Starting phenix.real_space_refine on Mon Jun 16 16:07:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8to9_41440/06_2025/8to9_41440.cif Found real_map, /net/cci-nas-00/data/ceres_data/8to9_41440/06_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_41440/06_2025/8to9_41440.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8to9_41440/06_2025/8to9_41440.map" model { file = "/net/cci-nas-00/data/ceres_data/8to9_41440/06_2025/8to9_41440.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8to9_41440/06_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 11.29, per 1000 atoms: 0.60 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: 5.60 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: 2.26 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: 6.67 Time building geometry restraints manager: 6.55 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: 3.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.770 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 44.310 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.120 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.990 ------------------------------------------------------------------------------- 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 : 2.030 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: 0.3025 time to fit residues: 72.9775 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 : 2.024 ------------------------------------------------------------------------------- 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 = 184014.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.040733 restraints weight = 105349.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.041675 restraints weight = 70035.764| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 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 : 2.022 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: 0.8429 (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: 0.8562 (t0) cc_final: 0.8328 (t0) REVERT: H 27 ASP cc_start: 0.8585 (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: 0.7266 (mpp) REVERT: Z 648 GLU cc_start: 0.9226 (mt-10) cc_final: 0.9006 (mt-10) outliers start: 2 outliers final: 0 residues processed: 122 average time/residue: 0.2614 time to fit residues: 53.3152 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 : 2.377 ------------------------------------------------------------------------------- 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: 9.9990 chunk 214 optimal weight: 10.0000 chunk 111 optimal weight: 5.9990 chunk 150 optimal weight: 20.0000 chunk 196 optimal weight: 0.5980 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: 4.7188 ------------------------------------------------------------------------------- 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** B 105 HIS C 105 HIS ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN ** F 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 GLN ** I 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 567 GLN ** Z 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.047192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.036625 restraints weight = 184975.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.037564 restraints weight = 103373.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.037713 restraints weight = 70932.192| |-----------------------------------------------------------------------------| r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3315 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= 0.244 Angle : 0.724 9.258 26283 Z= 0.354 Chirality : 0.047 0.249 3148 Planarity : 0.005 0.050 3170 Dihedral : 7.748 57.366 4095 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.20 % Favored : 91.75 % Rotamer: Outliers : 0.05 % Allowed : 5.81 % Favored : 94.14 % 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: -1.48 (0.18), residues: 2171 helix: 2.15 (0.28), residues: 329 sheet: -0.70 (0.22), residues: 603 loop : -2.11 (0.17), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP J 631 HIS 0.010 0.002 HIS A 287 PHE 0.023 0.002 PHE E 100F TYR 0.021 0.002 TYR E 52 ARG 0.007 0.001 ARG J 644 Details of bonding type rmsd link_NAG-ASN : bond 0.00527 ( 58) link_NAG-ASN : angle 2.15602 ( 174) link_BETA1-4 : bond 0.00505 ( 22) link_BETA1-4 : angle 2.67867 ( 66) hydrogen bonds : bond 0.04336 ( 528) hydrogen bonds : angle 5.73789 ( 1407) SS BOND : bond 0.00312 ( 39) SS BOND : angle 1.13005 ( 78) covalent geometry : bond 0.00528 (19154) covalent geometry : angle 0.69117 (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 113 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 112 time to evaluate : 2.