Starting phenix.real_space_refine on Thu Jun 4 21:54:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9x61_66604/06_2026/9x61_66604.cif Found real_map, /net/cci-nas-00/data/ceres_data/9x61_66604/06_2026/9x61_66604.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9x61_66604/06_2026/9x61_66604.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9x61_66604/06_2026/9x61_66604.map" model { file = "/net/cci-nas-00/data/ceres_data/9x61_66604/06_2026/9x61_66604.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9x61_66604/06_2026/9x61_66604.cif" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.069 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 72 5.16 5 C 9681 2.51 5 N 2622 2.21 5 O 3114 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15489 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 2539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2539 Classifications: {'peptide': 334} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 307} Chain: "V" Number of atoms: 695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 695 Classifications: {'peptide': 88} Link IDs: {'TRANS': 87} Chain: "B" Number of atoms: 2539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2539 Classifications: {'peptide': 334} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 307} Chain: "W" Number of atoms: 695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 695 Classifications: {'peptide': 88} Link IDs: {'TRANS': 87} Chain: "C" Number of atoms: 2539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2539 Classifications: {'peptide': 334} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 307} Chain: "X" Number of atoms: 695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 695 Classifications: {'peptide': 88} Link IDs: {'TRANS': 87} Chain: "H" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 904 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "L" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 831 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 101} Chain: "J" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 904 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "K" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 831 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 904 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "E" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 831 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 101} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "M" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "Q" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "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: 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: "T" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "U" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.53, per 1000 atoms: 0.23 Number of scatterers: 15489 At special positions: 0 Unit cell: (153.55, 140.27, 135.29, 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 72 16.00 O 3114 8.00 N 2622 7.00 C 9681 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 57 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 72 " distance=2.03 Simple disulfide: pdb=" SG CYS A 94 " - pdb=" SG CYS A 143 " distance=2.04 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 294 " - pdb=" SG CYS A 320 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 57 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 72 " distance=2.03 Simple disulfide: pdb=" SG CYS B 94 " - pdb=" SG CYS B 143 " distance=2.04 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 274 " distance=1.74 Simple disulfide: pdb=" SG CYS B 294 " - pdb=" SG CYS B 320 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 57 " distance=2.03 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 72 " distance=2.03 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 143 " distance=2.04 Simple disulfide: pdb=" SG CYS C 180 " - pdb=" SG CYS C 274 " distance=1.91 Simple disulfide: pdb=" SG CYS C 294 " - pdb=" SG CYS C 320 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 104 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 104 " distance=2.04 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 104 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 104 " distance=2.04 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 104 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 104 " distance=2.04 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=4, symmetry=0 Links applied ALPHA1-3 " BMA I 3 " - " MAN I 6 " " MAN I 4 " - " MAN I 5 " " BMA P 3 " - " MAN P 6 " " MAN P 4 " - " MAN P 5 " " BMA T 3 " - " MAN T 6 " " MAN T 4 " - " MAN T 5 " ALPHA1-6 " BMA I 3 " - " MAN I 4 " " BMA P 3 " - " MAN P 4 " " BMA T 3 " - " MAN T 4 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " BETA1-6 " NAG M 1 " - " FUC M 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG Q 1 " - " FUC Q 3 " " NAG U 1 " - " FUC U 3 " NAG-ASN " NAG A 401 " - " ASN A 25 " " NAG A 402 " - " ASN A 167 " " NAG B 401 " - " ASN B 25 " " NAG B 402 " - " ASN B 167 " " NAG C 401 " - " ASN C 25 " " NAG C 402 " - " ASN C 167 " " NAG F 1 " - " ASN A 303 " " NAG G 1 " - " ASN A 332 " " NAG I 1 " - " ASN A 145 " " NAG M 1 " - " ASN A 59 " " NAG N 1 " - " ASN B 303 " " NAG O 1 " - " ASN B 332 " " NAG P 1 " - " ASN B 145 " " NAG Q 1 " - " ASN B 59 " " NAG R 1 " - " ASN C 303 " " NAG S 1 " - " ASN C 332 " " NAG T 1 " - " ASN C 145 " " NAG U 1 " - " ASN C 59 " Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.49 Conformation dependent library (CDL) restraints added in 651.2 milliseconds 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3522 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 42 sheets defined 17.7% alpha, 29.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 61 through 68 Processing helix chain 'A' and resid 98 through 102 removed outlier: 3.541A pdb=" N ARG A 101 " --> pdb=" O MET A 98 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR A 102 " --> pdb=" O HIS A 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 98 through 102' Processing helix chain 'A' and resid 103 through 105 No H-bonds generated for 'chain 'A' and resid 103 through 105' Processing helix chain 'A' and resid 106 through 112 Processing helix chain 'A' and resid 196 through 204 removed outlier: 3.729A pdb=" N LYS A 201 " --> pdb=" O LYS A 197 " (cutoff:3.500A) Processing helix chain 'V' and resid 386 through 403 Processing helix chain 'V' and resid 420 through 455 removed outlier: 3.690A pdb=" N LEU V 424 " --> pdb=" O HIS V 420 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU V 425 " --> pdb=" O ASN V 421 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU V 426 " --> pdb=" O GLU V 422 " (cutoff:3.500A) Processing helix chain 'V' and resid 457 through 472 removed outlier: 4.091A pdb=" N ALA V 463 " --> pdb=" O GLU V 459 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU V 464 " --> pdb=" O HIS V 460 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS V 467 " --> pdb=" O ALA V 463 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LYS V 470 " --> pdb=" O ARG V 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 68 Processing helix chain 'B' and resid 98 through 102 removed outlier: 3.542A pdb=" N ARG B 101 " --> pdb=" O MET B 98 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR B 102 " --> pdb=" O HIS B 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 98 through 102' Processing helix chain 'B' and resid 103 through 105 No H-bonds generated for 'chain 'B' and resid 103 through 105' Processing helix chain 'B' and resid 106 through 112 Processing helix chain 'B' and resid 196 through 204 removed outlier: 3.729A pdb=" N LYS B 201 " --> pdb=" O LYS B 197 " (cutoff:3.500A) Processing helix chain 'W' and resid 386 through 403 Processing helix chain 'W' and resid 420 through 455 removed outlier: 3.690A pdb=" N LEU W 424 " --> pdb=" O HIS W 420 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU W 425 " --> pdb=" O ASN W 421 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU W 426 " --> pdb=" O GLU W 422 " (cutoff:3.500A) Processing helix chain 'W' and resid 457 through 472 removed outlier: 4.089A pdb=" N ALA W 463 " --> pdb=" O GLU W 459 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU W 464 " --> pdb=" O HIS W 460 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS W 467 " --> pdb=" O ALA W 463 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LYS W 470 " --> pdb=" O ARG W 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 68 Processing helix chain 'C' and resid 98 through 102 removed outlier: 3.542A pdb=" N ARG C 101 " --> pdb=" O MET C 98 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR C 102 " --> pdb=" O HIS C 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 98 through 102' Processing helix chain 'C' and resid 103 through 105 No H-bonds generated for 'chain 'C' and resid 103 through 105' Processing helix chain 'C' and resid 106 through 112 Processing helix chain 'C' and resid 196 through 204 removed outlier: 3.729A pdb=" N LYS C 201 " --> pdb=" O LYS C 197 " (cutoff:3.500A) Processing helix chain 'X' and resid 386 through 403 Processing helix chain 'X' and resid 420 through 455 removed outlier: 3.691A pdb=" N LEU X 424 " --> pdb=" O HIS X 420 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU X 425 " --> pdb=" O ASN X 421 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU X 426 " --> pdb=" O GLU X 422 " (cutoff:3.500A) Processing helix chain 'X' and resid 457 through 472 removed outlier: 4.089A pdb=" N ALA X 463 " --> pdb=" O GLU X 459 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU X 464 " --> pdb=" O HIS X 460 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS X 467 " --> pdb=" O ALA X 463 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LYS X 470 " --> pdb=" O ARG X 466 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 37 removed outlier: 3.676A pdb=" N ASN H 36 " --> pdb=" O ASN H 29 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE H 37 " --> pdb=" O PHE H 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 29 through 37' Processing helix chain 'H' and resid 95 through 99 removed outlier: 4.202A pdb=" N THR H 99 " --> pdb=" O PRO H 96 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 37 No H-bonds generated for 'chain 'L' and resid 30 through 37' Processing helix chain 'J' and resid 29 through 37 removed outlier: 3.676A pdb=" N ASN J 36 " --> pdb=" O ASN J 29 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE J 37 " --> pdb=" O PHE J 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 29 through 37' Processing helix chain 'J' and resid 95 through 99 removed outlier: 4.201A pdb=" N THR J 99 " --> pdb=" O PRO J 96 " (cutoff:3.500A) Processing helix chain 'K' and resid 30 through 37 No H-bonds generated for 'chain 'K' and resid 30 through 37' Processing helix chain 'D' and resid 29 through 37 removed outlier: 3.675A pdb=" N ASN D 36 " --> pdb=" O ASN D 29 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE D 37 " --> pdb=" O PHE D 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 29 through 37' Processing helix chain 'D' and resid 95 through 99 removed outlier: 4.201A pdb=" N THR D 99 " --> pdb=" O PRO D 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 37 No H-bonds generated for 'chain 'E' and resid 30 through 37' Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 17 Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 31 Processing sheet with id=AA3, first strand: chain 'A' and resid 43 through 44 removed outlier: 6.101A pdb=" N ASN A 43 " --> pdb=" O ALA A 292 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 49 through 50 Processing sheet with id=AA5, first strand: chain 'A' and resid 116 through 119 removed outlier: 7.390A pdb=" N VAL A 189 " --> pdb=" O PRO A 269 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N VAL A 266 " --> pdb=" O ALA A 159 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N TRP A 158 " --> pdb=" O GLY A 138 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 116 through 119 Processing sheet with id=AA7, first strand: chain 'A' and resid 172 through 176 Processing sheet with id=AA8, first strand: chain 'A' and resid 300 through 302 Processing sheet with id=AA9, first strand: chain 'A' and resid 308 through 309 Processing sheet with id=AB1, first strand: chain 'B' and resid 14 through 17 Processing sheet with id=AB2, first strand: chain 'B' and resid 29 through 31 Processing sheet with id=AB3, first strand: chain 'B' and resid 43 through 44 removed outlier: 6.101A pdb=" N ASN B 43 " --> pdb=" O ALA B 292 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 49 through 50 Processing sheet with id=AB5, first strand: chain 'B' and resid 116 through 119 removed outlier: 7.391A pdb=" N VAL B 189 " --> pdb=" O PRO B 269 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N VAL B 266 " --> pdb=" O ALA B 159 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N TRP B 158 " --> pdb=" O GLY B 138 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 116 through 119 Processing sheet with id=AB7, first strand: chain 'B' and resid 172 through 176 Processing sheet with id=AB8, first strand: chain 'B' and resid 300 through 302 Processing sheet with id=AB9, first strand: chain 'B' and resid 308 through 309 Processing sheet with id=AC1, first strand: chain 'C' and resid 14 through 17 Processing sheet with id=AC2, first strand: chain 'C' and resid 29 through 31 Processing sheet with id=AC3, first strand: chain 'C' and resid 43 through 44 removed outlier: 6.100A pdb=" N ASN C 43 " --> pdb=" O ALA C 292 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 49 through 50 Processing sheet with id=AC5, first strand: chain 'C' and resid 116 through 119 removed outlier: 7.390A pdb=" N VAL C 189 " --> pdb=" O PRO C 269 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N VAL C 266 " --> pdb=" O ALA C 159 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N TRP C 158 " --> pdb=" O GLY C 138 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 116 through 119 Processing sheet with id=AC7, first strand: chain 'C' and resid 172 through 176 Processing sheet with id=AC8, first strand: chain 'C' and resid 300 through 302 Processing sheet with id=AC9, first strand: chain 'C' and resid 308 through 309 Processing sheet with id=AD1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AD2, first strand: chain 'H' and resid 12 through 13 removed outlier: 6.711A pdb=" N MET H 39 " --> pdb=" O VAL H 55 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N VAL H 55 " --> pdb=" O MET H 39 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TRP H 41 " --> pdb=" O VAL H 53 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 12 through 13 Processing sheet with id=AD4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AD5, first strand: chain 'L' and resid 66 through 67 removed outlier: 6.292A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N TYR L 55 " --> pdb=" O LEU L 39 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LEU L 39 " --> pdb=" O TYR L 55 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AD7, first strand: chain 'J' and resid 12 through 13 removed outlier: 6.711A pdb=" N MET J 39 " --> pdb=" O VAL J 55 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N VAL J 55 " --> pdb=" O MET J 39 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TRP J 41 " --> pdb=" O VAL J 53 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 12 through 13 Processing sheet with id=AD9, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AE1, first strand: chain 'K' and resid 66 through 67 removed outlier: 6.292A pdb=" N TRP K 41 " --> pdb=" O LEU K 53 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N TYR K 55 " --> pdb=" O LEU K 39 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LEU K 39 " --> pdb=" O TYR K 55 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AE3, first strand: chain 'D' and resid 12 through 13 removed outlier: 6.712A pdb=" N MET D 39 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N VAL D 55 " --> pdb=" O MET D 39 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TRP D 41 " --> pdb=" O VAL D 53 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 12 through 13 Processing sheet with id=AE5, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AE6, first strand: chain 'E' and resid 66 through 67 removed outlier: 6.292A pdb=" N TRP E 41 " --> pdb=" O LEU E 53 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N TYR E 55 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LEU E 39 " --> pdb=" O TYR E 55 " (cutoff:3.500A) 597 hydrogen bonds defined for protein. 