Starting phenix.real_space_refine on Sun Aug 24 09:35:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8to9_41440/08_2025/8to9_41440.cif Found real_map, /net/cci-nas-00/data/ceres_data/8to9_41440/08_2025/8to9_41440.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8to9_41440/08_2025/8to9_41440.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8to9_41440/08_2025/8to9_41440.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8to9_41440/08_2025/8to9_41440.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8to9_41440/08_2025/8to9_41440.map" } resolution = 4.03 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= 0.001 sd= 0.012 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 123 5.16 5 C 11792 2.51 5 N 3108 2.21 5 O 3765 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18788 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 3204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3204 Classifications: {'peptide': 405} Link IDs: {'PTRANS': 22, 'TRANS': 382} Chain breaks: 8 Chain: "B" Number of atoms: 3204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3204 Classifications: {'peptide': 405} Link IDs: {'PTRANS': 22, 'TRANS': 382} Chain breaks: 8 Chain: "C" Number of atoms: 3204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3204 Classifications: {'peptide': 405} Link IDs: {'PTRANS': 22, 'TRANS': 382} Chain breaks: 8 Chain: "D" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 981 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "E" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 981 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "F" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 806 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "G" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 806 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "H" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 981 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "I" Number of atoms: 896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 896 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 1, 'TRANS': 110} Chain breaks: 1 Chain: "J" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 904 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 1, 'TRANS': 111} Chain breaks: 1 Chain: "L" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 806 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "Z" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 879 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 1, 'TRANS': 108} Chain breaks: 1 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: "M" 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: "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: 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: "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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "I" 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: "J" 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: "Z" 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 Time building chain proxies: 4.16, per 1000 atoms: 0.22 Number of scatterers: 18788 At special positions: 0 Unit cell: (112.05, 158.53, 162.68, 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 123 16.00 O 3765 8.00 N 3108 7.00 C 11792 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, 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 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS I 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.04 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS J 605 " 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=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.02 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS Z 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 598 " - pdb=" SG CYS I 604 " distance=2.03 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS Z 598 " - pdb=" SG CYS Z 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 K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG 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 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-ASN " NAG A 601 " - " ASN A 160 " " NAG A 602 " - " ASN A 197 " " NAG A 603 " - " ASN A 276 " " NAG A 604 " - " ASN A 295 " " NAG A 605 " - " ASN A 442 " " NAG A 606 " - " ASN A 448 " " NAG A 607 " - " ASN A 88 " " NAG A 608 " - " ASN A 301 " " NAG A 609 " - " ASN A 130 " " NAG A 610 " - " ASN A 392 " " NAG A 611 " - " ASN A 339 " " NAG A 612 " - " ASN A 156 " " NAG A 613 " - " ASN A 356 " " NAG B 601 " - " ASN B 160 " " NAG B 602 " - " ASN B 197 " " NAG B 603 " - " ASN B 276 " " NAG B 604 " - " ASN B 295 " " NAG B 605 " - " ASN B 392 " " NAG B 606 " - " ASN B 448 " " NAG B 607 " - " ASN B 88 " " NAG B 608 " - " ASN B 442 " " NAG B 609 " - " ASN B 339 " " NAG B 610 " - " ASN B 130 " " NAG B 611 " - " ASN B 301 " " NAG B 612 " - " ASN B 156 " " NAG B 613 " - " ASN B 356 " " NAG C 601 " - " ASN C 160 " " NAG C 602 " - " ASN C 197 " " NAG C 603 " - " ASN C 276 " " NAG C 604 " - " ASN C 295 " " NAG C 605 " - " ASN C 442 " " NAG C 606 " - " ASN C 392 " " NAG C 607 " - " ASN C 448 " " NAG C 608 " - " ASN C 88 " " NAG C 609 " - " ASN C 339 " " NAG C 610 " - " ASN C 301 " " NAG C 611 " - " ASN C 130 " " NAG C 612 " - " ASN C 156 " " NAG C 613 " - " ASN C 356 " " NAG I 701 " - " ASN I 637 " " NAG J 701 " - " ASN J 637 " " NAG K 1 " - " ASN A 230 " " NAG M 1 " - " ASN A 234 " " NAG N 1 " - " ASN A 241 " " NAG O 1 " - " ASN A 262 " " NAG Q 1 " - " ASN A 386 " " NAG R 1 " - " ASN B 230 " " NAG S 1 " - " ASN B 234 " " NAG T 1 " - " ASN B 241 " " NAG U 1 " - " ASN B 262 " " NAG V 1 " - " ASN B 332 " " NAG W 1 " - " ASN B 386 " " NAG X 1 " - " ASN C 230 " " NAG Y 1 " - " ASN C 234 " " NAG Z 701 " - " ASN Z 637 " " NAG a 1 " - " ASN C 241 " " NAG b 1 " - " ASN C 262 " " NAG d 1 " - " ASN C 386 " Time building additional restraints: 1.58 Conformation dependent library (CDL) restraints added in 692.