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.8233 (tmm) cc_final: 0.7746 (tmm) REVERT: A 154 MET cc_start: 0.8153 (mmp) cc_final: 0.7519 (mmp) REVERT: D 75 ASN cc_start: 0.8685 (t0) cc_final: 0.8282 (t0) REVERT: I 643 TYR cc_start: 0.9464 (m-80) cc_final: 0.9236 (m-80) REVERT: J 530 MET cc_start: 0.8306 (pmm) cc_final: 0.7952 (pmm) REVERT: Z 648 GLU cc_start: 0.9195 (mt-10) cc_final: 0.8964 (mt-10) outliers start: 1 outliers final: 1 residues processed: 112 average time/residue: 0.2763 time to fit residues: 50.5904 Evaluate side-chains 86 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 2.044 ------------------------------------------------------------------------------- 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: 8.9990 chunk 130 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 91 optimal weight: 0.0050 chunk 132 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 162 optimal weight: 9.9990 chunk 57 optimal weight: 10.0000 chunk 182 optimal weight: 4.9990 overall best weight: 2.2002 ------------------------------------------------------------------------------- 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 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 = 0.3456 r_free = 0.3456 target = 0.047984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.037722 restraints weight = 185256.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.038703 restraints weight = 101838.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.038984 restraints weight = 69015.483| |-----------------------------------------------------------------------------| r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19273 Z= 0.137 Angle : 0.610 9.337 26283 Z= 0.293 Chirality : 0.046 0.243 3148 Planarity : 0.004 0.044 3170 Dihedral : 7.209 55.431 4095 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.91 % Favored : 93.04 % Rotamer: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % 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: -1.37 (0.18), residues: 2171 helix: 2.15 (0.28), residues: 347 sheet: -0.68 (0.22), residues: 603 loop : -2.05 (0.17), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B 479 HIS 0.005 0.001 HIS A 287 PHE 0.013 0.001 PHE E 100F TYR 0.019 0.001 TYR E 52 ARG 0.004 0.000 ARG C 304 Details of bonding type rmsd link_NAG-ASN : bond 0.00296 ( 58) link_NAG-ASN : angle 2.02792 ( 174) link_BETA1-4 : bond 0.00371 ( 22) link_BETA1-4 : angle 2.56110 ( 66) hydrogen bonds : bond 0.03264 ( 528) hydrogen bonds : angle 5.35855 ( 1407) SS BOND : bond 0.00236 ( 39) SS BOND : angle 0.91657 ( 78) covalent geometry : bond 0.00301 (19154) covalent geometry : angle 0.57405 (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 119 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 2.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.8309 (tmm) cc_final: 0.7791 (tmm) REVERT: A 154 MET cc_start: 0.8125 (mmp) cc_final: 0.7647 (tpp) REVERT: D 75 ASN cc_start: 0.8637 (t0) cc_final: 0.8246 (t0) REVERT: H 35 ASN cc_start: 0.8614 (m110) cc_final: 0.8139 (t0) REVERT: J 530 MET cc_start: 0.8502 (pmm) cc_final: 0.8158 (pmm) REVERT: Z 530 MET cc_start: 0.7941 (mpp) cc_final: 0.7398 (mpp) REVERT: Z 648 GLU cc_start: 0.9170 (mt-10) cc_final: 0.8940 (mt-10) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.3157 time to fit residues: 59.6361 Evaluate side-chains 91 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 2.046 ------------------------------------------------------------------------------- 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: 0.0170 chunk 1 optimal weight: 8.9990 chunk 126 optimal weight: 5.9990 chunk 9 optimal weight: 0.0570 chunk 207 optimal weight: 0.8980 chunk 128 optimal weight: 10.0000 chunk 53 optimal weight: 0.6980 chunk 50 optimal weight: 10.0000 chunk 141 optimal weight: 7.9990 chunk 171 optimal weight: 8.9990 chunk 190 optimal weight: 10.0000 overall best weight: 1.5338 ------------------------------------------------------------------------------- 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 287 HIS ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 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 = 0.3466 r_free = 0.3466 target = 0.048303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.038072 restraints weight = 186012.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.039109 restraints weight = 102694.