Starting phenix.real_space_refine on Sun Sep 13 01:19:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6vo3_21258/09_2026/6vo3_21258.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vo3_21258/09_2026/6vo3_21258.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vo3_21258/09_2026/6vo3_21258.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vo3_21258/09_2026/6vo3_21258.map" model { file = "/net/cci-nas-00/data/ceres_data/6vo3_21258/09_2026/6vo3_21258.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vo3_21258/09_2026/6vo3_21258.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6vo3_21258/09_2026/6vo3_21258.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6vo3_21258/09_2026/6vo3_21258.cif" } resolution = 4.25 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= 0.049 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 120 5.16 5 C 12300 2.51 5 N 3300 2.21 5 O 3834 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19554 Number of models: 1 Model: "" Number of chains: 39 Chain: "H" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 994 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "L" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 784 Classifications: {'peptide': 100} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 92} Chain: "A" Number of atoms: 3402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3402 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 22, 'TRANS': 406} Chain breaks: 4 Chain: "B" Number of atoms: 992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 992 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "G" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 994 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "J" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 784 Classifications: {'peptide': 100} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 92} Chain: "C" Number of atoms: 3402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3402 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 22, 'TRANS': 406} Chain breaks: 4 Chain: "E" Number of atoms: 992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 992 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "I" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 994 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "K" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 784 Classifications: {'peptide': 100} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 92} Chain: "D" Number of atoms: 3402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3402 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 22, 'TRANS': 406} Chain breaks: 4 Chain: "F" Number of atoms: 992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 992 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen 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 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 chiralities: 2 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "Y" 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 chiralities: 2 Chain: "Z" 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 chiralities: 2 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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 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 chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.81, per 1000 atoms: 0.19 Number of scatterers: 19554 At special positions: 0 Unit cell: (144.1, 148.03, 116.59, 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 120 16.00 O 3834 8.00 N 3300 7.00 C 12300 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.05 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.02 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.13 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.04 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.02 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.05 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.02 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.04 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.13 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.04 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.02 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.05 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.02 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.04 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.04 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.13 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.04 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.02 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.03 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.03 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.03 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " 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=0, symmetry=0 Links applied ALPHA1-3 " BMA N 3 " - " MAN N 4 " " BMA U 3 " - " MAN U 4 " " BMA b 3 " - " MAN b 4 " ALPHA1-6 " BMA N 3 " - " MAN N 5 " " BMA U 3 " - " MAN U 5 " " BMA b 3 " - " MAN b 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " 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 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " NAG-ASN " NAG A 614 " - " ASN A 396 " " NAG A 615 " - " ASN A 448 " " NAG A 619 " - " ASN A 463 " " NAG A 622 " - " ASN A 234 " " NAG A 623 " - " ASN A 197 " " NAG B 701 " - " ASN B 625 " " NAG C 614 " - " ASN C 396 " " NAG C 615 " - " ASN C 448 " " NAG C 619 " - " ASN C 463 " " NAG C 622 " - " ASN C 234 " " NAG C 623 " - " ASN C 197 " " NAG D 614 " - " ASN D 396 " " NAG D 615 " - " ASN D 448 " " NAG D 619 " - " ASN D 463 " " NAG D 622 " - " ASN D 234 " " NAG D 623 " - " ASN D 197 " " NAG E 701 " - " ASN E 625 " " NAG F 701 " - " ASN F 625 " " NAG M 1 " - " ASN A 262 " " NAG N 1 " - " ASN A 276 " " NAG O 1 " - " ASN A 386 " " NAG P 1 " - " ASN A 392 " " NAG Q 1 " - " ASN A 362 " " NAG R 1 " - " ASN A 241 " " NAG S 1 " - " ASN A 88 " " NAG T 1 " - " ASN C 262 " " NAG U 1 " - " ASN C 276 " " NAG V 1 " - " ASN C 386 " " NAG W 1 " - " ASN C 392 " " NAG X 1 " - " ASN C 362 " " NAG Y 1 " - " ASN C 241 " " NAG Z 1 " - " ASN C 88 " " NAG a 1 " - " ASN D 262 " " NAG b 1 " - " ASN D 276 " " NAG c 1 " - " ASN D 386 " " NAG d 1 " - " ASN D 392 " " NAG e 1 " - " ASN D 362 " " NAG f 1 " - " ASN D 241 " " NAG g 1 " - " ASN D 88 " Time building additional restraints: 1.80 Conformation dependent library (CDL) restraints added in 809.5 milliseconds 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4338 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 45 sheets defined 24.4% alpha, 34.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'H' and resid 25 through 31 Processing helix chain 'H' and resid 60 through 66 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 77 through 83 Proline residue: L 80 - end of helix Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.206A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 334 through 353 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 390 Processing helix chain 'A' and resid 425 through 429 Processing helix chain 'A' and resid 474 through 484 removed outlier: 4.032A pdb=" N ASN A 478 " --> pdb=" O ASP A 474 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 Processing helix chain 'B' and resid 532 through 541 removed outlier: 4.764A pdb=" N THR B 538 " --> pdb=" O SER B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 596 Processing helix chain 'B' and resid 618 through 624 removed outlier: 3.560A pdb=" N ILE B 622 " --> pdb=" O SER B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.885A pdb=" N ARG B 633 " --> pdb=" O ILE B 629 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLU B 634 " --> pdb=" O GLU B 630 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE B 635 " --> pdb=" O TRP B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 651 Processing helix chain 'B' and resid 651 through 664 Processing helix chain 'G' and resid 25 through 31 Processing helix chain 'G' and resid 60 through 66 Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'J' and resid 77 through 83 Proline residue: J 80 - end of helix Processing helix chain 'C' and resid 70 through 74 Processing helix chain 'C' and resid 98 through 117 removed outlier: 4.206A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 334 through 353 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 390 Processing helix chain 'C' and resid 425 through 429 Processing helix chain 'C' and resid 474 through 484 removed outlier: 4.032A pdb=" N ASN C 478 " --> pdb=" O ASP C 474 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 528 Processing helix chain 'E' and resid 532 through 541 removed outlier: 4.764A pdb=" N THR E 538 " --> pdb=" O SER E 534 " (cutoff:3.500A) Processing helix chain 'E' and resid 570 through 596 Processing helix chain 'E' and resid 618 through 624 removed outlier: 3.561A pdb=" N ILE E 622 " --> pdb=" O SER E 618 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 636 removed outlier: 3.885A pdb=" N ARG E 633 " --> pdb=" O ILE E 629 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLU E 634 " --> pdb=" O GLU E 630 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE E 635 " --> pdb=" O TRP E 631 " (cutoff:3.500A) Processing helix chain 'E' and resid 638 through 651 Processing helix chain 'E' and resid 651 through 664 Processing helix chain 'I' and resid 25 through 31 Processing helix chain 'I' and resid 60 through 66 Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'K' and resid 77 through 83 Proline residue: K 80 - end of helix Processing helix chain 'D' and resid 70 through 74 Processing helix chain 'D' and resid 98 through 117 removed outlier: 4.207A pdb=" N GLU D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 334 through 353 Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 387 through 390 Processing helix chain 'D' and resid 425 through 429 Processing helix chain 'D' and resid 474 through 484 removed outlier: 4.032A pdb=" N ASN D 478 " --> pdb=" O ASP D 474 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLU D 482 " --> pdb=" O ASN D 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 528 Processing helix chain 'F' and resid 532 through 541 removed outlier: 4.764A pdb=" N THR F 538 " --> pdb=" O SER F 534 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 596 Processing helix chain 'F' and resid 618 through 624 removed outlier: 3.560A pdb=" N ILE F 622 " --> pdb=" O SER F 618 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 636 removed outlier: 3.885A pdb=" N ARG F 633 " --> pdb=" O ILE F 629 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLU F 634 " --> pdb=" O GLU F 630 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE F 635 " --> pdb=" O TRP F 631 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 651 Processing helix chain 'F' and resid 651 through 664 Processing sheet with id=AA1, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.671A pdb=" N ILE H 35 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N TRP H 50 " --> pdb=" O ILE H 35 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.688A pdb=" N CYS H 92 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA4, first strand: chain 'L' and resid 10 through 12 removed outlier: 5.951A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 12 removed outlier: 5.951A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 494 through 498 Processing sheet with id=AA7, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA8, first strand: chain 'A' and resid 75 through 76 removed outlier: 6.830A pdb=" N CYS A 54 " --> pdb=" O VAL A 75 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AB1, first strand: chain 'A' and resid 170 through 177 Processing sheet with id=AB2, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.160A pdb=" N VAL A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N TYR A 435 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LYS A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 259 through 260 removed outlier: 3.785A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 259 through 260 removed outlier: 3.785A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ALA A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 315 through 323A removed outlier: 7.394A pdb=" N TRP A 316 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE A 309 " --> pdb=" O TRP A 316 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N THR A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N LYS A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA A 322 " --> pdb=" O THR A 303 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 315 through 323A removed outlier: 7.394A pdb=" N TRP A 316 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE A 309 " --> pdb=" O TRP A 316 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N THR A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N LYS A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA A 322 " --> pdb=" O THR A 303 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.671A pdb=" N ILE G 35 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N TRP G 50 " --> pdb=" O ILE G 35 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 10 through 12 removed outlier: 5.688A pdb=" N CYS G 92 " --> pdb=" O GLY G 104 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AC1, first strand: chain 'J' and resid 10 through 12 removed outlier: 5.950A pdb=" N LEU J 11 " --> pdb=" O GLU J 105 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 10 through 12 removed outlier: 5.950A pdb=" N LEU J 11 " --> pdb=" O GLU J 105 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 494 through 498 Processing sheet with id=AC4, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AC5, first strand: chain 'C' and resid 75 through 76 removed outlier: 6.830A pdb=" N CYS C 54 " --> pdb=" O VAL C 75 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AC7, first strand: chain 'C' and resid 170 through 177 Processing sheet with id=AC8, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.161A pdb=" N VAL C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N TYR C 435 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LYS C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 259 through 260 removed outlier: 3.785A pdb=" N GLY C 451 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 259 through 260 removed outlier: 3.785A pdb=" N GLY C 451 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ALA C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 315 through 323A removed outlier: 7.394A pdb=" N TRP C 316 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE C 309 " --> pdb=" O TRP C 316 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N TYR C 318 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ILE C 307 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N THR C 320 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N LYS C 305 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA C 322 " --> pdb=" O THR C 303 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 315 through 323A removed outlier: 7.394A pdb=" N TRP C 316 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE C 309 " --> pdb=" O TRP C 316 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N TYR C 318 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ILE C 307 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N THR C 320 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N LYS C 305 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA C 322 " --> pdb=" O THR C 303 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.671A pdb=" N ILE I 35 " --> pdb=" O TRP I 50 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N TRP I 50 " --> pdb=" O ILE I 35 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 10 through 12 removed outlier: 5.687A pdb=" N CYS I 92 " --> pdb=" O GLY I 104 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AD7, first strand: chain 'K' and resid 10 through 12 removed outlier: 5.951A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 10 through 12 removed outlier: 5.951A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 494 through 498 Processing sheet with id=AE1, first strand: chain 'D' and resid 45 through 47 Processing sheet with id=AE2, first strand: chain 'D' and resid 75 through 76 removed outlier: 6.830A pdb=" N CYS D 54 " --> pdb=" O VAL D 75 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 91 through 94 Processing sheet with id=AE4, first strand: chain 'D' and resid 170 through 177 Processing sheet with id=AE5, first strand: chain 'D' and resid 200 through 203 removed outlier: 6.161A pdb=" N VAL D 200 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N TYR D 435 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LYS D 202 " --> pdb=" O TYR D 435 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 259 through 260 removed outlier: 3.786A pdb=" N GLY D 451 " --> pdb=" O LEU D 260 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 259 through 260 removed outlier: 3.786A pdb=" N GLY D 451 " --> pdb=" O LEU D 260 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ALA D 360 " --> pdb=" O PHE D 468 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 315 through 323A removed outlier: 7.393A pdb=" N TRP D 316 " --> pdb=" O ILE D 309 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE D 309 " --> pdb=" O TRP D 316 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N TYR D 318 " --> pdb=" O ILE D 307 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ILE D 307 " --> pdb=" O TYR D 318 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N THR D 320 " --> pdb=" O LYS D 305 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N LYS D 305 " --> pdb=" O THR D 320 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA D 322 " --> pdb=" O THR D 303 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N PHE D 382 " --> pdb=" O LYS D 421 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 315 through 323A removed outlier: 7.393A pdb=" N TRP D 316 " --> pdb=" O ILE D 309 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE D 309 " --> pdb=" O TRP D 316 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N TYR D 318 " --> pdb=" O ILE D 307 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ILE D 307 " --> pdb=" O TYR D 318 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N THR D 320 " --> pdb=" O LYS D 305 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N LYS D 305 " --> pdb=" O THR D 320 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA D 322 " --> pdb=" O THR D 303 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ASN D 300 " --> pdb=" O GLY D 441 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLY D 441 " --> pdb=" O ASN D 300 " (cutoff:3.500A) 807 hydrogen bonds defined for protein. 2016 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: 4.05 Time building geometry restraints manager: 2.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 4975 1.33 - 1.47: 6369 1.47 - 1.61: 8444 1.61 - 1.74: 12 1.74 - 1.88: 159 Bond restraints: 19959 Sorted by residual: bond pdb=" CB CYS L 88 " pdb=" SG CYS L 88 " ideal model delta sigma weight residual 1.808 1.635 0.173 3.30e-02 9.18e+02 2.75e+01 bond pdb=" CB CYS J 88 " pdb=" SG CYS J 88 " ideal model delta sigma weight residual 1.808 1.635 0.173 3.30e-02 9.18e+02 2.75e+01 bond pdb=" CB CYS K 88 " pdb=" SG CYS K 88 " ideal model delta sigma weight residual 1.808 1.635 0.173 3.30e-02 9.18e+02 2.74e+01 bond pdb=" CB HIS C 330 " pdb=" CG HIS C 330 " ideal model delta sigma weight residual 1.497 1.427 0.070 1.40e-02 5.10e+03 2.49e+01 bond pdb=" CB TYR H 100E" pdb=" CG TYR H 100E" ideal model delta sigma weight residual 1.512 1.402 0.110 2.20e-02 2.07e+03 2.49e+01 ... (remaining 19954 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 22093 2.18 - 4.36: 3949 4.36 - 6.53: 836 6.53 - 8.71: 176 8.71 - 10.89: 18 Bond angle restraints: 27072 Sorted by residual: angle pdb=" CA PHE A 53 " pdb=" CB PHE A 53 " pdb=" CG PHE A 53 " ideal model delta sigma weight residual 113.80 121.92 -8.12 1.00e+00 1.00e+00 6.59e+01 angle pdb=" CA PHE D 53 " pdb=" CB PHE D 53 " pdb=" CG PHE D 53 " ideal model delta sigma weight residual 113.80 121.91 -8.11 1.00e+00 1.00e+00 6.57e+01 angle pdb=" CA PHE C 53 " pdb=" CB PHE C 53 " pdb=" CG PHE C 53 " ideal model delta sigma weight residual 113.80 121.90 -8.10 1.00e+00 1.00e+00 6.56e+01 angle pdb=" N ILE A 181 " pdb=" CA ILE A 181 " pdb=" C ILE A 181 " ideal model delta sigma weight residual 108.17 119.06 -10.89 1.40e+00 5.10e-01 6.05e+01 angle pdb=" N ILE C 181 " pdb=" CA ILE C 181 " pdb=" C ILE C 181 " ideal model delta sigma weight residual 108.17 119.06 -10.89 1.40e+00 5.10e-01 6.05e+01 ... (remaining 27067 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 10817 17.69 - 35.38: 349 35.38 - 53.07: 135 53.07 - 70.76: 39 70.76 - 88.45: 9 Dihedral angle restraints: 11349 sinusoidal: 4635 harmonic: 6714 Sorted by residual: dihedral pdb=" C LEU E 537 " pdb=" N LEU E 537 " pdb=" CA LEU E 537 " pdb=" CB LEU E 537 " ideal model delta harmonic sigma weight residual -122.60 -112.27 -10.33 0 2.50e+00 1.60e-01 1.71e+01 dihedral pdb=" C LEU F 537 " pdb=" N LEU F 537 " pdb=" CA LEU F 537 " pdb=" CB LEU F 537 " ideal model delta harmonic sigma weight residual -122.60 -112.28 -10.32 0 2.50e+00 1.60e-01 1.70e+01 dihedral pdb=" C LEU B 537 " pdb=" N LEU B 537 " pdb=" CA LEU B 537 " pdb=" CB LEU B 537 " ideal model delta harmonic sigma weight residual -122.60 -112.30 -10.30 0 2.50e+00 1.60e-01 1.70e+01 ... (remaining 11346 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 2392 0.113 - 0.226: 729 0.226 - 0.339: 101 0.339 - 0.452: 3 0.452 - 0.565: 12 Chirality restraints: 3237 Sorted by residual: chirality pdb=" C1 BMA a 3 " pdb=" O4 NAG a 2 " pdb=" C2 BMA a 3 " pdb=" O5 BMA a 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.33e+01 chirality pdb=" C1 BMA M 3 " pdb=" O4 NAG M 2 " pdb=" C2 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.26e+01 chirality pdb=" C1 BMA T 3 " pdb=" O4 NAG T 2 " pdb=" C2 BMA T 3 " pdb=" O5 BMA T 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.18e+01 ... (remaining 3234 not shown) Planarity restraints: 3375 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG T 2 " -0.088 2.00e-02 2.50e+03 7.24e-02 6.55e+01 pdb=" C7 NAG T 2 " 0.023 2.00e-02 2.50e+03 pdb=" C8 NAG T 2 " -0.066 2.00e-02 2.50e+03 pdb=" N2 NAG T 2 " 0.115 2.00e-02 2.50e+03 pdb=" O7 NAG T 2 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG a 2 " -0.088 2.00e-02 2.50e+03 7.24e-02 6.54e+01 pdb=" C7 NAG a 2 " 0.023 2.00e-02 2.50e+03 pdb=" C8 NAG a 2 " -0.066 2.00e-02 2.50e+03 pdb=" N2 NAG a 2 " 0.115 2.00e-02 2.50e+03 pdb=" O7 NAG a 2 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 2 " -0.088 2.00e-02 2.50e+03 7.23e-02 6.54e+01 pdb=" C7 NAG M 2 " 0.023 2.00e-02 2.50e+03 pdb=" C8 NAG M 2 " -0.066 2.00e-02 2.50e+03 pdb=" N2 NAG M 2 " 0.115 2.00e-02 2.50e+03 pdb=" O7 NAG M 2 " 0.017 2.00e-02 2.50e+03 ... (remaining 3372 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.89: 7888 2.89 - 3.39: 17911 3.39 - 3.89: 34105 3.89 - 4.40: 39417 4.40 - 4.90: 62034 Nonbonded interactions: 161355 Sorted by model distance: nonbonded pdb=" N ASP C 57 " pdb=" OD1 ASP C 57 " model vdw 2.385 3.120 nonbonded pdb=" N ASP A 57 " pdb=" OD1 ASP A 57 " model vdw 2.385 3.120 nonbonded pdb=" N ASP D 57 " pdb=" OD1 ASP D 57 " model vdw 2.385 3.120 nonbonded pdb=" OD1 ASP H 27 " pdb=" NZ LYS C 207 " model vdw 2.387 3.120 nonbonded pdb=" NZ LYS A 207 " pdb=" OD1 ASP I 27 " model vdw 2.387 3.120 ... (remaining 161350 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'a' selection = chain 'c' selection = chain 'e' } ncs_group { reference = chain 'N' selection = chain 'U' selection = chain 'b' } ncs_group { reference = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'd' selection = chain 'f' selection = chain 'g' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.480 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: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 17.480 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 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 : 0.019 0.173 20073 Z= 1.012 Angle : 1.858 10.890 27378 Z= 1.171 Chirality : 0.106 0.565 3237 Planarity : 0.009 0.072 3336 Dihedral : 11.020 88.450 6903 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.53 % Allowed : 3.82 % Favored : 95.66 % Rotamer: Outliers : 0.44 % Allowed : 1.32 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.17), residues: 2280 helix: -0.25 (0.23), residues: 429 sheet: 0.78 (0.19), residues: 642 loop : 0.05 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 94 TYR 0.042 0.009 TYR C 486 PHE 0.032 0.006 PHE D 53 TRP 0.040 0.011 TRP B 571 HIS 0.016 0.004 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.01915 / 1.01 (19959) covalent geometry : angle 1.84077 / 1.17 (27072) SS BOND : bond 0.02869 / 2.27 ( 36) SS BOND : angle 2.11563 / 1.47 ( 72) hydrogen bonds : bond 0.15913 / 10.81 ( 768) hydrogen bonds : angle 8.13255 / 5.70 ( 2016) link_ALPHA1-3 : bond 0.04758 / 2.39 ( 3) link_ALPHA1-3 : angle 6.02560 / 3.60 ( 9) link_ALPHA1-6 : bond 0.04450 / 2.23 ( 3) link_ALPHA1-6 : angle 3.79895 / 2.29 ( 9) link_BETA1-4 : bond 0.03794 / 2.38 ( 33) link_BETA1-4 : angle 3.87154 / 2.55 ( 99) link_NAG-ASN : bond 0.03225 / 2.03 ( 39) link_NAG-ASN : angle 2.18944 / 1.57 ( 117) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 683 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 4 LEU cc_start: 0.8039 (mt) cc_final: 0.7023 (mt) REVERT: H 36 TRP cc_start: 0.9324 (m100) cc_final: 0.8905 (m100) REVERT: H 72 ASP cc_start: 0.7945 (t0) cc_final: 0.7462 (t0) REVERT: H 75 LEU cc_start: 0.9001 (mt) cc_final: 0.8752 (mt) REVERT: H 80 MET cc_start: 0.8778 (ttp) cc_final: 0.8493 (ttt) REVERT: H 81 ASP cc_start: 0.7892 (m-30) cc_final: 0.7628 (p0) REVERT: L 86 TYR cc_start: 0.8245 (m-80) cc_final: 0.7760 (m-10) REVERT: A 69 TRP cc_start: 0.7677 (m-90) cc_final: 0.6699 (m-90) REVERT: A 95 MET cc_start: 0.8697 (ptm) cc_final: 0.8492 (ptm) REVERT: A 195 ASN cc_start: 0.7968 (m-40) cc_final: 0.7672 (m110) REVERT: A 434 MET cc_start: 0.8486 (ttp) cc_final: 0.7924 (tmm) REVERT: A 494 LEU cc_start: 0.8870 (mt) cc_final: 0.8521 (pp) REVERT: B 622 ILE cc_start: 0.8882 (pt) cc_final: 0.8528 (mp) REVERT: G 4 LEU cc_start: 0.7919 (mt) cc_final: 0.7130 (mt) REVERT: G 13 LYS cc_start: 0.8714 (mmtt) cc_final: 0.8480 (mmmt) REVERT: G 36 TRP cc_start: 0.9353 (m100) cc_final: 0.9024 (m100) REVERT: G 72 ASP cc_start: 0.7949 (t0) cc_final: 0.7646 (t0) REVERT: G 80 MET cc_start: 0.8817 (ttp) cc_final: 0.6552 (ttp) REVERT: G 81 ASP cc_start: 0.8264 (m-30) cc_final: 0.7909 (p0) REVERT: J 86 TYR cc_start: 0.8331 (m-80) cc_final: 0.7812 (m-10) REVERT: J 102 THR cc_start: 0.8060 (p) cc_final: 0.7836 (m) REVERT: C 69 TRP cc_start: 0.7949 (m-90) cc_final: 0.7479 (m-90) REVERT: C 181 ILE cc_start: 0.8666 (mt) cc_final: 0.8423 (pt) REVERT: C 195 ASN cc_start: 0.8151 (m-40) cc_final: 0.7850 (m110) REVERT: C 475 MET cc_start: 0.8325 (mmt) cc_final: 0.7992 (mmt) REVERT: C 494 LEU cc_start: 0.8901 (mt) cc_final: 0.8603 (mt) REVERT: E 658 GLN cc_start: 0.8204 (tp40) cc_final: 0.8002 (tp40) REVERT: I 4 LEU cc_start: 0.8395 (mt) cc_final: 0.7691 (mt) REVERT: I 13 LYS cc_start: 0.8881 (mmtt) cc_final: 0.8655 (mmmt) REVERT: I 80 MET cc_start: 0.8728 (ttp) cc_final: 0.8138 (ttp) REVERT: I 81 ASP cc_start: 0.8262 (m-30) cc_final: 0.7859 (p0) REVERT: I 100 GLN cc_start: 0.5169 (mt0) cc_final: 0.4708 (mm110) REVERT: K 86 TYR cc_start: 0.8272 (m-80) cc_final: 0.7705 (m-10) REVERT: K 104 LEU cc_start: 0.8265 (mt) cc_final: 0.8018 (mt) REVERT: D 69 TRP cc_start: 0.8116 (m-90) cc_final: 0.7187 (m-90) REVERT: D 181 ILE cc_start: 0.8570 (mt) cc_final: 0.8331 (pt) REVERT: D 475 MET cc_start: 0.8386 (mmt) cc_final: 0.8137 (mmt) REVERT: D 494 LEU cc_start: 0.8740 (mt) cc_final: 0.8479 (mp) REVERT: F 576 LEU cc_start: 0.8748 (tp) cc_final: 0.8539 (tt) outliers start: 9 outliers final: 6 residues processed: 692 average time/residue: 0.1525 time to fit residues: 154.5443 Evaluate side-chains 340 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 334 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 43 GLN L 32 HIS A 72 HIS A 105 HIS A 195 ASN A 229 ASN A 377 ASN ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 43 GLN J 32 HIS ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 HIS C 105 HIS C 195 ASN C 229 ASN ** C 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 43 GLN K 32 HIS K 100 GLN D 72 HIS D 105 HIS D 229 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.077230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.062008 restraints weight = 84880.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.064106 restraints weight = 50940.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.065558 restraints weight = 35327.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.066553 restraints weight = 27242.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.067237 restraints weight = 22644.012| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 20073 Z= 0.229 Angle : 0.992 24.547 27378 Z= 0.486 Chirality : 0.055 0.401 3237 Planarity : 0.005 0.065 3336 Dihedral : 5.622 24.285 2496 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.75 % Allowed : 4.69 % Favored : 94.56 % Rotamer: Outliers : 0.10 % Allowed : 2.64 % Favored : 97.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.20 (0.17), residues: 2280 helix: 0.99 (0.25), residues: 408 sheet: 0.59 (0.19), residues: 654 loop : -0.36 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG I 94 TYR 0.051 0.003 TYR E 643 PHE 0.030 0.003 PHE G 76 TRP 0.034 0.003 TRP C 112 HIS 0.006 0.001 HIS D 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.23 (19959) covalent geometry : angle 0.89030 / 0.46 (27072) SS BOND : bond 0.00415 / 0.26 ( 36) SS BOND : angle 1.54095 / 1.12 ( 72) hydrogen bonds : bond 0.06198 / 4.17 ( 768) hydrogen bonds : angle 6.89117 / 4.80 ( 2016) link_ALPHA1-3 : bond 0.01286 / 0.64 ( 3) link_ALPHA1-3 : angle 3.87788 / 2.30 ( 9) link_ALPHA1-6 : bond 0.01153 / 0.58 ( 3) link_ALPHA1-6 : angle 1.24012 / 0.75 ( 9) link_BETA1-4 : bond 0.00741 / 0.44 ( 33) link_BETA1-4 : angle 3.48019 / 2.33 ( 99) link_NAG-ASN : bond 0.01030 / 0.65 ( 39) link_NAG-ASN : angle 5.83899 / 4.42 ( 117) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 484 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 4 LEU cc_start: 0.8326 (mt) cc_final: 0.6167 (mt) REVERT: H 28 ILE cc_start: 0.9555 (mm) cc_final: 0.9098 (mm) REVERT: H 34 LEU cc_start: 0.8943 (mt) cc_final: 0.8738 (mt) REVERT: H 72 ASP cc_start: 0.7597 (t0) cc_final: 0.7016 (t0) REVERT: H 75 LEU cc_start: 0.8963 (mt) cc_final: 0.8511 (mp) REVERT: H 81 ASP cc_start: 0.8158 (m-30) cc_final: 0.7706 (p0) REVERT: H 108 LEU cc_start: 0.8846 (tp) cc_final: 0.8616 (tp) REVERT: L 4 LEU cc_start: 0.8571 (tp) cc_final: 0.8263 (tp) REVERT: L 47 LEU cc_start: 0.9019 (mm) cc_final: 0.8466 (pp) REVERT: L 86 TYR cc_start: 0.8441 (m-80) cc_final: 0.7996 (m-10) REVERT: L 97 PHE cc_start: 0.8328 (m-10) cc_final: 0.7836 (m-80) REVERT: A 154 ILE cc_start: 0.9498 (tp) cc_final: 0.8869 (tp) REVERT: A 316 TRP cc_start: 0.6537 (m-90) cc_final: 0.6113 (m-90) REVERT: A 342 LEU cc_start: 0.9207 (mp) cc_final: 0.8995 (mm) REVERT: A 373 MET cc_start: 0.8826 (mtp) cc_final: 0.8468 (mtp) REVERT: B 584 GLU cc_start: 0.8667 (tm-30) cc_final: 0.8174 (tm-30) REVERT: B 596 TRP cc_start: 0.8383 (m-10) cc_final: 0.8146 (m-10) REVERT: B 628 TRP cc_start: 0.7840 (m100) cc_final: 0.7198 (m100) REVERT: B 630 GLU cc_start: 0.8615 (pt0) cc_final: 0.8049 (pt0) REVERT: B 647 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.8067 (pm20) REVERT: G 34 LEU cc_start: 0.8799 (mt) cc_final: 0.8421 (mt) REVERT: G 36 TRP cc_start: 0.9399 (m100) cc_final: 0.8641 (m-10) REVERT: G 72 ASP cc_start: 0.7435 (t0) cc_final: 