Starting phenix.real_space_refine on Mon May 19 17:59:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8to9_41440/05_2025/8to9_41440.cif Found real_map, /net/cci-nas-00/data/ceres_data/8to9_41440/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8to9_41440/05_2025/8to9_41440.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8to9_41440/05_2025/8to9_41440.map" model { file = "/net/cci-nas-00/data/ceres_data/8to9_41440/05_2025/8to9_41440.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8to9_41440/05_2025/8to9_41440.cif" } resolution = 4.03 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 13.00, per 1000 atoms: 0.69 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: 5.48 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 2.75 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: 6.73 Time building geometry restraints manager: 6.38 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: 2.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.850 Check model and map are aligned: 0.150 Set scattering table: 0.210 Process input model: 47.220 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.160 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:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.580 ------------------------------------------------------------------------------- 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 : 5.45 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.075 0.002 TRP B 479 HIS 0.012 0.001 HIS C 105 PHE 0.022 0.002 PHE A 210 TYR 0.017 0.001 TYR I 643 ARG 0.005 0.000 ARG D 41 Details of bonding type rmsd link_NAG-ASN : bond 0.00502 ( 58) link_NAG-ASN : angle 2.53309 ( 174) link_BETA1-4 : bond 0.00607 ( 22) link_BETA1-4 : angle 3.93677 ( 66) hydrogen bonds : bond 0.24529 ( 528) hydrogen bonds : angle 9.09606 ( 1407) SS BOND : bond 0.00276 ( 39) SS BOND : angle 0.95925 ( 78) covalent geometry : bond 0.00530 (19154) covalent geometry : angle 0.97654 (25965) *********************** 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 : 2.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.7857 (tmm) cc_final: 0.7620 (tmm) REVERT: A 154 MET cc_start: 0.7714 (mmp) cc_final: 0.7280 (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: 0.8422 (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: 0.9040 (mt) REVERT: H 27 ASP cc_start: 0.8234 (t70) cc_final: 0.7899 (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: 0.7397 (mmp) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.2890 time to fit residues: 69.5492 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 : 2.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 184 optimal weight: 10.0000 chunk 165 optimal weight: 10.0000 chunk 92 optimal weight: 8.9990 chunk 56 optimal weight: 6.9990 chunk 111 optimal weight: 5.9990 chunk 88 optimal weight: 7.9990 chunk 171 optimal weight: 10.0000 chunk 66 optimal weight: 0.6980 chunk 104 optimal weight: 4.9990 chunk 127 optimal weight: 0.7980 chunk 198 optimal weight: 7.9990 overall best weight: 3.8986 ------------------------------------------------------------------------------- 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** F 38 GLN G 27 GLN ** Z 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.050020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.039709 restraints weight = 184014.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.040732 restraints weight = 105346.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.041681 restraints weight = 70064.470| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.136 19273 Z= 0.215 Angle : 0.673 9.267 26283 Z= 0.327 Chirality : 0.047 0.247 3148 Planarity : 0.005 0.058 3170 Dihedral : 9.070 65.899 4095 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 0.10 % Allowed : 3.99 % Favored : 95.