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.039783 restraints weight = 68405.071| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19273 Z= 0.114 Angle : 0.586 9.428 26283 Z= 0.279 Chirality : 0.045 0.245 3148 Planarity : 0.003 0.042 3170 Dihedral : 6.866 54.583 4095 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.14 % Favored : 92.81 % Rotamer: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.24 (0.18), residues: 2171 helix: 2.36 (0.28), residues: 347 sheet: -0.50 (0.23), residues: 576 loop : -2.02 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP J 571 HIS 0.003 0.001 HIS C 287 PHE 0.012 0.001 PHE E 100F TYR 0.022 0.001 TYR A 318 ARG 0.007 0.000 ARG D 41 Details of bonding type rmsd link_NAG-ASN : bond 0.00296 ( 58) link_NAG-ASN : angle 1.96655 ( 174) link_BETA1-4 : bond 0.00379 ( 22) link_BETA1-4 : angle 2.53169 ( 66) hydrogen bonds : bond 0.03060 ( 528) hydrogen bonds : angle 5.08983 ( 1407) SS BOND : bond 0.00279 ( 39) SS BOND : angle 0.84924 ( 78) covalent geometry : bond 0.00250 (19154) covalent geometry : angle 0.55017 (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 116 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 2.060 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8821 (ppp) cc_final: 0.8616 (ppp) REVERT: A 150 MET cc_start: 0.8288 (tmm) cc_final: 0.7756 (tmm) REVERT: A 154 MET cc_start: 0.8109 (mmp) cc_final: 0.7580 (tpp) REVERT: A 376 PHE cc_start: 0.8355 (p90) cc_final: 0.8137 (p90) REVERT: D 75 ASN cc_start: 0.8642 (t0) cc_final: 0.8243 (t0) REVERT: H 35 ASN cc_start: 0.8707 (m110) cc_final: 0.8489 (t0) REVERT: I 626 MET cc_start: 0.6728 (ptt) cc_final: 0.6436 (ppp) REVERT: J 530 MET cc_start: 0.8495 (pmm) cc_final: 0.8157 (pmm) REVERT: L 11 LEU cc_start: 0.9302 (pt) cc_final: 0.8839 (mp) REVERT: Z 530 MET cc_start: 0.8043 (mpp) cc_final: 0.7544 (mpp) REVERT: Z 648 GLU cc_start: 0.9131 (mt-10) cc_final: 0.8888 (mt-10) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.2987 time to fit residues: 55.3846 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 : 2.277 ------------------------------------------------------------------------------- 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: 1.9990 chunk 196 optimal weight: 9.9990 chunk 102 optimal weight: 5.9990 chunk 129 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 90 optimal weight: 40.0000 chunk 182 optimal weight: 1.9990 chunk 57 optimal weight: 8.9990 chunk 210 optimal weight: 7.9990 chunk 51 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** H 35BASN ** 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 = 0.3296 r_free = 0.3296 target = 0.043915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.032956 restraints weight = 171037.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.034033 restraints weight = 93958.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.034725 restraints weight = 65529.918| |-----------------------------------------------------------------------------| r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 19273 Z= 0.195 Angle : 0.631 9.330 26283 Z= 0.304 Chirality : 0.045 0.234 3148 Planarity : 0.003 0.040 3170 Dihedral : 6.938 56.107 4095 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.01 % Favored : 91.94 % Rotamer: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % 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: -1.31 (0.18), residues: 2171 helix: 2.46 (0.29), residues: 335 sheet: -0.68 (0.21), residues: 645 loop : -2.06 (0.18), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP J 571 HIS 0.003 0.001 HIS B 374 PHE 0.020 0.002 PHE E 100F TYR 0.021 0.002 TYR F 86 ARG 0.005 0.000 ARG D 41 Details of bonding type rmsd link_NAG-ASN : bond 0.00317 ( 58) link_NAG-ASN : angle 2.05465 ( 174) link_BETA1-4 : bond 0.00334 ( 22) link_BETA1-4 : angle 2.49051 ( 66) hydrogen bonds : bond 0.03297 ( 528) hydrogen bonds : angle 5.07624 ( 1407) SS BOND : bond 0.00302 ( 39) SS BOND : angle 1.01908 ( 78) covalent geometry : bond 0.00430 (19154) covalent geometry : angle 0.59659 (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 102 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 2.008 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9036 (ppp) cc_final: 0.8762 (ppp) REVERT: A 150 MET cc_start: 0.8263 (tmm) cc_final: 0.7722 (tmm) REVERT: A 154 MET cc_start: 0.8428 (mmp) cc_final: 0.7762 (tpp) REVERT: D 75 ASN cc_start: 0.8810 (t0) cc_final: 0.8375 (t0) REVERT: I 626 MET cc_start: 0.7739 (ptt) cc_final: 0.7093 (ppp) REVERT: J 530 MET cc_start: 0.8715 (pmm) cc_final: 0.8491 (pmm) REVERT: L 11 LEU cc_start: 0.9574 (pt) cc_final: 0.9178 (mp) REVERT: Z 648 GLU cc_start: 0.9339 (mt-10) cc_final: 0.9073 (mt-10) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.2763 time to fit residues: 46.7263 Evaluate side-chains 85 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 2.019 ------------------------------------------------------------------------------- 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: 0.7980 chunk 75 optimal weight: 10.0000 chunk 37 optimal weight: 8.9990 chunk 164 optimal weight: 1.9990 chunk 82 optimal weight: 9.9990 chunk 55 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 24 optimal weight: 20.0000 chunk 92 optimal weight: 3.9990 chunk 152 optimal weight: 8.