Starting phenix.real_space_refine on Tue Nov 18 13:03:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d7g_46604/11_2025/9d7g_46604.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d7g_46604/11_2025/9d7g_46604.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9d7g_46604/11_2025/9d7g_46604.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d7g_46604/11_2025/9d7g_46604.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9d7g_46604/11_2025/9d7g_46604.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d7g_46604/11_2025/9d7g_46604.map" } resolution = 3.58 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= 0.031 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 107 5.16 5 C 8934 2.51 5 N 2391 2.21 5 O 2888 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14320 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 3403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3403 Classifications: {'peptide': 432} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 411} Chain breaks: 4 Chain: "B" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 971 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "C" Number of atoms: 3373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3373 Classifications: {'peptide': 429} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 406} Chain breaks: 4 Chain: "D" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1008 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 1, 'TRANS': 125} Chain breaks: 1 Chain: "E" Number of atoms: 3447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3447 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 415} Chain breaks: 3 Chain: "F" Number of atoms: 963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 963 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.84, per 1000 atoms: 0.27 Number of scatterers: 14320 At special positions: 0 Unit cell: (126.36, 125.28, 126.36, 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 107 16.00 O 2888 8.00 N 2391 7.00 C 8934 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.05 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 378 " distance=2.05 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 445 " distance=2.02 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.04 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.04 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.05 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=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 149 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.02 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 331 " - pdb=" SG CYS E 418 " 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=2.04 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=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 234 " " NAG A 604 " - " ASN A 301 " " NAG A 605 " - " ASN A 355 " " NAG A 606 " - " ASN A 386 " " NAG A 607 " - " ASN A 392 " " NAG A 608 " - " ASN A 448 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 234 " " NAG C 603 " - " ASN C 276 " " NAG C 604 " - " ASN C 295 " " NAG C 605 " - " ASN C 301 " " NAG C 606 " - " ASN C 332 " " NAG C 607 " - " ASN C 355 " " NAG C 608 " - " ASN C 392 " " NAG C 609 " - " ASN C 448 " " NAG D 701 " - " ASN D 637 " " NAG E 601 " - " ASN E 133 " " NAG E 602 " - " ASN E 137 " " NAG E 603 " - " ASN E 234 " " NAG E 604 " - " ASN E 301 " " NAG E 605 " - " ASN E 355 " " NAG E 606 " - " ASN E 392 " " NAG E 607 " - " ASN E 448 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 637 " " NAG G 1 " - " ASN A 148 " " NAG H 1 " - " ASN A 152 " " NAG I 1 " - " ASN A 197 " " NAG J 1 " - " ASN A 262 " " NAG K 1 " - " ASN A 276 " " NAG L 1 " - " ASN A 295 " " NAG M 1 " - " ASN A 332 " " NAG N 1 " - " ASN A 363 " " NAG O 1 " - " ASN C 133 " " NAG P 1 " - " ASN C 148 " " NAG Q 1 " - " ASN C 152 " " NAG R 1 " - " ASN C 197 " " NAG S 1 " - " ASN C 262 " " NAG T 1 " - " ASN C 363 " " NAG U 1 " - " ASN C 386 " " NAG V 1 " - " ASN E 88 " " NAG W 1 " - " ASN E 148 " " NAG X 1 " - " ASN E 152 " " NAG Y 1 " - " ASN E 262 " " NAG Z 1 " - " ASN E 276 " " NAG a 1 " - " ASN E 295 " " NAG b 1 " - " ASN E 332 " " NAG c 1 " - " ASN E 363 " " NAG d 1 " - " ASN E 386 " Time building additional restraints: 1.34 Conformation dependent library (CDL) restraints added in 620.1 milliseconds 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3120 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 25 sheets defined 22.3% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 99 through 116 removed outlier: 3.600A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.852A pdb=" N LEU A 125 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.783A pdb=" N ARG A 350 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 475 through 480 removed outlier: 3.952A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 535 removed outlier: 3.804A pdb=" N MET B 535 " --> pdb=" O ALA B 532 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 532 through 535' Processing helix chain 'B' and resid 536 through 543 removed outlier: 4.209A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 572 removed outlier: 3.668A pdb=" N GLY B 572 " --> pdb=" O THR B 569 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 569 through 572' Processing helix chain 'B' and resid 573 through 596 removed outlier: 3.760A pdb=" N ALA B 578 " --> pdb=" O LYS B 574 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ARG B 579 " --> pdb=" O GLN B 575 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL B 580 " --> pdb=" O LEU B 576 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 622 removed outlier: 3.796A pdb=" N GLU B 621 " --> pdb=" O ASN B 618 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE B 622 " --> pdb=" O LEU B 619 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 618 through 622' Processing helix chain 'B' and resid 627 through 634 Processing helix chain 'B' and resid 641 through 663 removed outlier: 4.205A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LEU B 663 " --> pdb=" O ASP B 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 116 removed outlier: 4.471A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 350 removed outlier: 3.776A pdb=" N ARG C 350 " --> pdb=" O VAL C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.520A pdb=" N THR C 373 " --> pdb=" O LEU C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 480 removed outlier: 3.763A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 541 removed outlier: 4.157A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA D 541 " --> pdb=" O LEU D 537 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 536 through 541' Processing helix chain 'D' and resid 542 through 544 No H-bonds generated for 'chain 'D' and resid 542 through 544' Processing helix chain 'D' and resid 569 through 596 removed outlier: 4.068A pdb=" N ILE D 573 " --> pdb=" O THR D 569 