Starting phenix.real_space_refine on Tue Nov 19 07:16:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8to9_41440/11_2024/8to9_41440.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8to9_41440/11_2024/8to9_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8to9_41440/11_2024/8to9_41440.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8to9_41440/11_2024/8to9_41440.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8to9_41440/11_2024/8to9_41440.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8to9_41440/11_2024/8to9_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-5513/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: 11.38, per 1000 atoms: 0.61 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: 5.13 Conformation dependent library (CDL) restraints added in 2.2 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: 2.25 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: 6.11 Time building geometry restraints manager: 5.86 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: 4.030 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: 0.040 Extract box with map and model: 0.790 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 41.800 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.130 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: 0.010 Load rotamer database and sin/cos tables:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.300 ------------------------------------------------------------------------------- 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 19154 Z= 0.326 Angle : 0.977 14.362 25965 Z= 0.497 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 *********************** 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 : 2.238 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: 0.3028 time to fit residues: 72.4326 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 : 2.132 ------------------------------------------------------------------------------- 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: 10.0000 chunk 56 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 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: 3.6986 ------------------------------------------------------------------------------- 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 F 38 GLN G 27 GLN ** Z 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 19154 Z= 0.278 Angle : 0.620 9.298 25965 Z= 0.312 Chirality : 0.046 0.262 3148 Planarity : 0.005 0.057 3170 Dihedral : 9.347 70.265 4095 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 0.10 % Allowed : 3.39 % Favored : 96.51 % 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: -1.66 (0.18), residues: 2171 helix: 1.18 (0.28), residues: 348 sheet: -0.40 (0.23), residues: 564 loop : -2.22 (0.16), residues: 1259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 479 HIS 0.004 0.001 HIS C 105 PHE 0.020 0.002 PHE E 100F TYR 0.019 0.002 TYR E 52 ARG 0.005 0.001 ARG A 327 *********************** 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 124 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 122 time to evaluate : 2.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.7648 (mmp) cc_final: 0.7435 (mmm) REVERT: A 376 PHE cc_start: 0.8482 (p90) cc_final: 0.8205 (p90) REVERT: D 64 GLU cc_start: 0.9055 (mm-30) cc_final: 0.8616 (mp0) REVERT: D 75 ASN cc_start: 0.8630 (t0) cc_final: 0.8403 (t0) REVERT: H 27 ASP cc_start: 0.8431 (t70) cc_final: 0.7934 (t0) REVERT: H 35 ASN cc_start: 0.9055 (m110) cc_final: 0.8853 (t0) REVERT: L 11 LEU cc_start: 0.9057 (pt) cc_final: 0.8309 (mp) REVERT: Z 530 MET cc_start: 0.7738 (mpp) cc_final: 0.7202 (mpp) outliers start: 2 outliers final: 0 residues processed: 124 average time/residue: 0.2802 time to fit residues: 58.0009 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 : 2.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 110 optimal weight: 9.9990 chunk 61 optimal weight: 0.9990 chunk 165 optimal weight: 0.4980 chunk 135 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 199 optimal weight: 0.9990 chunk 215 optimal weight: 0.7980 chunk 177 optimal weight: 7.9990 chunk 197 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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** ** D 35BASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35BASN ** Z 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 19154 Z= 0.126 Angle : 0.544 9.364 25965 Z= 0.264 Chirality : 0.046 0.252 3148 Planarity : 0.003 0.048 3170 Dihedral : 7.790 55.071 4095 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.03 % Favored : 93.92 % Rotamer: Outliers : 0.05 % Allowed : 2.98 % Favored : 96.97 % 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: 1.86 (0.28), residues: 347 sheet: -0.31 (0.23), residues: 591 loop : -2.08 (0.17), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 479 HIS 0.005 0.001 HIS C 105 PHE 0.009 0.001 PHE B 376 TYR 0.020 0.001 TYR I 643 ARG 0.003 0.000 ARG J 579 *********************** 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 132 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 131 time to evaluate : 2.