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** H 35BASN ** 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 = 0.3305 r_free = 0.3305 target = 0.044187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.033219 restraints weight = 164845.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.034320 restraints weight = 89903.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.035033 restraints weight = 62390.733| |-----------------------------------------------------------------------------| r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19273 Z= 0.144 Angle : 0.614 9.353 26283 Z= 0.291 Chirality : 0.045 0.234 3148 Planarity : 0.004 0.066 3170 Dihedral : 6.848 55.365 4095 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.60 % Favored : 92.35 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % 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: -1.28 (0.18), residues: 2171 helix: 2.49 (0.29), residues: 335 sheet: -0.71 (0.21), residues: 642 loop : -2.01 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP B 479 HIS 0.003 0.001 HIS B 374 PHE 0.014 0.001 PHE E 100F TYR 0.023 0.001 TYR B 318 ARG 0.014 0.001 ARG C 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00312 ( 58) link_NAG-ASN : angle 2.21477 ( 174) link_BETA1-4 : bond 0.00390 ( 22) link_BETA1-4 : angle 2.51750 ( 66) hydrogen bonds : bond 0.03167 ( 528) hydrogen bonds : angle 4.98690 ( 1407) SS BOND : bond 0.00222 ( 39) SS BOND : angle 0.91909 ( 78) covalent geometry : bond 0.00317 (19154) covalent geometry : angle 0.57425 (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 108 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 2.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9043 (ppp) cc_final: 0.8767 (ppp) REVERT: A 150 MET cc_start: 0.8265 (tmm) cc_final: 0.7712 (tmm) REVERT: A 154 MET cc_start: 0.8433 (mmp) cc_final: 0.7744 (tpp) REVERT: D 75 ASN cc_start: 0.8810 (t0) cc_final: 0.8367 (t0) REVERT: E 52 TYR cc_start: 0.8814 (t80) cc_final: 0.8560 (t80) REVERT: F 70 ASP cc_start: 0.9465 (t0) cc_final: 0.9165 (p0) REVERT: H 35 ASN cc_start: 0.9075 (m110) cc_final: 0.8598 (t0) REVERT: H 43 LYS cc_start: 0.8446 (pttm) cc_final: 0.8229 (mtmm) REVERT: I 626 MET cc_start: 0.7758 (ptt) cc_final: 0.7137 (ppp) REVERT: J 530 MET cc_start: 0.8749 (pmm) cc_final: 0.8538 (pmm) REVERT: L 11 LEU cc_start: 0.9579 (pt) cc_final: 0.9217 (mp) REVERT: Z 530 MET cc_start: 0.8243 (mpp) cc_final: 0.7678 (mpp) REVERT: Z 648 GLU cc_start: 0.9353 (mt-10) cc_final: 0.9081 (mt-10) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.3350 time to fit residues: 59.6427 Evaluate side-chains 87 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 2.614 ------------------------------------------------------------------------------- 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: 10.0000 chunk 47 optimal weight: 8.9990 chunk 205 optimal weight: 9.9990 chunk 64 optimal weight: 0.9980 chunk 11 optimal weight: 20.0000 chunk 48 optimal weight: 10.0000 chunk 201 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 chunk 33 optimal weight: 9.9990 chunk 134 optimal weight: 6.9990 chunk 135 optimal weight: 0.9980 overall best weight: 3.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 229 ASN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35BASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 567 GLN ** I 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.043412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.032464 restraints weight = 167722.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.033533 restraints weight = 92047.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.034227 restraints weight = 64157.384| |-----------------------------------------------------------------------------| r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.4385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19273 Z= 0.190 Angle : 0.643 9.324 26283 Z= 0.308 Chirality : 0.046 0.229 3148 Planarity : 0.004 0.050 3170 Dihedral : 6.954 56.069 4095 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.25 % Favored : 91.71 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % 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: -1.35 (0.18), residues: 2171 helix: 2.37 (0.28), residues: 335 sheet: -0.70 (0.21), residues: 648 loop : -2.07 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 479 HIS 0.005 0.001 HIS B 216 PHE 0.017 0.001 PHE E 100F TYR 0.023 0.002 TYR E 100E ARG 0.008 0.001 ARG C 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00334 ( 58) link_NAG-ASN : angle 2.17224 ( 174) link_BETA1-4 : bond 0.00332 ( 22) link_BETA1-4 : angle 2.51512 ( 66) hydrogen bonds : bond 0.03340 ( 528) hydrogen bonds : angle 5.06472 ( 1407) SS BOND : bond 0.00265 ( 39) SS BOND : angle 0.99903 ( 78) covalent geometry : bond 0.00418 (19154) covalent geometry : angle 0.60659 (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 105 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 2.