0.7168 (t0) REVERT: G 81 ASP cc_start: 0.8064 (m-30) cc_final: 0.7822 (p0) REVERT: J 47 LEU cc_start: 0.8940 (mp) cc_final: 0.8530 (pp) REVERT: J 86 TYR cc_start: 0.8668 (m-80) cc_final: 0.8116 (m-10) REVERT: J 104 LEU cc_start: 0.8585 (mt) cc_final: 0.8375 (mt) REVERT: C 69 TRP cc_start: 0.7593 (m-90) cc_final: 0.7289 (m-90) REVERT: C 256 SER cc_start: 0.8135 (p) cc_final: 0.7932 (m) REVERT: C 373 MET cc_start: 0.8723 (mtp) cc_final: 0.8456 (mtp) REVERT: C 475 MET cc_start: 0.8001 (mmt) cc_final: 0.7798 (mmt) REVERT: E 530 MET cc_start: 0.7351 (ptm) cc_final: 0.6619 (ptm) REVERT: E 546 SER cc_start: 0.8263 (t) cc_final: 0.7747 (p) REVERT: E 628 TRP cc_start: 0.7603 (m100) cc_final: 0.7318 (m100) REVERT: I 4 LEU cc_start: 0.7882 (mt) cc_final: 0.7430 (mt) REVERT: I 27 ASP cc_start: 0.9418 (p0) cc_final: 0.9212 (p0) REVERT: I 72 ASP cc_start: 0.6675 (t0) cc_final: 0.6269 (t0) REVERT: I 80 MET cc_start: 0.8722 (ttp) cc_final: 0.8262 (ttp) REVERT: I 81 ASP cc_start: 0.8360 (m-30) cc_final: 0.7732 (p0) REVERT: I 100 GLN cc_start: 0.5203 (mt0) cc_final: 0.4683 (mm110) REVERT: K 32 HIS cc_start: 0.7962 (m90) cc_final: 0.7707 (m-70) REVERT: K 33 MET cc_start: 0.7727 (ptp) cc_final: 0.6977 (tmm) REVERT: K 47 LEU cc_start: 0.9104 (mm) cc_final: 0.8518 (pp) REVERT: K 71 TYR cc_start: 0.6342 (t80) cc_final: 0.5921 (t80) REVERT: K 86 TYR cc_start: 0.8204 (m-80) cc_final: 0.7902 (m-10) REVERT: D 104 MET cc_start: 0.8986 (mmt) cc_final: 0.8677 (mmp) REVERT: D 373 MET cc_start: 0.8963 (mtp) cc_final: 0.8688 (mtp) REVERT: D 475 MET cc_start: 0.8155 (mmt) cc_final: 0.7681 (mmt) REVERT: F 530 MET cc_start: 0.6860 (ptt) cc_final: 0.6482 (ptt) REVERT: F 546 SER cc_start: 0.8183 (t) cc_final: 0.7904 (p) REVERT: F 574 LYS cc_start: 0.9278 (mttt) cc_final: 0.8825 (ttmm) REVERT: F 628 TRP cc_start: 0.7334 (m100) cc_final: 0.6686 (m100) outliers start: 2 outliers final: 0 residues processed: 484 average time/residue: 0.1360 time to fit residues: 100.4841 Evaluate side-chains 299 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 298 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 148 optimal weight: 5.9990 chunk 162 optimal weight: 0.8980 chunk 103 optimal weight: 9.9990 chunk 82 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 119 optimal weight: 0.9990 chunk 39 optimal weight: 10.0000 chunk 23 optimal weight: 0.9980 chunk 188 optimal weight: 6.9990 chunk 138 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 32 HIS L 90 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 95 GLN J 32 HIS C 302 ASN C 377 ASN C 425 ASN I 43 GLN D 302 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.077081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.061776 restraints weight = 84990.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.063912 restraints weight = 50542.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.065388 restraints weight = 35157.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.066419 restraints weight = 27025.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.067114 restraints weight = 22376.036| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.4419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20073 Z= 0.171 Angle : 0.858 21.937 27378 Z= 0.415 Chirality : 0.052 0.349 3237 Planarity : 0.005 0.065 3336 Dihedral : 5.407 23.579 2496 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.53 % Allowed : 5.22 % Favored : 94.25 % Rotamer: Outliers : 0.15 % Allowed : 2.39 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.08 (0.17), residues: 2280 helix: 0.79 (0.24), residues: 447 sheet: 0.59 (0.19), residues: 684 loop : -0.53 (0.18), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 166 TYR 0.020 0.002 TYR E 643 PHE 0.028 0.002 PHE G 76 TRP 0.038 0.002 TRP G 23 HIS 0.005 0.001 HIS D 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.17 (19959) covalent geometry : angle 0.77181 / 0.40 (27072) SS BOND : bond 0.00505 / 0.30 ( 36) SS BOND : angle 1.43902 / 1.05 ( 72) hydrogen bonds : bond 0.05017 / 3.36 ( 768) hydrogen bonds : angle 6.45770 / 4.51 ( 2016) link_ALPHA1-3 : bond 0.00999 / 0.50 ( 3) link_ALPHA1-3 : angle 3.32860 / 1.96 ( 9) link_ALPHA1-6 : bond 0.01132 / 0.57 ( 3) link_ALPHA1-6 : angle 1.28662 / 0.74 ( 9) link_BETA1-4 : bond 0.00636 / 0.39 ( 33) link_BETA1-4 : angle 2.66757 / 1.76 ( 99) link_NAG-ASN : bond 0.00819 / 0.55 ( 39) link_NAG-ASN : angle 5.09858 / 3.90 ( 117) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 422 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 27 ASP cc_start: 0.9405 (p0) cc_final: 0.9144 (p0) REVERT: H 28 ILE cc_start: 0.9431 (mm) cc_final: 0.9041 (mm) REVERT: H 43 GLN cc_start: 0.8828 (mm-40) cc_final: 0.7837 (mp10) REVERT: H 72 ASP cc_start: 0.7496 (t0) cc_final: 0.6911 (t0) REVERT: H 75 LEU cc_start: 0.8713 (mt) cc_final: 0.8437 (mp) REVERT: H 81 ASP cc_start: 0.8268 (m-30) cc_final: 0.7873 (p0) REVERT: H 108 LEU cc_start: 0.8817 (tp) cc_final: 0.8611 (tp) REVERT: L 4 LEU cc_start: 0.8457 (tp) cc_final: 0.8111 (tp) REVERT: L 33 MET cc_start: 0.7834 (pmm) cc_final: 0.7363 (pmm) REVERT: L 47 LEU cc_start: 0.9058 (mm) cc_final: 0.8500 (pp) REVERT: L 86 TYR cc_start: 0.8676 (m-80) cc_final: 0.8247 (m-10) REVERT: L 97 PHE cc_start: 0.8209 (m-10) cc_final: 0.7751 (m-10) REVERT: A 104 MET cc_start: 0.9246 (tpp) cc_final: 0.8985 (tpp) REVERT: A 373 MET cc_start: 0.8898 (mtp) cc_final: 0.8312 (mtm) REVERT: B 584 GLU cc_start: 0.8736 (tm-30) cc_final: 0.8222 (tm-30) REVERT: B 588 ARG cc_start: 0.8572 (tpp80) cc_final: 0.8051 (tpp80) REVERT: B 626 MET cc_start: 0.7422 (tpp) cc_final: 0.5914 (tpp) REVERT: B 647 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7867 (pm20) REVERT: G 4 LEU cc_start: 0.8277 (mt) cc_final: 0.7772 (mt) REVERT: G 6 GLN cc_start: 0.8361 (pm20) cc_final: 0.7919 (pm20) REVERT: G 27 ASP cc_start: 0.9403 (p0) cc_final: 0.9128 (p0) REVERT: G 34 LEU cc_start: 0.8702 (mt) cc_final: 0.8296 (mt) REVERT: G 36 TRP cc_start: 0.9365 (m100) cc_final: 0.8581 (m-10) REVERT: G 46 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7817 (mp0) REVERT: G 72 ASP cc_start: 0.7650 (t0) cc_final: 0.7106 (t0) REVERT: G 81 ASP cc_start: 0.8185 (m-30) cc_final: 0.7744 (p0) REVERT: G 108 LEU cc_start: 0.8996 (tp) cc_final: 0.8792 (tp) REVERT: J 33 MET cc_start: 0.7986 (pmm) cc_final: 0.7641 (pmm) REVERT: J 86 TYR cc_start: 0.8554 (m-80) cc_final: 0.8062 (m-10) REVERT: C 69 TRP cc_start: 0.7992 (m-90) cc_final: 0.7520 (m-90) REVERT: C 95 MET cc_start: 0.9044 (ppp) cc_final: 0.8842 (ppp) REVERT: C 100 MET cc_start: 0.9350 (mtt) cc_final: 0.9073 (mtt) REVERT: C 349 LEU cc_start: 0.9719 (mt) cc_final: 0.9490 (mp) REVERT: C 373 MET cc_start: 0.8747 (mtp) cc_final: 0.8342 (mtp) REVERT: C 420 ILE cc_start: 0.9062 (mm) cc_final: 0.8847 (mm) REVERT: E 530 MET cc_start: 0.7166 (ptm) cc_final: 0.6426 (ptp) REVERT: E 584 GLU cc_start: 0.8843 (tm-30) cc_final: 0.8576 (tm-30) REVERT: E 588 ARG cc_start: 0.8890 (tpp80) cc_final: 0.8478 (tpp80) REVERT: E 628 TRP cc_start: 0.7514 (m100) cc_final: 0.7305 (m100) REVERT: I 28 ILE cc_start: 0.9297 (mm) cc_final: 0.9074 (mt) REVERT: I 46 GLU cc_start: 0.8338 (mm-30) cc_final: 0.8030 (mp0) REVERT: I 72 ASP cc_start: 0.7036 (t0) cc_final: 0.6743 (t0) REVERT: I 81 ASP cc_start: 0.8272 (m-30) cc_final: 0.7773 (p0) REVERT: I 100 GLN cc_start: 0.5296 (mt0) cc_final: 0.4660 (mp10) REVERT: I 108 LEU cc_start: 0.8722 (tp) cc_final: 0.8521 (tp) REVERT: K 32 HIS cc_start: 0.7955 (m90) cc_final: 0.7647 (m-70) REVERT: K 33 MET cc_start: 0.7889 (ptp) cc_final: 0.6857 (tmm) REVERT: K 47 LEU cc_start: 0.8894 (mm) cc_final: 0.8524 (pp) REVERT: D 104 MET cc_start: 0.9052 (mmt) cc_final: 0.8495 (mmt) REVERT: D 373 MET cc_start: 0.9032 (mtp) cc_final: 0.8698 (mtp) REVERT: D 457 ASP cc_start: 0.5952 (m-30) cc_final: 0.5706 (m-30) REVERT: D 492 GLU cc_start: 0.8815 (tp30) cc_final: 0.7806 (tm-30) REVERT: F 535 MET cc_start: 0.8088 (tpp) cc_final: 0.7862 (tpp) REVERT: F 546 SER cc_start: 0.8207 (t) cc_final: 0.7863 (p) REVERT: F 574 LYS cc_start: 0.9224 (mttt) cc_final: 0.8930 (ttmm) REVERT: F 588 ARG cc_start: 0.8924 (tpp80) cc_final: 0.8656 (tpp80) REVERT: F 628 TRP cc_start: 0.7583 (m100) cc_final: 0.7104 (m100) REVERT: F 647 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7870 (pm20) REVERT: F 662 GLU cc_start: 0.7678 (tt0) cc_final: 0.7283 (tt0) outliers start: 3 outliers final: 1 residues processed: 423 average time/residue: 0.1360 time to fit residues: 87.8298 Evaluate side-chains 281 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 278 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 7 optimal weight: 6.9990 chunk 169 optimal weight: 20.0000 chunk 150 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 chunk 219 optimal weight: 0.9990 chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 10.0000 chunk 205 optimal weight: 7.9990 chunk 100 optimal weight: 20.0000 chunk 210 optimal weight: 7.9990 chunk 171 optimal weight: 2.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 79 HIS ** H 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 HIS G 95 GLN ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 590 GLN I 79 HIS K 90 GLN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 590 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.070482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.055678 restraints weight = 89217.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.057352 restraints weight = 57436.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.058534 restraints weight = 42154.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.059336 restraints weight = 33784.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.059887 restraints weight = 28912.808| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.5334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.143 20073 Z= 0.359 Angle : 1.001 21.923 27378 Z= 0.492 Chirality : 0.054 0.483 3237 Planarity : 0.006 0.054 3336 Dihedral : 5.811 23.133 2496 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 20.12 Ramachandran Plot: Outliers : 0.53 % Allowed : 6.58 % Favored : 92.89 % Rotamer: Outliers : 0.20 % Allowed : 3.18 % Favored : 96.