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.18), residues: 2171 helix: 1.32 (0.28), residues: 348 sheet: -0.61 (0.22), residues: 582 loop : -2.20 (0.16), residues: 1241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 479 HIS 0.004 0.001 HIS A 105 PHE 0.023 0.002 PHE E 100F TYR 0.019 0.002 TYR E 52 ARG 0.006 0.001 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00434 ( 58) link_NAG-ASN : angle 1.97856 ( 174) link_BETA1-4 : bond 0.00448 ( 22) link_BETA1-4 : angle 2.51106 ( 66) hydrogen bonds : bond 0.04118 ( 528) hydrogen bonds : angle 6.22301 ( 1407) SS BOND : bond 0.00280 ( 39) SS BOND : angle 0.90634 ( 78) covalent geometry : bond 0.00471 (19154) covalent geometry : angle 0.64320 (25965) *********************** 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 122 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 120 time to evaluate : 2.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.8088 (tmm) cc_final: 0.7648 (tmm) REVERT: A 154 MET cc_start: 0.7833 (mmp) cc_final: 0.7570 (mmm) REVERT: A 376 PHE cc_start: 0.8430 (p90) cc_final: 0.8148 (p90) REVERT: D 64 GLU cc_start: 0.8897 (mm-30) cc_final: 0.8583 (mp0) REVERT: D 75 ASN cc_start: 0.8563 (t0) cc_final: 0.8328 (t0) REVERT: H 27 ASP cc_start: 0.8583 (t70) cc_final: 0.8145 (t0) REVERT: L 11 LEU cc_start: 0.9010 (pt) cc_final: 0.8291 (mp) REVERT: Z 530 MET cc_start: 0.7818 (mpp) cc_final: 0.7265 (mpp) REVERT: Z 648 GLU cc_start: 0.9226 (mt-10) cc_final: 0.9005 (mt-10) outliers start: 2 outliers final: 0 residues processed: 122 average time/residue: 0.2727 time to fit residues: 55.0701 Evaluate side-chains 93 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 2.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 113 optimal weight: 6.9990 chunk 191 optimal weight: 4.9990 chunk 164 optimal weight: 8.9990 chunk 214 optimal weight: 9.9990 chunk 111 optimal weight: 5.9990 chunk 150 optimal weight: 20.0000 chunk 196 optimal weight: 0.0980 chunk 181 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 189 optimal weight: 9.9990 chunk 22 optimal weight: 8.9990 overall best weight: 4.6188 ------------------------------------------------------------------------------- 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** E 39 GLN G 38 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.044971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.034110 restraints weight = 167786.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.035194 restraints weight = 92864.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.035912 restraints weight = 64638.761| |-----------------------------------------------------------------------------| r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 19273 Z= 0.233 Angle : 0.677 9.181 26283 Z= 0.330 Chirality : 0.046 0.244 3148 Planarity : 0.004 0.050 3170 Dihedral : 7.889 59.355 4095 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.32 % Favored : 92.63 % Rotamer: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.18), residues: 2171 helix: 2.19 (0.29), residues: 330 sheet: -0.71 (0.21), residues: 621 loop : -2.11 (0.17), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP J 631 HIS 0.009 0.002 HIS C 105 PHE 0.021 0.002 PHE E 100F TYR 0.019 0.002 TYR E 52 ARG 0.007 0.001 ARG J 579 Details of bonding type rmsd link_NAG-ASN : bond 0.00431 ( 58) link_NAG-ASN : angle 2.08621 ( 174) link_BETA1-4 : bond 0.00345 ( 22) link_BETA1-4 : angle 2.59676 ( 66) hydrogen bonds : bond 0.04039 ( 528) hydrogen bonds : angle 5.81344 ( 1407) SS BOND : bond 0.00287 ( 39) SS BOND : angle 0.99899 ( 78) covalent geometry : bond 0.00503 (19154) covalent geometry : angle 0.64400 (25965) *********************** 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 110 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 2.