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.9498 (mtm) cc_final: 0.9271 (mtt) REVERT: A 104 MET cc_start: 0.9064 (ppp) cc_final: 0.8812 (ppp) REVERT: A 150 MET cc_start: 0.8332 (tmm) cc_final: 0.7767 (tmm) REVERT: A 154 MET cc_start: 0.8429 (mmp) cc_final: 0.7728 (tpp) REVERT: E 27 ASP cc_start: 0.9191 (t70) cc_final: 0.8694 (t70) REVERT: F 70 ASP cc_start: 0.9506 (t0) cc_final: 0.9207 (p0) REVERT: I 626 MET cc_start: 0.7823 (ptt) cc_final: 0.7279 (ppp) REVERT: J 530 MET cc_start: 0.8752 (pmm) cc_final: 0.8512 (pmm) REVERT: Z 530 MET cc_start: 0.8325 (mpp) cc_final: 0.7550 (mpp) REVERT: Z 648 GLU cc_start: 0.9347 (mt-10) cc_final: 0.9081 (mt-10) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.2936 time to fit residues: 50.0362 Evaluate side-chains 82 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 2.039 ------------------------------------------------------------------------------- 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: 20.0000 chunk 84 optimal weight: 8.9990 chunk 101 optimal weight: 5.9990 chunk 154 optimal weight: 7.9990 chunk 68 optimal weight: 10.0000 chunk 139 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 6.9990 chunk 76 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 332 ASN D 39 GLN ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 90 GLN ** H 35BASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.042034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.031121 restraints weight = 170634.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.032154 restraints weight = 94029.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.032821 restraints weight = 65895.922| |-----------------------------------------------------------------------------| r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.5134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 19273 Z= 0.302 Angle : 0.769 9.669 26283 Z= 0.373 Chirality : 0.047 0.233 3148 Planarity : 0.004 0.046 3170 Dihedral : 7.590 57.420 4095 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.23 % Favored : 89.73 % Rotamer: Outliers : 0.05 % Allowed : 0.81 % Favored : 99.14 % 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: -1.74 (0.18), residues: 2171 helix: 1.79 (0.27), residues: 341 sheet: -1.00 (0.20), residues: 660 loop : -2.24 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP B 479 HIS 0.007 0.002 HIS B 216 PHE 0.030 0.002 PHE E 100F TYR 0.024 0.002 TYR F 86 ARG 0.009 0.001 ARG C 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00527 ( 58) link_NAG-ASN : angle 2.42975 ( 174) link_BETA1-4 : bond 0.00449 ( 22) link_BETA1-4 : angle 2.69443 ( 66) hydrogen bonds : bond 0.03910 ( 528) hydrogen bonds : angle 5.55814 ( 1407) SS BOND : bond 0.00403 ( 39) SS BOND : angle 1.27984 ( 78) covalent geometry : bond 0.00661 (19154) covalent geometry : angle 0.73184 (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 95 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 94 time to evaluate : 3.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9084 (ppp) cc_final: 0.8823 (ppp) REVERT: E 52 TYR cc_start: 0.8975 (t80) cc_final: 0.8749 (t80) REVERT: F 70 ASP cc_start: 0.9521 (t0) cc_final: 0.9268 (p0) REVERT: G 90 GLN cc_start: 0.9056 (OUTLIER) cc_final: 0.8812 (pp30) REVERT: I 626 MET cc_start: 0.8062 (ptt) cc_final: 0.7513 (ppp) REVERT: J 530 MET cc_start: 0.8714 (pmm) cc_final: 0.8316 (pmm) REVERT: Z 530 MET cc_start: 0.8347 (mpp) cc_final: 0.7496 (mpp) REVERT: Z 648 GLU cc_start: 0.9363 (mt-10) cc_final: 0.9102 (mt-10) outliers start: 1 outliers final: 0 residues processed: 95 average time/residue: 0.3625 time to fit residues: 54.6186 Evaluate side-chains 74 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 73 time to evaluate : 4.423 ------------------------------------------------------------------------------- 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: 2.9990 chunk 202 optimal weight: 6.9990 chunk 181 optimal weight: 4.9990 chunk 193 optimal weight: 7.9990 chunk 161 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 119 optimal weight: 0.7980 chunk 150 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 210 optimal weight: 8.9990 chunk 76 optimal weight: 3.