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8852 (ppp) cc_final: 0.7849 (ppp) REVERT: A 150 MET cc_start: 0.8160 (tmm) cc_final: 0.7533 (tmm) REVERT: A 154 MET cc_start: 0.7795 (mmp) cc_final: 0.7584 (mmm) REVERT: A 376 PHE cc_start: 0.8388 (p90) cc_final: 0.8170 (p90) REVERT: B 475 MET cc_start: 0.7183 (ttm) cc_final: 0.6617 (ttm) REVERT: D 30 LYS cc_start: 0.9217 (mmmm) cc_final: 0.8912 (mmmm) REVERT: D 64 GLU cc_start: 0.9048 (mm-30) cc_final: 0.8533 (mp0) REVERT: D 75 ASN cc_start: 0.8657 (t0) cc_final: 0.8258 (t0) REVERT: H 27 ASP cc_start: 0.8423 (t70) cc_final: 0.7877 (t0) REVERT: H 35 ASN cc_start: 0.8971 (m110) cc_final: 0.8757 (t0) REVERT: L 11 LEU cc_start: 0.9082 (pt) cc_final: 0.8388 (mp) REVERT: Z 530 MET cc_start: 0.7609 (mpp) cc_final: 0.7163 (mpp) outliers start: 1 outliers final: 0 residues processed: 132 average time/residue: 0.2934 time to fit residues: 62.6365 Evaluate side-chains 95 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 2.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 196 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 95 optimal weight: 20.0000 chunk 133 optimal weight: 0.3980 chunk 199 optimal weight: 20.0000 chunk 211 optimal weight: 8.9990 chunk 104 optimal weight: 2.9990 chunk 189 optimal weight: 10.0000 chunk 57 optimal weight: 8.9990 overall best weight: 4.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN G 38 GLN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 19154 Z= 0.333 Angle : 0.666 9.663 25965 Z= 0.333 Chirality : 0.046 0.232 3148 Planarity : 0.004 0.045 3170 Dihedral : 7.233 57.428 4095 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.65 % Favored : 92.31 % Rotamer: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % 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: 2.40 (0.29), residues: 329 sheet: -0.66 (0.22), residues: 591 loop : -2.06 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 479 HIS 0.009 0.002 HIS A 287 PHE 0.020 0.002 PHE E 100F TYR 0.028 0.002 TYR H 100E ARG 0.008 0.001 ARG H 100D *********************** 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 111 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 2.105 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8869 (ppp) cc_final: 0.8591 (ppp) REVERT: A 150 MET cc_start: 0.8258 (tmm) cc_final: 0.7543 (tmm) REVERT: A 154 MET cc_start: 0.8142 (mmp) cc_final: 0.7816 (mmm) REVERT: D 30 LYS cc_start: 0.9237 (mmmm) cc_final: 0.8961 (mmmm) REVERT: D 64 GLU cc_start: 0.9149 (mm-30) cc_final: 0.8874 (mm-30) REVERT: D 75 ASN cc_start: 0.8728 (t0) cc_final: 0.8247 (t0) REVERT: J 530 MET cc_start: 0.8366 (pmm) cc_final: 0.8042 (pmm) REVERT: J 584 GLU cc_start: 0.8851 (mp0) cc_final: 0.8564 (mp0) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.3191 time to fit residues: 57.4368 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 : 2.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 176 optimal weight: 7.9990 chunk 120 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 157 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 chunk 180 optimal weight: 3.9990 chunk 146 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 108 optimal weight: 0.9980 chunk 190 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 GLN ** H 35BASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 567 GLN ** Z 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19154 Z= 0.233 Angle : 0.578 9.286 25965 Z= 0.287 Chirality : 0.045 0.234 3148 Planarity : 0.003 0.043 3170 Dihedral : 6.942 54.928 4095 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.00 % Favored : 92.95 % Rotamer: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % 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: -1.27 (0.18), residues: 2171 helix: 2.39 (0.29), residues: 347 sheet: -0.63 (0.22), residues: 603 loop : -2.03 (0.17), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 479 HIS 0.008 0.001 HIS C 105 PHE 0.020 0.001 PHE E 100F TYR 0.021 0.002 TYR E 52 ARG 0.004 0.000 ARG C 304 *********************** 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 108 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 2.