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4186 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 49 sheets defined 18.7% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.611A pdb=" N ASP A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 352 removed outlier: 3.633A pdb=" N GLU A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.512A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU A 429 " --> pdb=" O MET A 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 425 through 429' Processing helix chain 'A' and resid 475 through 481 Processing helix chain 'B' and resid 94 through 97 removed outlier: 3.544A pdb=" N LYS B 97 " --> pdb=" O ASN B 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 94 through 97' Processing helix chain 'B' and resid 98 through 117 removed outlier: 4.123A pdb=" N ASP B 102 " --> pdb=" O ASN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 350 removed outlier: 4.107A pdb=" N LYS B 348 " --> pdb=" O ARG B 344 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS B 350 " --> pdb=" O LYS B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 429 removed outlier: 3.626A pdb=" N GLN B 428 " --> pdb=" O ASN B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 481 removed outlier: 3.808A pdb=" N ASN B 478 " --> pdb=" O ASP B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 486 removed outlier: 4.320A pdb=" N LYS B 485 " --> pdb=" O GLU B 482 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 117 Processing helix chain 'C' and resid 334 through 350 removed outlier: 3.552A pdb=" N TRP C 338 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS C 348 " --> pdb=" O ARG C 344 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS C 350 " --> pdb=" O LYS C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 429 Processing helix chain 'C' and resid 474 through 481 removed outlier: 4.190A pdb=" N ASN C 478 " --> pdb=" O ASP C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 484 No H-bonds generated for 'chain 'C' and resid 482 through 484' Processing helix chain 'D' and resid 73 through 75 No H-bonds generated for 'chain 'D' and resid 73 through 75' Processing helix chain 'E' and resid 73 through 75 No H-bonds generated for 'chain 'E' and resid 73 through 75' Processing helix chain 'G' and resid 79 through 83 removed outlier: 3.999A pdb=" N PHE G 83 " --> pdb=" O ILE G 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'I' and resid 522 through 526 removed outlier: 4.313A pdb=" N ALA I 525 " --> pdb=" O PHE I 522 " (cutoff:3.500A) Processing helix chain 'I' and resid 529 through 540 removed outlier: 3.539A pdb=" N ALA I 533 " --> pdb=" O THR I 529 " (cutoff:3.500A) Processing helix chain 'I' and resid 566 through 595 Processing helix chain 'I' and resid 618 through 622 Processing helix chain 'I' and resid 627 through 635 removed outlier: 3.915A pdb=" N TRP I 631 " --> pdb=" O THR I 627 " (cutoff:3.500A) Processing helix chain 'I' and resid 638 through 655 Processing helix chain 'J' and resid 522 through 526 removed outlier: 4.093A pdb=" N ALA J 525 " --> pdb=" O PHE J 522 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 540 removed outlier: 3.676A pdb=" N ALA J 533 " --> pdb=" O THR J 529 " (cutoff:3.500A) Processing helix chain 'J' and resid 566 through 596 removed outlier: 3.756A pdb=" N TRP J 596 " --> pdb=" O LEU J 592 " (cutoff:3.500A) Processing helix chain 'J' and resid 618 through 622 removed outlier: 3.750A pdb=" N ILE J 622 " --> pdb=" O GLN J 619 " (cutoff:3.500A) Processing helix chain 'J' and resid 627 through 636 removed outlier: 4.375A pdb=" N TRP J 631 " --> pdb=" O THR J 627 " (cutoff:3.500A) Processing helix chain 'J' and resid 638 through 656 removed outlier: 3.510A pdb=" N GLN J 650 " --> pdb=" O LEU J 646 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.012A pdb=" N PHE L 83 " --> pdb=" O ILE L 80 " (cutoff:3.500A) Processing helix chain 'Z' and resid 522 through 526 removed outlier: 4.232A pdb=" N ALA Z 525 " --> pdb=" O PHE Z 522 " (cutoff:3.500A) Processing helix chain 'Z' and resid 529 through 540 Processing helix chain 'Z' and resid 566 through 596 removed outlier: 3.811A pdb=" N TRP Z 596 " --> pdb=" O LEU Z 592 " (cutoff:3.500A) Processing helix chain 'Z' and resid 618 through 622 removed outlier: 3.617A pdb=" N ILE Z 622 " --> pdb=" O GLN Z 619 " (cutoff:3.500A) Processing helix chain 'Z' and resid 627 through 636 removed outlier: 3.961A pdb=" N TRP Z 631 " --> pdb=" O THR Z 627 " (cutoff:3.500A) Processing helix chain 'Z' and resid 638 through 653 removed outlier: 3.538A pdb=" N GLN Z 653 " --> pdb=" O SER Z 649 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 39 removed outlier: 3.659A pdb=" N THR A 499 " --> pdb=" O TRP A 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 46 Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 56 removed outlier: 3.770A pdb=" N CYS A 218 " --> pdb=" O PHE A 53 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 92 Processing sheet with id=AA5, first strand: chain 'A' and resid 129 through 130 removed outlier: 4.503A pdb=" N ARG A 192 " --> pdb=" O VAL A 182 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL A 182 " --> pdb=" O ARG A 192 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 132 through 133 removed outlier: 4.174A pdb=" N LYS A 155 " --> pdb=" O PHE A 176 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N PHE A 176 " --> pdb=" O LYS A 155 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 158 through 159 Processing sheet with id=AA8, first strand: chain 'A' and resid 200 through 201 removed outlier: 6.944A pdb=" N THR A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 256 through 257 removed outlier: 3.508A pdb=" N SER A 375 " --> pdb=" O THR A 257 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 271 through 273 removed outlier: 4.242A pdb=" N ILE A 271 " --> pdb=" O HIS A 287 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N HIS A 287 " --> pdb=" O ILE A 271 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 305 through 306 removed outlier: 3.723A pdb=" N ALA A 319 " --> pdb=" O LYS A 305 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 331 through 332 Processing sheet with id=AB4, first strand: chain 'B' and resid 496 through 499 removed outlier: 3.956A pdb=" N CYS J 604 " --> pdb=" O VAL B 38 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 45 through 46 removed outlier: 4.744A pdb=" N VAL B 242 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU B 86 " --> pdb=" O VAL B 242 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N MET B 84 " --> pdb=" O THR B 244 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 53 through 56 removed outlier: 3.580A pdb=" N PHE B 53 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N CYS B 218 " --> pdb=" O PHE B 53 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA B 55 " --> pdb=" O HIS B 216 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 91 through 92 removed outlier: 3.653A pdb=" N GLU B 91 " --> pdb=" O CYS B 239 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 129 through 130 removed outlier: 4.578A pdb=" N ARG B 192 " --> pdb=" O VAL B 182 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL B 182 " --> pdb=" O ARG B 192 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 132 through 133 Processing sheet with id=AC1, first strand: chain 'B' and resid 200 through 201 removed outlier: 6.615A pdb=" N THR B 200 " --> pdb=" O ALA B 433 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'B' and resid 271 through 273 removed outlier: 4.122A pdb=" N ILE B 271 " --> pdb=" O HIS B 287 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LYS B 360 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 374 through 377 Processing sheet with id=AC4, first strand: chain 'C' and resid 495 through 499 removed outlier: 3.568A pdb=" N THR C 37 " --> pdb=" O ALA C 497 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR C 499 " --> pdb=" O TRP C 35 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N VAL Z 