1566 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.54 Time building geometry restraints manager: 1.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 2532 1.29 - 1.43: 4009 1.43 - 1.57: 9152 1.57 - 1.70: 6 1.70 - 1.84: 102 Bond restraints: 15801 Sorted by residual: bond pdb=" C GLU C 184 " pdb=" O GLU C 184 " ideal model delta sigma weight residual 1.235 1.165 0.071 1.22e-02 6.72e+03 3.37e+01 bond pdb=" CD GLU C 184 " pdb=" OE1 GLU C 184 " ideal model delta sigma weight residual 1.249 1.155 0.094 1.90e-02 2.77e+03 2.44e+01 bond pdb=" C CYS C 180 " pdb=" O CYS C 180 " ideal model delta sigma weight residual 1.235 1.175 0.061 1.26e-02 6.30e+03 2.31e+01 bond pdb=" C THR A 181 " pdb=" O THR A 181 " ideal model delta sigma weight residual 1.235 1.181 0.055 1.19e-02 7.06e+03 2.12e+01 bond pdb=" C THR C 49 " pdb=" O THR C 49 " ideal model delta sigma weight residual 1.236 1.180 0.056 1.21e-02 6.83e+03 2.11e+01 ... (remaining 15796 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.82: 20935 2.82 - 5.63: 402 5.63 - 8.45: 85 8.45 - 11.26: 11 11.26 - 14.08: 5 Bond angle restraints: 21438 Sorted by residual: angle pdb=" N GLY A 183 " pdb=" CA GLY A 183 " pdb=" C GLY A 183 " ideal model delta sigma weight residual 113.79 103.44 10.35 1.17e+00 7.31e-01 7.82e+01 angle pdb=" N GLY B 183 " pdb=" CA GLY B 183 " pdb=" C GLY B 183 " ideal model delta sigma weight residual 114.25 103.01 11.24 1.30e+00 5.92e-01 7.47e+01 angle pdb=" C THR C 181 " pdb=" N GLU C 182 " pdb=" CA GLU C 182 " ideal model delta sigma weight residual 121.54 135.62 -14.08 1.91e+00 2.74e-01 5.43e+01 angle pdb=" C THR B 181 " pdb=" N GLU B 182 " pdb=" CA GLU B 182 " ideal model delta sigma weight residual 121.54 135.29 -13.75 1.91e+00 2.74e-01 5.19e+01 angle pdb=" CA THR B 181 " pdb=" CB THR B 181 " pdb=" OG1 THR B 181 " ideal model delta sigma weight residual 109.60 99.00 10.60 1.50e+00 4.44e-01 4.99e+01 ... (remaining 21433 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.61: 9299 21.61 - 43.22: 649 43.22 - 64.83: 78 64.83 - 86.44: 48 86.44 - 108.05: 21 Dihedral angle restraints: 10095 sinusoidal: 4578 harmonic: 5517 Sorted by residual: dihedral pdb=" C GLU C 182 " pdb=" N GLU C 182 " pdb=" CA GLU C 182 " pdb=" CB GLU C 182 " ideal model delta harmonic sigma weight residual -122.60 -147.73 25.13 0 2.50e+00 1.60e-01 1.01e+02 dihedral pdb=" C GLU B 182 " pdb=" N GLU B 182 " pdb=" CA GLU B 182 " pdb=" CB GLU B 182 " ideal model delta harmonic sigma weight residual -122.60 -147.60 25.00 0 2.50e+00 1.60e-01 1.00e+02 dihedral pdb=" N GLU C 182 " pdb=" C GLU C 182 " pdb=" CA GLU C 182 " pdb=" CB GLU C 182 " ideal model delta harmonic sigma weight residual 122.80 146.89 -24.09 0 2.50e+00 1.60e-01 9.29e+01 ... (remaining 10092 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.203: 2514 0.203 - 0.406: 14 0.406 - 0.609: 1 0.609 - 0.811: 0 0.811 - 1.014: 3 Chirality restraints: 2532 Sorted by residual: chirality pdb=" CA GLU B 182 " pdb=" N GLU B 182 " pdb=" C GLU B 182 " pdb=" CB GLU B 182 " both_signs ideal model delta sigma weight residual False 2.51 1.50 1.01 2.00e-01 2.50e+01 2.57e+01 chirality pdb=" CA GLU C 182 " pdb=" N GLU C 182 " pdb=" C GLU C 182 " pdb=" CB GLU C 182 " both_signs ideal model delta sigma weight residual False 2.51 1.50 1.01 2.00e-01 2.50e+01 2.57e+01 chirality pdb=" CA GLU A 182 " pdb=" N GLU A 182 " pdb=" C GLU A 182 " pdb=" CB GLU A 182 " both_signs ideal model delta sigma weight residual False 2.51 1.69 0.82 2.00e-01 2.50e+01 1.70e+01 ... (remaining 2529 not shown) Planarity restraints: 2721 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 182 " 0.017 2.00e-02 2.50e+03 3.60e-02 1.29e+01 pdb=" C GLU B 182 " -0.062 2.00e-02 2.50e+03 pdb=" O GLU B 182 " 0.025 2.00e-02 2.50e+03 pdb=" N GLY B 183 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 182 " -0.015 2.00e-02 2.50e+03 3.22e-02 1.04e+01 pdb=" C GLU A 182 " 0.056 2.00e-02 2.50e+03 pdb=" O GLU A 182 " -0.022 2.00e-02 2.50e+03 pdb=" N GLY A 183 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 48 " 0.014 2.00e-02 2.50e+03 2.93e-02 8.59e+00 pdb=" C ARG B 48 " -0.051 2.00e-02 2.50e+03 pdb=" O ARG B 48 " 0.019 2.00e-02 2.50e+03 pdb=" N THR B 49 " 0.018 2.00e-02 2.50e+03 ... (remaining 2718 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 126 2.61 - 3.18: 11754 3.18 - 3.75: 22861 3.75 - 4.33: 33544 4.33 - 4.90: 57317 Nonbonded interactions: 125602 Sorted by model distance: nonbonded pdb=" NH2 ARG A 48 " pdb=" CG PRO A 77 " model vdw 2.033 3.520 nonbonded pdb=" O THR A 181 " pdb=" OG1 THR A 181 " model vdw 2.137 3.040 nonbonded pdb=" O THR C 181 " pdb=" OG1 THR C 181 " model vdw 2.139 3.040 nonbonded pdb=" O THR B 181 " pdb=" OG1 THR B 181 " model vdw 2.167 3.040 nonbonded pdb=" OH TYR B 178 " pdb=" O GLU B 184 " model vdw 2.271 3.040 ... (remaining 125597 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'N' selection = chain 'O' selection = chain 'R' selection = chain 'S' } ncs_group { reference = chain 'I' selection = chain 'P' selection = chain 'T' } ncs_group { reference = chain 'M' selection = chain 'Q' selection = chain 'U' } ncs_group { reference = chain 'V' selection = chain 'W' selection = chain 'X' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.740 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 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 : 0.008 0.327 15871 Z= 0.442 Angle : 1.080 30.396 21615 Z= 0.581 Chirality : 0.067 1.014 2532 Planarity : 0.008 0.072 2703 Dihedral : 15.774 108.046 6510 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.58 % Favored : 95.21 % Rotamer: Outliers : 2.24 % Allowed : 4.61 % Favored : 93.15 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.60 (0.16), residues: 1920 helix: -1.93 (0.25), residues: 276 sheet: -0.58 (0.20), residues: 579 loop : -2.41 (0.15), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 88 TYR 0.014 0.002 TYR C 262 PHE 0.024 0.003 PHE K 107 TRP 0.019 0.002 TRP K 115 HIS 0.005 0.002 HIS D 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00703 / 0.33 (15801) covalent geometry : angle 1.02816 / 0.56 (21438) SS BOND : bond 0.06926 / 5.26 ( 21) SS BOND : angle 6.57508 / 3.42 ( 42) hydrogen bonds : bond 0.13463 / 8.98 ( 558) hydrogen bonds : angle 7.16961 / 4.82 ( 1566) Misc. bond : bond 0.16354 / 12.98 ( 4) link_ALPHA1-3 : bond 0.00086 / 0.05 ( 6) link_ALPHA1-3 : angle 2.90015 / 2.05 ( 18) link_ALPHA1-6 : bond 0.00137 / 0.08 ( 3) link_ALPHA1-6 : angle 1.75139 / 1.06 ( 9) link_BETA1-4 : bond 0.00588 / 0.39 ( 15) link_BETA1-4 : angle 2.16776 / 1.43 ( 45) link_BETA1-6 : bond 0.00051 / 0.03 ( 3) link_BETA1-6 : angle 1.66557 / 0.98 ( 9) link_NAG-ASN : bond 0.00364 / 0.25 ( 18) link_NAG-ASN : angle 2.47363 / 1.61 ( 54) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 259 time to evaluate : 0.549 Fit side-chains revert: symmetry clash REVERT: A 86 GLU cc_start: 0.7277 (mm-30) cc_final: 0.7019 (mt-10) REVERT: A 199 GLN cc_start: 0.7833 (mm-40) cc_final: 0.7515 (mm-40) REVERT: A 298 LYS cc_start: 0.7719 (mttm) cc_final: 0.7228 (tptp) REVERT: B 80 LYS cc_start: 0.8507 (mttt) cc_final: 0.8077 (mptt) REVERT: W 396 LYS cc_start: 0.7853 (mttt) cc_final: 0.7639 (mtpt) REVERT: C 199 GLN cc_start: 0.7718 (mm-40) cc_final: 0.7364 (mm-40) REVERT: C 304 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8531 (tttm) REVERT: H 39 MET cc_start: 0.8449 (mmm) cc_final: 0.8207 (mmt) REVERT: J 39 MET cc_start: 0.8440 (mmm) cc_final: 0.8232 (mmt) REVERT: D 39 MET cc_start: 0.8389 (mmm) cc_final: 0.8024 (mmt) REVERT: D 93 SER cc_start: 0.8413 (OUTLIER) cc_final: 0.8178 (p) outliers start: 37 outliers final: 2 residues processed: 293 average time/residue: 0.6087 time to fit residues: 196.3815 Evaluate side-chains 184 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 180 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain D residue 93 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 HIS A 233 GLN V 399 ASN V 408 ASN ** V 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 HIS B 233 GLN W 408 ASN W 421 ASN C 233 GLN X 399 ASN X 408 ASN X 421 ASN H 82 ASN L 44 GLN L 48 GLN L 106 HIS J 82 ASN K 44 GLN K 106 HIS K 120 GLN D 82 ASN E 44 GLN E 48 GLN E 106 HIS ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.155422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.122765 restraints weight = 18912.079| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.61 r_work: 0.3328 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15871 Z= 0.146 Angle : 0.609 6.246 21615 Z= 0.306 Chirality : 0.044 0.194 2532 Planarity : 0.005 0.057 2703 Dihedral : 8.974 76.908 2997 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.42 % Allowed : 13.21 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.18), residues: 1920 helix: -0.08 (0.32), residues: 285 sheet: -0.29 (0.21), residues: 576 loop : -1.59 (0.17), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 95 TYR 0.010 0.001 TYR L 55 PHE 0.013 0.002 PHE B 192 TRP 0.017 0.001 TRP L 115 HIS 0.003 0.001 HIS B 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (15801) covalent geometry : angle 0.58390 / 0.30 (21438) SS BOND : bond 0.00416 / 0.29 ( 21) SS BOND : angle 1.57668 / 0.96 ( 42) hydrogen bonds : bond 0.03782 / 2.57 ( 558) hydrogen bonds : angle 5.59621 / 3.84 ( 1566) Misc. bond : bond 0.00464 / 0.26 ( 4) link_ALPHA1-3 : bond 0.00604 / 0.41 ( 6) link_ALPHA1-3 : angle 2.51378 / 1.56 ( 18) link_ALPHA1-6 : bond 0.00283 / 0.16 ( 3) link_ALPHA1-6 : angle 2.05321 / 1.21 ( 9) link_BETA1-4 : bond 0.00287 / 0.20 ( 15) link_BETA1-4 : angle 1.78394 / 1.25 ( 45) link_BETA1-6 : bond 0.00109 / 0.06 ( 3) link_BETA1-6 : angle 1.46209 / 0.88 ( 9) link_NAG-ASN : bond 0.00147 / 0.10 ( 18) link_NAG-ASN : angle 2.29999 / 1.52 ( 54) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 189 time to evaluate : 0.578 Fit side-chains REVERT: A 21 GLN cc_start: 0.7762 (mp10) cc_final: 0.7510 (mp10) REVERT: A 199 GLN cc_start: 0.8306 (mm-40) cc_final: 0.8043 (mm-40) REVERT: B 86 GLU cc_start: 0.7405 (mm-30) cc_final: 0.7123 (mt-10) REVERT: W 396 LYS cc_start: 0.7949 (mttt) cc_final: 0.7689 (mtmt) REVERT: W 405 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7822 (pm20) REVERT: C 199 GLN cc_start: 0.8306 (mm-40) cc_final: 0.7978 (mm-40) REVERT: H 39 MET cc_start: 0.8922 (mmm) cc_final: 0.8666 (mmt) REVERT: J 20 ARG cc_start: 0.8858 (ttt-90) cc_final: 0.8644 (ttt-90) REVERT: J 116 ASP cc_start: 0.8496 (m-30) cc_final: 0.8237 (m-30) outliers start: 40 outliers final: 26 residues processed: 213 average time/residue: 0.6181 time to fit residues: 144.5309 Evaluate side-chains 194 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 167 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain V residue 400 SER Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain W residue 385 LYS Chi-restraints excluded: chain W residue 400 SER Chi-restraints excluded: chain W residue 405 GLU Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain X residue 439 SER Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 36 SER Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 91 MET Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 126 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 106 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 181 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 chunk 113 optimal weight: 0.0370 chunk 90 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 chunk 140 optimal weight: 0.9980 chunk 146 optimal weight: 3.9990 overall best weight: 1.8064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 399 ASN V 441 GLN B 196 ASN W 421 ASN W 441 GLN C 233 GLN X 399 ASN X 441 GLN ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.154375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.123107 restraints weight = 18913.554| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.48 r_work: 0.3361 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 15871 Z= 0.252 Angle : 0.694 7.948 21615 Z= 0.343 Chirality : 0.047 0.203 2532 Planarity : 0.005 0.080 2703 Dihedral : 8.379 73.242 2988 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.76 % Allowed : 14.36 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.19), residues: 1920 helix: 0.51 (0.33), residues: 285 sheet: -0.14 (0.21), residues: 609 loop : -1.29 (0.18), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 95 TYR 0.014 0.002 TYR L 55 PHE 0.019 0.003 PHE B 192 TRP 0.015 0.002 TRP K 115 HIS 0.006 0.002 HIS D 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00606 / 0.25 (15801) covalent geometry : angle 0.67019 / 0.34 (21438) SS BOND : bond 0.00620 / 0.44 ( 21) SS BOND : angle 1.96685 / 1.26 ( 42) hydrogen bonds : bond 0.04067 / 2.76 ( 558) hydrogen bonds : angle 5.49768 / 3.77 ( 1566) Misc. bond : bond 0.00411 / 0.24 ( 4) link_ALPHA1-3 : bond 0.00572 / 0.38 ( 6) link_ALPHA1-3 : angle 2.67906 / 1.79 ( 18) link_ALPHA1-6 : bond 0.00214 / 0.12 ( 3) link_ALPHA1-6 : angle 2.35438 / 1.39 ( 9) link_BETA1-4 : bond 0.00486 / 0.32 ( 15) link_BETA1-4 : angle 1.85074 / 1.23 ( 45) link_BETA1-6 : bond 0.00146 / 0.08 ( 3) link_BETA1-6 : angle 1.32855 / 0.78 ( 9) link_NAG-ASN : bond 0.00216 / 0.15 ( 18) link_NAG-ASN : angle 2.18984 / 1.45 ( 54) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 186 time to evaluate : 0.609 Fit side-chains REVERT: A 199 GLN cc_start: 0.8311 (mm-40) cc_final: 0.7992 (mm-40) REVERT: V 385 LYS cc_start: 0.6244 (OUTLIER) cc_final: 0.6018 (mmpt) REVERT: V 428 GLU cc_start: 0.7433 (mt-10) cc_final: 0.7044 (pt0) REVERT: B 23 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7801 (tt0) REVERT: W 396 LYS cc_start: 0.7775 (mttt) cc_final: 0.7457 (mtpt) REVERT: W 405 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7826 (pm20) REVERT: W 428 GLU cc_start: 0.7545 (mt-10) cc_final: 0.7193 (pt0) REVERT: C 199 GLN cc_start: 0.8303 (mm-40) cc_final: 0.7971 (mm-40) REVERT: X 405 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7835 (pm20) REVERT: X 428 GLU cc_start: 0.7478 (mt-10) cc_final: 0.7073 (pt0) REVERT: H 95 ARG cc_start: 0.7200 (mtt-85) cc_final: 0.6860 (mtm-85) REVERT: J 20 ARG cc_start: 0.8855 (ttt-90) cc_final: 0.8502 (ttt-90) REVERT: J 116 ASP cc_start: 0.8464 (m-30) cc_final: 0.8119 (m-30) REVERT: E 88 THR cc_start: 0.8256 (OUTLIER) cc_final: 0.7980 (p) outliers start: 62 outliers final: 37 residues processed: 229 average time/residue: 0.6056 time to fit residues: 153.1201 Evaluate side-chains 195 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 153 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain V residue 385 LYS Chi-restraints excluded: chain V residue 400 SER Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 94 CYS Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain W residue 400 SER Chi-restraints excluded: chain W residue 405 GLU Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain X residue 405 GLU Chi-restraints excluded: chain X residue 439 SER Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 36 SER Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 88 THR Chi-restraints excluded: chain E residue 126 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 107 optimal weight: 1.9990 chunk 157 optimal weight: 6.9990 chunk 117 