET cc_start: 0.7713 (tpp) cc_final: 0.7388 (tpp) REVERT: A 69 TRP cc_start: 0.8527 (m100) cc_final: 0.8208 (m-90) REVERT: A 100 MET cc_start: 0.8725 (mtp) cc_final: 0.8413 (mtm) REVERT: A 131 CYS cc_start: 0.5963 (m) cc_final: 0.5420 (m) REVERT: A 180 ASP cc_start: 0.8502 (m-30) cc_final: 0.7933 (m-30) REVERT: B 661 LEU cc_start: 0.5701 (mt) cc_final: 0.5112 (mt) outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 0.1016 time to fit residues: 37.3373 Evaluate side-chains 173 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 66 optimal weight: 1.9990 chunk 98 optimal weight: 7.9990 chunk 127 optimal weight: 5.9990 chunk 151 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 chunk 85 optimal weight: 0.3980 chunk 170 optimal weight: 30.0000 chunk 177 optimal weight: 30.0000 chunk 112 optimal weight: 9.9990 chunk 129 optimal weight: 0.7980 chunk 78 optimal weight: 5.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 ASN D 625 ASN ** D 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 585 HIS ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.074911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.060399 restraints weight = 65981.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.061841 restraints weight = 40657.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.062845 restraints weight = 29762.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.063495 restraints weight = 24169.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.063884 restraints weight = 21090.319| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.5466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16226 Z= 0.167 Angle : 0.677 11.155 22245 Z= 0.328 Chirality : 0.046 0.455 2793 Planarity : 0.004 0.048 2680 Dihedral : 4.564 27.477 2009 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % 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: 0.23 (0.21), residues: 1666 helix: 1.52 (0.27), residues: 419 sheet: 0.11 (0.24), residues: 457 loop : -0.51 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 273 TYR 0.017 0.002 TYR C 486 PHE 0.019 0.002 PHE E 53 TRP 0.029 0.002 TRP C 45 HIS 0.010 0.001 HIS F 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (16098) covalent geometry : angle 0.62680 / 0.32 (21894) SS BOND : bond 0.00334 / 0.20 ( 33) SS BOND : angle 1.11870 / 0.75 ( 66) hydrogen bonds : bond 0.04151 / 2.82 ( 591) hydrogen bonds : angle 4.52253 / 3.22 ( 2202) link_ALPHA1-3 : bond 0.00451 / 0.23 ( 3) link_ALPHA1-3 : angle 1.65400 / 1.04 ( 9) link_ALPHA1-6 : bond 0.00423 / 0.21 ( 3) link_ALPHA1-6 : angle 1.49033 / 1.07 ( 9) link_BETA1-4 : bond 0.00359 / 0.21 ( 24) link_BETA1-4 : angle 1.25862 / 0.84 ( 72) link_NAG-ASN : bond 0.00466 / 0.35 ( 65) link_NAG-ASN : angle 2.64473 / 1.89 ( 195) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 577 GLN cc_start: 0.8632 (tm-30) cc_final: 0.8306 (tm-30) REVERT: D 634 GLU cc_start: 0.8744 (tt0) cc_final: 0.7908 (mt-10) REVERT: D 643 TYR cc_start: 0.8478 (m-80) cc_final: 0.8171 (m-80) REVERT: D 652 GLN cc_start: 0.8895 (tp-100) cc_final: 0.8382 (tp-100) REVERT: E 104 MET cc_start: 0.8703 (tpp) cc_final: 0.8463 (mmm) REVERT: E 161 MET cc_start: 0.8470 (tpp) cc_final: 0.8090 (tpp) REVERT: E 217 TYR cc_start: 0.7986 (m-80) cc_final: 0.7525 (m-80) REVERT: E 390 LEU cc_start: 0.9595 (mt) cc_final: 0.9386 (mm) REVERT: E 452 LEU cc_start: 0.9368 (mm) cc_final: 0.8571 (tp) REVERT: F 571 TRP cc_start: 0.8286 (t60) cc_final: 0.7820 (t60) REVERT: F 626 MET cc_start: 0.7731 (tpp) cc_final: 0.7330 (tpp) REVERT: A 69 TRP cc_start: 0.8660 (m100) cc_final: 0.8261 (m-90) REVERT: A 131 CYS cc_start: 0.5985 (m) cc_final: 0.5526 (m) REVERT: A 161 MET cc_start: 0.8030 (ttt) cc_final: 0.7795 (ttt) REVERT: A 180 ASP cc_start: 0.8543 (m-30) cc_final: 0.7930 (m-30) REVERT: B 661 LEU cc_start: 0.5708 (mt) cc_final: 0.5082 (mt) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.1099 time to fit residues: 37.7192 Evaluate side-chains 164 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 30.0000 chunk 107 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 182 optimal weight: 30.0000 chunk 177 optimal weight: 30.0000 chunk 70 optimal weight: 2.9990 chunk 148 optimal weight: 0.6980 chunk 94 optimal weight: 0.8980 chunk 169 optimal weight: 20.0000 chunk 90 optimal weight: 10.0000 chunk 151 optimal weight: 10.0000 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 72 HIS ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 ASN D 625 ASN ** D 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN B 653 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.073447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.059287 restraints weight = 65974.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.060706 restraints weight = 40624.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.061673 restraints weight = 29587.