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N VAL C 38 " --> pdb=" O THR Z 606 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N THR Z 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 45 through 46 removed outlier: 3.521A pdb=" N LYS C 487 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 53 through 56 removed outlier: 3.604A pdb=" N CYS C 218 " --> pdb=" O PHE C 53 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 91 through 92 removed outlier: 3.571A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AC9, first strand: chain 'C' and resid 181 through 182 removed outlier: 4.102A pdb=" N ARG C 192 " --> pdb=" O VAL C 182 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 200 through 202 Processing sheet with id=AD2, first strand: chain 'C' and resid 256 through 257 removed outlier: 3.676A pdb=" N SER C 375 " --> pdb=" O THR C 257 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS C 331 " --> pdb=" O LEU C 416 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 271 through 273 removed outlier: 3.991A pdb=" N ILE C 271 " --> pdb=" O HIS C 287 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 305 through 306 Processing sheet with id=AD5, first strand: chain 'C' and resid 360 through 361 removed outlier: 6.432A pdb=" N LYS C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'D' and resid 3 through 7 removed outlier: 4.344A pdb=" N ARG D 77 " --> pdb=" O ASP D 72 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASP D 72 " --> pdb=" O ARG D 77 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER D 70 " --> pdb=" O SER D 79 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 34 through 35 removed outlier: 3.838A pdb=" N THR D 102 " --> pdb=" O ARG D 94 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL D 96 " --> pdb=" O LEU D 100G" (cutoff:3.500A) removed outlier: 5.825A pdb=" N LEU D 100G" --> pdb=" O VAL D 96 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 57 through 59 removed outlier: 5.549A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N THR D 89 " --> pdb=" O GLN D 39 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.741A pdb=" N LEU E 20 " --> pdb=" O LEU E 80 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ARG E 77 " --> pdb=" O ASP E 72 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP E 72 " --> pdb=" O ARG E 77 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 34 through 35 removed outlier: 3.683A pdb=" N THR E 102 " --> pdb=" O ARG E 94 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL E 96 " --> pdb=" O LEU E 100G" (cutoff:3.500A) removed outlier: 5.610A pdb=" N LEU E 100G" --> pdb=" O VAL E 96 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 57 through 59 removed outlier: 5.362A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR E 89 " --> pdb=" O GLN E 39 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.613A pdb=" N LEU F 11 " --> pdb=" O LYS F 103 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR F 102 " --> pdb=" O TYR F 86 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR F 86 " --> pdb=" O THR F 102 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 20 through 22 removed outlier: 3.533A pdb=" N ASP F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 4 through 7 removed outlier: 3.574A pdb=" N THR G 5 " --> pdb=" O ARG G 24 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER G 7 " --> pdb=" O THR G 22 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N THR G 22 " --> pdb=" O SER G 7 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASP G 70 " --> pdb=" O SER G 67 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 10 through 13 Processing sheet with id=AE7, first strand: chain 'G' and resid 53 through 54 removed outlier: 6.732A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N TYR G 49 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N LEU G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.582A pdb=" N THR H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ARG H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASP H 72 " --> pdb=" O ARG H 77 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER H 70 " --> pdb=" O SER H 79 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AF1, first strand: chain 'H' and resid 34 through 35A removed outlier: 3.692A pdb=" N THR H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL H 96 " --> pdb=" O LEU H 100G" (cutoff:3.500A) removed outlier: 5.643A pdb=" N LEU H 100G" --> pdb=" O VAL H 96 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 57 through 59 removed outlier: 5.517A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N THR H 89 " --> pdb=" O GLN H 39 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.650A pdb=" N THR L 5 " --> pdb=" O ARG L 24 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG L 24 " --> pdb=" O THR L 5 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER L 65 " --> pdb=" O THR L 72 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 53 through 54 removed outlier: 5.308A pdb=" N VAL L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N GLN L 37 " --> pdb=" O VAL L 46 " (cutoff:3.500A) 528 hydrogen bonds defined for protein. 1407 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: 2.64 Time building geometry restraints manager: 2.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5756 1.34 - 1.47: 4860 1.47 - 1.59: 8370 1.59 - 1.72: 0 1.72 - 1.84: 168 Bond restraints: 19154 Sorted by residual: bond pdb=" N GLN C 328 " pdb=" CA GLN C 328 " ideal model delta sigma weight residual 1.453 1.491 -0.038 1.37e-02 5.33e+03 7.89e+00 bond pdb=" N GLN A 328 " pdb=" CA GLN A 328 " ideal model delta sigma weight residual 1.452 1.491 -0.039 1.41e-02 5.03e+03 7.63e+00 bond pdb=" N CYS A 331 " pdb=" CA CYS A 331 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.16e-02 7.43e+03 7.48e+00 bond pdb=" N HIS C 330 " pdb=" CA HIS C 330 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.23e-02 6.61e+03 6.70e+00 bond pdb=" N LYS C 357 " pdb=" CA LYS C 357 " ideal model delta sigma weight residual 1.456 1.487 -0.032 1.25e-02 6.40e+03 6.46e+00 ... (remaining 19149 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.87: 25430 2.87 - 5.74: 446 5.74 - 8.62: 72 8.62 - 11.49: 15 11.49 - 14.36: 2 Bond angle restraints: 25965 Sorted by residual: angle pdb=" N ILE I 635 " pdb=" CA ILE I 635 " pdb=" C ILE I 635 " ideal model delta sigma weight residual 112.29 104.34 7.95 9.40e-01 1.13e+00 7.15e+01 angle pdb=" N THR J 606 " pdb=" CA THR J 606 " pdb=" C THR J 606 " ideal model delta sigma weight residual 107.73 116.47 -8.74 1.34e+00 5.57e-01 4.25e+01 angle pdb=" N GLU J 584 " pdb=" CA GLU J 584 " pdb=" CB GLU J 584 " ideal model delta sigma weight residual 110.39 119.10 -8.71 1.66e+00 3.63e-01 2.75e+01 angle pdb=" C ASN C 160 " pdb=" N THR C 161 " pdb=" CA THR C 161 " ideal model delta sigma weight residual 122.61 130.10 -7.49 1.56e+00 4.11e-01 2.31e+01 angle pdb=" CB MET A 150 " pdb=" CG MET A 150 " pdb=" SD MET A 150 " ideal model delta sigma weight residual 112.70 