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 153 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 28 optimal weight: 0.3980 chunk 184 optimal weight: 5.9990 chunk 94 optimal weight: 0.4980 chunk 173 optimal weight: 3.9990 chunk 154 optimal weight: 0.6980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 399 ASN W 421 ASN C 233 GLN X 399 ASN ** K 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.157095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.125156 restraints weight = 18726.772| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.56 r_work: 0.3381 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15871 Z= 0.167 Angle : 0.593 7.518 21615 Z= 0.292 Chirality : 0.044 0.186 2532 Planarity : 0.004 0.060 2703 Dihedral : 7.800 67.415 2988 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.45 % Allowed : 16.24 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.19), residues: 1920 helix: 0.99 (0.34), residues: 282 sheet: -0.12 (0.21), residues: 627 loop : -1.02 (0.18), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 95 TYR 0.009 0.001 TYR K 38 PHE 0.015 0.002 PHE E 107 TRP 0.016 0.001 TRP L 115 HIS 0.004 0.001 HIS H 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 (15801) covalent geometry : angle 0.57259 / 0.29 (21438) SS BOND : bond 0.00501 / 0.35 ( 21) SS BOND : angle 1.46851 / 0.96 ( 42) hydrogen bonds : bond 0.03430 / 2.32 ( 558) hydrogen bonds : angle 5.26311 / 3.62 ( 1566) Misc. bond : bond 0.00494 / 0.27 ( 4) link_ALPHA1-3 : bond 0.00662 / 0.46 ( 6) link_ALPHA1-3 : angle 2.33200 / 1.53 ( 18) link_ALPHA1-6 : bond 0.00125 / 0.07 ( 3) link_ALPHA1-6 : angle 2.17171 / 1.27 ( 9) link_BETA1-4 : bond 0.00409 / 0.26 ( 15) link_BETA1-4 : angle 1.58287 / 1.08 ( 45) link_BETA1-6 : bond 0.00099 / 0.05 ( 3) link_BETA1-6 : angle 1.42542 / 0.85 ( 9) link_NAG-ASN : bond 0.00163 / 0.11 ( 18) link_NAG-ASN : angle 1.97417 / 1.30 ( 54) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 160 time to evaluate : 0.586 Fit side-chains revert: symmetry clash REVERT: A 199 GLN cc_start: 0.8277 (mm-40) cc_final: 0.7983 (mm-40) REVERT: V 428 GLU cc_start: 0.7396 (mt-10) cc_final: 0.7056 (pt0) REVERT: V 451 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8229 (tt0) REVERT: B 23 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7791 (mt-10) REVERT: B 69 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.7725 (ptt-90) REVERT: B 250 MET cc_start: 0.8966 (mtp) cc_final: 0.8703 (mtp) REVERT: W 396 LYS cc_start: 0.7838 (mttt) cc_final: 0.7514 (mtmt) REVERT: W 428 GLU cc_start: 0.7618 (mt-10) cc_final: 0.7161 (pt0) REVERT: C 23 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7565 (tt0) REVERT: C 199 GLN cc_start: 0.8284 (mm-40) cc_final: 0.8007 (mm-40) REVERT: X 405 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7813 (pm20) REVERT: X 428 GLU cc_start: 0.7503 (mt-10) cc_final: 0.7075 (pt0) REVERT: H 95 ARG cc_start: 0.7235 (mtt-85) cc_final: 0.6910 (mtm-85) REVERT: L 120 GLN cc_start: 0.7766 (mp10) cc_final: 0.7408 (pm20) REVERT: J 20 ARG cc_start: 0.8716 (ttt-90) cc_final: 0.8502 (tpt-90) REVERT: J 116 ASP cc_start: 0.8508 (m-30) cc_final: 0.8124 (m-30) REVERT: D 116 ASP cc_start: 0.8319 (m-30) cc_final: 0.8090 (m-30) outliers start: 57 outliers final: 40 residues processed: 200 average time/residue: 0.5489 time to fit residues: 122.1355 Evaluate side-chains 195 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 150 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 69 ARG Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain V residue 451 GLU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 94 CYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain W residue 385 LYS Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain X residue 405 GLU Chi-restraints excluded: chain X residue 439 SER Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain L residue 126 ILE Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain K residue 126 ILE Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 91 MET Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 126 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 92 optimal weight: 0.5980 chunk 64 optimal weight: 4.9990 chunk 130 optimal weight: 0.9980 chunk 172 optimal weight: 0.8980 chunk 145 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 182 optimal weight: 8.9990 chunk 50 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN B 199 GLN W 421 ASN C 233 GLN X 399 ASN ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.149344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.113203 restraints weight = 18483.303| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.61 r_work: 0.3140 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15871 Z= 0.126 Angle : 0.540 7.156 21615 Z= 0.265 Chirality : 0.043 0.196 2532 Planarity : 0.004 0.048 2703 Dihedral : 7.101 59.841 2988 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.52 % Allowed : 17.21 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.19), residues: 1920 helix: 1.48 (0.34), residues: 279 sheet: -0.01 (0.21), residues: 627 loop : -0.84 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 95 TYR 0.008 0.001 TYR C 309 PHE 0.016 0.002 PHE E 107 TRP 0.015 0.001 TRP L 115 HIS 0.003 0.001 HIS C 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (15801) covalent geometry : angle 0.52222 / 0.26 (21438) SS BOND : bond 0.00380 / 0.27 ( 21) SS BOND : angle 1.17271 / 0.76 ( 42) hydrogen bonds : bond 0.03075 / 2.08 ( 558) hydrogen bonds : angle 5.02433 / 3.46 ( 1566) Misc. bond : bond 0.00264 / 0.16 ( 4) link_ALPHA1-3 : bond 0.00804 / 0.56 ( 6) link_ALPHA1-3 : angle 2.15103 / 1.40 ( 18) link_ALPHA1-6 : bond 0.00023 / 0.01 ( 3) link_ALPHA1-6 : angle 2.13691 / 1.24 ( 9) link_BETA1-4 : bond 0.00450 / 0.30 ( 15) link_BETA1-4 : angle 1.44461 / 0.98 ( 45) link_BETA1-6 : bond 0.00120 / 0.07 ( 3) link_BETA1-6 : angle 1.42710 / 0.85 ( 9) link_NAG-ASN : bond 0.00160 / 0.12 ( 18) link_NAG-ASN : angle 1.70159 / 1.13 ( 54) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 167 time to evaluate : 0.572 Fit side-chains revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7783 (mm-30) REVERT: A 69 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.8218 (ptt90) REVERT: A 87 VAL cc_start: 0.6309 (OUTLIER) cc_final: 0.6095 (m) REVERT: V 428 GLU cc_start: 0.7045 (mt-10) cc_final: 0.6632 (pt0) REVERT: V 451 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.8023 (tt0) REVERT: B 23 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7917 (mt-10) REVERT: B 69 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.7474 (ptt-90) REVERT: W 396 LYS cc_start: 0.7445 (mttt) cc_final: 0.7081 (mtmt) REVERT: W 428 GLU cc_start: 0.7112 (mt-10) cc_final: 0.6911 (mt-10) REVERT: C 23 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7703 (mm-30) REVERT: C 199 GLN cc_start: 0.8089 (mm-40) cc_final: 0.7806 (mm-40) REVERT: X 396 LYS cc_start: 0.7544 (mttm) cc_final: 0.7109 (mtpt) REVERT: X 405 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7743 (pm20) REVERT: H 20 ARG cc_start: 0.8790 (ttt-90) cc_final: 0.8440 (tpt-90) REVERT: H 95 ARG cc_start: 0.7078 (mtt-85) cc_final: 0.6806 (mtm-85) REVERT: H 116 ASP cc_start: 0.8330 (m-30) cc_final: 0.8051 (m-30) REVERT: L 120 GLN cc_start: 0.7675 (mp10) cc_final: 0.7231 (pm20) REVERT: J 116 ASP cc_start: 0.8430 (m-30) cc_final: 0.8029 (m-30) REVERT: D 116 ASP cc_start: 0.8223 (m-30) cc_final: 0.7887 (m-30) REVERT: E 2 ILE cc_start: 0.8495 (OUTLIER) cc_final: 0.7791 (mp) outliers start: 58 outliers final: 36 residues processed: 212 average time/residue: 0.5192 time to fit residues: 122.8312 Evaluate side-chains 210 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 166 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 69 ARG Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain V residue 400 SER Chi-restraints excluded: chain V residue 451 GLU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 94 CYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain W residue 385 LYS Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 69 ARG Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain X residue 405 GLU Chi-restraints excluded: chain X residue 439 SER Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain L residue 126 ILE Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 125 THR Chi-restraints excluded: chain K residue 36 SER Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain K residue 126 ILE Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain E residue 2 ILE Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 126 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 133 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 109 optimal weight: 0.8980 chunk 138 optimal weight: 0.9990 chunk 168 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 86 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 123 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 421 ASN C 233 GLN X 399 ASN ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.143751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.105352 restraints weight = 18159.083| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.59 r_work: 0.3100 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15871 Z= 0.140 Angle : 0.560 9.148 21615 Z= 0.273 Chirality : 0.043 0.209 2532 Planarity : 0.004 0.053 2703 Dihedral : 6.916 56.896 2988 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.64 % Allowed : 17.70 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.19), residues: 1920 helix: 1.75 (0.33), residues: 279 sheet: 0.03 (0.21), residues: 606 loop : -0.75 (0.19), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 95 TYR 0.009 0.001 TYR L 55 PHE 0.014 0.002 PHE J 76 TRP 0.014 0.001 TRP K 115 HIS 0.004 0.001 HIS B 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (15801) covalent geometry : angle 0.54038 / 0.27 (21438) SS BOND : bond 0.00421 / 0.30 ( 21) SS BOND : angle 1.33348 / 0.86 ( 42) hydrogen bonds : bond 0.03112 / 2.11 ( 558) hydrogen bonds : angle 5.01297 / 3.46 ( 1566) Misc. bond : bond 0.00280 / 0.17 ( 4) link_ALPHA1-3 : bond 0.00739 / 0.51 ( 6) link_ALPHA1-3 : angle 2.23485 / 1.45 ( 18) link_ALPHA1-6 : bond 0.00160 / 0.09 ( 3) link_ALPHA1-6 : angle 2.20922 / 1.28 ( 9) link_BETA1-4 : bond 0.00447 / 0.28 ( 15) link_BETA1-4 : angle 1.48550 / 1.01 ( 45) link_BETA1-6 : bond 0.00135 / 0.08 ( 3) link_BETA1-6 : angle 1.39089 / 0.83 ( 9) link_NAG-ASN : bond 0.00158 / 0.12 ( 18) link_NAG-ASN : angle 1.83775 / 1.18 ( 54) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 163 time to evaluate : 0.624 Fit side-chains revert: symmetry clash REVERT: A 69 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.8168 (ptt90) REVERT: A 87 VAL cc_start: 0.6750 (OUTLIER) cc_final: 0.6537 (m) REVERT: V 428 GLU cc_start: 0.7114 (mt-10) cc_final: 0.6621 (pt0) REVERT: V 451 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.8064 (tt0) REVERT: B 23 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8116 (mt-10) REVERT: B 69 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.7363 (ptt-90) REVERT: B 86 GLU cc_start: 0.7453 (mm-30) cc_final: 0.7091 (mt-10) REVERT: W 396 LYS cc_start: 0.7357 (mttt) cc_final: 0.6963 (mtmt) REVERT: W 428 GLU cc_start: 0.7213 (mt-10) cc_final: 0.6972 (mt-10) REVERT: C 23 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7816 (mm-30) REVERT: C 199 GLN cc_start: 0.8142 (mm-40) cc_final: 0.7852 (mm-40) REVERT: X 396 LYS cc_start: 0.7408 (mttm) cc_final: 0.6966 (mtpt) REVERT: X 405 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.7895 (pm20) REVERT: H 20 ARG cc_start: 0.8731 (ttt-90) cc_final: 0.8376 (tpt-90) REVERT: H 95 ARG cc_start: 0.6932 (mtt-85) cc_final: 0.6649 (mtm-85) REVERT: H 116 ASP cc_start: 0.8534 (m-30) cc_final: 0.8245 (m-30) REVERT: L 120 GLN cc_start: 0.7727 (mp10) cc_final: 0.7224 (pm20) REVERT: J 20 ARG cc_start: 0.8810 (ttt-90) cc_final: 0.8566 (tpt-90) REVERT: J 116 ASP cc_start: 0.8630 (m-30) cc_final: 0.8197 (m-30) REVERT: K 86 ASP cc_start: 0.7231 (OUTLIER) cc_final: 0.6977 (m-30) REVERT: D 116 ASP cc_start: 0.8442 (m-30) cc_final: 0.8032 (m-30) REVERT: E 2 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.7721 (mp) REVERT: E 88 THR cc_start: 0.7901 (OUTLIER) cc_final: 0.7595 (p) outliers start: 60 outliers final: 38 residues processed: 211 average time/residue: 0.5220 time to fit residues: 123.0403 Evaluate side-chains 209 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 162 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 69 ARG Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain V residue 400 SER Chi-restraints excluded: chain V residue 451 GLU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 94 CYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain W residue 400 SER Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain X residue 405 GLU Chi-restraints excluded: chain X residue 439 SER Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain L residue 126 ILE Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 125 THR Chi-restraints excluded: chain K residue 36 SER Chi-restraints excluded: chain K residue 86 ASP Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain K residue 126 ILE Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain E residue 2 ILE Chi-restraints excluded: chain E residue 88 THR Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 126 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 20 optimal weight: 0.4980 chunk 10 optimal weight: 0.9980 chunk 155 optimal weight: 0.8980 chunk 143 optimal weight: 0.5980 chunk 171 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 111 optimal weight: 0.0770 chunk 7 optimal weight: 0.8980 chunk 184 optimal weight: 8.9990 chunk 25 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 421 ASN C 233 GLN X 399 ASN D 40 HIS ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.143152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.106293 restraints weight = 18031.834| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.78 r_work: 0.3120 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 15871 Z= 0.106 Angle : 0.528 8.288 21615 Z= 0.256 Chirality : 0.042 0.226 2532 Planarity : 0.004 0.042 2703 Dihedral : 6.482 50.790 2988 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.52 % Allowed : 18.30 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.19), residues: 1920 helix: 2.06 (0.33), residues: 279 sheet: 0.14 (0.22), residues: 603 loop : -0.64 (0.19), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 95 TYR 0.008 0.001 TYR C 309 PHE 0.013 0.001 PHE E 107 TRP 0.015 0.001 TRP K 115 HIS 0.003 0.001 HIS C 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (15801) covalent geometry : angle 0.51041 / 0.25 (21438) SS BOND : bond 0.00344 / 0.24 ( 21) SS BOND : angle 1.03208 / 0.67 ( 42) hydrogen bonds : bond 0.02844 / 1.92 ( 558) hydrogen bonds : angle 4.88666 / 3.38 ( 1566) Misc. bond : bond 0.00306 / 0.18 ( 4) link_ALPHA1-3 : bond 0.00865 / 0.60 ( 6) link_ALPHA1-3 : angle 2.00176 / 1.29 ( 18) link_ALPHA1-6 : bond 0.00015 / 0.01 ( 3) link_ALPHA1-6 : angle 2.11050 / 1.21 ( 9) link_BETA1-4 : bond 0.00529 / 0.36 ( 15) link_BETA1-4 : angle 1.34188 / 0.91 ( 45) link_BETA1-6 : bond 0.00120 / 0.07 ( 3) link_BETA1-6 : angle 1.43521 / 0.86 ( 9) link_NAG-ASN : bond 0.00188 / 0.13 ( 18) link_NAG-ASN : angle 1.82361 / 1.30 ( 54) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 167 time to evaluate : 0.609 Fit side-chains revert: symmetry clash REVERT: A 87 VAL cc_start: 0.6938 (OUTLIER) cc_final: 0.6734 (m) REVERT: V 451 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7863 (tp30) REVERT: B 86 GLU cc_start: 0.7468 (mm-30) cc_final: 0.7237 (mt-10) REVERT: W 396 LYS cc_start: 0.7511 (mttt) cc_final: 0.7126 (mtmt) REVERT: C 23 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7818 (mm-30) REVERT: C 199 GLN cc_start: 0.8179 (mm-40) cc_final: 0.7794 (mm-40) REVERT: X 396 LYS cc_start: 0.7562 (mttm) cc_final: 