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS D 574 " --> pdb=" O VAL D 570 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU D 592 " --> pdb=" O ARG D 588 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU D 593 " --> pdb=" O ASP D 589 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 633 removed outlier: 4.106A pdb=" N LYS D 633 " --> pdb=" O LEU D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 661 removed outlier: 3.566A pdb=" N ILE D 642 " --> pdb=" O TYR D 638 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY D 644 " --> pdb=" O GLN D 640 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU D 661 " --> pdb=" O GLU D 657 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 116 removed outlier: 4.413A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU E 116 " --> pdb=" O TRP E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 198 Processing helix chain 'E' and resid 335 through 354 removed outlier: 4.161A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 474 through 479 removed outlier: 3.788A pdb=" N ASP E 477 " --> pdb=" O ASP E 474 " (cutoff:3.500A) Processing helix chain 'F' and resid 536 through 542 removed outlier: 3.941A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA F 541 " --> pdb=" O LEU F 537 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 596 removed outlier: 3.572A pdb=" N TRP F 596 " --> pdb=" O LEU F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 623 removed outlier: 3.640A pdb=" N ILE F 622 " --> pdb=" O ASN F 618 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TRP F 623 " --> pdb=" O LEU F 619 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 618 through 623' Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 659 removed outlier: 4.149A pdb=" N ILE F 642 " --> pdb=" O TYR F 638 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS F 655 " --> pdb=" O ASN F 651 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASN F 656 " --> pdb=" O GLN F 652 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU F 657 " --> pdb=" O GLN F 653 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ASP F 659 " --> pdb=" O LYS F 655 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 4.205A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.260A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 3.516A pdb=" N VAL A 75 " --> pdb=" O CYS A 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.616A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 161 through 169 Processing sheet with id=AA6, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 312 removed outlier: 6.787A pdb=" N ASN A 301 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ILE A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 315 through 322 current: chain 'A' and resid 465 through 470 Processing sheet with id=AA7, first strand: chain 'A' and resid 423 through 424 Processing sheet with id=AA8, first strand: chain 'C' and resid 494 through 499 removed outlier: 3.532A pdb=" N THR C 499 " --> pdb=" O TRP C 35 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.120A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AB2, first strand: chain 'C' and resid 92 through 94 removed outlier: 3.582A pdb=" N GLY C 237 " --> pdb=" O PHE C 93 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 130 through 133 Processing sheet with id=AB4, first strand: chain 'C' and resid 173 through 175 Processing sheet with id=AB5, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.659A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 260 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 260 through 261 current: chain 'C' and resid 329 through 334 removed outlier: 3.511A pdb=" N VAL C 333 " --> pdb=" O ILE C 414 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 304 through 308 Processing sheet with id=AB8, first strand: chain 'C' and resid 393 through 395 removed outlier: 3.571A pdb=" N ILE C 359 " --> pdb=" O TRP C 395 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 374 through 378 removed outlier: 3.608A pdb=" N GLU C 381 " --> pdb=" O CYS C 378 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS C 421 " --> pdb=" O PHE C 382 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 495 through 499 removed outlier: 3.517A pdb=" N GLY E 495 " --> pdb=" O TYR E 39 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.715A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 75 through 76 removed outlier: 4.379A pdb=" N VAL E 75 " --> pdb=" O CYS E 54 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER E 56 " --> pdb=" O VAL E 75 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE E 53 " --> pdb=" O CYS E 218 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 161 through 169 removed outlier: 3.604A pdb=" N LYS E 189 " --> pdb=" O CYS E 131 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 202 through 203 removed outlier: 6.978A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'E' and resid 271 through 273 removed outlier: 7.674A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR E 297 " --> pdb=" O HIS E 330 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N HIS E 330 " --> pdb=" O THR E 297 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 329 through 334 current: chain 'E' and resid 383 through 384 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 383 through 384 current: chain 'E' and resid 465 through 470 Processing sheet with id=AC7, first strand: chain 'E' and resid 304 through 308 350 hydrogen bonds defined for protein. 987 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: 2.28 Time building geometry restraints manager: 1.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 2466 1.33 - 1.46: 5479 1.46 - 1.60: 6492 1.60 - 1.74: 1 1.74 - 1.87: 142 Bond restraints: 14580 Sorted by residual: bond pdb=" CA ASN E 356 " pdb=" CB ASN E 356 " ideal model delta sigma weight residual 1.527 1.707 -0.180 2.48e-02 1.63e+03 5.27e+01 bond pdb=" C THR E 123 " pdb=" N PRO E 124 " ideal model delta sigma weight residual 1.335 1.394 -0.059 9.40e-03 1.13e+04 3.94e+01 bond pdb=" C ASP C 78 " pdb=" N PRO C 79 " ideal model delta sigma weight residual 1.334 1.414 -0.080 2.34e-02 1.83e+03 1.17e+01 bond pdb=" CA GLU E 268 " pdb=" CB GLU E 268 " ideal model delta sigma weight residual 1.530 1.573 -0.043 1.69e-02 3.50e+03 6.41e+00 bond pdb=" CB GLU E 268 " pdb=" CG GLU E 268 " ideal model delta sigma weight residual 1.520 1.596 -0.076 3.00e-02 1.11e+03 6.38e+00 ... (remaining 14575 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.81: 19207 2.81 - 5.62: 485 5.62 - 8.43: 64 8.43 - 11.24: 20 11.24 - 14.05: 8 Bond angle restraints: 19784 Sorted by residual: angle pdb=" C LYS E 351 " pdb=" N HIS E 352 " pdb=" CA HIS E 352 " ideal model delta sigma weight residual 121.54 135.59 -14.05 1.91e+00 2.74e-01 5.41e+01 angle pdb=" C GLY E 431 " pdb=" N GLN E 432 " pdb=" CA GLN E 432 " ideal model delta sigma weight