127.06 -14.36 3.00e+00 1.11e-01 2.29e+01 ... (remaining 25960 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.79: 11581 21.79 - 43.57: 789 43.57 - 65.36: 135 65.36 - 87.15: 44 87.15 - 108.93: 16 Dihedral angle restraints: 12565 sinusoidal: 6094 harmonic: 6471 Sorted by residual: dihedral pdb=" CB CYS C 54 " pdb=" SG CYS C 54 " pdb=" SG CYS C 74 " pdb=" CB CYS C 74 " ideal model delta sinusoidal sigma weight residual 93.00 10.02 82.98 1 1.00e+01 1.00e-02 8.43e+01 dihedral pdb=" CB CYS F 23 " pdb=" SG CYS F 23 " pdb=" SG CYS F 88 " pdb=" CB CYS F 88 " ideal model delta sinusoidal sigma weight residual 93.00 169.88 -76.88 1 1.00e+01 1.00e-02 7.42e+01 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 -86.00 -162.55 76.55 1 1.00e+01 1.00e-02 7.37e+01 ... (remaining 12562 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2474 0.071 - 0.142: 575 0.142 - 0.213: 76 0.213 - 0.285: 15 0.285 - 0.356: 8 Chirality restraints: 3148 Sorted by residual: chirality pdb=" C2 NAG C 611 " pdb=" C1 NAG C 611 " pdb=" C3 NAG C 611 " pdb=" N2 NAG C 611 " both_signs ideal model delta sigma weight residual False -2.49 -2.14 -0.36 2.00e-01 2.50e+01 3.16e+00 chirality pdb=" CB ILE A 270 " pdb=" CA ILE A 270 " pdb=" CG1 ILE A 270 " pdb=" CG2 ILE A 270 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 3.02e+00 chirality pdb=" CB ILE B 423 " pdb=" CA ILE B 423 " pdb=" CG1 ILE B 423 " pdb=" CG2 ILE B 423 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.86e+00 ... (remaining 3145 not shown) Planarity restraints: 3228 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 613 " -0.088 2.00e-02 2.50e+03 7.29e-02 6.65e+01 pdb=" C7 NAG B 613 " 0.027 2.00e-02 2.50e+03 pdb=" C8 NAG B 613 " -0.068 2.00e-02 2.50e+03 pdb=" N2 NAG B 613 " 0.115 2.00e-02 2.50e+03 pdb=" O7 NAG B 613 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 613 " -0.076 2.00e-02 2.50e+03 6.29e-02 4.95e+01 pdb=" C7 NAG C 613 " 0.020 2.00e-02 2.50e+03 pdb=" C8 NAG C 613 " -0.058 2.00e-02 2.50e+03 pdb=" N2 NAG C 613 " 0.100 2.00e-02 2.50e+03 pdb=" O7 NAG C 613 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 479 " 0.031 2.00e-02 2.50e+03 2.77e-02 1.91e+01 pdb=" CG TRP B 479 " -0.075 2.00e-02 2.50e+03 pdb=" CD1 TRP B 479 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP B 479 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 479 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 479 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 479 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 479 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 479 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 479 " 0.005 2.00e-02 2.50e+03 ... (remaining 3225 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 5823 2.84 - 3.36: 16712 3.36 - 3.87: 30278 3.87 - 4.39: 31731 4.39 - 4.90: 55916 Nonbonded interactions: 140460 Sorted by model distance: nonbonded pdb=" OG SER L 26 " pdb=" OE1 GLN L 27 " model vdw 2.328 3.040 nonbonded pdb=" OG1 THR J 606 " pdb=" N ALA J 607 " model vdw 2.339 3.120 nonbonded pdb=" O VAL C 36 " pdb=" OG1 THR Z 606 " model vdw 2.347 3.040 nonbonded pdb=" O ILE Z 635 " pdb=" OG1 THR Z 639 " model vdw 2.355 3.040 nonbonded pdb=" NZ LYS C 421 " pdb=" O ILE C 423 " model vdw 2.356 3.120 ... (remaining 140455 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' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'L' } ncs_group { reference = (chain 'I' and (resid 520 through 653 or resid 701)) selection = (chain 'J' and (resid 520 through 653 or resid 701)) selection = chain 'Z' } ncs_group { reference = chain 'K' selection = chain 'N' selection = chain 'O' selection = chain 'P' 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' selection = chain 'd' } ncs_group { reference = chain 'M' selection = chain 'S' selection = chain 'Y' selection = chain 'c' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.340 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.070 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:1.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 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 0.054 19273 Z= 0.276 Angle : 1.013 14.362 26283 Z= 0.504 Chirality : 0.062 0.356 3148 Planarity : 0.006 0.076 3170 Dihedral : 14.793 108.935 8262 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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 aren not related in a simple way. whole: -2.52 (0.17), residues: 2171 helix: -1.03 (0.23), residues: 328 sheet: -0.35 (0.23), residues: 537 loop : -2.57 (0.15), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 41 TYR 0.017 0.001 TYR I 643 PHE 0.022 0.002 PHE A 210 TRP 0.075 0.002 TRP B 479 HIS 0.012 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00530 (19154) covalent geometry : angle 0.97654 (25965) SS BOND : bond 0.00276 ( 39) SS BOND : angle 0.95925 ( 78) hydrogen bonds : bond 0.24529 ( 528) hydrogen bonds : angle 9.09606 ( 1407) link_BETA1-4 : bond 0.00607 ( 22) link_BETA1-4 : angle 3.93677 ( 66) link_NAG-ASN : bond 0.00502 ( 58) link_NAG-ASN : angle 2.53309 ( 174) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.7857 (tmm) cc_final: 0.7619 (tmm) REVERT: A 154 MET cc_start: 0.7714 (mmp) cc_final: 0.7281 (mmm) REVERT: A 376 PHE cc_start: 0.8524 (p90) cc_final: 0.8272 (p90) REVERT: B 45 TRP cc_start: 0.7457 (p90) cc_final: 0.7069 (p90) REVERT: D 64 GLU cc_start: 0.8902 (mm-30) cc_final: 0.8421 (mp0) REVERT: D 97 ARG cc_start: 0.8764 (ptm-80) cc_final: 0.7998 (tmt170) REVERT: F 47 LEU cc_start: 0.9347 (mt) cc_final: 0.9041 (mt) REVERT: H 27 ASP cc_start: 0.8234 (t70) cc_final: 0.7897 (t0) REVERT: J 535 ASN cc_start: 0.9013 (m-40) cc_final: 0.8793 (m-40) REVERT: L 11 LEU cc_start: 0.8743 (pt) cc_final: 0.7953 (mp) REVERT: Z 629 MET cc_start: 0.7937 (mmp) cc_final: 0.7398 (mmp) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.1282 time to fit residues: 31.0323 Evaluate side-chains 107 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 216 optimal weight: 0.4980 chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 0.0000 chunk 212 optimal weight: 7.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 GLN C 203 GLN C 249 HIS ** E 35BASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 27 GLN ** Z 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.047962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.037603 restraints weight = 165978.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.038766 restraints weight = 92427.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.039530 restraints weight = 63677.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.040049 restraints weight = 49777.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.040384 restraints weight = 42397.815| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 19273 Z= 0.180 Angle : 0.635 9.162 26283 Z= 0.308 Chirality : 0.046 0.248 3148 Planarity : 0.004 0.055 3170 Dihedral : 8.827 60.981 4095 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 0.10 % Allowed : 3.94 % Favored : 95.