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.46 (0.17), residues: 2280 helix: 0.36 (0.24), residues: 432 sheet: 0.27 (0.20), residues: 564 loop : -0.78 (0.17), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 66 TYR 0.027 0.003 TYR B 638 PHE 0.032 0.003 PHE A 391 TRP 0.083 0.004 TRP B 596 HIS 0.009 0.002 HIS H 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00777 / 0.36 (19959) covalent geometry : angle 0.92485 / 0.48 (27072) SS BOND : bond 0.00603 / 0.43 ( 36) SS BOND : angle 1.51477 / 1.03 ( 72) hydrogen bonds : bond 0.05598 / 3.79 ( 768) hydrogen bonds : angle 6.73807 / 4.72 ( 2016) link_ALPHA1-3 : bond 0.00737 / 0.37 ( 3) link_ALPHA1-3 : angle 3.28347 / 1.93 ( 9) link_ALPHA1-6 : bond 0.00943 / 0.49 ( 3) link_ALPHA1-6 : angle 1.78565 / 1.11 ( 9) link_BETA1-4 : bond 0.00384 / 0.23 ( 33) link_BETA1-4 : angle 2.75192 / 1.90 ( 99) link_NAG-ASN : bond 0.00885 / 0.59 ( 39) link_NAG-ASN : angle 5.24385 / 3.97 ( 117) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 342 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 4 LEU cc_start: 0.8739 (mt) cc_final: 0.8481 (mt) REVERT: H 13 LYS cc_start: 0.8748 (mmtt) cc_final: 0.8266 (mmmm) REVERT: H 27 ASP cc_start: 0.9118 (p0) cc_final: 0.8860 (p0) REVERT: H 28 ILE cc_start: 0.9333 (mm) cc_final: 0.8247 (mm) REVERT: H 72 ASP cc_start: 0.7660 (t0) cc_final: 0.7435 (t0) REVERT: H 75 LEU cc_start: 0.9090 (mt) cc_final: 0.8758 (mt) REVERT: H 108 LEU cc_start: 0.9085 (tp) cc_final: 0.8730 (tp) REVERT: L 4 LEU cc_start: 0.8530 (tp) cc_final: 0.8319 (tp) REVERT: L 33 MET cc_start: 0.7247 (pmm) cc_final: 0.6858 (pmm) REVERT: L 47 LEU cc_start: 0.9062 (mm) cc_final: 0.8458 (pp) REVERT: L 96 GLU cc_start: 0.8839 (pm20) cc_final: 0.8164 (pm20) REVERT: L 97 PHE cc_start: 0.8538 (m-10) cc_final: 0.7533 (m-10) REVERT: A 104 MET cc_start: 0.9139 (tpp) cc_final: 0.8865 (tpp) REVERT: A 342 LEU cc_start: 0.9434 (mp) cc_final: 0.9174 (mm) REVERT: A 373 MET cc_start: 0.8978 (mtp) cc_final: 0.7827 (mmm) REVERT: B 584 GLU cc_start: 0.8709 (tm-30) cc_final: 0.8258 (tm-30) REVERT: B 588 ARG cc_start: 0.8622 (tpp80) cc_final: 0.7739 (tpp-160) REVERT: B 626 MET cc_start: 0.7213 (tpp) cc_final: 0.6091 (tpp) REVERT: G 4 LEU cc_start: 0.8673 (mt) cc_final: 0.8297 (mp) REVERT: G 13 LYS cc_start: 0.8617 (mmtt) cc_final: 0.8212 (mmmt) REVERT: G 28 ILE cc_start: 0.9437 (mm) cc_final: 0.9228 (mt) REVERT: G 34 LEU cc_start: 0.8837 (mt) cc_final: 0.8435 (mt) REVERT: G 36 TRP cc_start: 0.9145 (m100) cc_final: 0.8557 (m-10) REVERT: G 46 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7724 (mm-30) REVERT: G 72 ASP cc_start: 0.8082 (t0) cc_final: 0.7695 (t0) REVERT: G 108 LEU cc_start: 0.9249 (tp) cc_final: 0.9037 (tp) REVERT: J 33 MET cc_start: 0.7873 (pmm) cc_final: 0.7505 (pmm) REVERT: J 86 TYR cc_start: 0.8709 (m-80) cc_final: 0.8490 (m-10) REVERT: J 96 GLU cc_start: 0.8797 (pm20) cc_final: 0.8487 (pm20) REVERT: J 97 PHE cc_start: 0.8580 (m-80) cc_final: 0.8295 (m-80) REVERT: C 69 TRP cc_start: 0.8108 (m-90) cc_final: 0.7813 (m-90) REVERT: C 95 MET cc_start: 0.9163 (ppp) cc_final: 0.8903 (ppp) REVERT: C 116 LEU cc_start: 0.9228 (tt) cc_final: 0.8917 (tt) REVERT: C 316 TRP cc_start: 0.7973 (m-90) cc_final: 0.7660 (m-90) REVERT: C 373 MET cc_start: 0.8944 (mtp) cc_final: 0.8129 (ttm) REVERT: E 537 LEU cc_start: 0.8106 (mt) cc_final: 0.7832 (mt) REVERT: E 546 SER cc_start: 0.8527 (t) cc_final: 0.8199 (p) REVERT: E 603 ILE cc_start: 0.9041 (pt) cc_final: 0.8709 (tt) REVERT: E 659 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8426 (mm-30) REVERT: E 662 GLU cc_start: 0.7815 (pt0) cc_final: 0.7173 (pt0) REVERT: I 13 LYS cc_start: 0.8761 (mmtt) cc_final: 0.8342 (mmmt) REVERT: I 26 GLU cc_start: 0.8804 (tm-30) cc_final: 0.8410 (tm-30) REVERT: I 28 ILE cc_start: 0.9228 (mm) cc_final: 0.9014 (mm) REVERT: I 31 ARG cc_start: 0.7640 (tpm170) cc_final: 0.7371 (tpm170) REVERT: I 46 GLU cc_start: 0.8353 (mm-30) cc_final: 0.7774 (mm-30) REVERT: I 108 LEU cc_start: 0.9048 (tp) cc_final: 0.8700 (tp) REVERT: K 86 TYR cc_start: 0.8339 (m-10) cc_final: 0.8111 (m-10) REVERT: D 95 MET cc_start: 0.9141 (ppp) cc_final: 0.8865 (ppp) REVERT: D 104 MET cc_start: 0.8886 (mmt) cc_final: 0.8508 (mmt) REVERT: D 373 MET cc_start: 0.9065 (mtp) cc_final: 0.7582 (mmm) REVERT: F 530 MET cc_start: 0.7315 (ptm) cc_final: 0.6867 (ptm) REVERT: F 546 SER cc_start: 0.8725 (t) cc_final: 0.8355 (p) REVERT: F 628 TRP cc_start: 0.8513 (m100) cc_final: 0.7163 (m100) outliers start: 4 outliers final: 2 residues processed: 345 average time/residue: 0.1381 time to fit residues: 73.3979 Evaluate side-chains 249 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 247 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 42 optimal weight: 10.0000 chunk 170 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 160 optimal weight: 7.9990 chunk 103 optimal weight: 0.9990 chunk 108 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 70 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.071217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.056055 restraints weight = 85936.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.057913 restraints weight = 52831.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.059197 restraints weight = 37697.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.060082 restraints weight = 29709.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.060662 restraints weight = 25041.613| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.5834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 20073 Z= 0.228 Angle : 0.863 20.815 27378 Z= 0.424 Chirality : 0.051 0.306 3237 Planarity : 0.005 0.048 3336 Dihedral : 5.685 21.536 2496 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.62 % Favored : 93.07 % Rotamer: Outliers : 0.15 % Allowed : 2.20 % Favored : 97.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.48 (0.17), residues: 2280 helix: 0.47 (0.24), residues: 426 sheet: 0.08 (0.20), residues: 606 loop : -0.77 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 315 TYR 0.024 0.002 TYR B 638 PHE 0.033 0.003 PHE I 76 TRP 0.047 0.003 TRP D 479 HIS 0.006 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.23 (19959) covalent geometry : angle 0.78822 / 0.41 (27072) SS BOND : bond 0.00459 / 0.28 ( 36) SS BOND : angle 1.65092 / 1.10 ( 72) hydrogen bonds : bond 0.05075 / 3.43 ( 768) hydrogen bonds : angle 6.46713 / 4.56 ( 2016) link_ALPHA1-3 : bond 0.00682 / 0.34 ( 3) link_ALPHA1-3 : angle 3.13465 / 1.83 ( 9) link_ALPHA1-6 : bond 0.01339 / 0.67 ( 3) link_ALPHA1-6 : angle 1.40186 / 0.84 ( 9) link_BETA1-4 : bond 0.00336 / 0.21 ( 33) link_BETA1-4 : angle 2.29908 / 1.52 ( 99) link_NAG-ASN : bond 0.00688 / 0.47 ( 39) link_NAG-ASN : angle 4.85884 / 3.71 ( 117) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 340 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 4 LEU cc_start: 0.8896 (mt) cc_final: 0.8328 (mp) REVERT: H 28 ILE cc_start: 0.9374 (mm) cc_final: 0.9119 (tt) REVERT: H 72 ASP cc_start: 0.7809 (t0) cc_final: 0.7279 (t0) REVERT: H 108 LEU cc_start: 0.8997 (tp) cc_final: 0.8663 (tp) REVERT: L 4 LEU cc_start: 0.8680 (tp) cc_final: 0.8337 (tp) REVERT: L 33 MET cc_start: 0.7433 (pmm) cc_final: 0.6998 (pmm) REVERT: L 47 LEU cc_start: 0.9027 (mm) cc_final: 0.8526 (pp) REVERT: L 96 GLU cc_start: 0.8724 (pm20) cc_final: 0.8093 (pm20) REVERT: L 97 PHE cc_start: 0.8641 (m-10) cc_final: 0.7450 (m-10) REVERT: A 95 MET cc_start: 0.9234 (ppp) cc_final: 0.8976 (ppp) REVERT: A 195 ASN cc_start: 0.8622 (m110) cc_final: 0.8400 (m110) REVERT: A 308 HIS cc_start: 0.8696 (m90) cc_final: 0.7671 (m90) REVERT: A 373 MET cc_start: 0.9077 (mtp) cc_final: 0.8335 (ttm) REVERT: B 584 GLU cc_start: 0.8927 (tm-30) cc_final: 0.8604 (tm-30) REVERT: B 588 ARG cc_start: 0.8861 (tpp80) cc_final: 0.8285 (tpp80) REVERT: G 13 LYS cc_start: 0.8663 (mmtt) cc_final: 0.8179 (mmmt) REVERT: G 28 ILE cc_start: 0.9482 (mm) cc_final: 0.8933 (mt) REVERT: G 34 LEU cc_start: 0.8640 (mt) cc_final: 0.8339 (mt) REVERT: G 36 TRP cc_start: 0.9177 (m100) cc_final: 0.8303 (m-10) REVERT: G 46 GLU cc_start: 0.8382 (mm-30) cc_final: 0.7894 (mm-30) REVERT: G 72 ASP cc_start: 0.7899 (t0) cc_final: 0.7423 (t0) REVERT: G 75 LEU cc_start: 0.9070 (mp) cc_final: 0.8843 (mm) REVERT: G 81 ASP cc_start: 0.7595 (p0) cc_final: 0.7288 (p0) REVERT: G 108 LEU cc_start: 0.9232 (tp) cc_final: 0.8987 (tp) REVERT: J 33 MET cc_start: 0.7841 (pmm) cc_final: 0.7410 (pmm) REVERT: J 86 TYR cc_start: 0.8793 (m-80) cc_final: 0.8573 (m-10) REVERT: J 97 PHE cc_start: 0.8538 (m-80) cc_final: 0.8168 (m-80) REVERT: C 95 MET cc_start: 0.9149 (ppp) cc_final: 0.8859 (ppp) REVERT: C 104 MET cc_start: 0.9343 (mmm) cc_final: 0.8823 (mmt) REVERT: C 373 MET cc_start: 0.9003 (mtp) cc_final: 0.7652 (mmm) REVERT: C 475 MET cc_start: 0.8158 (mmm) cc_final: 0.7888 (mmt) REVERT: E 647 GLU cc_start: 0.8454 (pp20) cc_final: 0.8185 (pp20) REVERT: E 655 LYS cc_start: 0.9267 (pttp) cc_final: 0.8770 (pttm) REVERT: I 4 LEU cc_start: 0.8272 (mt) cc_final: 0.7964 (mt) REVERT: I 13 LYS cc_start: 0.8804 (mmtt) cc_final: 0.8413 (mmmm) REVERT: I 26 GLU cc_start: 0.8862 (tm-30) cc_final: 0.8073 (tm-30) REVERT: I 46 GLU cc_start: 0.8450 (mm-30) cc_final: 0.7990 (mm-30) REVERT: I 72 ASP cc_start: 0.7811 (t0) cc_final: 0.7326 (t0) REVERT: I 81 ASP cc_start: 0.7451 (p0) cc_final: 0.7188 (p0) REVERT: I 108 LEU cc_start: 0.8971 (tp) cc_final: 0.8612 (tp) REVERT: D 95 MET cc_start: 0.9103 (ppp) cc_final: 0.8764 (ppp) REVERT: D 308 HIS cc_start: 0.8734 (m90) cc_final: 0.7998 (m-70) REVERT: D 316 TRP cc_start: 0.8067 (m-90) cc_final: 0.7835 (m-90) REVERT: D 373 MET cc_start: 0.9094 (mtp) cc_final: 0.7755 (mmm) REVERT: D 475 MET cc_start: 0.8625 (mmm) cc_final: 0.8336 (mmt) REVERT: F 546 SER cc_start: 0.8802 (t) cc_final: 0.8368 (p) REVERT: F 574 LYS cc_start: 0.9351 (mttt) cc_final: 0.9092 (ttmt) REVERT: F 628 TRP cc_start: 0.8572 (m100) cc_final: 0.8094 (m100) outliers start: 3 outliers final: 0 residues processed: 343 average time/residue: 0.1401 time to fit residues: 74.4573 Evaluate side-chains 244 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 157 optimal weight: 7.9990 chunk 199 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 183 optimal weight: 0.6980 chunk 16 optimal weight: 0.2980 chunk 3 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 203 optimal weight: 6.9990 chunk 15 optimal weight: 7.9990 chunk 173 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.073667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.058286 restraints weight = 84725.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.060245 restraints weight = 51511.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.061607 restraints weight = 36435.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.062535 restraints weight = 28493.