residual 121.26 131.11 -9.85 1.49e+00 4.50e-01 4.37e+01 angle pdb=" CA GLN B 658 " pdb=" CB GLN B 658 " pdb=" CG GLN B 658 " ideal model delta sigma weight residual 114.10 126.96 -12.86 2.00e+00 2.50e-01 4.13e+01 angle pdb=" N GLN B 658 " pdb=" CA GLN B 658 " pdb=" CB GLN B 658 " ideal model delta sigma weight residual 110.33 119.62 -9.29 1.50e+00 4.44e-01 3.83e+01 angle pdb=" CA GLU E 268 " pdb=" CB GLU E 268 " pdb=" CG GLU E 268 " ideal model delta sigma weight residual 114.10 126.42 -12.32 2.00e+00 2.50e-01 3.79e+01 ... (remaining 19779 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 8897 17.98 - 35.96: 761 35.96 - 53.93: 167 53.93 - 71.91: 44 71.91 - 89.89: 16 Dihedral angle restraints: 9885 sinusoidal: 5074 harmonic: 4811 Sorted by residual: dihedral pdb=" CB CYS A 228 " pdb=" SG CYS A 228 " pdb=" SG CYS A 239 " pdb=" CB CYS A 239 " ideal model delta sinusoidal sigma weight residual 93.00 -177.11 -89.89 1 1.00e+01 1.00e-02 9.58e+01 dihedral pdb=" CB CYS A 296 " pdb=" SG CYS A 296 " pdb=" SG CYS A 378 " pdb=" CB CYS A 378 " ideal model delta sinusoidal sigma weight residual -86.00 -173.32 87.32 1 1.00e+01 1.00e-02 9.15e+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 -171.42 85.42 1 1.00e+01 1.00e-02 8.83e+01 ... (remaining 9882 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 2291 0.110 - 0.220: 171 0.220 - 0.330: 13 0.330 - 0.440: 5 0.440 - 0.550: 3 Chirality restraints: 2483 Sorted by residual: chirality pdb=" C1 NAG E 606 " pdb=" ND2 ASN E 392 " pdb=" C2 NAG E 606 " pdb=" O5 NAG E 606 " both_signs ideal model delta sigma weight residual False -2.40 -1.85 -0.55 2.00e-01 2.50e+01 7.56e+00 chirality pdb=" CB ILE E 430 " pdb=" CA ILE E 430 " pdb=" CG1 ILE E 430 " pdb=" CG2 ILE E 430 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.49 2.00e-01 2.50e+01 5.96e+00 chirality pdb=" C1 NAG L 1 " pdb=" ND2 ASN A 295 " pdb=" C2 NAG L 1 " pdb=" O5 NAG L 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 4.97e+00 ... (remaining 2480 not shown) Planarity restraints: 2460 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 78 " -0.043 2.00e-02 2.50e+03 8.07e-02 6.52e+01 pdb=" C ASP C 78 " 0.140 2.00e-02 2.50e+03 pdb=" O ASP C 78 " -0.053 2.00e-02 2.50e+03 pdb=" N PRO C 79 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP E 78 " 0.040 2.00e-02 2.50e+03 7.83e-02 6.13e+01 pdb=" C ASP E 78 " -0.135 2.00e-02 2.50e+03 pdb=" O ASP E 78 " 0.052 2.00e-02 2.50e+03 pdb=" N PRO E 79 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER D 546 " -0.031 2.00e-02 2.50e+03 6.22e-02 3.87e+01 pdb=" C SER D 546 " 0.108 2.00e-02 2.50e+03 pdb=" O SER D 546 " -0.041 2.00e-02 2.50e+03 pdb=" N GLY D 547 " -0.035 2.00e-02 2.50e+03 ... (remaining 2457 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3716 2.81 - 3.34: 11863 3.34 - 3.86: 22082 3.86 - 4.38: 23759 4.38 - 4.90: 42429 Nonbonded interactions: 103849 Sorted by model distance: nonbonded pdb=" OG1 THR C 37 " pdb=" O CYS D 604 " model vdw 2.293 3.040 nonbonded pdb=" O LEU A 369 " pdb=" OG1 THR A 373 " model vdw 2.297 3.040 nonbonded pdb=" O LEU E 369 " pdb=" OG1 THR E 373 " model vdw 2.313 3.040 nonbonded pdb=" O VAL E 36 " pdb=" OG1 THR F 606 " model vdw 2.314 3.040 nonbonded pdb=" O ILE D 635 " pdb=" OG1 THR D 639 " model vdw 2.335 3.040 ... (remaining 103844 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 34 through 135 or resid 144 through 396 or resid 412 throu \ gh 607)) selection = (chain 'C' and (resid 34 through 77 or resid 82 through 177 or resid 189 through \ 396 or resid 412 through 607)) selection = (chain 'E' and (resid 34 through 77 or resid 82 through 135 or resid 144 through \ 177 or resid 189 through 396 or resid 412 through 607)) } ncs_group { reference = (chain 'B' and resid 521 through 701) selection = (chain 'D' and (resid 521 through 546 or resid 569 through 701)) selection = (chain 'F' and resid 521 through 701) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'a' selection = chain 'b' } ncs_group { reference = chain 'J' selection = chain 'P' selection = chain 'S' selection = chain 'Y' selection = chain 'Z' selection = chain 'c' selection = chain 'd' } 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: 2.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 14.490 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 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 : 0.005 0.180 14697 Z= 0.257 Angle : 1.182 17.872 20102 Z= 0.586 Chirality : 0.063 0.550 2483 Planarity : 0.008 0.088 2407 Dihedral : 13.414 89.308 6666 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.77 % Favored : 94.11 % Rotamer: Outliers : 0.07 % Allowed : 0.54 % Favored : 99.39 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.25 % 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: -2.68 (0.19), residues: 1629 helix: -1.36 (0.24), residues: 352 sheet: -1.36 (0.24), residues: 438 loop : -2.18 (0.19), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG F 585 TYR 0.026 0.002 TYR D 638 PHE 0.017 0.002 PHE C 233 TRP 0.023 0.002 TRP E 69 HIS 0.010 0.001 HIS E 352 Details of bonding type rmsd covalent geometry : bond 0.00523 (14580) covalent geometry : angle 1.09094 (19784) SS BOND : bond 0.00800 ( 33) SS BOND : angle 3.29801 ( 66) hydrogen bonds : bond 0.19960 ( 350) hydrogen bonds : angle 7.60177 ( 987) link_BETA1-4 : bond 0.00886 ( 31) link_BETA1-4 : angle 2.53006 ( 93) link_NAG-ASN : bond 0.00953 ( 53) link_NAG-ASN : angle 4.52077 ( 159) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 228 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ASP cc_start: 0.8734 (t70) cc_final: 0.8217 (t0) REVERT: A 217 TYR cc_start: 0.7923 (m-80) cc_final: 0.7360 (m-80) REVERT: B 530 MET cc_start: 0.8378 (mmm) cc_final: 0.7835 (mmm) REVERT: B 584 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7860 (tm-30) REVERT: B 588 ARG cc_start: 0.8067 (ttm-80) cc_final: 0.7573 (ttm110) REVERT: C 213 ILE cc_start: 0.8508 (tp) cc_final: 0.8265 (pt) REVERT: C 426 MET cc_start: 0.7947 (mmm) cc_final: 0.7709 (mtp) REVERT: D 590 GLN cc_start: 0.7968 (tp40) cc_final: 0.6806 (tm-30) REVERT: D 659 ASP cc_start: 0.8229 (t70) cc_final: 0.7863 (t0) REVERT: E 110 SER cc_start: 0.8900 (t) cc_final: 0.8682 (t) REVERT: F 647 GLU cc_start: 0.8169 (tp30) cc_final: 0.7839 (tt0) REVERT: F 656 ASN cc_start: 0.7683 (t0) cc_final: 0.7448 (m-40) REVERT: F 657 GLU cc_start: 0.8687 (tm-30) cc_final: 0.8329 (tm-30) outliers start: 1 outliers final: 1 residues processed: 229 average time/residue: 0.1108 time to fit residues: 39.2537 Evaluate side-chains 179 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 178 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 356 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.0020 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN A 374 HIS C 99 ASN C 302 ASN D 540 GLN E 103 GLN E 136 ASN ** E 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 630 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.135926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.108326 restraints weight = 23107.