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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 aren not related in a simple way. whole: -1.62 (0.18), residues: 2171 helix: 1.33 (0.28), residues: 348 sheet: -0.36 (0.23), residues: 546 loop : -2.23 (0.16), residues: 1277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 41 TYR 0.016 0.002 TYR H 33 PHE 0.019 0.002 PHE E 100F TRP 0.024 0.002 TRP A 479 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00383 (19154) covalent geometry : angle 0.60399 (25965) SS BOND : bond 0.00290 ( 39) SS BOND : angle 0.82251 ( 78) hydrogen bonds : bond 0.03681 ( 528) hydrogen bonds : angle 6.07608 ( 1407) link_BETA1-4 : bond 0.00489 ( 22) link_BETA1-4 : angle 2.56931 ( 66) link_NAG-ASN : bond 0.00354 ( 58) link_NAG-ASN : angle 1.89539 ( 174) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 121 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.8048 (tmm) cc_final: 0.7598 (tmm) REVERT: A 154 MET cc_start: 0.7944 (mmp) cc_final: 0.7574 (mmm) REVERT: A 376 PHE cc_start: 0.8531 (p90) cc_final: 0.8185 (p90) REVERT: D 64 GLU cc_start: 0.9016 (mm-30) cc_final: 0.8611 (mp0) REVERT: D 75 ASN cc_start: 0.8652 (t0) cc_final: 0.8277 (t0) REVERT: H 27 ASP cc_start: 0.8392 (t70) cc_final: 0.7827 (t0) REVERT: H 35 ASN cc_start: 0.9027 (m110) cc_final: 0.8779 (t0) REVERT: L 11 LEU cc_start: 0.9158 (pt) cc_final: 0.8422 (mp) REVERT: Z 530 MET cc_start: 0.7833 (mpp) cc_final: 0.7297 (mpp) REVERT: Z 648 GLU cc_start: 0.9312 (mt-10) cc_final: 0.9062 (mt-10) outliers start: 2 outliers final: 0 residues processed: 123 average time/residue: 0.1262 time to fit residues: 25.7324 Evaluate side-chains 91 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 211 optimal weight: 9.9990 chunk 121 optimal weight: 20.0000 chunk 142 optimal weight: 3.9990 chunk 207 optimal weight: 0.8980 chunk 158 optimal weight: 0.1980 chunk 118 optimal weight: 5.9990 chunk 136 optimal weight: 0.6980 chunk 95 optimal weight: 8.9990 chunk 150 optimal weight: 20.0000 chunk 88 optimal weight: 9.9990 chunk 201 optimal weight: 1.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 328 GLN ** D 35BASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35BASN H 35BASN ** I 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.047932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.037543 restraints weight = 166524.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.038732 restraints weight = 91867.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.039499 restraints weight = 63079.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.040009 restraints weight = 49394.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.040349 restraints weight = 42070.519| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 19273 Z= 0.110 Angle : 0.578 9.394 26283 Z= 0.273 Chirality : 0.045 0.252 3148 Planarity : 0.003 0.049 3170 Dihedral : 7.575 54.545 4095 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.03 % Favored : 93.92 % Rotamer: Outliers : 0.10 % Allowed : 3.08 % Favored : 96.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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 aren not related in a simple way. whole: -1.30 (0.18), residues: 2171 helix: 1.93 (0.28), residues: 348 sheet: -0.31 (0.23), residues: 567 loop : -2.07 (0.16), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 63 TYR 0.020 0.001 TYR I 643 PHE 0.010 0.001 PHE G 71 TRP 0.018 0.001 TRP J 631 HIS 0.005 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00234 (19154) covalent geometry : angle 0.54441 (25965) SS BOND : bond 0.00146 ( 39) SS BOND : angle 0.63490 ( 78) hydrogen bonds : bond 0.03484 ( 528) hydrogen bonds : angle 5.56368 ( 1407) link_BETA1-4 : bond 0.00436 ( 22) link_BETA1-4 : angle 2.62870 ( 66) link_NAG-ASN : bond 0.00326 ( 58) link_NAG-ASN : angle 1.83543 ( 174) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 125 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8726 (ppp) cc_final: 0.7766 (ppp) REVERT: A 150 MET cc_start: 0.8136 (tmm) cc_final: 0.7663 (tmm) REVERT: A 154 MET cc_start: 0.8033 (mmp) cc_final: 0.7361 (mmm) REVERT: A 376 PHE cc_start: 0.8452 (p90) cc_final: 0.8210 (p90) REVERT: B 475 MET cc_start: 0.7304 (ttm) cc_final: 0.6793 (ttm) REVERT: D 30 LYS cc_start: 0.9255 (mmmm) cc_final: 0.8973 (mmmm) REVERT: D 64 GLU cc_start: 0.9021 (mm-30) cc_final: 0.8451 (mp0) REVERT: D 75 ASN cc_start: 0.8672 (t0) cc_final: 0.8237 (t0) REVERT: H 27 ASP cc_start: 0.8438 (t70) cc_final: 0.7854 (t0) REVERT: H 35 ASN cc_start: 0.8958 (m-40) cc_final: 0.8682 (t0) REVERT: L 11 LEU cc_start: 0.9233 (pt) cc_final: 0.8575 (mp) REVERT: Z 530 MET cc_start: 0.7710 (mpp) cc_final: 0.7218 (mpp) REVERT: Z 648 GLU cc_start: 0.9284 (mt-10) cc_final: 0.9010 (mt-10) outliers start: 2 outliers final: 1 residues processed: 127 average time/residue: 0.1395 time to fit residues: 28.4345 Evaluate side-chains 94 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 93 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 70 optimal weight: 10.0000 chunk 155 optimal weight: 8.9990 chunk 162 optimal weight: 5.9990 chunk 58 optimal weight: 8.9990 chunk 114 optimal weight: 6.9990 chunk 164 optimal weight: 4.9990 chunk 92 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 36 optimal weight: 20.0000 chunk 89 optimal weight: 0.8980 chunk 48 optimal weight: 7.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 HIS ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN ** F 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN G 38 GLN G 90 GLN ** I 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 567 GLN ** Z 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.046909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.036238 restraints weight = 186992.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.037145 restraints weight = 104185.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.037304 restraints weight = 72341.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.037437 restraints weight = 73679.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.037637 restraints weight = 65466.985| |-----------------------------------------------------------------------------| r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 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 : 0.006 0.071 19273 Z= 0.282 Angle : 0.747 11.177 26283 Z= 0.365 Chirality : 0.047 0.227 3148 Planarity : 0.005 0.052 3170 Dihedral : 7.401 57.758 4095 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.25 % Favored : 91.71 % Rotamer: Outliers : 0.05 % Allowed : 4.19 % Favored : 95.