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.8209 (tmm) cc_final: 0.7718 (tmm) REVERT: A 154 MET cc_start: 0.8294 (mmp) cc_final: 0.7745 (mmm) REVERT: D 30 LYS cc_start: 0.9296 (mmmm) cc_final: 0.8984 (mmmm) REVERT: D 64 GLU cc_start: 0.9175 (mm-30) cc_final: 0.8929 (mm-30) REVERT: D 75 ASN cc_start: 0.8747 (t0) cc_final: 0.8310 (t0) REVERT: J 530 MET cc_start: 0.8535 (pmm) cc_final: 0.8190 (pmm) REVERT: J 584 GLU cc_start: 0.8860 (mp0) cc_final: 0.8565 (mp0) REVERT: Z 648 GLU cc_start: 0.9385 (mt-10) cc_final: 0.9114 (mt-10) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.2808 time to fit residues: 50.2479 Evaluate side-chains 88 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 1.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 109 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 32 optimal weight: 8.9990 chunk 91 optimal weight: 9.9990 chunk 132 optimal weight: 4.9990 chunk 122 optimal weight: 8.9990 chunk 61 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 chunk 162 optimal weight: 7.9990 chunk 57 optimal weight: 10.0000 chunk 182 optimal weight: 30.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.047254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.036730 restraints weight = 186085.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.037681 restraints weight = 104081.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.037973 restraints weight = 70869.000| |-----------------------------------------------------------------------------| r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 19273 Z= 0.218 Angle : 0.657 9.206 26283 Z= 0.319 Chirality : 0.046 0.243 3148 Planarity : 0.004 0.058 3170 Dihedral : 7.359 55.606 4095 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.65 % Favored : 92.31 % Rotamer: Outliers : 0.05 % Allowed : 3.34 % Favored : 96.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.18), residues: 2171 helix: 2.24 (0.29), residues: 335 sheet: -0.72 (0.21), residues: 609 loop : -2.13 (0.17), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 479 HIS 0.007 0.001 HIS A 287 PHE 0.024 0.002 PHE E 100F TYR 0.019 0.002 TYR E 52 ARG 0.004 0.001 ARG B 476 Details of bonding type rmsd link_NAG-ASN : bond 0.00336 ( 58) link_NAG-ASN : angle 2.12803 ( 174) link_BETA1-4 : bond 0.00331 ( 22) link_BETA1-4 : angle 2.55707 ( 66) hydrogen bonds : bond 0.03550 ( 528) hydrogen bonds : angle 5.51337 ( 1407) SS BOND : bond 0.00264 ( 39) SS BOND : angle 1.07472 ( 78) covalent geometry : bond 0.00475 (19154) covalent geometry : angle 0.62144 (25965) *********************** 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 112 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 111 time to evaluate : 2.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.8276 (tmm) cc_final: 0.7783 (tmm) REVERT: A 154 MET cc_start: 0.8180 (mmp) cc_final: 0.7697 (tpp) REVERT: D 75 ASN cc_start: 0.8681 (t0) cc_final: 0.8274 (t0) REVERT: I 626 MET cc_start: 0.6902 (ptt) cc_final: 0.6453 (ppp) REVERT: J 530 MET cc_start: 0.8500 (pmm) cc_final: 0.8182 (pmm) REVERT: Z 530 MET cc_start: 0.8000 (mpp) cc_final: 0.7248 (mpp) REVERT: Z 648 GLU cc_start: 0.9176 (mt-10) cc_final: 0.8953 (mt-10) outliers start: 1 outliers final: 0 residues processed: 112 average time/residue: 0.2817 time to fit residues: 51.5410 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 : 2.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 64 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 126 optimal weight: 9.9990 chunk 9 optimal weight: 0.0970 chunk 207 optimal weight: 6.9990 chunk 128 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 141 optimal weight: 0.9980 chunk 171 optimal weight: 9.9990 chunk 190 optimal weight: 8.9990 overall best weight: 5.4184 ------------------------------------------------------------------------------- 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 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 ASN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.042739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.032292 restraints weight = 171497.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.033194 restraints weight = 87243.