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** G 90 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.042881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.032029 restraints weight = 168137.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.033093 restraints weight = 91957.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.033786 restraints weight = 64012.854| |-----------------------------------------------------------------------------| r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.5060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19273 Z= 0.171 Angle : 0.658 12.655 26283 Z= 0.313 Chirality : 0.046 0.245 3148 Planarity : 0.004 0.038 3170 Dihedral : 7.290 56.479 4095 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.15 % Favored : 91.80 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % 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: -1.55 (0.18), residues: 2171 helix: 1.86 (0.27), residues: 359 sheet: -0.91 (0.20), residues: 660 loop : -2.12 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 479 HIS 0.004 0.001 HIS B 374 PHE 0.016 0.001 PHE E 100F TYR 0.019 0.002 TYR F 86 ARG 0.012 0.001 ARG C 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00292 ( 58) link_NAG-ASN : angle 2.25270 ( 174) link_BETA1-4 : bond 0.00365 ( 22) link_BETA1-4 : angle 2.65510 ( 66) hydrogen bonds : bond 0.03425 ( 528) hydrogen bonds : angle 5.19010 ( 1407) SS BOND : bond 0.00263 ( 39) SS BOND : angle 1.07379 ( 78) covalent geometry : bond 0.00382 (19154) covalent geometry : angle 0.61831 (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 : 2.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.9562 (mtm) cc_final: 0.9332 (mtt) REVERT: A 104 MET cc_start: 0.9098 (ppp) cc_final: 0.8862 (ppp) REVERT: A 154 MET cc_start: 0.8260 (mmp) cc_final: 0.8033 (mmm) REVERT: E 27 ASP cc_start: 0.9235 (t70) cc_final: 0.8723 (t70) REVERT: F 70 ASP cc_start: 0.9508 (t0) cc_final: 0.9226 (p0) REVERT: H 43 LYS cc_start: 0.8650 (pttm) cc_final: 0.8406 (mtmm) REVERT: I 626 MET cc_start: 0.8054 (ptt) cc_final: 0.7494 (ppp) REVERT: J 530 MET cc_start: 0.8655 (pmm) cc_final: 0.8418 (pmm) REVERT: Z 530 MET cc_start: 0.8339 (mpp) cc_final: 0.7379 (mpp) REVERT: Z 648 GLU cc_start: 0.9356 (mt-10) cc_final: 0.9086 (mt-10) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.3116 time to fit residues: 51.7119 Evaluate side-chains 75 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 2.005 ------------------------------------------------------------------------------- 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: 10.0000 chunk 187 optimal weight: 0.0970 chunk 98 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 202 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 91 optimal weight: 9.9990 chunk 100 optimal weight: 6.9990 chunk 209 optimal weight: 20.0000 chunk 173 optimal weight: 4.9990 chunk 131 optimal weight: 0.4980 overall best weight: 1.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.043418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.032547 restraints weight = 167749.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.033632 restraints weight = 91011.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.034334 restraints weight = 63075.490| |-----------------------------------------------------------------------------| r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.4956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19273 Z= 0.124 Angle : 0.622 10.518 26283 Z= 0.293 Chirality : 0.046 0.243 3148 Planarity : 0.003 0.036 3170 Dihedral : 7.029 58.251 4095 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.83 % Favored : 92.12 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % 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: 1.98 (0.28), residues: 359 sheet: -0.79 (0.20), residues: 684 loop : -2.06 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B 479 HIS 0.004 0.001 HIS B 330 PHE 0.012 0.001 PHE E 100F TYR 0.017 0.001 TYR I 643 ARG 0.008 0.000 ARG C 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00300 ( 58) link_NAG-ASN : angle 2.17566 ( 174) link_BETA1-4 : bond 0.00420 ( 22) link_BETA1-4 : angle 2.63511 ( 66) hydrogen bonds : bond 0.03173 ( 528) hydrogen bonds : angle 4.97820 ( 1407) SS BOND : bond 0.00217 ( 39) SS BOND : angle 0.95437 ( 78) covalent geometry : bond 0.00277 (19154) covalent geometry : angle 0.58321 (25965) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5572.74 seconds wall clock time: 99 minutes 26.17 seconds (5966.17 seconds total)