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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 aren not related in a simple way. whole: -1.48 (0.18), residues: 2171 helix: 2.19 (0.28), residues: 335 sheet: -0.73 (0.22), residues: 585 loop : -2.12 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 100D TYR 0.023 0.002 TYR E 33 PHE 0.020 0.002 PHE D 100F TRP 0.030 0.002 TRP B 479 HIS 0.010 0.002 HIS A 287 Details of bonding type rmsd covalent geometry : bond 0.00610 (19154) covalent geometry : angle 0.71478 (25965) SS BOND : bond 0.00375 ( 39) SS BOND : angle 1.25474 ( 78) hydrogen bonds : bond 0.03788 ( 528) hydrogen bonds : angle 5.63317 ( 1407) link_BETA1-4 : bond 0.00463 ( 22) link_BETA1-4 : angle 2.50048 ( 66) link_NAG-ASN : bond 0.00537 ( 58) link_NAG-ASN : angle 2.22997 ( 174) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.8296 (tmm) cc_final: 0.7782 (tmm) REVERT: A 154 MET cc_start: 0.8110 (mmp) cc_final: 0.7765 (mmm) REVERT: D 75 ASN cc_start: 0.8691 (t0) cc_final: 0.8247 (t0) REVERT: I 643 TYR cc_start: 0.9496 (m-80) cc_final: 0.9186 (m-80) REVERT: J 530 MET cc_start: 0.8460 (pmm) cc_final: 0.8143 (pmm) REVERT: Z 648 GLU cc_start: 0.9173 (mt-10) cc_final: 0.8948 (mt-10) outliers start: 1 outliers final: 0 residues processed: 110 average time/residue: 0.1370 time to fit residues: 24.3427 Evaluate side-chains 83 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 194 optimal weight: 8.9990 chunk 22 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 212 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 152 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 177 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 154 optimal weight: 4.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 HIS ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.048091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.037808 restraints weight = 184566.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.038519 restraints weight = 101799.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.039077 restraints weight = 73318.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.039156 restraints weight = 72356.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.039198 restraints weight = 61779.912| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19273 Z= 0.129 Angle : 0.614 9.818 26283 Z= 0.292 Chirality : 0.046 0.235 3148 Planarity : 0.003 0.043 3170 Dihedral : 6.979 54.862 4095 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.54 % Favored : 93.41 % Rotamer: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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 aren not related in a simple way. whole: -1.29 (0.18), residues: 2171 helix: 2.31 (0.28), residues: 347 sheet: -0.61 (0.22), residues: 609 loop : -2.04 (0.17), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 644 TYR 0.015 0.001 TYR I 643 PHE 0.013 0.001 PHE E 100F TRP 0.044 0.002 TRP B 479 HIS 0.004 0.001 HIS A 287 Details of bonding type rmsd covalent geometry : bond 0.00284 (19154) covalent geometry : angle 0.57901 (25965) SS BOND : bond 0.00212 ( 39) SS BOND : angle 0.88495 ( 78) hydrogen bonds : bond 0.03177 ( 528) hydrogen bonds : angle 5.23520 ( 1407) link_BETA1-4 : bond 0.00393 ( 22) link_BETA1-4 : angle 2.52850 ( 66) link_NAG-ASN : bond 0.00294 ( 58) link_NAG-ASN : angle 2.02999 ( 174) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8893 (ppp) cc_final: 0.7824 (ppp) REVERT: A 150 MET cc_start: 0.8274 (tmm) cc_final: 0.7729 (tmm) REVERT: A 154 MET cc_start: 0.8149 (mmp) cc_final: 0.7826 (mmm) REVERT: A 376 PHE cc_start: 0.8331 (p90) cc_final: 0.8109 (p90) REVERT: B 288 LEU cc_start: 0.8706 (tp) cc_final: 0.8395 (tp) REVERT: D 75 ASN cc_start: 0.8629 (t0) cc_final: 0.8220 (t0) REVERT: H 35 ASN cc_start: 0.8670 (m-40) cc_final: 0.8388 (t0) REVERT: J 530 MET cc_start: 0.8519 (pmm) cc_final: 0.8232 (pmm) REVERT: Z 629 MET cc_start: 0.8600 (mmp) cc_final: 0.8275 (mmt) REVERT: Z 648 GLU cc_start: 0.9173 (mt-10) cc_final: 0.8937 (mt-10) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.1422 time to fit residues: 26.0567 Evaluate side-chains 91 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 184 optimal weight: 7.9990 chunk 90 optimal weight: 40.0000 chunk 61 optimal weight: 4.9990 chunk 22 optimal weight: 10.0000 chunk 151 optimal weight: 20.0000 chunk 158 optimal weight: 6.9990 chunk 193 optimal weight: 20.0000 chunk 164 optimal weight: 2.9990 chunk 180 optimal weight: 8.9990 chunk 110 optimal weight: 9.9990 chunk 179 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 HIS ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 ASN B 287 HIS ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.042686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.032232 restraints weight = 170246.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.033081 restraints weight = 86481.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.033529 restraints weight = 61193.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.033607 restraints weight = 56388.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.033675 restraints weight = 51619.394| |-----------------------------------------------------------------------------| r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.4416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 19273 Z= 0.306 Angle : 0.759 10.017 26283 Z= 0.371 Chirality : 0.047 0.224 3148 Planarity : 0.004 0.041 3170 Dihedral : 7.457 57.669 4095 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 17.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.17 % Favored : 90.79 % Rotamer: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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 aren not related in a simple way. whole: -1.66 (0.18), residues: 2171 helix: 1.90 (0.28), residues: 341 sheet: -0.81 (0.21), residues: 609 loop : -2.26 (0.17), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 476 TYR 0.021 0.002 TYR H 33 PHE 0.031 0.002 PHE E 100F TRP 0.040 0.003 TRP B 479 HIS 0.009 0.002 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00666 (19154) covalent geometry : angle 0.72482 (25965) SS BOND : bond 0.00399 ( 39) SS BOND : angle 1.30054 ( 78) hydrogen bonds : bond 0.03965 ( 528) hydrogen bonds : angle 5.65022 ( 1407) link_BETA1-4 : bond 0.00515 ( 22) link_BETA1-4 : angle 2.62710 ( 66) link_NAG-ASN : bond 0.00538 ( 58) link_NAG-ASN : angle 2.29821 ( 174) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9007 (ppp) cc_final: 0.8722 (ppp) REVERT: A 150 MET cc_start: 0.8272 (tmm) cc_final: 0.7727 (tmm) REVERT: A 154 MET cc_start: 0.8504 (mmp) cc_final: 0.7841 (tpp) REVERT: B 104 MET cc_start: 0.9580 (tmm) cc_final: 0.9367 (ppp) REVERT: B 475 MET cc_start: 0.8531 (ptm) cc_final: 0.8283 (ptm) REVERT: D 75 ASN cc_start: 0.8794 (t0) cc_final: 0.8311 (t0) REVERT: I 626 MET cc_start: 0.7927 (ptt) cc_final: 0.7140 (ppp) REVERT: J 584 GLU cc_start: 0.8911 (mp0) cc_final: 0.8605 (mp0) REVERT: Z 648 GLU cc_start: 0.9352 (mt-10) cc_final: 0.9079 (mt-10) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1317 time to fit residues: 21.0649 Evaluate side-chains 77 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 187 optimal weight: 0.0000 chunk 52 optimal weight: 0.6980 chunk 102 optimal weight: 5.9990 chunk 198 optimal weight: 8.9990 chunk 62 optimal weight: 9.9990 chunk 96 optimal weight: 7.9990 chunk 43 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 156 optimal weight: 0.7980 chunk 144 optimal weight: 2.9990 chunk 176 optimal weight: 5.9990 overall best weight: 1.