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.112028 restraints weight = 13677.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.114500 restraints weight = 9915.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.116067 restraints weight = 8060.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.117180 restraints weight = 7064.686| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14697 Z= 0.203 Angle : 0.794 13.707 20102 Z= 0.374 Chirality : 0.050 0.469 2483 Planarity : 0.005 0.054 2407 Dihedral : 8.740 73.074 3523 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.32 % Favored : 93.55 % Rotamer: Outliers : 1.69 % Allowed : 8.50 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.20), residues: 1629 helix: 0.02 (0.28), residues: 356 sheet: -1.21 (0.24), residues: 447 loop : -2.17 (0.19), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 588 TYR 0.017 0.002 TYR C 217 PHE 0.016 0.002 PHE A 376 TRP 0.015 0.002 TRP C 112 HIS 0.005 0.002 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00482 (14580) covalent geometry : angle 0.71396 (19784) SS BOND : bond 0.00668 ( 33) SS BOND : angle 2.09099 ( 66) hydrogen bonds : bond 0.04492 ( 350) hydrogen bonds : angle 5.38630 ( 987) link_BETA1-4 : bond 0.00605 ( 31) link_BETA1-4 : angle 2.05831 ( 93) link_NAG-ASN : bond 0.00652 ( 53) link_NAG-ASN : angle 3.46274 ( 159) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 194 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8777 (ttt) cc_final: 0.8233 (ttt) REVERT: A 110 SER cc_start: 0.8551 (t) cc_final: 0.8330 (t) REVERT: A 121 LYS cc_start: 0.8554 (tptm) cc_final: 0.8173 (tppt) REVERT: A 142 MET cc_start: 0.8693 (tpp) cc_final: 0.8241 (tpp) REVERT: A 165 TYR cc_start: 0.8887 (p90) cc_final: 0.8553 (p90) REVERT: A 217 TYR cc_start: 0.8566 (m-80) cc_final: 0.7659 (m-80) REVERT: A 229 LYS cc_start: 0.7815 (mmmt) cc_final: 0.7396 (mttm) REVERT: A 475 MET cc_start: 0.8616 (mmm) cc_final: 0.8314 (tpp) REVERT: B 588 ARG cc_start: 0.8174 (ttm-80) cc_final: 0.7735 (ttm110) REVERT: B 658 GLN cc_start: 0.8435 (pm20) cc_final: 0.7969 (pm20) REVERT: C 67 ASN cc_start: 0.8121 (p0) cc_final: 0.7769 (p0) REVERT: C 213 ILE cc_start: 0.8672 (tp) cc_final: 0.8379 (pt) REVERT: D 659 ASP cc_start: 0.8316 (t70) cc_final: 0.8110 (t0) REVERT: E 475 MET cc_start: 0.8478 (tpp) cc_final: 0.8028 (tpp) REVERT: E 484 TYR cc_start: 0.8856 (p90) cc_final: 0.8656 (p90) REVERT: F 542 ARG cc_start: 0.8318 (mtp85) cc_final: 0.8031 (mtp85) REVERT: F 656 ASN cc_start: 0.7805 (t0) cc_final: 0.7513 (m-40) REVERT: F 657 GLU cc_start: 0.8485 (tm-30) cc_final: 0.8260 (tm-30) outliers start: 25 outliers final: 19 residues processed: 205 average time/residue: 0.1127 time to fit residues: 34.9700 Evaluate side-chains 195 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 176 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain E residue 136 ASN Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 595 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 59 optimal weight: 0.9990 chunk 15 optimal weight: 0.0870 chunk 119 optimal weight: 2.9990 chunk 139 optimal weight: 0.1980 chunk 23 optimal weight: 0.9980 chunk 151 optimal weight: 2.9990 chunk 145 optimal weight: 0.8980 chunk 93 optimal weight: 7.9990 chunk 11 optimal weight: 0.9990 chunk 133 optimal weight: 4.9990 chunk 147 optimal weight: 1.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 136 ASN ** E 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 356 ASN F 630 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.138207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.110351 restraints weight = 23021.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.114207 restraints weight = 13396.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.116750 restraints weight = 9594.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.118436 restraints weight = 7734.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.119503 restraints weight = 6705.860| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14697 Z= 0.128 Angle : 0.707 13.451 20102 Z= 0.328 Chirality : 0.048 0.438 2483 Planarity : 0.004 0.043 2407 Dihedral : 8.286 69.162 3521 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.22 % Favored : 94.66 % Rotamer: Outliers : 1.35 % Allowed : 11.81 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.20), residues: 1629 helix: 0.56 (0.29), residues: 356 sheet: -1.05 (0.24), residues: 460 loop : -2.08 (0.19), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 542 TYR 0.016 0.001 TYR C 486 PHE 0.010 0.001 PHE E 376 TRP 0.010 0.001 TRP C 112 HIS 0.003 0.001 HIS E 352 Details of bonding type rmsd covalent geometry : bond 0.00293 (14580) covalent geometry : angle 0.62463 (19784) SS BOND : bond 0.00500 ( 33) SS BOND : angle 1.87635 ( 66) hydrogen bonds : bond 0.03847 ( 350) hydrogen bonds : angle 4.97507 ( 987) link_BETA1-4 : bond 0.00591 ( 31) link_BETA1-4 : angle 1.98206 ( 93) link_NAG-ASN : bond 0.00652 ( 53) link_NAG-ASN : angle 3.31294 ( 159) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 191 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8072 (mttt) cc_final: 0.7834 (mttp) REVERT: A 92 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7749 (mm-30) REVERT: A 104 MET cc_start: 0.8817 (ttt) cc_final: 0.8333 (ttt) REVERT: A 121 LYS cc_start: 0.8362 (tptm) cc_final: 0.7985 (tppt) REVERT: A 142 MET cc_start: 0.8707 (tpp) cc_final: 0.8280 (tpp) REVERT: A 165 TYR cc_start: 0.8916 (p90) cc_final: 0.8591 (p90) REVERT: A 217 TYR cc_start: 0.8567 (m-80) cc_final: 0.7597 (m-80) REVERT: B 588 ARG cc_start: 0.8140 (ttm-80) cc_final: 0.7733 (ttm110) REVERT: C 67 ASN cc_start: 0.8007 (p0) cc_final: 0.7722 (p0) REVERT: C 213 ILE cc_start: 0.8651 (tp) cc_final: 0.8340 (pt) REVERT: C 278 THR cc_start: 0.7794 (p) cc_final: 0.7554 (p) REVERT: E 265 LEU cc_start: 0.8966 (mm) cc_final: 0.8625 (mm) REVERT: E 289 ASN cc_start: 0.8258 (m110) cc_final: 0.7942 (m-40) REVERT: E 475 MET cc_start: 0.8350 (tpp) cc_final: 0.7910 (tpp) REVERT: F 647 GLU cc_start: 0.8536 (tp30) cc_final: 0.8144 (tt0) REVERT: F 656 ASN cc_start: 0.7727 (t0) cc_final: 0.7506 (m-40) REVERT: F 657 GLU cc_start: 0.8501 (tm-30) cc_final: 0.8239 (tm-30) outliers start: 20 outliers final: 14 residues processed: 201 average time/residue: 0.1195 time to fit residues: 36.2381 Evaluate side-chains 185 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 171 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 626 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 54 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 126 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 129 optimal weight: 0.5980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 HIS E 356 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.132777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.105044 restraints weight = 23104.