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.033623 restraints weight = 60896.161| |-----------------------------------------------------------------------------| r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.4345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 19273 Z= 0.278 Angle : 0.737 9.803 26283 Z= 0.360 Chirality : 0.047 0.234 3148 Planarity : 0.004 0.043 3170 Dihedral : 7.522 57.777 4095 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.26 % Favored : 90.70 % Rotamer: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.18), residues: 2171 helix: 2.02 (0.28), residues: 341 sheet: -0.91 (0.21), residues: 624 loop : -2.22 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP J 571 HIS 0.007 0.002 HIS C 105 PHE 0.029 0.002 PHE E 100F TYR 0.017 0.002 TYR E 33 ARG 0.007 0.001 ARG J 579 Details of bonding type rmsd link_NAG-ASN : bond 0.00450 ( 58) link_NAG-ASN : angle 2.28331 ( 174) link_BETA1-4 : bond 0.00440 ( 22) link_BETA1-4 : angle 2.60142 ( 66) hydrogen bonds : bond 0.03929 ( 528) hydrogen bonds : angle 5.61006 ( 1407) SS BOND : bond 0.00365 ( 39) SS BOND : angle 1.24400 ( 78) covalent geometry : bond 0.00607 (19154) covalent geometry : angle 0.70198 (25965) *********************** 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 105 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 2.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9097 (ppp) cc_final: 0.8828 (ppp) REVERT: A 150 MET cc_start: 0.8312 (tmm) cc_final: 0.7777 (tmm) REVERT: A 154 MET cc_start: 0.8458 (mmp) cc_final: 0.7762 (tpp) REVERT: D 75 ASN cc_start: 0.8829 (t0) cc_final: 0.8367 (t0) REVERT: E 52 TYR cc_start: 0.8845 (t80) cc_final: 0.8617 (t80) REVERT: I 626 MET cc_start: 0.8010 (ptt) cc_final: 0.7249 (ppp) REVERT: I 643 TYR cc_start: 0.9712 (m-80) cc_final: 0.9255 (m-80) REVERT: J 530 MET cc_start: 0.8686 (pmm) cc_final: 0.8421 (pmm) REVERT: J 584 GLU cc_start: 0.8918 (mp0) cc_final: 0.8585 (mp0) REVERT: L 11 LEU cc_start: 0.9584 (pt) cc_final: 0.9202 (mp) REVERT: Z 648 GLU cc_start: 0.9347 (mt-10) cc_final: 0.9084 (mt-10) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.3050 time to fit residues: 50.6856 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 : 2.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 77 optimal weight: 4.9990 chunk 196 optimal weight: 9.9990 chunk 102 optimal weight: 2.9990 chunk 129 optimal weight: 9.9990 chunk 76 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 chunk 90 optimal weight: 40.0000 chunk 182 optimal weight: 6.9990 chunk 57 optimal weight: 20.0000 chunk 210 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 HIS ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 332 ASN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.042295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.031358 restraints weight = 171067.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.032387 restraints weight = 94275.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.033078 restraints weight = 65898.545| |-----------------------------------------------------------------------------| r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.4822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 19273 Z= 0.283 Angle : 0.735 9.201 26283 Z= 0.358 Chirality : 0.047 0.235 3148 Planarity : 0.005 0.073 3170 Dihedral : 7.745 57.721 4095 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.94 % Favored : 91.02 % Rotamer: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.18), residues: 2171 helix: 1.87 (0.27), residues: 341 sheet: -0.88 (0.21), residues: 609 loop : -2.33 (0.17), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP Z 596 HIS 0.008 0.001 HIS C 105 PHE 0.032 0.002 PHE E 100F TYR 0.018 0.002 TYR C 191 ARG 0.016 0.001 ARG C 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00465 ( 58) link_NAG-ASN : angle 2.47778 ( 174) link_BETA1-4 : bond 0.00389 ( 22) link_BETA1-4 : angle 2.66649 ( 66) hydrogen bonds : bond 0.03850 ( 528) hydrogen bonds : angle 5.62094 ( 1407) SS BOND : bond 0.00392 ( 39) SS BOND : angle 1.32928 ( 78) covalent geometry : bond 0.00617 (19154) covalent geometry : angle 0.69480 (25965) *********************** 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 101 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 2.