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 GLN ** D 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 567 GLN ** I 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.044352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.033459 restraints weight = 163721.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.034582 restraints weight = 87557.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.035322 restraints weight = 60076.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.035795 restraints weight = 47376.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.036117 restraints weight = 40763.691| |-----------------------------------------------------------------------------| r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 19273 Z= 0.109 Angle : 0.627 9.438 26283 Z= 0.296 Chirality : 0.046 0.234 3148 Planarity : 0.003 0.050 3170 Dihedral : 6.934 55.108 4095 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.49 % Favored : 93.46 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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 aren not related in a simple way. whole: -1.31 (0.18), residues: 2171 helix: 2.49 (0.28), residues: 329 sheet: -0.67 (0.21), residues: 636 loop : -2.05 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 304 TYR 0.019 0.001 TYR I 643 PHE 0.010 0.001 PHE B 376 TRP 0.044 0.001 TRP B 479 HIS 0.005 0.001 HIS B 216 Details of bonding type rmsd covalent geometry : bond 0.00239 (19154) covalent geometry : angle 0.58708 (25965) SS BOND : bond 0.00222 ( 39) SS BOND : angle 0.95491 ( 78) hydrogen bonds : bond 0.03145 ( 528) hydrogen bonds : angle 5.07471 ( 1407) link_BETA1-4 : bond 0.00466 ( 22) link_BETA1-4 : angle 2.61067 ( 66) link_NAG-ASN : bond 0.00346 ( 58) link_NAG-ASN : angle 2.21014 ( 174) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.761 Fit side-chains revert: symmetry clash REVERT: A 104 MET cc_start: 0.8992 (ppp) cc_final: 0.8703 (ppp) REVERT: A 150 MET cc_start: 0.8302 (tmm) cc_final: 0.7717 (tmm) REVERT: A 154 MET cc_start: 0.8452 (mmp) cc_final: 0.8034 (mmm) REVERT: D 75 ASN cc_start: 0.8768 (t0) cc_final: 0.8323 (t0) REVERT: E 27 ASP cc_start: 0.9188 (t70) cc_final: 0.8664 (t70) REVERT: E 52 TYR cc_start: 0.8597 (t80) cc_final: 0.8231 (t80) REVERT: H 35 ASN cc_start: 0.9016 (m-40) cc_final: 0.8517 (t0) REVERT: H 43 LYS cc_start: 0.8444 (pttm) cc_final: 0.8227 (mtmm) REVERT: I 626 MET cc_start: 0.7719 (ptt) cc_final: 0.7091 (ppp) REVERT: J 584 GLU cc_start: 0.8810 (mp0) cc_final: 0.8481 (mp0) REVERT: L 11 LEU cc_start: 0.9551 (pp) cc_final: 0.8965 (mp) REVERT: Z 648 GLU cc_start: 0.9324 (mt-10) cc_final: 0.9037 (mt-10) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.1415 time to fit residues: 24.4380 Evaluate side-chains 86 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 205 optimal weight: 9.9990 chunk 209 optimal weight: 20.0000 chunk 94 optimal weight: 4.9990 chunk 187 optimal weight: 10.0000 chunk 141 optimal weight: 7.9990 chunk 189 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 126 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 GLN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 332 ASN D 39 GLN ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.042043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.031601 restraints weight = 172138.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.032408 restraints weight = 87905.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.032875 restraints weight = 62546.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.032959 restraints weight = 57367.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.033029 restraints weight = 52280.667| |-----------------------------------------------------------------------------| r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.4907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 19273 Z= 0.350 Angle : 0.800 10.974 26283 Z= 0.389 Chirality : 0.048 0.235 3148 Planarity : 0.005 0.055 3170 Dihedral : 7.578 57.333 4095 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.90 % Favored : 90.05 % Rotamer: Outliers : 0.05 % Allowed : 1.06 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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 aren not related in a simple way. whole: -1.70 (0.18), residues: 2171 helix: 1.92 (0.27), residues: 341 sheet: -0.78 (0.21), residues: 609 loop : -2.33 (0.17), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 192 TYR 0.020 0.003 TYR I 643 PHE 0.033 0.003 PHE E 100F TRP 0.042 0.003 TRP B 479 HIS 0.011 0.002 HIS B 216 Details of bonding type rmsd covalent geometry : bond 0.00759 (19154) covalent geometry : angle 0.76223 (25965) SS BOND : bond 0.00456 ( 39) SS BOND : angle 1.34939 ( 78) hydrogen bonds : bond 0.04072 ( 528) hydrogen bonds : angle 5.60145 ( 1407) link_BETA1-4 : bond 0.00495 ( 22) link_BETA1-4 : angle 2.68043 ( 66) link_NAG-ASN : bond 0.00703 ( 58) link_NAG-ASN : angle 2.54722 ( 174) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 93 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.9551 (mtm) cc_final: 0.9341 (mtt) REVERT: A 104 MET cc_start: 0.9042 (ppp) cc_final: 0.8777 (ppp) REVERT: A 150 MET cc_start: 0.8348 (tmm) cc_final: 0.7780 (tmm) REVERT: A 154 MET cc_start: 0.8538 (mmp) cc_final: 0.8248 (mmm) REVERT: B 104 MET cc_start: 0.9236 (ppp) cc_final: 0.8764 (ppp) REVERT: E 52 TYR cc_start: 0.8932 (t80) cc_final: 0.8639 (t80) REVERT: F 70 ASP cc_start: 0.9525 (t0) cc_final: 0.9286 (p0) REVERT: I 626 MET cc_start: 0.7996 (ptt) cc_final: 0.7339 (ppp) REVERT: J 584 GLU cc_start: 0.8850 (mp0) cc_final: 0.8533 (mp0) REVERT: L 11 LEU cc_start: 0.9596 (pp) cc_final: 0.9048 (mp) REVERT: Z 648 GLU cc_start: 0.9357 (mt-10) cc_final: 0.9083 (mt-10) outliers start: 1 outliers final: 0 residues processed: 94 average time/residue: 0.1439 time to fit residues: 21.5831 Evaluate side-chains 72 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 110 optimal weight: 0.9990 chunk 150 optimal weight: 10.0000 chunk 164 optimal weight: 0.8980 chunk 72 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 chunk 192 optimal weight: 0.5980 chunk 156 optimal weight: 4.9990 chunk 189 optimal weight: 8.9990 chunk 98 optimal weight: 0.7980 chunk 19 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 ASN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.043484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.032584 restraints weight = 167023.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.033664 restraints weight = 90774.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.034367 restraints weight = 63023.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.034815 restraints weight = 50246.