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.108672 restraints weight = 13683.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.111098 restraints weight = 9954.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.112697 restraints weight = 8106.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.113721 restraints weight = 7074.892| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14697 Z= 0.187 Angle : 0.749 13.351 20102 Z= 0.351 Chirality : 0.049 0.502 2483 Planarity : 0.004 0.041 2407 Dihedral : 8.266 71.778 3521 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.75 % Favored : 93.06 % Rotamer: Outliers : 2.36 % Allowed : 13.97 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.20), residues: 1629 helix: 0.77 (0.30), residues: 357 sheet: -1.26 (0.23), residues: 475 loop : -1.98 (0.20), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 542 TYR 0.018 0.002 TYR C 486 PHE 0.013 0.002 PHE A 376 TRP 0.015 0.001 TRP C 112 HIS 0.005 0.001 HIS E 216 Details of bonding type rmsd covalent geometry : bond 0.00448 (14580) covalent geometry : angle 0.67205 (19784) SS BOND : bond 0.00522 ( 33) SS BOND : angle 2.09131 ( 66) hydrogen bonds : bond 0.04167 ( 350) hydrogen bonds : angle 4.80294 ( 987) link_BETA1-4 : bond 0.00593 ( 31) link_BETA1-4 : angle 1.96164 ( 93) link_NAG-ASN : bond 0.00636 ( 53) link_NAG-ASN : angle 3.27205 ( 159) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 187 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8059 (mttt) cc_final: 0.7829 (mttp) REVERT: A 92 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7766 (mm-30) REVERT: A 104 MET cc_start: 0.8862 (ttt) cc_final: 0.8593 (ttt) REVERT: A 110 SER cc_start: 0.8652 (t) cc_final: 0.8447 (t) REVERT: A 121 LYS cc_start: 0.8471 (tptm) cc_final: 0.8108 (tppt) REVERT: A 142 MET cc_start: 0.8696 (tpp) cc_final: 0.8209 (tpp) REVERT: A 165 TYR cc_start: 0.8922 (p90) cc_final: 0.8598 (p90) REVERT: A 217 TYR cc_start: 0.8860 (m-80) cc_final: 0.8355 (m-80) REVERT: A 229 LYS cc_start: 0.8371 (mmmm) cc_final: 0.7888 (mtmt) REVERT: B 584 GLU cc_start: 0.8153 (tm-30) cc_final: 0.7925 (tm-30) REVERT: B 588 ARG cc_start: 0.8146 (ttm-80) cc_final: 0.7759 (ttm110) REVERT: B 621 GLU cc_start: 0.6601 (pm20) cc_final: 0.6085 (pp20) REVERT: B 658 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.8157 (pm20) REVERT: C 46 LYS cc_start: 0.8472 (mmmt) cc_final: 0.7917 (mttm) REVERT: C 67 ASN cc_start: 0.8016 (p0) cc_final: 0.7815 (p0) REVERT: C 207 LYS cc_start: 0.7661 (mmmt) cc_final: 0.7374 (tmtt) REVERT: C 213 ILE cc_start: 0.8842 (tp) cc_final: 0.8439 (pt) REVERT: D 627 THR cc_start: 0.9108 (m) cc_final: 0.8865 (p) REVERT: E 93 PHE cc_start: 0.6997 (m-10) cc_final: 0.6735 (m-10) REVERT: E 265 LEU cc_start: 0.8848 (mm) cc_final: 0.8485 (mm) REVERT: E 475 MET cc_start: 0.8394 (tpp) cc_final: 0.8004 (tpp) REVERT: F 542 ARG cc_start: 0.8237 (mtp85) cc_final: 0.7918 (mtp85) REVERT: F 647 GLU cc_start: 0.8528 (tp30) cc_final: 0.8277 (tt0) REVERT: F 656 ASN cc_start: 0.7942 (t0) cc_final: 0.7571 (m-40) REVERT: F 657 GLU cc_start: 0.8657 (tm-30) cc_final: 0.8217 (tm-30) outliers start: 35 outliers final: 23 residues processed: 205 average time/residue: 0.1175 time to fit residues: 36.3842 Evaluate side-chains 196 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 172 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 530 MET Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain E residue 385 CYS Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 626 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 113 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 2 optimal weight: 0.3980 chunk 102 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 141 optimal weight: 0.8980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 356 ASN E 374 HIS F 543 ASN F 630 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.132339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.104899 restraints weight = 23251.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.108530 restraints weight = 13668.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.110987 restraints weight = 9890.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.112591 restraints weight = 8020.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.113637 restraints weight = 6990.306| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14697 Z= 0.170 Angle : 0.717 13.325 20102 Z= 0.334 Chirality : 0.050 0.738 2483 Planarity : 0.004 0.044 2407 Dihedral : 8.206 70.935 3521 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.14 % Favored : 93.68 % Rotamer: Outliers : 2.50 % Allowed : 14.37 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.21), residues: 1629 helix: 0.90 (0.30), residues: 358 sheet: -1.22 (0.23), residues: 485 loop : -1.96 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 588 TYR 0.018 0.001 TYR C 486 PHE 0.012 0.001 PHE E 376 TRP 0.012 0.001 TRP C 112 HIS 0.004 0.001 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00406 (14580) covalent geometry : angle 0.64158 (19784) SS BOND : bond 0.00450 ( 33) SS BOND : angle 1.98604 ( 66) hydrogen bonds : bond 0.03810 ( 350) hydrogen bonds : angle 4.63433 ( 987) link_BETA1-4 : bond 0.00593 ( 31) link_BETA1-4 : angle 1.95265 ( 93) link_NAG-ASN : bond 0.00606 ( 53) link_NAG-ASN : angle 3.14998 ( 159) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 183 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8110 (mttt) cc_final: 0.7811 (mttp) REVERT: A 92 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7725 (mm-30) REVERT: A 104 MET cc_start: 0.8918 (ttt) cc_final: 0.8647 (ttt) REVERT: A 110 SER cc_start: 0.8606 (t) cc_final: 0.8386 (t) REVERT: A 121 LYS cc_start: 0.8408 (tptm) cc_final: 0.8014 (tppt) REVERT: A 142 MET cc_start: 0.8690 (tpp) cc_final: 0.8202 (tpp) REVERT: A 165 TYR cc_start: 0.8963 (p90) cc_final: 0.8598 (p90) REVERT: A 217 TYR cc_start: 0.8956 (m-80) cc_final: 0.8439 (m-80) REVERT: A 229 LYS cc_start: 0.8343 (mmmm) cc_final: 0.7845 (mtmt) REVERT: B 584 GLU cc_start: 0.8159 (tm-30) cc_final: 0.7938 (tm-30) REVERT: B 587 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8003 (mm) REVERT: B 588 ARG cc_start: 0.8102 (ttm-80) cc_final: 0.7679 (ttm110) REVERT: B 658 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.7875 (pm20) REVERT: C 46 LYS cc_start: 0.8458 (mmmt) cc_final: 0.8099 (mttm) REVERT: C 207 LYS cc_start: 0.7693 (mmmt) cc_final: 0.7377 (tmtt) REVERT: C 213 ILE cc_start: 0.8814 (tp) cc_final: 0.8388 (pt) REVERT: D 627 THR cc_start: 0.9076 (m) cc_final: 0.8847 (p) REVERT: E 265 LEU cc_start: 0.8843 (mm) cc_final: 0.8498 (mm) REVERT: E 434 MET cc_start: 0.8710 (ttp) cc_final: 0.8462 (ttp) REVERT: E 475 MET cc_start: 0.8341 (tpp) cc_final: 0.7918 (tpp) REVERT: F 542 ARG cc_start: 0.8316 (mtp85) cc_final: 0.8100 (mtp85) REVERT: F 587 