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.063194 restraints weight = 23947.783| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.6108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 20073 Z= 0.155 Angle : 0.813 20.555 27378 Z= 0.393 Chirality : 0.051 0.278 3237 Planarity : 0.005 0.158 3336 Dihedral : 5.391 23.982 2496 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.92 % Favored : 93.77 % Rotamer: Outliers : 0.05 % Allowed : 1.17 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.28 (0.17), residues: 2280 helix: 0.77 (0.25), residues: 408 sheet: 0.19 (0.20), residues: 588 loop : -0.65 (0.17), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG H 94 TYR 0.022 0.002 TYR F 638 PHE 0.025 0.002 PHE G 76 TRP 0.064 0.003 TRP F 631 HIS 0.005 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (19959) covalent geometry : angle 0.74083 / 0.38 (27072) SS BOND : bond 0.00398 / 0.21 ( 36) SS BOND : angle 1.53150 / 1.04 ( 72) hydrogen bonds : bond 0.04558 / 3.08 ( 768) hydrogen bonds : angle 6.25527 / 4.44 ( 2016) link_ALPHA1-3 : bond 0.00752 / 0.38 ( 3) link_ALPHA1-3 : angle 2.99279 / 1.74 ( 9) link_ALPHA1-6 : bond 0.01084 / 0.54 ( 3) link_ALPHA1-6 : angle 1.26847 / 0.74 ( 9) link_BETA1-4 : bond 0.00412 / 0.26 ( 33) link_BETA1-4 : angle 2.07826 / 1.35 ( 99) link_NAG-ASN : bond 0.00728 / 0.50 ( 39) link_NAG-ASN : angle 4.64694 / 3.57 ( 117) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 356 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 72 ASP cc_start: 0.7666 (t0) cc_final: 0.6903 (t0) REVERT: H 75 LEU cc_start: 0.8959 (mt) cc_final: 0.8690 (mp) REVERT: H 100 TRP cc_start: 0.7313 (m-10) cc_final: 0.7104 (m-10) REVERT: L 4 LEU cc_start: 0.8577 (tp) cc_final: 0.8233 (tp) REVERT: L 33 MET cc_start: 0.7811 (pmm) cc_final: 0.7521 (pmm) REVERT: L 47 LEU cc_start: 0.9104 (mm) cc_final: 0.8599 (pp) REVERT: L 53 LYS cc_start: 0.9144 (mtpt) cc_final: 0.8876 (mtmm) REVERT: L 86 TYR cc_start: 0.8633 (m-10) cc_final: 0.8349 (m-10) REVERT: L 96 GLU cc_start: 0.8683 (pm20) cc_final: 0.7773 (pm20) REVERT: L 97 PHE cc_start: 0.8549 (m-80) cc_final: 0.7434 (m-10) REVERT: A 69 TRP cc_start: 0.7755 (m-90) cc_final: 0.7050 (m-90) REVERT: A 95 MET cc_start: 0.9161 (ppp) cc_final: 0.8928 (ppp) REVERT: A 308 HIS cc_start: 0.8837 (m90) cc_final: 0.7737 (m90) REVERT: A 373 MET cc_start: 0.9055 (mtp) cc_final: 0.8644 (mtp) REVERT: A 475 MET cc_start: 0.8368 (mmm) cc_final: 0.7960 (mmt) REVERT: B 584 GLU cc_start: 0.9006 (tm-30) cc_final: 0.8376 (tm-30) REVERT: B 588 ARG cc_start: 0.8988 (tpp80) cc_final: 0.8477 (tpp80) REVERT: B 628 TRP cc_start: 0.8595 (m100) cc_final: 0.8115 (m100) REVERT: B 630 GLU cc_start: 0.8680 (pt0) cc_final: 0.8313 (pt0) REVERT: B 655 LYS cc_start: 0.9423 (mmmt) cc_final: 0.9018 (mmmm) REVERT: G 4 LEU cc_start: 0.8629 (mt) cc_final: 0.8183 (mt) REVERT: G 34 LEU cc_start: 0.8688 (mt) cc_final: 0.8314 (mt) REVERT: G 36 TRP cc_start: 0.9130 (m100) cc_final: 0.8056 (m-10) REVERT: G 37 VAL cc_start: 0.9445 (t) cc_final: 0.9198 (p) REVERT: G 46 GLU cc_start: 0.8440 (mm-30) cc_final: 0.7825 (mm-30) REVERT: G 72 ASP cc_start: 0.7872 (t0) cc_final: 0.7265 (t0) REVERT: G 81 ASP cc_start: 0.7552 (p0) cc_final: 0.7247 (p0) REVERT: G 108 LEU cc_start: 0.9020 (tp) cc_final: 0.8795 (tp) REVERT: J 33 MET cc_start: 0.7788 (pmm) cc_final: 0.7168 (pmm) REVERT: J 47 LEU cc_start: 0.9277 (mp) cc_final: 0.8555 (pp) REVERT: J 86 TYR cc_start: 0.8818 (m-80) cc_final: 0.8517 (m-10) REVERT: C 69 TRP cc_start: 0.7776 (m-90) cc_final: 0.7485 (m-90) REVERT: C 95 MET cc_start: 0.9109 (ppp) cc_final: 0.8814 (ppp) REVERT: C 316 TRP cc_start: 0.8025 (m-90) cc_final: 0.7640 (m-90) REVERT: C 373 MET cc_start: 0.8996 (mtp) cc_final: 0.7902 (mmm) REVERT: C 475 MET cc_start: 0.8423 (mmm) cc_final: 0.7989 (mmt) REVERT: E 596 TRP cc_start: 0.8586 (m-10) cc_final: 0.8061 (m-90) REVERT: E 655 LYS cc_start: 0.9204 (pttp) cc_final: 0.8770 (pttm) REVERT: I 6 GLN cc_start: 0.8484 (pm20) cc_final: 0.8180 (pm20) REVERT: I 28 ILE cc_start: 0.9228 (mt) cc_final: 0.8847 (mt) REVERT: I 46 GLU cc_start: 0.8279 (mm-30) cc_final: 0.7935 (mm-30) REVERT: I 72 ASP cc_start: 0.7372 (t0) cc_final: 0.6651 (t0) REVERT: I 81 ASP cc_start: 0.7463 (p0) cc_final: 0.7209 (p0) REVERT: I 108 LEU cc_start: 0.8902 (tp) cc_final: 0.8580 (tp) REVERT: K 32 HIS cc_start: 0.7815 (m90) cc_final: 0.7374 (m-70) REVERT: K 86 TYR cc_start: 0.8056 (m-10) cc_final: 0.7735 (m-10) REVERT: D 69 TRP cc_start: 0.7735 (m-90) cc_final: 0.6762 (m-90) REVERT: D 95 MET cc_start: 0.9020 (ppp) cc_final: 0.8723 (ppp) REVERT: D 308 HIS cc_start: 0.8734 (m90) cc_final: 0.7897 (m90) REVERT: D 373 MET cc_start: 0.9066 (mtp) cc_final: 0.7718 (mmm) REVERT: D 475 MET cc_start: 0.8531 (mmm) cc_final: 0.7851 (mmt) REVERT: F 546 SER cc_start: 0.8361 (t) cc_final: 0.7911 (p) REVERT: F 574 LYS cc_start: 0.9362 (mttt) cc_final: 0.8988 (ttmt) REVERT: F 596 TRP cc_start: 0.8458 (m-10) cc_final: 0.8099 (m-90) REVERT: F 628 TRP cc_start: 0.8427 (m100) cc_final: 0.7895 (m100) REVERT: F 647 GLU cc_start: 0.8640 (pm20) cc_final: 0.8403 (pm20) outliers start: 1 outliers final: 0 residues processed: 357 average time/residue: 0.1387 time to fit residues: 77.1271 Evaluate side-chains 256 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 144 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 183 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 88 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 17 optimal weight: 0.3980 chunk 91 optimal weight: 0.0970 overall best weight: 1.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 90 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.072603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.057310 restraints weight = 86436.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.059206 restraints weight = 53032.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.060516 restraints weight = 37800.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.061424 restraints weight = 29762.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.062021 restraints weight = 25071.925| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.6366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 20073 Z= 0.177 Angle : 0.806 20.371 27378 Z= 0.393 Chirality : 0.050 0.351 3237 Planarity : 0.005 0.138 3336 Dihedral : 5.343 26.278 2496 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.62 % Favored : 93.07 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.17), residues: 2280 helix: 0.49 (0.25), residues: 426 sheet: 0.15 (0.20), residues: 597 loop : -0.63 (0.18), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 94 TYR 0.019 0.002 TYR H 100E PHE 0.020 0.002 PHE D 53 TRP 0.046 0.003 TRP C 479 HIS 0.005 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.18 (19959) covalent geometry : angle 0.73233 / 0.38 (27072) SS BOND : bond 0.00534 / 0.30 ( 36) SS BOND : angle 1.65949 / 1.24 ( 72) hydrogen bonds : bond 0.04573 / 3.08 ( 768) hydrogen bonds : angle 6.20114 / 4.39 ( 2016) link_ALPHA1-3 : bond 0.00734 / 0.37 ( 3) link_ALPHA1-3 : angle 3.02574 / 1.77 ( 9) link_ALPHA1-6 : bond 0.01066 / 0.54 ( 3) link_ALPHA1-6 : angle 1.30560 / 0.81 ( 9) link_BETA1-4 : bond 0.00340 / 0.22 ( 33) link_BETA1-4 : angle 2.08045 / 1.37 ( 99) link_NAG-ASN : bond 0.00728 / 0.48 ( 39) link_NAG-ASN : angle 4.64886 / 3.58 ( 117) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 335 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 4 LEU cc_start: 0.8854 (mp) cc_final: 0.8514 (mp) REVERT: H 72 ASP cc_start: 0.7817 (t0) cc_final: 0.7018 (t0) REVERT: H 75 LEU cc_start: 0.9031 (mt) cc_final: 0.8730 (mp) REVERT: L 30 TYR cc_start: 0.8132 (m-80) cc_final: 0.7911 (m-80) REVERT: L 33 MET cc_start: 0.7817 (pmm) cc_final: 0.7548 (pmm) REVERT: L 47 LEU cc_start: 0.9085 (mm) cc_final: 0.8556 (pp) REVERT: L 96 GLU cc_start: 0.8660 (pm20) cc_final: 0.8046 (pm20) REVERT: L 97 PHE cc_start: 0.8513 (m-80) cc_final: 0.7512 (m-80) REVERT: A 69 TRP cc_start: 0.7634 (m-90) cc_final: 0.6729 (m-90) REVERT: A 95 MET cc_start: 0.9150 (ppp) cc_final: 0.8838 (ppp) REVERT: A 308 HIS cc_start: 0.8809 (m90) cc_final: 0.7702 (m90) REVERT: A 373 MET cc_start: 0.9030 (mtp) cc_final: 0.8581 (mtp) REVERT: A 475 MET cc_start: 0.8368 (mmm) cc_final: 0.7961 (mmt) REVERT: B 584 GLU cc_start: 0.8976 (tm-30) cc_final: 0.8526 (tm-30) REVERT: B 588 ARG cc_start: 0.8963 (tpp80) cc_final: 0.8520 (tpp80) REVERT: B 628 TRP cc_start: 0.8374 (m100) cc_final: 0.7505 (m100) REVERT: G 4 LEU cc_start: 0.8623 (mt) cc_final: 0.8339 (mt) REVERT: G 34 LEU cc_start: 0.8769 (mt) cc_final: 0.8429 (mt) REVERT: G 36 TRP cc_start: 0.9048 (m100) cc_final: 0.8180 (m-10) REVERT: G 37 VAL cc_start: 0.9376 (t) cc_final: 0.9138 (p) REVERT: G 46 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7694 (mm-30) REVERT: G 60 SER cc_start: 0.8885 (t) cc_final: 0.8567 (p) REVERT: G 72 ASP cc_start: 0.8007 (t0) cc_final: 0.7654 (t0) REVERT: G 75 LEU cc_start: 0.9073 (mp) cc_final: 0.8833 (mm) REVERT: G 81 ASP cc_start: 0.7402 (p0) cc_final: 0.7141 (p0) REVERT: J 33 MET cc_start: 0.8104 (pmm) cc_final: 0.7741 (pmm) REVERT: J 47 LEU cc_start: 0.9227 (mp) cc_final: 0.8591 (pp) REVERT: C 95 MET cc_start: 0.9226 (ppp) cc_final: 0.8916 (ppp) REVERT: C 316 TRP cc_start: 0.7851 (m-90) cc_final: 0.7473 (m-90) REVERT: C 373 MET cc_start: 0.9027 (mtp) cc_final: 0.7912 (mmm) REVERT: C 475 MET cc_start: 0.8393 (mmm) cc_final: 0.8124 (mmt) REVERT: E 575 GLN cc_start: 0.8654 (pp30) cc_final: 0.8077 (pp30) REVERT: E 596 TRP cc_start: 0.8604 (m-10) cc_final: 0.8138 (m-90) REVERT: I 4 LEU cc_start: 0.8597 (mt) cc_final: 0.8151 (mt) REVERT: I 37 VAL cc_start: 0.9370 (t) cc_final: 0.9087 (p) REVERT: I 46 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7838 (mm-30) REVERT: I 60 SER cc_start: 0.9124 (t) cc_final: 0.8909 (p) REVERT: I 72 ASP cc_start: 0.7875 (t0) cc_final: 0.7035 (t0) REVERT: I 96 LYS cc_start: 0.7312 (mtmm) cc_final: 0.6970 (mttm) REVERT: I 108 LEU cc_start: 0.8973 (tp) cc_final: 0.8623 (tp) REVERT: K 4 LEU cc_start: 0.8784 (tp) cc_final: 0.8569 (tp) REVERT: K 86 TYR cc_start: 0.8032 (m-10) cc_final: 0.7375 (m-10) REVERT: D 69 TRP cc_start: 0.7510 (m-90) cc_final: 0.6784 (m-90) REVERT: D 95 MET cc_start: 0.8961 (ppp) cc_final: 0.8643 (ppp) REVERT: D 195 ASN cc_start: 0.8461 (m110) cc_final: 0.8233 (m110) REVERT: D 308 HIS cc_start: 0.8736 (m90) cc_final: 0.8012 (m-70) REVERT: D 316 TRP cc_start: 0.8114 (m-90) cc_final: 0.7808 (m-90) REVERT: D 373 MET cc_start: 0.9062 (mtp) cc_final: 0.7719 (mmm) REVERT: D 475 MET cc_start: 0.8573 (mmm) cc_final: 0.7993 (mmt) REVERT: F 546 SER cc_start: 0.8210 (t) cc_final: 0.7790 (p) REVERT: F 574 LYS cc_start: 0.9359 (mttt) cc_final: 0.9094 (ttmt) REVERT: F 588 ARG cc_start: 0.8866 (ttm170) cc_final: 0.8526 (ttp-170) REVERT: F 596 TRP cc_start: 0.8457 (m-10) cc_final: 0.8193 (m-90) REVERT: F 647 GLU cc_start: 0.8577 (pm20) cc_final: 0.8350 (pm20) outliers start: 0 outliers final: 0 residues processed: 335 average time/residue: 0.1374 time to fit residues: 71.5081 Evaluate side-chains 252 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 162 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 225 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 46 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 160 optimal weight: 0.2980 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 HIS J 70 GLN C 105 HIS ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 70 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.072934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.057719 restraints weight = 87313.