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.035103 restraints weight = 43635.393| |-----------------------------------------------------------------------------| r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.4679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19273 Z= 0.123 Angle : 0.636 9.389 26283 Z= 0.303 Chirality : 0.047 0.238 3148 Planarity : 0.004 0.040 3170 Dihedral : 7.111 55.093 4095 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.09 % Favored : 92.86 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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 aren not related in a simple way. whole: -1.43 (0.18), residues: 2171 helix: 1.92 (0.28), residues: 365 sheet: -0.79 (0.20), residues: 660 loop : -2.08 (0.18), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 192 TYR 0.019 0.001 TYR I 643 PHE 0.010 0.001 PHE E 100F TRP 0.044 0.002 TRP B 479 HIS 0.004 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00273 (19154) covalent geometry : angle 0.59713 (25965) SS BOND : bond 0.00233 ( 39) SS BOND : angle 1.04907 ( 78) hydrogen bonds : bond 0.03283 ( 528) hydrogen bonds : angle 5.11659 ( 1407) link_BETA1-4 : bond 0.00420 ( 22) link_BETA1-4 : angle 2.62129 ( 66) link_NAG-ASN : bond 0.00311 ( 58) link_NAG-ASN : angle 2.21086 ( 174) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.9534 (mtm) cc_final: 0.9279 (mtt) REVERT: A 104 MET cc_start: 0.9019 (ppp) cc_final: 0.8711 (ppp) REVERT: A 150 MET cc_start: 0.8345 (tmm) cc_final: 0.7747 (tmm) REVERT: A 154 MET cc_start: 0.8453 (mmp) cc_final: 0.8131 (mmm) REVERT: B 45 TRP cc_start: 0.8531 (p90) cc_final: 0.8004 (p90) REVERT: B 104 MET cc_start: 0.9230 (ppp) cc_final: 0.8729 (ppp) REVERT: E 27 ASP cc_start: 0.9237 (t70) cc_final: 0.8706 (t70) REVERT: E 52 TYR cc_start: 0.8658 (t80) cc_final: 0.8279 (t80) REVERT: F 70 ASP cc_start: 0.9477 (t0) cc_final: 0.9179 (p0) REVERT: H 35 ASN cc_start: 0.9024 (m-40) cc_final: 0.8475 (m-40) REVERT: H 43 LYS cc_start: 0.8543 (pttm) cc_final: 0.8314 (mtmm) REVERT: I 626 MET cc_start: 0.7861 (ptt) cc_final: 0.7296 (ppp) REVERT: L 11 LEU cc_start: 0.9549 (pp) cc_final: 0.8974 (mp) REVERT: Z 648 GLU cc_start: 0.9327 (mt-10) cc_final: 0.9051 (mt-10) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.1425 time to fit residues: 24.9262 Evaluate side-chains 81 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 48 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 chunk 81 optimal weight: 4.9990 chunk 203 optimal weight: 4.9990 chunk 150 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 104 optimal weight: 20.0000 chunk 202 optimal weight: 7.9990 chunk 31 optimal weight: 9.9990 chunk 151 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 567 GLN ** Z 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.042006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.031574 restraints weight = 171428.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.032439 restraints weight = 87505.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.032833 restraints weight = 61450.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.032926 restraints weight = 56927.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.033020 restraints weight = 52050.772| |-----------------------------------------------------------------------------| r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.5216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 19273 Z= 0.304 Angle : 0.760 10.021 26283 Z= 0.369 Chirality : 0.047 0.237 3148 Planarity : 0.004 0.043 3170 Dihedral : 7.556 57.824 4095 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.09 % Favored : 89.87 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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 aren not related in a simple way. whole: -1.70 (0.18), residues: 2171 helix: 1.91 (0.28), residues: 341 sheet: -0.78 (0.21), residues: 612 loop : -2.33 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 192 TYR 0.022 0.002 TYR I 643 PHE 0.025 0.002 PHE E 100F TRP 0.031 0.003 TRP C 427 HIS 0.007 0.002 HIS B 216 Details of bonding type rmsd covalent geometry : bond 0.00665 (19154) covalent geometry : angle 0.72261 (25965) SS BOND : bond 0.00380 ( 39) SS BOND : angle 1.26252 ( 78) hydrogen bonds : bond 0.03883 ( 528) hydrogen bonds : angle 5.52434 ( 1407) link_BETA1-4 : bond 0.00444 ( 22) link_BETA1-4 : angle 2.71380 ( 66) link_NAG-ASN : bond 0.00517 ( 58) link_NAG-ASN : angle 2.40304 ( 174) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9068 (ppp) cc_final: 0.8762 (ppp) REVERT: B 104 MET cc_start: 0.9290 (ppp) cc_final: 0.8795 (ppp) REVERT: F 70 ASP cc_start: 0.9535 (t0) cc_final: 0.9304 (p0) REVERT: I 626 MET cc_start: 0.8066 (ptt) cc_final: 0.7464 (ppp) REVERT: J 584 GLU cc_start: 0.8866 (mp0) cc_final: 0.8611 (mp0) REVERT: Z 648 GLU cc_start: 0.9368 (mt-10) cc_final: 0.9092 (mt-10) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.1431 time to fit residues: 21.7089 Evaluate side-chains 67 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 21 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 109 optimal weight: 8.9990 chunk 189 optimal weight: 2.9990 chunk 199 optimal weight: 30.0000 chunk 33 optimal weight: 6.9990 chunk 216 optimal weight: 0.0070 chunk 185 optimal weight: 2.9990 chunk 207 optimal weight: 0.7980 chunk 128 optimal weight: 5.9990 overall best weight: 1.9604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.043159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.032258 restraints weight = 168129.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.033348 restraints weight = 90808.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.034052 restraints weight = 62894.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.034503 restraints weight = 50063.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.034800 restraints weight = 43432.082| |-----------------------------------------------------------------------------| r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.5035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19273 Z= 0.131 Angle : 0.641 10.526 26283 Z= 0.305 Chirality : 0.046 0.239 3148 Planarity : 0.004 0.041 3170 Dihedral : 7.191 59.226 4095 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.65 % Favored : 92.31 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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 aren not related in a simple way. whole: -1.49 (0.18), residues: 2171 helix: 1.84 (0.28), residues: 365 sheet: -0.78 (0.21), residues: 645 loop : -2.13 (0.17), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 192 TYR 0.019 0.001 TYR I 643 PHE 0.012 0.001 PHE E 100F TRP 0.039 0.002 TRP B 479 HIS 0.004 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00295 (19154) covalent geometry : angle 0.60174 (25965) SS BOND : bond 0.00229 ( 39) SS BOND : angle 1.03212 ( 78) hydrogen bonds : bond 0.03299 ( 528) hydrogen bonds : angle 5.14164 ( 1407) link_BETA1-4 : bond 0.00420 ( 22) link_BETA1-4 : angle 2.67961 ( 66) link_NAG-ASN : bond 0.00304 ( 58) link_NAG-ASN : angle 2.20886 ( 174) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2975.39 seconds wall clock time: 52 minutes 44.05 seconds (3164.05 seconds total)