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8050 (mt) REVERT: F 656 ASN cc_start: 0.7991 (t0) cc_final: 0.7652 (m-40) REVERT: F 657 GLU cc_start: 0.8710 (tm-30) cc_final: 0.8236 (tm-30) outliers start: 37 outliers final: 23 residues processed: 206 average time/residue: 0.1173 time to fit residues: 36.5631 Evaluate side-chains 198 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 172 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 530 MET Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain E residue 356 ASN Chi-restraints excluded: chain E residue 385 CYS Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 626 MET Chi-restraints excluded: chain F residue 641 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 112 optimal weight: 7.9990 chunk 116 optimal weight: 0.0170 chunk 98 optimal weight: 5.9990 chunk 138 optimal weight: 0.9980 chunk 162 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 104 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 155 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 overall best weight: 0.9620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 356 ASN E 377 ASN F 630 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.132092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.104804 restraints weight = 23276.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.108486 restraints weight = 13651.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.110963 restraints weight = 9855.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.112553 restraints weight = 7982.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.113656 restraints weight = 6955.486| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14697 Z= 0.149 Angle : 0.697 13.281 20102 Z= 0.325 Chirality : 0.048 0.450 2483 Planarity : 0.004 0.042 2407 Dihedral : 8.066 70.198 3521 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.51 % Favored : 93.31 % Rotamer: Outliers : 2.56 % Allowed : 16.33 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.21), residues: 1629 helix: 1.05 (0.30), residues: 355 sheet: -1.15 (0.23), residues: 484 loop : -1.89 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 588 TYR 0.021 0.001 TYR C 486 PHE 0.011 0.001 PHE E 376 TRP 0.012 0.001 TRP C 112 HIS 0.003 0.001 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00352 (14580) covalent geometry : angle 0.62555 (19784) SS BOND : bond 0.00454 ( 33) SS BOND : angle 1.84364 ( 66) hydrogen bonds : bond 0.03655 ( 350) hydrogen bonds : angle 4.50720 ( 987) link_BETA1-4 : bond 0.00588 ( 31) link_BETA1-4 : angle 1.92377 ( 93) link_NAG-ASN : bond 0.00575 ( 53) link_NAG-ASN : angle 3.02659 ( 159) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 183 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8109 (mttt) cc_final: 0.7807 (mttp) REVERT: A 92 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7635 (mm-30) REVERT: A 104 MET cc_start: 0.8946 (ttt) cc_final: 0.8686 (ttt) REVERT: A 110 SER cc_start: 0.8586 (t) cc_final: 0.8369 (t) REVERT: A 121 LYS cc_start: 0.8397 (tptm) cc_final: 0.7992 (tppt) REVERT: A 142 MET cc_start: 0.8697 (tpp) cc_final: 0.8203 (tpp) REVERT: A 165 TYR cc_start: 0.8970 (p90) cc_final: 0.8596 (p90) REVERT: A 217 TYR cc_start: 0.8980 (m-80) cc_final: 0.8478 (m-80) REVERT: A 229 LYS cc_start: 0.8324 (mmmm) cc_final: 0.7827 (mtmt) REVERT: B 584 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7889 (tm-30) REVERT: B 587 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.7992 (mm) REVERT: B 588 ARG cc_start: 0.8133 (ttm-80) cc_final: 0.7692 (ttm110) REVERT: B 621 GLU cc_start: 0.6991 (pm20) cc_final: 0.6351 (pp20) REVERT: B 658 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.8058 (pm20) REVERT: C 46 LYS cc_start: 0.8378 (mmmt) cc_final: 0.7982 (mttm) REVERT: C 92 GLU cc_start: 0.7775 (mp0) cc_final: 0.7452 (mp0) REVERT: C 207 LYS cc_start: 0.7643 (mmmt) cc_final: 0.7396 (tmtt) REVERT: C 213 ILE cc_start: 0.8787 (tp) cc_final: 0.8381 (pt) REVERT: D 627 THR cc_start: 0.9073 (m) cc_final: 0.8867 (p) REVERT: E 265 LEU cc_start: 0.8786 (mm) cc_final: 0.8459 (mm) REVERT: E 475 MET cc_start: 0.8327 (tpp) cc_final: 0.7896 (tpp) REVERT: F 542 ARG cc_start: 0.8288 (mtp85) cc_final: 0.8042 (mtp85) REVERT: F 656 ASN cc_start: 0.8048 (t0) cc_final: 0.7660 (m-40) REVERT: F 657 GLU cc_start: 0.8734 (tm-30) cc_final: 0.8268 (tm-30) outliers start: 38 outliers final: 20 residues processed: 208 average time/residue: 0.1172 time to fit residues: 37.0344 Evaluate side-chains 192 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 170 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 530 MET Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain E residue 385 CYS Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 626 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 45 optimal weight: 4.9990 chunk 159 optimal weight: 10.0000 chunk 65 optimal weight: 0.0980 chunk 49 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 107 optimal weight: 0.5980 chunk 75 optimal weight: 0.4980 chunk 67 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 356 ASN E 377 ASN F 630 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.137193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.109728 restraints weight = 23141.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.113348 restraints weight = 13873.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.115806 restraints weight = 10153.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.117421 restraints weight = 8323.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.118518 restraints weight = 7287.780| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14697 Z= 0.120 Angle : 0.676 14.963 20102 Z= 0.312 Chirality : 0.047 0.412 2483 Planarity : 0.003 0.039 2407 Dihedral : 7.844 68.460 3521 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.83 % Favored : 93.98 % Rotamer: Outliers : 2.70 % Allowed : 16.80 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.21), residues: 1629 helix: 1.28 (0.31), residues: 351 sheet: -1.07 (0.23), residues: 478 loop : -1.83 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 542 TYR 0.020 0.001 TYR C 486 PHE 0.010 0.001 PHE E 376 TRP 0.010 0.001 TRP E 96 HIS 0.002 0.001 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00275 (14580) covalent geometry : angle 0.60632 (19784) SS BOND : bond 0.00393 ( 33) SS BOND : angle 1.73137 ( 66) hydrogen bonds : bond 0.03307 ( 350) hydrogen bonds : angle 4.34785 ( 987) link_BETA1-4 : bond 0.00587 ( 31) link_BETA1-4 : angle 1.84138 ( 93) link_NAG-ASN : bond 0.00556 ( 53) link_NAG-ASN : angle 2.97204 ( 159) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 181 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8131 (mttt) cc_final: 0.7834 (mttp) REVERT: A 92 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7631 (mm-30) REVERT: A 104 MET cc_start: 0.8991 (ttt) cc_final: 0.8730 (ttt) REVERT: A 110 SER cc_start: 