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9094 (ppp) cc_final: 0.8850 (ppp) REVERT: A 150 MET cc_start: 0.8395 (tmm) cc_final: 0.7832 (tmm) REVERT: A 154 MET cc_start: 0.8537 (mmp) cc_final: 0.8200 (mmm) REVERT: B 104 MET cc_start: 0.9557 (tmm) cc_final: 0.9350 (tmm) REVERT: E 52 TYR cc_start: 0.8823 (t80) cc_final: 0.8602 (t80) REVERT: H 43 LYS cc_start: 0.8656 (pttm) cc_final: 0.8416 (mtmm) REVERT: I 626 MET cc_start: 0.8101 (ptt) cc_final: 0.7483 (ppp) REVERT: J 647 GLU cc_start: 0.9597 (tm-30) cc_final: 0.9387 (pp20) REVERT: Z 530 MET cc_start: 0.8363 (mpp) cc_final: 0.7546 (mpp) REVERT: Z 648 GLU cc_start: 0.9375 (mt-10) cc_final: 0.9120 (mt-10) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.2936 time to fit residues: 47.7617 Evaluate side-chains 78 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 2.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 20 optimal weight: 9.9990 chunk 86 optimal weight: 0.9990 chunk 75 optimal weight: 8.9990 chunk 37 optimal weight: 9.9990 chunk 164 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 55 optimal weight: 0.0040 chunk 70 optimal weight: 7.9990 chunk 24 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 chunk 152 optimal weight: 6.9990 overall best weight: 3.2000 ------------------------------------------------------------------------------- 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 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 ASN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN F 37 GLN ** I 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 650 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.042861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.031943 restraints weight = 166562.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.033009 restraints weight = 91708.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.033691 restraints weight = 64070.645| |-----------------------------------------------------------------------------| r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.4829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19273 Z= 0.176 Angle : 0.655 9.346 26283 Z= 0.313 Chirality : 0.046 0.243 3148 Planarity : 0.004 0.042 3170 Dihedral : 7.469 56.137 4095 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.61 % Favored : 91.34 % Rotamer: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.18), residues: 2171 helix: 2.06 (0.28), residues: 341 sheet: -0.87 (0.21), residues: 630 loop : -2.26 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP J 571 HIS 0.004 0.001 HIS B 374 PHE 0.018 0.001 PHE E 100F TYR 0.023 0.002 TYR I 643 ARG 0.012 0.001 ARG C 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00301 ( 58) link_NAG-ASN : angle 2.32281 ( 174) link_BETA1-4 : bond 0.00364 ( 22) link_BETA1-4 : angle 2.64904 ( 66) hydrogen bonds : bond 0.03480 ( 528) hydrogen bonds : angle 5.35220 ( 1407) SS BOND : bond 0.00272 ( 39) SS BOND : angle 1.14792 ( 78) covalent geometry : bond 0.00389 (19154) covalent geometry : angle 0.61322 (25965) *********************** 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 105 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 2.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.9556 (mtm) cc_final: 0.9315 (mtt) REVERT: A 104 MET cc_start: 0.9103 (ppp) cc_final: 0.8874 (ppp) REVERT: A 150 MET cc_start: 0.8371 (tmm) cc_final: 0.7784 (tmm) REVERT: A 154 MET cc_start: 0.8486 (mmp) cc_final: 0.8133 (mmm) REVERT: B 104 MET cc_start: 0.9560 (tmm) cc_final: 0.9286 (tmm) REVERT: D 64 GLU cc_start: 0.9124 (mm-30) cc_final: 0.8920 (mm-30) REVERT: E 27 ASP cc_start: 0.9290 (t70) cc_final: 0.8780 (t70) REVERT: H 43 LYS cc_start: 0.8662 (pttm) cc_final: 0.8409 (mtmm) REVERT: I 626 MET cc_start: 0.8034 (ptt) cc_final: 0.7441 (ppp) REVERT: J 647 GLU cc_start: 0.9582 (tm-30) cc_final: 0.9376 (pp20) REVERT: L 11 LEU cc_start: 0.9575 (pt) cc_final: 0.9243 (mp) REVERT: Z 530 MET cc_start: 0.8371 (mpp) cc_final: 0.7460 (mpp) REVERT: Z 648 GLU cc_start: 0.9361 (mt-10) cc_final: 0.9105 (mt-10) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.2901 time to fit residues: 48.8953 Evaluate side-chains 79 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 2.