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.8323 (tmm) cc_final: 0.7713 (tmm) REVERT: A 154 MET cc_start: 0.8194 (mmp) cc_final: 0.7541 (tpp) REVERT: D 30 LYS cc_start: 0.9226 (mmmm) cc_final: 0.8927 (mmmm) REVERT: D 64 GLU cc_start: 0.9155 (mm-30) cc_final: 0.8868 (mm-30) REVERT: D 75 ASN cc_start: 0.8706 (t0) cc_final: 0.8219 (t0) REVERT: H 35 ASN cc_start: 0.9046 (m110) cc_final: 0.8593 (t0) REVERT: J 530 MET cc_start: 0.8574 (pmm) cc_final: 0.8330 (pmm) REVERT: Z 629 MET cc_start: 0.8772 (mmp) cc_final: 0.8454 (mmt) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.2937 time to fit residues: 52.0530 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 : 2.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 71 optimal weight: 10.0000 chunk 190 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 124 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 211 optimal weight: 10.0000 chunk 175 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 17 optimal weight: 8.9990 chunk 70 optimal weight: 7.9990 chunk 111 optimal weight: 0.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 HIS ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 ASN ** C 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 GLN H 35BASN ** I 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 19154 Z= 0.314 Angle : 0.640 9.263 25965 Z= 0.319 Chirality : 0.046 0.229 3148 Planarity : 0.004 0.041 3170 Dihedral : 7.063 56.509 4095 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.38 % Favored : 91.57 % Rotamer: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.18), residues: 2171 helix: 2.18 (0.28), residues: 353 sheet: -0.79 (0.21), residues: 639 loop : -2.10 (0.17), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP J 571 HIS 0.010 0.001 HIS C 105 PHE 0.024 0.002 PHE E 100F TYR 0.028 0.002 TYR F 86 ARG 0.004 0.001 ARG J 579 *********************** 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 103 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 2.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8903 (ppp) cc_final: 0.8693 (ppp) REVERT: A 150 MET cc_start: 0.8324 (tmm) cc_final: 0.7744 (tmm) REVERT: A 154 MET cc_start: 0.8270 (mmp) cc_final: 0.7539 (tpp) REVERT: B 104 MET cc_start: 0.9117 (tmm) cc_final: 0.8909 (tmm) REVERT: D 30 LYS cc_start: 0.9218 (mmmm) cc_final: 0.8894 (mmmm) REVERT: D 75 ASN cc_start: 0.8771 (t0) cc_final: 0.8326 (t0) REVERT: F 70 ASP cc_start: 0.9623 (t0) cc_final: 0.9349 (p0) REVERT: H 35 ASN cc_start: 0.9117 (m-40) cc_final: 0.8604 (m-40) REVERT: J 530 MET cc_start: 0.8561 (pmm) cc_final: 0.8280 (pmm) REVERT: J 584 GLU cc_start: 0.8890 (mp0) cc_final: 0.8598 (mp0) REVERT: L 11 LEU cc_start: 0.9457 (pt) cc_final: 0.9017 (mp) REVERT: Z 530 MET cc_start: 0.7907 (mpp) cc_final: 0.7443 (mpp) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.3224 time to fit residues: 52.6541 Evaluate side-chains 83 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 2.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 204 optimal weight: 9.9990 chunk 23 optimal weight: 8.9990 chunk 120 optimal weight: 0.9980 chunk 154 optimal weight: 8.9990 chunk 119 optimal weight: 0.4980 chunk 178 optimal weight: 9.9990 chunk 118 optimal weight: 0.9980 chunk 211 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 chunk 97 optimal weight: 9.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- 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** B 287 HIS ** C 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 567 GLN ** I 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19154 Z= 0.189 Angle : 0.568 9.284 25965 Z= 0.280 Chirality : 0.045 0.231 3148 Planarity : 0.003 0.042 3170 Dihedral : 6.820 55.003 4095 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.82 % Favored : 93.14 % Rotamer: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % 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: 2.33 (0.28), residues: 353 sheet: -0.71 (0.21), residues: 639 loop : -2.02 (0.18), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP J 571 HIS 0.008 0.001 HIS C 105 PHE 0.012 0.001 PHE E 100F TYR 0.016 0.001 TYR F 86 ARG 0.004 0.000 ARG C 304 *********************** 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 107 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 2.