Starting phenix.real_space_refine on Fri Jun 5 22:53:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9x5x_66600/06_2026/9x5x_66600.cif Found real_map, /net/cci-nas-00/data/ceres_data/9x5x_66600/06_2026/9x5x_66600.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9x5x_66600/06_2026/9x5x_66600.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9x5x_66600/06_2026/9x5x_66600.map" model { file = "/net/cci-nas-00/data/ceres_data/9x5x_66600/06_2026/9x5x_66600.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9x5x_66600/06_2026/9x5x_66600.cif" } resolution = 2.76 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= 0.001 sd= 0.065 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 10056 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 9936 2.51 5 N 2718 2.21 5 O 3156 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15882 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 2570 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 336, 2550 Classifications: {'peptide': 336} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 310} Conformer: "B" Number of residues, atoms: 336, 2550 Classifications: {'peptide': 336} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 310} bond proxies already assigned to first conformer: 2587 Chain: "B" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 807 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain breaks: 1 Chain: "C" Number of atoms: 2570 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 336, 2550 Classifications: {'peptide': 336} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 310} Conformer: "B" Number of residues, atoms: 336, 2550 Classifications: {'peptide': 336} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 310} bond proxies already assigned to first conformer: 2587 Chain: "D" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 807 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain breaks: 1 Chain: "E" Number of atoms: 2570 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 336, 2550 Classifications: {'peptide': 336} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 310} Conformer: "B" Number of residues, atoms: 336, 2550 Classifications: {'peptide': 336} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 310} bond proxies already assigned to first conformer: 2587 Chain: "F" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 807 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain breaks: 1 Chain: "H" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 955 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "L" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 822 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "G" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 955 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "I" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 822 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "J" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 955 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "K" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 822 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Residues with excluded nonbonded symmetry interactions: 9 residue: pdb=" N ASER A 39 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 39 " occ=0.50 residue: pdb=" N AASN A 43 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN A 43 " occ=0.50 residue: pdb=" N ASER A 306 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 306 " occ=0.50 residue: pdb=" N ASER C 39 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER C 39 " occ=0.50 residue: pdb=" N AASN C 43 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN C 43 " occ=0.50 residue: pdb=" N ASER C 306 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER C 306 " occ=0.50 residue: pdb=" N ASER E 39 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER E 39 " occ=0.50 residue: pdb=" N AASN E 43 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN E 43 " occ=0.50 residue: pdb=" N ASER E 306 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER E 306 " occ=0.50 Time building chain proxies: 5.24, per 1000 atoms: 0.33 Number of scatterers: 15882 At special positions: 0 Unit cell: (137.78, 148.57, 158.53, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 3156 8.00 N 2718 7.00 C 9936 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 57 " distance=2.04 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 72 " distance=2.03 Simple disulfide: pdb=" SG CYS A 94 " - pdb=" SG CYS A 143 " distance=2.03 Simple disulfide: pdb=" SG CYS A 181 " - pdb=" SG CYS A 275 " distance=2.04 Simple disulfide: pdb=" SG CYS A 295 " - pdb=" SG CYS A 321 " distance=2.04 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 57 " distance=2.04 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 72 " distance=2.03 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 143 " distance=2.03 Simple disulfide: pdb=" SG CYS C 181 " - pdb=" SG CYS C 275 " distance=2.04 Simple disulfide: pdb=" SG CYS C 295 " - pdb=" SG CYS C 321 " distance=2.04 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 57 " distance=2.04 Simple disulfide: pdb=" SG CYS E 60 " - pdb=" SG CYS E 72 " distance=2.03 Simple disulfide: pdb=" SG CYS E 94 " - pdb=" SG CYS E 143 " distance=2.02 Simple disulfide: pdb=" SG CYS E 181 " - pdb=" SG CYS E 275 " distance=2.04 Simple disulfide: pdb=" SG CYS E 295 " - pdb=" SG CYS E 321 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 104 " distance=2.02 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 104 " distance=2.02 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 104 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A 401 " - " ASN A 145 " " NAG A 402 " - " ASN A 233 " " NAG A 403 " - " ASN A 25 " " NAG A 404 " - " ASN A 59 " " NAG C 401 " - " ASN C 145 " " NAG C 402 " - " ASN C 233 " " NAG C 403 " - " ASN C 25 " " NAG C 404 " - " ASN C 59 " " NAG E 401 " - " ASN E 145 " " NAG E 402 " - " ASN E 233 " " NAG E 403 " - " ASN E 25 " " NAG E 404 " - " ASN E 59 " " NAG M 1 " - " ASN A 304 " " NAG N 1 " - " ASN A 333 " " NAG O 1 " - " ASN A 197 " " NAG P 1 " - " ASN C 304 " " NAG Q 1 " - " ASN C 333 " " NAG R 1 " - " ASN C 197 " " NAG S 1 " - " ASN E 304 " " NAG T 1 " - " ASN E 333 " " NAG U 1 " - " ASN E 197 " Time building additional restraints: 1.33 Conformation dependent library (CDL) restraints added in 1.0 seconds 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3672 