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 211 optimal weight: 9.9990 chunk 47 optimal weight: 0.9990 chunk 205 optimal weight: 10.0000 chunk 64 optimal weight: 0.4980 chunk 11 optimal weight: 20.0000 chunk 48 optimal weight: 0.0570 chunk 201 optimal weight: 0.7980 chunk 136 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 134 optimal weight: 7.9990 chunk 135 optimal weight: 0.9990 overall best weight: 0.6300 ------------------------------------------------------------------------------- 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 ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 GLN ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35BASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 650 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.043978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.033134 restraints weight = 166403.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.034239 restraints weight = 89687.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.034976 restraints weight = 61935.777| |-----------------------------------------------------------------------------| r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.4638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 19273 Z= 0.108 Angle : 0.627 9.459 26283 Z= 0.297 Chirality : 0.046 0.245 3148 Planarity : 0.004 0.070 3170 Dihedral : 7.057 56.649 4095 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.14 % Favored : 92.81 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.18), residues: 2171 helix: 2.11 (0.28), residues: 352 sheet: -0.77 (0.21), residues: 654 loop : -2.13 (0.17), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP J 571 HIS 0.003 0.001 HIS B 330 PHE 0.009 0.001 PHE G 71 TYR 0.021 0.001 TYR B 318 ARG 0.010 0.000 ARG B 304 Details of bonding type rmsd link_NAG-ASN : bond 0.00356 ( 58) link_NAG-ASN : angle 2.17489 ( 174) link_BETA1-4 : bond 0.00444 ( 22) link_BETA1-4 : angle 2.64251 ( 66) hydrogen bonds : bond 0.03152 ( 528) hydrogen bonds : angle 5.07005 ( 1407) SS BOND : bond 0.00220 ( 39) SS BOND : angle 0.96011 ( 78) covalent geometry : bond 0.00237 (19154) covalent geometry : angle 0.58786 (25965) *********************** 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 110 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 2.210 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.9512 (mtm) cc_final: 0.9265 (mtt) REVERT: A 104 MET cc_start: 0.9092 (ppp) cc_final: 0.8857 (ppp) REVERT: A 150 MET cc_start: 0.8342 (tmm) cc_final: 0.7799 (tmm) REVERT: A 154 MET cc_start: 0.8441 (mmp) cc_final: 0.7781 (tpp) REVERT: B 104 MET cc_start: 0.9559 (tmm) cc_final: 0.9254 (tmm) REVERT: D 64 GLU cc_start: 0.9114 (mm-30) cc_final: 0.8877 (mm-30) REVERT: E 27 ASP cc_start: 0.9251 (t70) cc_final: 0.8743 (t70) REVERT: H 43 LYS cc_start: 0.8589 (pttm) cc_final: 0.8387 (mtmm) REVERT: I 626 MET cc_start: 0.7859 (ptt) cc_final: 0.7272 (ppp) REVERT: J 584 GLU cc_start: 0.8875 (mp0) cc_final: 0.8607 (mp0) REVERT: J 647 GLU cc_start: 0.9577 (tm-30) cc_final: 0.9374 (pp20) REVERT: L 11 LEU cc_start: 0.9580 (pt) cc_final: 0.9235 (mp) REVERT: Z 530 MET cc_start: 0.8353 (mpp) cc_final: 0.7425 (mpp) REVERT: Z 648 GLU cc_start: 0.9348 (mt-10) cc_final: 0.9074 (mt-10) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.2850 time to fit residues: 50.9937 Evaluate side-chains 80 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 2.