0.8653 (t) cc_final: 0.8450 (t) REVERT: A 142 MET cc_start: 0.8746 (tpp) cc_final: 0.8282 (tpp) REVERT: A 217 TYR cc_start: 0.8947 (m-80) cc_final: 0.8447 (m-80) REVERT: B 588 ARG cc_start: 0.8108 (ttm-80) cc_final: 0.7715 (ttm110) REVERT: B 621 GLU cc_start: 0.6619 (pm20) cc_final: 0.6164 (pp20) REVERT: B 658 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.8033 (pm20) REVERT: C 46 LYS cc_start: 0.8450 (mmmt) cc_final: 0.8073 (mttm) REVERT: C 92 GLU cc_start: 0.7778 (mp0) cc_final: 0.7488 (mp0) REVERT: C 207 LYS cc_start: 0.7642 (mmmt) cc_final: 0.7434 (tmtt) REVERT: C 213 ILE cc_start: 0.8770 (tp) cc_final: 0.8403 (pt) REVERT: C 346 VAL cc_start: 0.9518 (p) cc_final: 0.9258 (t) REVERT: E 265 LEU cc_start: 0.8773 (mm) cc_final: 0.8545 (mm) REVERT: E 475 MET cc_start: 0.8364 (tpp) cc_final: 0.7934 (tpp) REVERT: F 542 ARG cc_start: 0.8165 (mtp85) cc_final: 0.7876 (mtp85) REVERT: F 657 GLU cc_start: 0.8709 (tm-30) cc_final: 0.8261 (tm-30) outliers start: 40 outliers final: 24 residues processed: 205 average time/residue: 0.1163 time to fit residues: 36.5805 Evaluate side-chains 197 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 172 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 530 MET Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 385 CYS Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 595 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 143 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 chunk 111 optimal weight: 0.0770 chunk 17 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 93 optimal weight: 9.9990 chunk 79 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 overall best weight: 2.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 630 GLN E 356 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.128018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.101081 restraints weight = 23453.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.104418 restraints weight = 14016.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.106728 restraints weight = 10365.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.108231 restraints weight = 8518.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.109172 restraints weight = 7494.849| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.083 14697 Z= 0.346 Angle : 0.904 13.722 20102 Z= 0.427 Chirality : 0.054 0.602 2483 Planarity : 0.005 0.054 2407 Dihedral : 8.553 72.316 3521 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.10 % Favored : 91.71 % Rotamer: Outliers : 2.90 % Allowed : 16.73 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.20), residues: 1629 helix: 0.60 (0.29), residues: 358 sheet: -1.11 (0.23), residues: 459 loop : -2.17 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 542 TYR 0.027 0.003 TYR C 486 PHE 0.022 0.003 PHE C 151 TRP 0.022 0.002 TRP C 112 HIS 0.007 0.002 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00836 (14580) covalent geometry : angle 0.83944 (19784) SS BOND : bond 0.00740 ( 33) SS BOND : angle 2.40012 ( 66) hydrogen bonds : bond 0.05100 ( 350) hydrogen bonds : angle 4.95827 ( 987) link_BETA1-4 : bond 0.00633 ( 31) link_BETA1-4 : angle 2.07463 ( 93) link_NAG-ASN : bond 0.00722 ( 53) link_NAG-ASN : angle 3.26319 ( 159) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 175 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8129 (mttt) cc_final: 0.7849 (mttp) REVERT: A 110 SER cc_start: 0.8827 (t) cc_final: 0.8535 (t) REVERT: A 142 MET cc_start: 0.8712 (tpp) cc_final: 0.8144 (tpp) REVERT: A 229 LYS cc_start: 0.8355 (mmmm) cc_final: 0.7937 (mtmt) REVERT: B 587 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8100 (mm) REVERT: B 588 ARG cc_start: 0.8171 (ttm-80) cc_final: 0.7731 (ttm110) REVERT: B 621 GLU cc_start: 0.6897 (pm20) cc_final: 0.6544 (pp20) REVERT: B 658 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.7771 (pm20) REVERT: C 46 LYS cc_start: 0.8416 (mmmt) cc_final: 0.7944 (mttm) REVERT: C 67 ASN cc_start: 0.7916 (p0) cc_final: 0.7467 (p0) REVERT: C 213 ILE cc_start: 0.8959 (tp) cc_final: 0.8437 (pt) REVERT: C 217 TYR cc_start: 0.9075 (m-80) cc_final: 0.8849 (m-80) REVERT: C 232 LYS cc_start: 0.8552 (mtmm) cc_final: 0.8314 (mttm) REVERT: C 285 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8666 (tt) REVERT: E 145 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.7067 (tt0) REVERT: E 265 LEU cc_start: 0.8946 (mm) cc_final: 0.8532 (mm) REVERT: E 269 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7461 (tp30) REVERT: E 475 MET cc_start: 0.8469 (tpp) cc_final: 0.8091 (tpp) REVERT: F 542 ARG cc_start: 0.8262 (mtp85) cc_final: 0.7883 (mtp85) REVERT: F 657 GLU cc_start: 0.8811 (tm-30) cc_final: 0.8587 (tm-30) outliers start: 43 outliers final: 27 residues processed: 206 average time/residue: 0.1271 time to fit residues: 38.8317 Evaluate side-chains 192 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 161 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 359 ILE Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 385 CYS Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 595 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 72 optimal weight: 0.9980 chunk 134 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 154 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 105 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 71 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 356 ASN E 377 ASN F 630 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.133681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.106501 restraints weight = 23242.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.110119 restraints weight = 13816.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.112556 restraints weight = 10087.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.114166 restraints weight = 8238.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.115164 restraints weight = 7196.096| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14697 Z= 0.139 Angle : 0.728 13.316 20102 Z= 0.339 Chirality : 0.048 0.447 2483 Planarity : 0.004 0.040 2407 Dihedral : 8.007 69.614 3521 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.71 % Favored : 94.17 % Rotamer: Outliers : 1.89 % Allowed : 18.69 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.21), residues: 1629 helix: 1.20 (0.30), residues: 350 sheet: -1.10 (0.23), residues: 482 loop : -1.97 (0.20), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 170 TYR 0.021 0.001 TYR B 638 PHE 0.017 0.001 PHE C 361 TRP 0.016 0.001 TRP E 45 HIS 0.003 0.001 HIS C 85 Details of bonding type rmsd covalent geometry : bond 0.00325 (14580) covalent geometry : angle 0.66048 (19784) SS BOND : bond 0.00478 ( 33) SS BOND : angle 1.95988 ( 66) hydrogen bonds : bond 0.03682 ( 350) hydrogen bonds : angle 4.52226 ( 987) link_BETA1-4 : bond 0.00554 ( 31) link_BETA1-4 : angle 1.89192 ( 93) link_NAG-ASN : bond 0.00555 ( 53) link_NAG-ASN : angle 3.00043 ( 159) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 180 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8142 (mttt) cc_final: 0.7871 (mttp) REVERT: A 92 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7585 (mm-30) REVERT: A 110 SER cc_start: 0.8809 (t) cc_final: 0.8574 (t) REVERT: A 142 MET cc_start: 0.8741 (tpp) cc_final: 0.8224 (tpp) REVERT: A 217 TYR cc_start: 0.8883 (m-80) cc_final: 0.8418 (m-80) REVERT: A 475 MET cc_start: 0.8533 (mmt) cc_final: 0.8321 (tpp) REVERT: B 587 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8102 (mm) REVERT: B 626 MET cc_start: 0.8134 (ttp) cc_final: 0.7922 (ttm) REVERT: B 658 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.7992 (pm20) REVERT: C 46 LYS cc_start: 0.8508 (mmmt) cc_final: 0.8043 (mttm) REVERT: C 67 ASN cc_start: 0.7842 (p0) cc_final: 0.7389 (p0) REVERT: C 213 ILE cc_start: 0.8872 (tp) cc_final: 0.8444 (pt) REVERT: E 265 LEU cc_start: 0.8880 (mm) cc_final: 0.8481 (mm) REVERT: E 475 MET cc_start: 0.8365 (tpp) cc_final: 0.7978 (tpp) REVERT: F 657 GLU cc_start: 0.8761 (tm-30) cc_final: 0.8365 (tm-30) outliers start: 28 outliers final: 21 residues processed: 200 average time/residue: 0.1176 time to fit residues: 35.8747 Evaluate side-chains 197 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 174 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 356 ASN Chi-restraints excluded: chain E residue 385 CYS Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 629 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 158 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 152 optimal weight: 0.5980 chunk 2 optimal weight: 8.9990 chunk 97 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 656 ASN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 356 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.133594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.106547 restraints weight = 23072.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.110140 restraints weight = 13716.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.112586 restraints weight = 10041.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.114189 restraints weight = 8192.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.115279 restraints weight = 7160.222| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.144 14697 Z= 0.170 Angle : 0.898 59.163 20102 Z= 0.470 Chirality : 0.048 0.445 2483 Planarity : 0.004 0.062 2407 Dihedral : 8.018 69.591 3521 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.02 % Favored : 93.86 % Rotamer: Outliers : 1.69 % Allowed : 19.03 % Favored : 79.28 % 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: -1.49 (0.21), residues: 1629 helix: 1.22 (0.30), residues: 350 sheet: -1.10 (0.23), residues: 482 loop : -1.95 (0.20), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 542 TYR 0.021 0.001 TYR B 638 PHE 0.015 0.001 PHE C 361 TRP 0.014 0.001 TRP E 45 HIS 0.003 0.001 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00379 (14580) covalent geometry : angle 0.84788 (19784) SS BOND : bond 0.00628 ( 33) SS BOND : angle 1.96974 ( 66) hydrogen bonds : bond 0.03686 ( 350) hydrogen bonds : angle 4.51647 ( 987) link_BETA1-4 : bond 0.00547 ( 31) link_BETA1-4 : angle 1.88269 ( 93) link_NAG-ASN : bond 0.00549 ( 53) link_NAG-ASN : angle 2.98837 ( 159) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 176 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8132 (mttt) cc_final: 0.7852 (mttp) REVERT: A 92 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7575 (mm-30) REVERT: A 110 SER cc_start: 0.8754 (t) cc_final: 0.8514 (t) REVERT: A 142 MET cc_start: 0.8705 (tpp) cc_final: 0.8182 (tpp) REVERT: A 217 TYR cc_start: 0.8719 (m-80) cc_final: 0.8431 (m-80) REVERT: A 475 MET cc_start: 0.8528 (mmt) cc_final: 0.8310 (tpp) REVERT: B 587 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8035 (mm) REVERT: B 588 ARG cc_start: 0.8023 (ttm-80) cc_final: 0.7737 (ttm-80) REVERT: B 621 GLU cc_start: 0.8609 (pp20) cc_final: 0.8099 (pp20) REVERT: B 626 MET cc_start: 0.8129 (ttp) cc_final: 0.7929 (ttm) REVERT: B 658 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.7987 (pm20) REVERT: C 46 LYS cc_start: 0.8477 (mmmt) cc_final: 0.7985 (mttm) REVERT: C 67 ASN cc_start: 0.7858 (p0) cc_final: 0.7396 (p0) REVERT: C 213 ILE cc_start: 0.8854 (tp) cc_final: 0.8401 (pt) REVERT: E 265 LEU cc_start: 0.8859 (mm) cc_final: 0.8477 (mm) REVERT: E 475 MET cc_start: 0.8354 (tpp) cc_final: 0.7934 (tpp) REVERT: F 657 GLU cc_start: 0.8767 (tm-30) cc_final: 0.8363 (tm-30) outliers start: 25 outliers final: 20 residues processed: 193 average time/residue: 0.1214 time to fit residues: 35.2809 Evaluate side-chains 198 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 176 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 267 GLU Chi-restraints excluded: chain E residue 385 CYS Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 629 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 152 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 141 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 chunk 2 optimal weight: 0.1980 chunk 107 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 348 GLN ** E 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.133327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.106307 restraints weight = 23076.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.109808 restraints weight = 13817.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.112265 restraints weight = 10138.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.113885 restraints weight = 8266.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.114976 restraints weight = 7213.353| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.144 14697 Z= 0.170 Angle : 0.898 59.163 20102 Z= 0.470 Chirality : 0.048 0.445 2483 Planarity : 0.004 0.062 2407 Dihedral : 8.018 69.591 3521 Min Nonbonded Distance : 1.013 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.02 % Favored : 93.86 % Rotamer: Outliers : 1.55 % Allowed : 19.23 % Favored : 79.22 % 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: -1.49 (0.21), residues: 1629 helix: 1.22 (0.30), residues: 350 sheet: -1.10 (0.23), residues: 482 loop : -1.95 (0.20), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 542 TYR 0.021 0.001 TYR B 638 PHE 0.015 0.001 PHE C 361 TRP 0.014 0.001 TRP E 45 HIS 0.003 0.001 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00379 (14580) covalent geometry : angle 0.84787 (19784) SS BOND : bond 0.00778 ( 33) SS BOND : angle 1.96664 ( 66) hydrogen bonds : bond 0.03686 ( 350) hydrogen bonds : angle 4.51647 ( 987) link_BETA1-4 : bond 0.00547 ( 31) link_BETA1-4 : angle 1.88269 ( 93) link_NAG-ASN : bond 0.00549 ( 53) link_NAG-ASN : angle 2.98837 ( 159) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2253.98 seconds wall clock time: 40 minutes 0.30 seconds (2400.30 seconds total)