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.059643 restraints weight = 53187.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.060979 restraints weight = 37637.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.061888 restraints weight = 29550.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.062517 restraints weight = 24855.183| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.6606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20073 Z= 0.155 Angle : 0.806 20.112 27378 Z= 0.391 Chirality : 0.050 0.403 3237 Planarity : 0.006 0.183 3336 Dihedral : 5.323 27.165 2496 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.18 % Favored : 93.51 % Rotamer: Outliers : 0.10 % Allowed : 0.59 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.32 (0.17), residues: 2280 helix: 0.54 (0.25), residues: 411 sheet: 0.14 (0.20), residues: 597 loop : -0.60 (0.18), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.001 ARG G 94 TYR 0.014 0.001 TYR D 191 PHE 0.025 0.002 PHE I 76 TRP 0.055 0.003 TRP H 36 HIS 0.005 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (19959) covalent geometry : angle 0.73491 / 0.38 (27072) SS BOND : bond 0.00399 / 0.23 ( 36) SS BOND : angle 1.57005 / 1.11 ( 72) hydrogen bonds : bond 0.04492 / 3.03 ( 768) hydrogen bonds : angle 6.13284 / 4.35 ( 2016) link_ALPHA1-3 : bond 0.00736 / 0.37 ( 3) link_ALPHA1-3 : angle 2.96474 / 1.73 ( 9) link_ALPHA1-6 : bond 0.01076 / 0.54 ( 3) link_ALPHA1-6 : angle 1.23998 / 0.73 ( 9) link_BETA1-4 : bond 0.00378 / 0.24 ( 33) link_BETA1-4 : angle 1.96576 / 1.29 ( 99) link_NAG-ASN : bond 0.00684 / 0.46 ( 39) link_NAG-ASN : angle 4.63918 / 3.60 ( 117) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 342 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 4 LEU cc_start: 0.8951 (mp) cc_final: 0.8689 (mp) REVERT: H 60 SER cc_start: 0.9161 (t) cc_final: 0.8872 (p) REVERT: H 72 ASP cc_start: 0.7734 (t0) cc_final: 0.7041 (t0) REVERT: H 75 LEU cc_start: 0.9022 (mt) cc_final: 0.8757 (mp) REVERT: L 4 LEU cc_start: 0.8632 (tp) cc_final: 0.8224 (tp) REVERT: L 33 MET cc_start: 0.7895 (pmm) cc_final: 0.7602 (pmm) REVERT: L 47 LEU cc_start: 0.9080 (mm) cc_final: 0.8547 (pp) REVERT: L 96 GLU cc_start: 0.8581 (pm20) cc_final: 0.8175 (pm20) REVERT: L 97 PHE cc_start: 0.8212 (m-80) cc_final: 0.7482 (m-80) REVERT: A 69 TRP cc_start: 0.7506 (m-90) cc_final: 0.6679 (m-90) REVERT: A 95 MET cc_start: 0.9136 (ppp) cc_final: 0.8750 (ppp) REVERT: A 308 HIS cc_start: 0.8872 (m90) cc_final: 0.7809 (m90) REVERT: A 373 MET cc_start: 0.8991 (mtp) cc_final: 0.8526 (mtp) REVERT: B 584 GLU cc_start: 0.9098 (tm-30) cc_final: 0.8562 (tm-30) REVERT: B 588 ARG cc_start: 0.8958 (tpp80) cc_final: 0.8513 (tpp80) REVERT: B 628 TRP cc_start: 0.8427 (m100) cc_final: 0.7724 (m100) REVERT: B 662 GLU cc_start: 0.8077 (tt0) cc_final: 0.7150 (tt0) REVERT: G 4 LEU cc_start: 0.8642 (mt) cc_final: 0.8373 (mt) REVERT: G 28 ILE cc_start: 0.9442 (mt) cc_final: 0.9180 (mt) REVERT: G 36 TRP cc_start: 0.9106 (m100) cc_final: 0.8135 (m-10) REVERT: G 37 VAL cc_start: 0.9450 (t) cc_final: 0.9201 (p) REVERT: G 46 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7687 (mm-30) REVERT: G 60 SER cc_start: 0.8952 (t) cc_final: 0.8609 (p) REVERT: G 72 ASP cc_start: 0.7939 (t0) cc_final: 0.7537 (t0) REVERT: G 81 ASP cc_start: 0.7468 (p0) cc_final: 0.7167 (p0) REVERT: G 94 ARG cc_start: 0.7694 (tmm160) cc_final: 0.7025 (tmm-80) REVERT: G 108 LEU cc_start: 0.9036 (tp) cc_final: 0.8834 (tp) REVERT: J 33 MET cc_start: 0.7756 (pmm) cc_final: 0.7508 (pmm) REVERT: J 47 LEU cc_start: 0.9302 (mp) cc_final: 0.8635 (pp) REVERT: J 70 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.7997 (pp30) REVERT: J 86 TYR cc_start: 0.8738 (m-10) cc_final: 0.8099 (m-10) REVERT: J 104 LEU cc_start: 0.8365 (mt) cc_final: 0.8136 (mt) REVERT: C 95 MET cc_start: 0.9202 (ppp) cc_final: 0.8735 (ppp) REVERT: C 316 TRP cc_start: 0.7829 (m-90) cc_final: 0.7484 (m-90) REVERT: C 373 MET cc_start: 0.9001 (mtp) cc_final: 0.7864 (mmm) REVERT: C 475 MET cc_start: 0.8458 (mmm) cc_final: 0.8103 (mmt) REVERT: E 530 MET cc_start: 0.7844 (ttm) cc_final: 0.7311 (ttp) REVERT: E 596 TRP cc_start: 0.8517 (m-10) cc_final: 0.8123 (m-90) REVERT: I 4 LEU cc_start: 0.8258 (mt) cc_final: 0.7785 (mt) REVERT: I 37 VAL cc_start: 0.9433 (t) cc_final: 0.9091 (p) REVERT: I 46 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7831 (mm-30) REVERT: I 72 ASP cc_start: 0.7992 (t0) cc_final: 0.7588 (t0) REVERT: I 81 ASP cc_start: 0.7464 (p0) cc_final: 0.7067 (p0) REVERT: I 108 LEU cc_start: 0.8895 (tp) cc_final: 0.8579 (tp) REVERT: K 4 LEU cc_start: 0.8695 (tp) cc_final: 0.8471 (tp) REVERT: K 86 TYR cc_start: 0.7760 (m-10) cc_final: 0.7497 (m-10) REVERT: D 69 TRP cc_start: 0.7555 (m-90) cc_final: 0.6874 (m-90) REVERT: D 95 MET cc_start: 0.8963 (ppp) cc_final: 0.8605 (ppp) REVERT: D 104 MET cc_start: 0.9224 (tpp) cc_final: 0.9021 (mmt) REVERT: D 308 HIS cc_start: 0.8830 (m90) cc_final: 0.7943 (m90) REVERT: D 373 MET cc_start: 0.9112 (mtp) cc_final: 0.7769 (mmm) REVERT: D 475 MET cc_start: 0.8586 (mmm) cc_final: 0.7665 (mmt) REVERT: F 546 SER cc_start: 0.8459 (t) cc_final: 0.7962 (p) REVERT: F 574 LYS cc_start: 0.9327 (mttt) cc_final: 0.9035 (ttmt) REVERT: F 588 ARG cc_start: 0.8898 (ttm170) cc_final: 0.8689 (ttp-170) REVERT: F 628 TRP cc_start: 0.8236 (m100) cc_final: 0.7533 (m100) REVERT: F 655 LYS cc_start: 0.8835 (pttp) cc_final: 0.8346 (pttm) outliers start: 2 outliers final: 0 residues processed: 344 average time/residue: 0.1344 time to fit residues: 72.2949 Evaluate side-chains 242 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 241 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 0 optimal weight: 8.9990 chunk 51 optimal weight: 9.9990 chunk 214 optimal weight: 5.9990 chunk 152 optimal weight: 9.9990 chunk 204 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 197 optimal weight: 9.9990 chunk 46 optimal weight: 10.0000 chunk 100 optimal weight: 8.9990 chunk 188 optimal weight: 5.9990 chunk 177 optimal weight: 4.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 413 HIS B 651 ASN ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 413 HIS E 651 ASN I 3 GLN ** K 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 HIS F 651 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.067018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.052208 restraints weight = 90058.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.053958 restraints weight = 54623.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.055161 restraints weight = 38695.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.056003 restraints weight = 30403.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.056599 restraints weight = 25611.463| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.7148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.089 20073 Z= 0.396 Angle : 1.031 20.684 27378 Z= 0.511 Chirality : 0.056 0.440 3237 Planarity : 0.008 0.189 3336 Dihedral : 6.170 27.938 2496 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 22.37 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.29 % Favored : 91.40 % Rotamer: Outliers : 0.05 % Allowed : 0.93 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.00 (0.17), residues: 2280 helix: -0.28 (0.23), residues: 432 sheet: 0.16 (0.21), residues: 534 loop : -1.16 (0.17), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG L 54 TYR 0.028 0.003 TYR K 30 PHE 0.032 0.004 PHE H 76 TRP 0.059 0.004 TRP H 36 HIS 0.008 0.002 HIS C 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00848 / 0.40 (19959) covalent geometry : angle 0.96638 / 0.50 (27072) SS BOND : bond 0.00641 / 0.41 ( 36) SS BOND : angle 1.68872 / 1.14 ( 72) hydrogen bonds : bond 0.05780 / 3.89 ( 768) hydrogen bonds : angle 6.68579 / 4.71 ( 2016) link_ALPHA1-3 : bond 0.00525 / 0.26 ( 3) link_ALPHA1-3 : angle 3.04661 / 1.79 ( 9) link_ALPHA1-6 : bond 0.00675 / 0.34 ( 3) link_ALPHA1-6 : angle 1.79818 / 1.17 ( 9) link_BETA1-4 : bond 0.00440 / 0.28 ( 33) link_BETA1-4 : angle 2.65405 / 1.84 ( 99) link_NAG-ASN : bond 0.00932 / 0.60 ( 39) link_NAG-ASN : angle 4.91650 / 3.70 ( 117) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 280 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 4 LEU cc_start: 0.9064 (mp) cc_final: 0.8674 (mp) REVERT: H 13 LYS cc_start: 0.8636 (mmtt) cc_final: 0.8083 (mmmm) REVERT: H 46 GLU cc_start: 0.7592 (mp0) cc_final: 0.7227 (mp0) REVERT: H 72 ASP cc_start: 0.7747 (t0) cc_final: 0.7529 (t0) REVERT: H 75 LEU cc_start: 0.9300 (mt) cc_final: 0.9056 (mt) REVERT: L 33 MET cc_start: 0.7717 (pmm) cc_final: 0.7388 (pmm) REVERT: L 86 TYR cc_start: 0.8514 (m-10) cc_final: 0.8292 (m-10) REVERT: L 96 GLU cc_start: 0.8609 (pm20) cc_final: 0.8119 (pm20) REVERT: L 97 PHE cc_start: 0.8465 (m-80) cc_final: 0.7374 (m-10) REVERT: A 95 MET cc_start: 0.9241 (ppp) cc_final: 0.7976 (ppp) REVERT: A 308 HIS cc_start: 0.8852 (m90) cc_final: 0.7796 (m90) REVERT: A 373 MET cc_start: 0.9240 (mtp) cc_final: 0.8376 (mtm) REVERT: A 475 MET cc_start: 0.8821 (mmm) cc_final: 0.8551 (mmt) REVERT: B 584 GLU cc_start: 0.9153 (tm-30) cc_final: 0.8732 (tm-30) REVERT: B 588 ARG cc_start: 0.8908 (tpp80) cc_final: 0.8344 (tpp80) REVERT: B 630 GLU cc_start: 0.8795 (pt0) cc_final: 0.8432 (pt0) REVERT: G 4 LEU cc_start: 0.9002 (mt) cc_final: 0.8785 (mt) REVERT: G 13 LYS cc_start: 0.8807 (mmtt) cc_final: 0.8260 (mmmm) REVERT: G 37 VAL cc_start: 0.9494 (t) cc_final: 0.9220 (p) REVERT: G 43 GLN cc_start: 0.9349 (mm110) cc_final: 0.9003 (mm-40) REVERT: G 46 GLU cc_start: 0.8358 (mm-30) cc_final: 0.7632 (mm-30) REVERT: G 81 ASP cc_start: 0.7768 (p0) cc_final: 0.7502 (p0) REVERT: G 100 TYR cc_start: 0.6151 (m-80) cc_final: 0.5853 (m-80) REVERT: G 108 LEU cc_start: 0.9199 (tp) cc_final: 0.8949 (tp) REVERT: J 30 TYR cc_start: 0.8433 (m-80) cc_final: 0.8097 (m-10) REVERT: J 33 MET cc_start: 0.7763 (pmm) cc_final: 0.7525 (pmm) REVERT: J 97 PHE cc_start: 0.8652 (m-80) cc_final: 0.8303 (m-80) REVERT: C 68 VAL cc_start: 0.8674 (t) cc_final: 0.8244 (t) REVERT: C 95 MET cc_start: 0.9324 (ppp) cc_final: 0.8318 (ppp) REVERT: C 