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 23 optimal weight: 9.9990 chunk 84 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 154 optimal weight: 6.9990 chunk 68 optimal weight: 9.9990 chunk 139 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 chunk 76 optimal weight: 9.9990 chunk 42 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 203 GLN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 650 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.043147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.032292 restraints weight = 168304.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.033383 restraints weight = 91414.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.034089 restraints weight = 63210.778| |-----------------------------------------------------------------------------| r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.4835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19273 Z= 0.167 Angle : 0.642 9.375 26283 Z= 0.304 Chirality : 0.046 0.244 3148 Planarity : 0.004 0.050 3170 Dihedral : 7.056 58.244 4095 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.43 % Favored : 91.52 % Rotamer: Outliers : 0.05 % Allowed : 0.40 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.18), residues: 2171 helix: 1.75 (0.28), residues: 377 sheet: -0.73 (0.21), residues: 651 loop : -2.10 (0.18), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP J 571 HIS 0.004 0.001 HIS B 216 PHE 0.020 0.001 PHE E 100F TYR 0.022 0.002 TYR B 318 ARG 0.007 0.000 ARG C 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00310 ( 58) link_NAG-ASN : angle 2.28021 ( 174) link_BETA1-4 : bond 0.00364 ( 22) link_BETA1-4 : angle 2.59150 ( 66) hydrogen bonds : bond 0.03247 ( 528) hydrogen bonds : angle 5.05097 ( 1407) SS BOND : bond 0.00285 ( 39) SS BOND : angle 1.00780 ( 78) covalent geometry : bond 0.00371 (19154) covalent geometry : angle 0.60167 (25965) *********************** 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 99 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 98 time to evaluate : 2.112 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9111 (ppp) cc_final: 0.8883 (ppp) REVERT: A 150 MET cc_start: 0.8375 (tmm) cc_final: 0.7755 (tmm) REVERT: A 154 MET cc_start: 0.8458 (mmp) cc_final: 0.8169 (mmm) REVERT: D 64 GLU cc_start: 0.9112 (mm-30) cc_final: 0.8880 (mm-30) REVERT: E 27 ASP cc_start: 0.9231 (t70) cc_final: 0.8758 (t70) REVERT: F 70 ASP cc_start: 0.9509 (t0) cc_final: 0.9229 (p0) REVERT: H 43 LYS cc_start: 0.8627 (pttm) cc_final: 0.8395 (mtmm) REVERT: I 626 MET cc_start: 0.7931 (ptt) cc_final: 0.7347 (ppp) REVERT: J 584 GLU cc_start: 0.8884 (mp0) cc_final: 0.8622 (mp0) REVERT: J 626 MET cc_start: 0.8481 (ptm) cc_final: 0.8273 (ptm) REVERT: J 647 GLU cc_start: 0.9567 (tm-30) cc_final: 0.9359 (pp20) REVERT: Z 530 MET cc_start: 0.8382 (mpp) cc_final: 0.7386 (mpp) REVERT: Z 648 GLU cc_start: 0.9340 (mt-10) cc_final: 0.9072 (mt-10) outliers start: 1 outliers final: 0 residues processed: 99 average time/residue: 0.3008 time to fit residues: 48.4421 Evaluate side-chains 78 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 2.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 111 optimal weight: 9.9990 chunk 202 optimal weight: 0.5980 chunk 181 optimal weight: 4.9990 chunk 193 optimal weight: 0.0980 chunk 161 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 119 optimal weight: 0.7980 chunk 150 optimal weight: 20.0000 chunk 33 optimal weight: 5.9990 chunk 210 optimal weight: 20.0000 chunk 76 optimal weight: 8.9990 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.043332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.032463 restraints weight = 167076.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.033540 restraints weight = 91064.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.034229 restraints weight = 63196.404| |-----------------------------------------------------------------------------| r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.4896 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= 0.143 Angle : 0.629 9.406 26283 Z= 0.297 Chirality : 0.046 0.236 3148 Planarity : 0.003 0.043 3170 Dihedral : 7.002 59.740 4095 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.97 % Favored : 91.