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.8326 (tmm) cc_final: 0.7702 (tmm) REVERT: A 154 MET cc_start: 0.8252 (mmp) cc_final: 0.7502 (tpp) REVERT: B 104 MET cc_start: 0.9079 (tmm) cc_final: 0.8837 (tmm) REVERT: D 64 GLU cc_start: 0.9120 (mm-30) cc_final: 0.8899 (mm-30) REVERT: D 75 ASN cc_start: 0.8752 (t0) cc_final: 0.8315 (t0) REVERT: F 70 ASP cc_start: 0.9629 (t0) cc_final: 0.9330 (p0) REVERT: H 35 ASN cc_start: 0.8994 (m-40) cc_final: 0.8535 (m-40) REVERT: J 530 MET cc_start: 0.8546 (pmm) cc_final: 0.8322 (pmm) REVERT: J 584 GLU cc_start: 0.8818 (mp0) cc_final: 0.8490 (mp0) REVERT: L 11 LEU cc_start: 0.9454 (pt) cc_final: 0.9014 (mp) REVERT: Z 530 MET cc_start: 0.8148 (mpp) cc_final: 0.7517 (mpp) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.2876 time to fit residues: 50.6352 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 : 2.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 130 optimal weight: 9.9990 chunk 84 optimal weight: 9.9990 chunk 126 optimal weight: 8.9990 chunk 63 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 chunk 40 optimal weight: 10.0000 chunk 134 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 104 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 chunk 165 optimal weight: 30.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 105 HIS ** C 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.4685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 19154 Z= 0.432 Angle : 0.715 9.372 25965 Z= 0.358 Chirality : 0.047 0.222 3148 Planarity : 0.004 0.040 3170 Dihedral : 7.384 57.184 4095 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.53 % Favored : 90.42 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % 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: -1.57 (0.18), residues: 2171 helix: 2.03 (0.28), residues: 341 sheet: -0.80 (0.21), residues: 624 loop : -2.20 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 479 HIS 0.009 0.002 HIS C 105 PHE 0.028 0.002 PHE E 100F TYR 0.023 0.002 TYR F 86 ARG 0.027 0.001 ARG C 192 *********************** 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 98 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 2.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8877 (ppp) cc_final: 0.8663 (ppp) REVERT: A 150 MET cc_start: 0.8285 (tmm) cc_final: 0.7717 (tmm) REVERT: A 154 MET cc_start: 0.8386 (mmp) cc_final: 0.8112 (mmm) REVERT: B 104 MET cc_start: 0.9145 (tmm) cc_final: 0.8884 (tmm) REVERT: F 70 ASP cc_start: 0.9646 (t0) cc_final: 0.9394 (p0) REVERT: H 35 ASN cc_start: 0.9054 (m-40) cc_final: 0.8450 (m-40) REVERT: J 530 MET cc_start: 0.8628 (pmm) cc_final: 0.8424 (pmm) REVERT: L 11 LEU cc_start: 0.9490 (pt) cc_final: 0.9066 (mp) REVERT: Z 530 MET cc_start: 0.8223 (mpp) cc_final: 0.7441 (mpp) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.2987 time to fit residues: 47.3964 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 : 2.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 192 optimal weight: 0.9990 chunk 202 optimal weight: 1.9990 chunk 184 optimal weight: 10.0000 chunk 196 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 154 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 177 optimal weight: 8.9990 chunk 186 optimal weight: 10.0000 chunk 129 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 105 HIS ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.4540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19154 Z= 0.188 Angle : 0.592 9.391 25965 Z= 0.292 Chirality : 0.046 0.236 3148 Planarity : 0.003 0.052 3170 Dihedral : 7.052 55.004 4095 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.19 % Favored : 92.77 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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: -1.36 (0.18), residues: 2171 helix: 2.02 (0.28), residues: 359 sheet: -0.82 (0.20), residues: 678 loop : -1.98 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP C 427 HIS 0.006 0.001 HIS C 105 PHE 0.013 0.001 PHE F 98 TYR 0.018 0.001 TYR F 86 ARG 0.014 0.000 ARG C 192 *********************** 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 107 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 1.990 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8857 (ppp) cc_final: 0.8610 (ppp) REVERT: A 150 MET cc_start: 0.8276 (tmm) cc_final: 0.7685 (tmm) REVERT: A 154 MET cc_start: 0.8320 (mmp) cc_final: 0.7566 (tpp) REVERT: B 104 MET cc_start: 0.9135 (tmm) cc_final: 0.8864 (tmm) REVERT: D 64 GLU cc_start: 0.9081 (mm-30) cc_final: 0.8875 (mm-30) REVERT: E 27 ASP cc_start: 0.9123 (t70) cc_final: 0.8755 (t70) REVERT: F 70 ASP cc_start: 0.9628 (t0) cc_final: 0.9339 (p0) REVERT: H 35 ASN cc_start: 0.8969 (m-40) cc_final: 0.8487 (m-40) REVERT: J 584 GLU cc_start: 0.8880 (mp0) cc_final: 0.8625 (mp0) REVERT: L 11 LEU cc_start: 0.9498 (pt) cc_final: 0.9113 (mp) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.3131 time to fit residues: 53.4173 Evaluate side-chains 84 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 2.