316 TRP cc_start: 0.8240 (m-90) cc_final: 0.7799 (m-90) REVERT: C 373 MET cc_start: 0.8934 (mtp) cc_final: 0.7575 (mtt) REVERT: C 474 ASP cc_start: 0.8870 (t0) cc_final: 0.8664 (t0) REVERT: C 475 MET cc_start: 0.8625 (mmm) cc_final: 0.8289 (mmt) REVERT: I 4 LEU cc_start: 0.8650 (mt) cc_final: 0.8142 (mt) REVERT: I 13 LYS cc_start: 0.8959 (mmtt) cc_final: 0.8383 (mmmm) REVERT: I 37 VAL cc_start: 0.9576 (t) cc_final: 0.9239 (p) REVERT: I 46 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8058 (mm-30) REVERT: I 72 ASP cc_start: 0.8003 (t0) cc_final: 0.7486 (t0) REVERT: I 75 LEU cc_start: 0.9098 (mt) cc_final: 0.8812 (mt) REVERT: K 86 TYR cc_start: 0.8017 (m-10) cc_final: 0.7649 (m-10) REVERT: D 69 TRP cc_start: 0.7846 (m-90) cc_final: 0.7090 (m-90) REVERT: D 95 MET cc_start: 0.9261 (ppp) cc_final: 0.8748 (ppp) REVERT: D 308 HIS cc_start: 0.8908 (m90) cc_final: 0.8041 (m90) REVERT: D 316 TRP cc_start: 0.8521 (m-90) cc_final: 0.8114 (m-90) REVERT: D 373 MET cc_start: 0.9033 (mtp) cc_final: 0.7765 (mmm) REVERT: D 475 MET cc_start: 0.8569 (mmm) cc_final: 0.7972 (mmt) REVERT: F 546 SER cc_start: 0.9048 (t) cc_final: 0.8719 (p) REVERT: F 651 ASN cc_start: 0.7107 (OUTLIER) cc_final: 0.6654 (m110) outliers start: 1 outliers final: 0 residues processed: 281 average time/residue: 0.1405 time to fit residues: 60.8515 Evaluate side-chains 212 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 211 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 111 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 225 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 133 optimal weight: 0.9990 chunk 176 optimal weight: 5.9990 chunk 216 optimal weight: 0.9990 chunk 165 optimal weight: 0.8980 chunk 213 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 163 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN A 80 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 616 ASN J 70 GLN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** 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 = 0.3443 r_free = 0.3443 target = 0.071707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.056259 restraints weight = 88750.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.058252 restraints weight = 51348.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.059626 restraints weight = 35569.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.060562 restraints weight = 27588.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.061200 restraints weight = 23088.418| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.7234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 20073 Z= 0.163 Angle : 0.859 19.795 27378 Z= 0.420 Chirality : 0.052 0.422 3237 Planarity : 0.006 0.113 3336 Dihedral : 5.688 28.657 2496 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.71 % Favored : 92.98 % Rotamer: Outliers : 0.05 % Allowed : 0.39 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.66 (0.17), residues: 2280 helix: 0.13 (0.24), residues: 426 sheet: 0.43 (0.21), residues: 567 loop : -1.05 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG L 54 TYR 0.019 0.001 TYR J 71 PHE 0.052 0.003 PHE H 76 TRP 0.037 0.003 TRP G 23 HIS 0.008 0.001 HIS I 35A Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 (19959) covalent geometry : angle 0.79576 / 0.41 (27072) SS BOND : bond 0.00443 / 0.22 ( 36) SS BOND : angle 1.60378 / 1.08 ( 72) hydrogen bonds : bond 0.04786 / 3.24 ( 768) hydrogen bonds : angle 6.35735 / 4.52 ( 2016) link_ALPHA1-3 : bond 0.00656 / 0.33 ( 3) link_ALPHA1-3 : angle 2.89947 / 1.68 ( 9) link_ALPHA1-6 : bond 0.01295 / 0.65 ( 3) link_ALPHA1-6 : angle 1.21230 / 0.68 ( 9) link_BETA1-4 : bond 0.00383 / 0.25 ( 33) link_BETA1-4 : angle 1.96450 / 1.28 ( 99) link_NAG-ASN : bond 0.00672 / 0.46 ( 39) link_NAG-ASN : angle 4.54592 / 3.48 ( 117) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 325 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 4 LEU cc_start: 0.8837 (mp) cc_final: 0.8578 (mp) REVERT: H 13 LYS cc_start: 0.8597 (mmtt) cc_final: 0.8005 (mmmm) REVERT: H 72 ASP cc_start: 0.8076 (t0) cc_final: 0.7573 (p0) REVERT: H 102 LEU cc_start: 0.7080 (mp) cc_final: 0.6830 (mp) REVERT: L 4 LEU cc_start: 0.8677 (tp) cc_final: 0.8450 (tp) REVERT: L 33 MET cc_start: 0.7984 (pmm) cc_final: 0.7610 (pmm) REVERT: L 42 GLN cc_start: 0.9220 (tp40) cc_final: 0.8708 (tp-100) REVERT: L 96 GLU cc_start: 0.8544 (pm20) cc_final: 0.8196 (pm20) REVERT: L 97 PHE cc_start: 0.8326 (m-80) cc_final: 0.7531 (m-10) REVERT: A 69 TRP cc_start: 0.7926 (m-90) cc_final: 0.7194 (m-90) REVERT: A 95 MET cc_start: 0.9161 (ppp) cc_final: 0.8362 (ppp) REVERT: A 308 HIS cc_start: 0.8901 (m90) cc_final: 0.7802 (m90) REVERT: A 373 MET cc_start: 0.9121 (mtp) cc_final: 0.8296 (ttm) REVERT: A 475 MET cc_start: 0.8950 (mmm) cc_final: 0.8687 (mmt) REVERT: B 535 MET cc_start: 0.8172 (tpp) cc_final: 0.7934 (tpp) REVERT: B 584 GLU cc_start: 0.9184 (tm-30) cc_final: 0.8708 (tm-30) REVERT: B 588 ARG cc_start: 0.9051 (tpp80) cc_final: 0.8541 (tpp80) REVERT: B 596 TRP cc_start: 0.8152 (m-10) cc_final: 0.7930 (m-90) REVERT: B 619 LEU cc_start: 0.9451 (tp) cc_final: 0.9178 (tp) REVERT: B 628 TRP cc_start: 0.8230 (m100) cc_final: 0.7759 (m100) REVERT: B 630 GLU cc_start: 0.8929 (pt0) cc_final: 0.8577 (pt0) REVERT: B 662 GLU cc_start: 0.8203 (tt0) cc_final: 0.7322 (tt0) REVERT: G 4 LEU cc_start: 0.8878 (mt) cc_final: 0.8618 (mt) REVERT: G 13 LYS cc_start: 0.8685 (mmtt) cc_final: 0.8148 (mmmm) REVERT: G 36 TRP cc_start: 0.9177 (m100) cc_final: 0.8321 (m-10) REVERT: G 37 VAL cc_start: 0.9423 (t) cc_final: 0.9108 (p) REVERT: G 46 GLU cc_start: 0.8332 (mm-30) cc_final: 0.7579 (mm-30) REVERT: G 72 ASP cc_start: 0.7596 (t0) cc_final: 0.6911 (t0) REVERT: G 80 MET cc_start: 0.8695 (ttt) cc_final: 0.7987 (ttt) REVERT: G 81 ASP cc_start: 0.7467 (p0) cc_final: 0.7149 (p0) REVERT: G 108 LEU cc_start: 0.9047 (tp) cc_final: 0.8750 (tp) REVERT: J 4 LEU cc_start: 0.8795 (tp) cc_final: 0.8590 (tp) REVERT: J 47 LEU cc_start: 0.9266 (mp) cc_final: 0.8635 (pp) REVERT: J 86 TYR cc_start: 0.8845 (m-10) cc_final: 0.8448 (m-10) REVERT: C 95 MET cc_start: 0.9244 (ppp) cc_final: 0.8504 (ppp) REVERT: C 308 HIS cc_start: 0.8982 (m90) cc_final: 0.8213 (m-70) REVERT: C 316 TRP cc_start: 0.8173 (m-90) cc_final: 0.7842 (m-90) REVERT: C 373 MET cc_start: 0.8931 (mtp) cc_final: 0.7855 (mmm) REVERT: C 474 ASP cc_start: 0.8761 (t0) cc_final: 0.8508 (t0) REVERT: C 475 MET cc_start: 0.8517 (mmm) cc_final: 0.8027 (mmt) REVERT: E 596 TRP cc_start: 0.8639 (m-10) cc_final: 0.8139 (m-90) REVERT: I 4 LEU cc_start: 0.8574 (mt) cc_final: 0.8210 (mt) REVERT: I 13 LYS cc_start: 0.8840 (mmtt) cc_final: 0.8266 (mmmm) REVERT: I 37 VAL cc_start: 0.9485 (t) cc_final: 0.9111 (p) REVERT: I 46 GLU cc_start: 0.8468 (mm-30) cc_final: 0.7934 (mm-30) REVERT: I 72 ASP cc_start: 0.7852 (t0) cc_final: 0.7291 (t0) REVERT: I 96 LYS cc_start: 0.7780 (mtmm) cc_final: 0.7232 (mttt) REVERT: I 108 LEU cc_start: 0.8854 (tp) cc_final: 0.8530 (tp) REVERT: K 33 MET cc_start: 0.7569 (pmm) cc_final: 0.7211 (pmm) REVERT: K 47 LEU cc_start: 0.9017 (mp) cc_final: 0.8543 (pp) REVERT: K 77 ARG cc_start: 0.8380 (mmp80) cc_final: 0.8026 (mmp80) REVERT: K 78 MET cc_start: 0.7160 (mtp) cc_final: 0.6483 (ttm) REVERT: K 86 TYR cc_start: 0.8400 (m-10) cc_final: 0.7857 (m-10) REVERT: D 69 TRP cc_start: 0.7774 (m-90) cc_final: 0.6788 (m-90) REVERT: D 95 MET cc_start: 0.9077 (ppp) cc_final: 0.8607 (ppp) REVERT: D 195 ASN cc_start: 0.8420 (m110) cc_final: 0.8194 (m110) REVERT: D 308 HIS cc_start: 0.9070 (m90) cc_final: 0.8260 (m90) REVERT: D 316 TRP cc_start: 0.8337 (m-90) cc_final: 0.7957 (m-90) REVERT: D 373 MET cc_start: 0.9088 (mtp) cc_final: 0.8011 (mmm) REVERT: D 475 MET cc_start: 0.8488 (mmm) cc_final: 0.7352 (mmt) REVERT: D 479 TRP cc_start: 0.8641 (m-10) cc_final: 0.7964 (m-10) REVERT: F 546 SER cc_start: 0.8851 (t) cc_final: 0.8552 (p) REVERT: F 574 LYS cc_start: 0.9235 (mtpt) cc_final: 0.8972 (pttp) REVERT: F 579 ARG cc_start: 0.8983 (mtp180) cc_final: 0.8713 (mtp180) REVERT: F 654 GLU cc_start: 0.8989 (mm-30) cc_final: 0.8579 (tp30) REVERT: F 655 LYS cc_start: 0.8909 (pttp) cc_final: 0.8609 (mtmm) outliers start: 1 outliers final: 0 residues processed: 326 average time/residue: 0.1378 time to fit residues: 70.1418 Evaluate side-chains 238 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 222 optimal weight: 0.9990 chunk 14 optimal weight: 7.9990 chunk 206 optimal weight: 5.9990 chunk 201 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 158 optimal weight: 0.7980 chunk 154 optimal weight: 1.9990 chunk 226 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 chunk 124 optimal weight: 9.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 GLN J 66 GLN J 70 GLN ** K 66 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 = 0.3449 r_free = 0.3449 target = 0.072053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.056592 restraints weight = 86343.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.058590 restraints weight = 49933.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.059972 restraints weight = 34433.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.060921 restraints weight = 26582.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.061584 restraints weight = 22123.814| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.7387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 20073 Z= 0.158 Angle : 0.816 19.937 27378 Z= 0.398 Chirality : 0.050 0.411 3237 Planarity : 0.005 0.085 3336 Dihedral : 5.495 24.546 2496 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.71 % Favored : 92.98 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.17), residues: 2280 helix: 0.24 (0.25), residues: 432 sheet: 0.27 (0.21), residues: 540 loop : -0.98 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG L 54 TYR 0.024 0.002 TYR J 71 PHE 0.024 0.002 PHE D 317 TRP 0.029 0.003 TRP I 23 HIS 0.003 0.001 HIS D 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 (19959) covalent geometry : angle 0.75044 / 0.38 (27072) SS BOND : bond 0.00450 / 0.24 ( 36) SS BOND : angle 1.64503 / 1.15 ( 72) hydrogen bonds : bond 0.04473 / 3.02 ( 768) hydrogen bonds : angle 6.20400 / 4.42 ( 2016) link_ALPHA1-3 : bond 0.00750 / 0.38 ( 3) link_ALPHA1-3 : angle 2.87477 / 1.67 ( 9) link_ALPHA1-6 : bond 0.01105 / 0.56 ( 3) link_ALPHA1-6 : angle 1.26707 / 0.76 ( 9) link_BETA1-4 : bond 0.00346 / 0.22 ( 33) link_BETA1-4 : angle 1.91818 / 1.27 ( 99) link_NAG-ASN : bond 0.00679 / 0.46 ( 39) link_NAG-ASN : angle 4.45342 / 3.42 ( 117) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3141.64 seconds wall clock time: 55 minutes 25.33 seconds (3325.33 seconds total)