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.18), residues: 2171 helix: 1.75 (0.28), residues: 377 sheet: -0.71 (0.21), residues: 651 loop : -2.06 (0.18), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP E 47 HIS 0.003 0.001 HIS B 330 PHE 0.017 0.001 PHE E 100F TYR 0.020 0.001 TYR I 643 ARG 0.007 0.000 ARG C 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00289 ( 58) link_NAG-ASN : angle 2.19752 ( 174) link_BETA1-4 : bond 0.00389 ( 22) link_BETA1-4 : angle 2.61786 ( 66) hydrogen bonds : bond 0.03149 ( 528) hydrogen bonds : angle 4.98262 ( 1407) SS BOND : bond 0.00240 ( 39) SS BOND : angle 0.99416 ( 78) covalent geometry : bond 0.00318 (19154) covalent geometry : angle 0.58932 (25965) ********************** 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 103 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 2.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.9525 (mtm) cc_final: 0.9297 (mtt) REVERT: A 104 MET cc_start: 0.9106 (ppp) cc_final: 0.8851 (ppp) REVERT: D 64 GLU cc_start: 0.9105 (mm-30) cc_final: 0.8858 (mm-30) REVERT: E 27 ASP cc_start: 0.9211 (t70) cc_final: 0.8755 (t70) REVERT: F 70 ASP cc_start: 0.9514 (t0) cc_final: 0.9228 (p0) REVERT: H 43 LYS cc_start: 0.8636 (pttm) cc_final: 0.8423 (mtmm) REVERT: I 626 MET cc_start: 0.7892 (ptt) cc_final: 0.7307 (ppp) REVERT: J 584 GLU cc_start: 0.8852 (mp0) cc_final: 0.8563 (mp0) REVERT: J 647 GLU cc_start: 0.9578 (tm-30) cc_final: 0.9367 (pp20) REVERT: Z 530 MET cc_start: 0.8384 (mpp) cc_final: 0.7375 (mpp) REVERT: Z 648 GLU cc_start: 0.9326 (mt-10) cc_final: 0.9059 (mt-10) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.2899 time to fit residues: 47.6886 Evaluate side-chains 78 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 1.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 25 optimal weight: 50.0000 chunk 187 optimal weight: 10.0000 chunk 98 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 202 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 chunk 91 optimal weight: 9.9990 chunk 100 optimal weight: 4.9990 chunk 209 optimal weight: 20.0000 chunk 173 optimal weight: 5.9990 chunk 131 optimal weight: 0.8980 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.043166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.032319 restraints weight = 168036.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.033392 restraints weight = 91390.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.034076 restraints weight = 63485.820| |-----------------------------------------------------------------------------| r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.4981 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= 0.151 Angle : 0.638 10.783 26283 Z= 0.301 Chirality : 0.046 0.233 3148 Planarity : 0.003 0.040 3170 Dihedral : 6.986 58.511 4095 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.20 % Favored : 91.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.18), residues: 2171 helix: 1.67 (0.28), residues: 383 sheet: -0.71 (0.21), residues: 651 loop : -2.06 (0.18), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 47 HIS 0.003 0.001 HIS B 330 PHE 0.016 0.001 PHE E 100F TYR 0.019 0.001 TYR I 643 ARG 0.007 0.000 ARG C 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00308 ( 58) link_NAG-ASN : angle 2.22416 ( 174) link_BETA1-4 : bond 0.00380 ( 22) link_BETA1-4 : angle 2.61969 ( 66) hydrogen bonds : bond 0.03130 ( 528) hydrogen bonds : angle 4.95868 ( 1407) SS BOND : bond 0.00236 ( 39) SS BOND : angle 1.01249 ( 78) covalent geometry : bond 0.00336 (19154) covalent geometry : angle 0.59820 (25965) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5234.97 seconds wall clock time: 93 minutes 31.00 seconds (5611.00 seconds total)