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 207 optimal weight: 0.7980 chunk 126 optimal weight: 5.9990 chunk 98 optimal weight: 9.9990 chunk 144 optimal weight: 0.3980 chunk 218 optimal weight: 0.8980 chunk 200 optimal weight: 5.9990 chunk 173 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 134 optimal weight: 8.9990 chunk 106 optimal weight: 4.9990 chunk 138 optimal weight: 9.9990 overall best weight: 2.6184 ------------------------------------------------------------------------------- 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** ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.4649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19154 Z= 0.217 Angle : 0.594 9.395 25965 Z= 0.292 Chirality : 0.046 0.243 3148 Planarity : 0.003 0.048 3170 Dihedral : 6.961 55.351 4095 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.11 % Favored : 91.85 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.18), residues: 2171 helix: 2.09 (0.28), residues: 359 sheet: -0.70 (0.21), residues: 645 loop : -2.03 (0.18), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 427 HIS 0.003 0.001 HIS B 330 PHE 0.015 0.001 PHE E 100F TYR 0.018 0.001 TYR E 52 ARG 0.011 0.000 ARG C 192 ********************** 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 101 residues out of total 1979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 2.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8857 (ppp) cc_final: 0.8621 (ppp) REVERT: A 154 MET cc_start: 0.8215 (mmp) cc_final: 0.7907 (tpp) REVERT: B 104 MET cc_start: 0.9131 (tmm) cc_final: 0.8848 (tmm) REVERT: D 64 GLU cc_start: 0.9073 (mm-30) cc_final: 0.8856 (mm-30) REVERT: E 27 ASP cc_start: 0.9081 (t70) cc_final: 0.8745 (t70) REVERT: F 70 ASP cc_start: 0.9626 (t0) cc_final: 0.9333 (p0) REVERT: H 35 ASN cc_start: 0.8980 (m-40) cc_final: 0.8462 (m-40) REVERT: J 584 GLU cc_start: 0.8860 (mp0) cc_final: 0.8589 (mp0) REVERT: Z 530 MET cc_start: 0.8184 (mpp) cc_final: 0.7389 (mpp) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.2937 time to fit residues: 48.3227 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 : 1.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 185 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 160 optimal weight: 10.0000 chunk 25 optimal weight: 50.0000 chunk 48 optimal weight: 4.9990 chunk 174 optimal weight: 8.9990 chunk 72 optimal weight: 10.0000 chunk 178 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 152 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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** ** D 105 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 = 0.3272 r_free = 0.3272 target = 0.043293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.032421 restraints weight = 168513.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.033495 restraints weight = 92025.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.034188 restraints weight = 63960.172| |-----------------------------------------------------------------------------| r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.4783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19154 Z= 0.234 Angle : 0.599 10.939 25965 Z= 0.295 Chirality : 0.046 0.248 3148 Planarity : 0.003 0.045 3170 Dihedral : 6.983 56.136 4095 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.43 % Favored : 91.52 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.18), residues: 2171 helix: 2.10 (0.28), residues: 359 sheet: -0.80 (0.20), residues: 675 loop : -1.98 (0.18), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 427 HIS 0.003 0.001 HIS B 374 PHE 0.016 0.001 PHE E 100F TYR 0.019 0.002 TYR B 318 ARG 0.011 0.000 ARG C 192 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2993.22 seconds wall clock time: 57 minutes 4.50 seconds (3424.50 seconds total)