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.062269 restraints weight = 23993.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.062713 restraints weight = 21053.736| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.5643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 16226 Z= 0.209 Angle : 0.715 11.406 22245 Z= 0.347 Chirality : 0.048 0.417 2793 Planarity : 0.004 0.052 2680 Dihedral : 4.695 31.066 2009 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % 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: 0.03 (0.20), residues: 1666 helix: 1.42 (0.26), residues: 419 sheet: -0.05 (0.24), residues: 437 loop : -0.63 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 503 TYR 0.017 0.002 TYR C 177 PHE 0.020 0.002 PHE E 53 TRP 0.038 0.002 TRP C 45 HIS 0.011 0.001 HIS F 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.21 (16098) covalent geometry : angle 0.66929 / 0.34 (21894) SS BOND : bond 0.00376 / 0.23 ( 33) SS BOND : angle 1.14212 / 0.78 ( 66) hydrogen bonds : bond 0.04369 / 2.95 ( 591) hydrogen bonds : angle 4.58577 / 3.26 ( 2202) link_ALPHA1-3 : bond 0.00387 / 0.20 ( 3) link_ALPHA1-3 : angle 1.78823 / 1.11 ( 9) link_ALPHA1-6 : bond 0.00379 / 0.19 ( 3) link_ALPHA1-6 : angle 1.53092 / 1.12 ( 9) link_BETA1-4 : bond 0.00355 / 0.21 ( 24) link_BETA1-4 : angle 1.23098 / 0.83 ( 72) link_NAG-ASN : bond 0.00520 / 0.37 ( 65) link_NAG-ASN : angle 2.60710 / 1.88 ( 195) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 MET cc_start: 0.8720 (tpp) cc_final: 0.7952 (tpp) REVERT: C 195 ASN cc_start: 0.8738 (p0) cc_final: 0.8445 (p0) REVERT: C 217 TYR cc_start: 0.7396 (m-10) cc_final: 0.5653 (m-10) REVERT: D 577 GLN cc_start: 0.8630 (tm-30) cc_final: 0.8315 (tm-30) REVERT: D 634 GLU cc_start: 0.8727 (tt0) cc_final: 0.8023 (mt-10) REVERT: D 643 TYR cc_start: 0.8598 (m-80) cc_final: 0.8131 (m-80) REVERT: E 42 VAL cc_start: 0.8248 (t) cc_final: 0.7819 (m) REVERT: E 95 MET cc_start: 0.8556 (ppp) cc_final: 0.8324 (ppp) REVERT: E 104 MET cc_start: 0.8632 (tpp) cc_final: 0.8075 (tpp) REVERT: E 161 MET cc_start: 0.8429 (tpp) cc_final: 0.8058 (tpp) REVERT: E 217 TYR cc_start: 0.7942 (m-80) cc_final: 0.6390 (m-80) REVERT: F 571 TRP cc_start: 0.8155 (t60) cc_final: 0.7737 (t60) REVERT: F 596 TRP cc_start: 0.8360 (m-10) cc_final: 0.8139 (m-10) REVERT: F 626 MET cc_start: 0.7716 (tpp) cc_final: 0.7335 (tpp) REVERT: A 69 TRP cc_start: 0.8634 (m100) cc_final: 0.8204 (m-90) REVERT: A 131 CYS cc_start: 0.6122 (m) cc_final: 0.5728 (m) REVERT: A 180 ASP cc_start: 0.8482 (m-30) cc_final: 0.7928 (m-30) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.1130 time to fit residues: 37.3036 Evaluate side-chains 154 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 121 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 119 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 ASN D 625 ASN D 652 GLN F 585 HIS ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN B 575 GLN B 653 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.074719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.060538 restraints weight = 64997.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.062029 restraints weight = 39795.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.063009 restraints weight = 28810.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.063671 restraints weight = 23329.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.064072 restraints weight = 20304.000| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.5720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16226 Z= 0.120 Angle : 0.667 15.709 22245 Z= 0.319 Chirality : 0.045 0.391 2793 Planarity : 0.004 0.049 2680 Dihedral : 4.513 27.095 2009 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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: 0.07 (0.20), residues: 1666 helix: 1.49 (0.26), residues: 419 sheet: 0.01 (0.24), residues: 416 loop : -0.64 (0.21), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 273 TYR 0.027 0.002 TYR C 319 PHE 0.017 0.002 PHE E 53 TRP 0.027 0.002 TRP C 45 HIS 0.008 0.001 HIS F 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (16098) covalent geometry : angle 0.60596 / 0.31 (21894) SS BOND : bond 0.00320 / 0.17 ( 33) SS BOND : angle 1.13844 / 0.78 ( 66) hydrogen bonds : bond 0.04107 / 2.76 ( 591) hydrogen bonds : angle 4.48516 / 3.22 ( 2202) link_ALPHA1-3 : bond 0.00463 / 0.24 ( 3) link_ALPHA1-3 : angle 1.55181 / 0.99 ( 9) link_ALPHA1-6 : bond 0.00456 / 0.23 ( 3) link_ALPHA1-6 : angle 1.40779 / 0.99 ( 9) link_BETA1-4 : bond 0.00418 / 0.24 ( 24) link_BETA1-4 : angle 1.11842 / 0.75 ( 72) link_NAG-ASN : bond 0.00527 / 0.36 ( 65) link_NAG-ASN : angle 2.89744 / 2.14 ( 195) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2240.92 seconds wall clock time: 39 minutes 46.84 seconds (2386.84 seconds total)