0.7173 (mtpt) REVERT: X 405 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8080 (pt0) REVERT: H 20 ARG cc_start: 0.8689 (ttt-90) cc_final: 0.8471 (tpt-90) REVERT: H 95 ARG cc_start: 0.6981 (mtt-85) cc_final: 0.6746 (mtm-85) REVERT: H 116 ASP cc_start: 0.8569 (m-30) cc_final: 0.8259 (m-30) REVERT: L 120 GLN cc_start: 0.7704 (mp10) cc_final: 0.7260 (pm20) REVERT: J 20 ARG cc_start: 0.8726 (ttt-90) cc_final: 0.8474 (tpt-90) REVERT: J 116 ASP cc_start: 0.8636 (m-30) cc_final: 0.8250 (m-30) REVERT: D 116 ASP cc_start: 0.8418 (m-30) cc_final: 0.8009 (m-30) REVERT: E 88 THR cc_start: 0.7942 (OUTLIER) cc_final: 0.7612 (p) outliers start: 58 outliers final: 35 residues processed: 213 average time/residue: 0.5233 time to fit residues: 124.4559 Evaluate side-chains 203 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 163 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain V residue 400 SER Chi-restraints excluded: chain V residue 451 GLU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 94 CYS Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain W residue 385 LYS Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 69 ARG Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain X residue 405 GLU Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain L residue 126 ILE Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 125 THR Chi-restraints excluded: chain K residue 36 SER Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain K residue 126 ILE Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 88 THR Chi-restraints excluded: chain E residue 126 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 141 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 47 optimal weight: 0.4980 chunk 5 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 177 optimal weight: 10.0000 chunk 144 optimal weight: 1.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 421 ASN C 233 GLN X 399 ASN D 40 HIS ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.150457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.112223 restraints weight = 18197.353| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.47 r_work: 0.3201 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 15871 Z= 0.290 Angle : 0.698 9.755 21615 Z= 0.341 Chirality : 0.048 0.304 2532 Planarity : 0.005 0.089 2703 Dihedral : 7.429 60.660 2988 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.82 % Allowed : 18.06 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.19), residues: 1920 helix: 1.61 (0.33), residues: 282 sheet: -0.01 (0.21), residues: 630 loop : -0.72 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 20 TYR 0.016 0.002 TYR L 55 PHE 0.020 0.003 PHE B 192 TRP 0.010 0.002 TRP H 52 HIS 0.007 0.002 HIS B 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00699 / 0.29 (15801) covalent geometry : angle 0.67586 / 0.34 (21438) SS BOND : bond 0.00676 / 0.47 ( 21) SS BOND : angle 2.06569 / 1.33 ( 42) hydrogen bonds : bond 0.03873 / 2.62 ( 558) hydrogen bonds : angle 5.27179 / 3.63 ( 1566) Misc. bond : bond 0.00536 / 0.32 ( 4) link_ALPHA1-3 : bond 0.00417 / 0.29 ( 6) link_ALPHA1-3 : angle 2.70702 / 1.79 ( 18) link_ALPHA1-6 : bond 0.00527 / 0.30 ( 3) link_ALPHA1-6 : angle 2.46511 / 1.45 ( 9) link_BETA1-4 : bond 0.00559 / 0.39 ( 15) link_BETA1-4 : angle 1.97887 / 1.32 ( 45) link_BETA1-6 : bond 0.00130 / 0.07 ( 3) link_BETA1-6 : angle 1.31612 / 0.77 ( 9) link_NAG-ASN : bond 0.00313 / 0.17 ( 18) link_NAG-ASN : angle 1.89816 / 1.22 ( 54) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 164 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: V 396 LYS cc_start: 0.7863 (mtpm) cc_final: 0.7385 (mtpt) REVERT: V 416 MET cc_start: 0.7698 (OUTLIER) cc_final: 0.5901 (mmm) REVERT: V 451 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8242 (tt0) REVERT: B 23 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8094 (mt-10) REVERT: W 396 LYS cc_start: 0.7751 (mttt) cc_final: 0.7352 (mtmt) REVERT: C 23 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7717 (mm-30) REVERT: C 199 GLN cc_start: 0.8331 (mm-40) cc_final: 0.8060 (mm-40) REVERT: X 396 LYS cc_start: 0.7775 (mttm) cc_final: 0.7351 (mtpt) REVERT: H 20 ARG cc_start: 0.8756 (ttt-90) cc_final: 0.8461 (tpt-90) REVERT: L 120 GLN cc_start: 0.7745 (mp10) cc_final: 0.7318 (pm20) REVERT: J 116 ASP cc_start: 0.8587 (OUTLIER) cc_final: 0.8158 (m-30) REVERT: K 86 ASP cc_start: 0.7510 (OUTLIER) cc_final: 0.7188 (m-30) REVERT: D 116 ASP cc_start: 0.8450 (m-30) cc_final: 0.7735 (m-30) REVERT: E 2 ILE cc_start: 0.8582 (OUTLIER) cc_final: 0.7841 (mp) REVERT: E 88 THR cc_start: 0.8313 (OUTLIER) cc_final: 0.8032 (p) outliers start: 63 outliers final: 41 residues processed: 208 average time/residue: 0.4953 time to fit residues: 116.0885 Evaluate side-chains 209 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 160 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain V residue 400 SER Chi-restraints excluded: chain V residue 416 MET Chi-restraints excluded: chain V residue 421 ASN Chi-restraints excluded: chain V residue 451 GLU Chi-restraints excluded: chain V residue 464 LEU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 94 CYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain W residue 400 SER Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 69 ARG Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain X residue 439 SER Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain L residue 126 ILE Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 116 ASP Chi-restraints excluded: chain J residue 125 THR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 36 SER Chi-restraints excluded: chain K residue 86 ASP Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain K residue 126 ILE Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain E residue 2 ILE Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 88 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 53 optimal weight: 0.0870 chunk 74 optimal weight: 0.9980 chunk 170 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 113 optimal weight: 0.6980 chunk 117 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 421 ASN C 233 GLN X 399 ASN ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.155872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.117916 restraints weight = 18084.538| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.49 r_work: 0.3266 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 15871 Z= 0.118 Angle : 0.551 8.455 21615 Z= 0.271 Chirality : 0.043 0.208 2532 Planarity : 0.004 0.039 2703 Dihedral : 6.658 51.792 2988 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.61 % Allowed : 19.70 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.20), residues: 1920 helix: 2.01 (0.33), residues: 282 sheet: 0.11 (0.21), residues: 633 loop : -0.55 (0.19), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 20 TYR 0.009 0.001 TYR C 309 PHE 0.014 0.001 PHE E 107 TRP 0.018 0.001 TRP K 115 HIS 0.003 0.001 HIS H 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (15801) covalent geometry : angle 0.53486 / 0.27 (21438) SS BOND : bond 0.00379 / 0.27 ( 21) SS BOND : angle 1.15210 / 0.76 ( 42) hydrogen bonds : bond 0.03017 / 2.04 ( 558) hydrogen bonds : angle 5.01845 / 3.47 ( 1566) Misc. bond : bond 0.00338 / 0.20 ( 4) link_ALPHA1-3 : bond 0.00880 / 0.58 ( 6) link_ALPHA1-3 : angle 2.07671 / 1.34 ( 18) link_ALPHA1-6 : bond 0.00154 / 0.09 ( 3) link_ALPHA1-6 : angle 2.14040 / 1.23 ( 9) link_BETA1-4 : bond 0.00492 / 0.32 ( 15) link_BETA1-4 : angle 1.41744 / 0.97 ( 45) link_BETA1-6 : bond 0.00111 / 0.06 ( 3) link_BETA1-6 : angle 1.46310 / 0.88 ( 9) link_NAG-ASN : bond 0.00203 / 0.12 ( 18) link_NAG-ASN : angle 1.65678 / 1.09 ( 54) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 166 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: V 396 LYS cc_start: 0.7786 (mtpm) cc_final: 0.7334 (mtpt) REVERT: V 416 MET cc_start: 0.7461 (OUTLIER) cc_final: 0.5714 (mmm) REVERT: B 23 GLU cc_start: 0.8353 (mt-10) cc_final: 0.8101 (mt-10) REVERT: W 396 LYS cc_start: 0.7711 (mttt) cc_final: 0.7316 (mtmt) REVERT: C 23 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7729 (mm-30) REVERT: C 199 GLN cc_start: 0.8252 (mm-40) cc_final: 0.7915 (mm110) REVERT: X 396 LYS cc_start: 0.7722 (mttm) cc_final: 0.7352 (mtpt) REVERT: H 95 ARG cc_start: 0.7123 (mtt-85) cc_final: 0.6867 (mtm-85) REVERT: H 116 ASP cc_start: 0.8357 (m-30) cc_final: 0.8108 (m-30) REVERT: L 120 GLN cc_start: 0.7690 (mp10) cc_final: 0.7257 (pm20) REVERT: J 116 ASP cc_start: 0.8585 (OUTLIER) cc_final: 0.8158 (m-30) REVERT: D 20 ARG cc_start: 0.8757 (tpt-90) cc_final: 0.8534 (OUTLIER) REVERT: D 116 ASP cc_start: 0.8450 (m-30) cc_final: 0.7991 (m-30) REVERT: E 2 ILE cc_start: 0.8569 (OUTLIER) cc_final: 0.7821 (mp) REVERT: E 88 THR cc_start: 0.8133 (OUTLIER) cc_final: 0.7825 (p) outliers start: 43 outliers final: 34 residues processed: 198 average time/residue: 0.5606 time to fit residues: 123.4132 Evaluate side-chains 198 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 160 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain V residue 400 SER Chi-restraints excluded: chain V residue 416 MET Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 94 CYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain W residue 400 SER Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 69 ARG Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain L residue 88 THR Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain L residue 126 ILE Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 116 ASP Chi-restraints excluded: chain J residue 125 THR Chi-restraints excluded: chain K residue 36 SER Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain K residue 126 ILE Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain E residue 2 ILE Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 88 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 0.9990 chunk 54 optimal weight: 0.5980 chunk 126 optimal weight: 3.9990 chunk 156 optimal weight: 9.9990 chunk 72 optimal weight: 0.9990 chunk 171 optimal weight: 0.7980 chunk 67 optimal weight: 0.0670 chunk 22 optimal weight: 1.9990 chunk 8 optimal weight: 0.0980 chunk 13 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 overall best weight: 0.5120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 421 ASN C 233 GLN X 399 ASN ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.149883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.112246 restraints weight = 18248.317| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.85 r_work: 0.3201 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 15871 Z= 0.111 Angle : 0.535 7.594 21615 Z= 0.262 Chirality : 0.043 0.211 2532 Planarity : 0.004 0.044 2703 Dihedral : 6.272 46.618 2988 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.30 % Allowed : 19.94 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.20), residues: 1920 helix: 2.29 (0.33), residues: 279 sheet: 0.17 (0.21), residues: 633 loop : -0.48 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 20 TYR 0.008 0.001 TYR C 309 PHE 0.014 0.001 PHE E 107 TRP 0.015 0.001 TRP E 115 HIS 0.003 0.001 HIS J 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (15801) covalent geometry : angle 0.51920 / 0.26 (21438) SS BOND : bond 0.00352 / 0.25 ( 21) SS BOND : angle 1.06561 / 0.70 ( 42) hydrogen bonds : bond 0.02877 / 1.95 ( 558) hydrogen bonds : angle 4.92802 / 3.40 ( 1566) Misc. bond : bond 0.00315 / 0.19 ( 4) link_ALPHA1-3 : bond 0.00844 / 0.58 ( 6) link_ALPHA1-3 : angle 2.02884 / 1.31 ( 18) link_ALPHA1-6 : bond 0.00013 / 0.01 ( 3) link_ALPHA1-6 : angle 2.09110 / 1.20 ( 9) link_BETA1-4 : bond 0.00525 / 0.37 ( 15) link_BETA1-4 : angle 1.39211 / 0.95 ( 45) link_BETA1-6 : bond 0.00162 / 0.09 ( 3) link_BETA1-6 : angle 1.39288 / 0.83 ( 9) link_NAG-ASN : bond 0.00189 / 0.12 ( 18) link_NAG-ASN : angle 1.60714 / 1.05 ( 54) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 162 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: V 396 LYS cc_start: 0.7736 (mtpm) cc_final: 0.7313 (mtpt) REVERT: V 416 MET cc_start: 0.7428 (OUTLIER) cc_final: 0.5690 (mmm) REVERT: W 396 LYS cc_start: 0.7612 (mttt) cc_final: 0.7225 (mtmt) REVERT: C 23 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7779 (mm-30) REVERT: C 199 GLN cc_start: 0.8180 (mm-40) cc_final: 0.7858 (mm110) REVERT: X 396 LYS cc_start: 0.7679 (mttm) cc_final: 0.7312 (mtpt) REVERT: H 95 ARG cc_start: 0.7068 (mtt-85) cc_final: 0.6816 (mtm-85) REVERT: L 120 GLN cc_start: 0.7721 (mp10) cc_final: 0.7296 (pm20) REVERT: J 20 ARG cc_start: 0.8649 (tpt-90) cc_final: 0.8284 (mmm-85) REVERT: J 116 ASP cc_start: 0.8587 (OUTLIER) cc_final: 0.8150 (m-30) REVERT: D 116 ASP cc_start: 0.8426 (m-30) cc_final: 0.7911 (m-30) REVERT: E 2 ILE cc_start: 0.8523 (OUTLIER) cc_final: 0.7780 (mp) REVERT: E 88 THR cc_start: 0.8056 (OUTLIER) cc_final: 0.7728 (p) outliers start: 38 outliers final: 31 residues processed: 193 average time/residue: 0.5379 time to fit residues: 115.8818 Evaluate side-chains 194 residues out of total 1650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 158 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain V residue 400 SER Chi-restraints excluded: chain V residue 416 MET Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 94 CYS Chi-restraints excluded: chain W residue 400 SER Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 69 ARG Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain L residue 88 THR Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain L residue 126 ILE Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 116 ASP Chi-restraints excluded: chain J residue 125 THR Chi-restraints excluded: chain K residue 36 SER Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain K residue 126 ILE Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain E residue 2 ILE Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 88 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 144 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 chunk 95 optimal weight: 0.5980 chunk 68 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 120 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 172 optimal weight: 4.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 421 ASN C 233 GLN X 399 ASN ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.153839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.115790 restraints weight = 18005.295| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.49 r_work: 0.3246 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 15871 Z= 0.177 Angle : 0.595 7.817 21615 Z= 0.291 Chirality : 0.044 0.203 2532 Planarity : 0.004 0.061 2703 Dihedral : 6.540 49.086 2988 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.97 % Allowed : 19.70 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.20), residues: 1920 helix: 2.12 (0.33), residues: 282 sheet: 0.13 (0.21), residues: 636 loop : -0.45 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 20 TYR 0.011 0.001 TYR K 55 PHE 0.015 0.002 PHE B 192 TRP 0.010 0.002 TRP K 115 HIS 0.005 0.001 HIS B 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 (15801) covalent geometry : angle 0.57624 / 0.29 (21438) SS BOND : bond 0.00517 / 0.36 ( 21) SS BOND : angle 1.53745 / 1.00 ( 42) hydrogen bonds : bond 0.03284 / 2.23 ( 558) hydrogen bonds : angle 5.06584 / 3.49 ( 1566) Misc. bond : bond 0.00375 / 0.22 ( 4) link_ALPHA1-3 : bond 0.00678 / 0.46 ( 6) link_ALPHA1-3 : angle 2.30809 / 1.49 ( 18) link_ALPHA1-6 : bond 0.00181 / 0.10 ( 3) link_ALPHA1-6 : angle 2.21557 / 1.28 ( 9) link_BETA1-4 : bond 0.00478 / 0.33 ( 15) link_BETA1-4 : angle 1.61735 / 1.09 ( 45) link_BETA1-6 : bond 0.00167 / 0.09 ( 3) link_BETA1-6 : angle 1.34607 / 0.80 ( 9) link_NAG-ASN : bond 0.00182 / 0.10 ( 18) link_NAG-ASN : angle 1.70191 / 1.11 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5601.75 seconds wall clock time: 96 minutes 19.70 seconds (5779.70 seconds total)