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 41 sheets defined 14.9% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 61 through 67 Processing helix chain 'A' and resid 98 through 102 removed outlier: 3.630A pdb=" N ARG A 101 " --> pdb=" O MET A 98 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N THR A 102 " --> pdb=" O HIS A 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 98 through 102' Processing helix chain 'A' and resid 103 through 105 No H-bonds generated for 'chain 'A' and resid 103 through 105' Processing helix chain 'A' and resid 106 through 112 Processing helix chain 'A' and resid 197 through 205 removed outlier: 3.639A pdb=" N ALA A 202 " --> pdb=" O GLU A 198 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS A 203 " --> pdb=" O THR A 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 403 removed outlier: 4.191A pdb=" N ILE B 395 " --> pdb=" O ALA B 391 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS B 397 " --> pdb=" O ASN B 393 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASN B 398 " --> pdb=" O LYS B 394 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU B 402 " --> pdb=" O ASN B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 469 removed outlier: 3.659A pdb=" N LEU B 425 " --> pdb=" O HIS B 421 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP B 437 " --> pdb=" O ASP B 433 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU B 458 " --> pdb=" O ILE B 454 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ASP B 459 " --> pdb=" O ILE B 455 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLU B 460 " --> pdb=" O ASN B 456 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU B 466 " --> pdb=" O LEU B 462 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU B 469 " --> pdb=" O LEU B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 472 No H-bonds generated for 'chain 'B' and resid 470 through 472' Processing helix chain 'C' and resid 61 through 67 Processing helix chain 'C' and resid 98 through 102 removed outlier: 3.519A pdb=" N ARG C 101 " --> pdb=" O MET C 98 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N THR C 102 " --> pdb=" O HIS C 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 98 through 102' Processing helix chain 'C' and resid 103 through 105 No H-bonds generated for 'chain 'C' and resid 103 through 105' Processing helix chain 'C' and resid 106 through 112 Processing helix chain 'C' and resid 197 through 205 removed outlier: 3.643A pdb=" N ALA C 202 " --> pdb=" O GLU C 198 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS C 203 " --> pdb=" O THR C 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 394 removed outlier: 3.676A pdb=" N ILE D 392 " --> pdb=" O THR D 388 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS D 394 " --> pdb=" O GLU D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 403 Processing helix chain 'D' and resid 421 through 456 removed outlier: 3.629A pdb=" N LEU D 425 " --> pdb=" O HIS D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 457 through 468 removed outlier: 3.768A pdb=" N HIS D 461 " --> pdb=" O SER D 457 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 67 Processing helix chain 'E' and resid 98 through 102 removed outlier: 3.512A pdb=" N ARG E 101 " --> pdb=" O MET E 98 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR E 102 " --> pdb=" O HIS E 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 98 through 102' Processing helix chain 'E' and resid 103 through 105 No H-bonds generated for 'chain 'E' and resid 103 through 105' Processing helix chain 'E' and resid 106 through 112 Processing helix chain 'E' and resid 197 through 205 removed outlier: 3.586A pdb=" N ALA E 202 " --> pdb=" O GLU E 198 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS E 203 " --> pdb=" O THR E 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 394 Processing helix chain 'F' and resid 397 through 403 Processing helix chain 'F' and resid 423 through 456 removed outlier: 3.536A pdb=" N ASP F 437 " --> pdb=" O ASP F 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 457 through 473 removed outlier: 3.866A pdb=" N LEU F 465 " --> pdb=" O HIS F 461 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N GLU F 466 " --> pdb=" O LEU F 462 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LYS F 471 " --> pdb=" O ARG F 467 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 99 removed outlier: 3.875A pdb=" N THR H 99 " --> pdb=" O ALA H 96 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 99 removed outlier: 3.766A pdb=" N THR G 99 " --> pdb=" O ALA G 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 95 through 99 removed outlier: 3.907A pdb=" N THR J 99 " --> pdb=" O ALA J 96 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 17 Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 31 Processing sheet with id=AA3, first strand: chain 'A' and resid 43 through 44 removed outlier: 6.023A pdb=" N AASN A 43 " --> pdb=" O ALA A 293 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 49 through 50 Processing sheet with id=AA5, first strand: chain 'A' and resid 116 through 119 removed outlier: 7.386A pdb=" N VAL A 190 " --> pdb=" O PRO A 270 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ILE A 267 " --> pdb=" O ALA A 159 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 116 through 119 Processing sheet with id=AA7, first strand: chain 'A' and resid 173 through 177 Processing sheet with id=AA8, first strand: chain 'A' and resid 301 through 302 Processing sheet with id=AA9, first strand: chain 'A' and resid 309 through 310 Processing sheet with id=AB1, first strand: chain 'C' and resid 14 through 17 Processing sheet with id=AB2, first strand: chain 'C' and resid 29 through 31 Processing sheet with id=AB3, first strand: chain 'C' and resid 43 through 44 removed outlier: 5.984A pdb=" N AASN C 43 " --> pdb=" O ALA C 293 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 49 through 50 Processing sheet with id=AB5, first strand: chain 'C' and resid 116 through 119 removed outlier: 7.414A pdb=" N VAL C 190 " --> pdb=" O PRO C 270 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ILE C 267 " --> pdb=" O ALA C 159 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 116 through 119 Processing sheet with id=AB7, first strand: chain 'C' and resid 173 through 177 Processing sheet with id=AB8, first strand: chain 'C' and resid 301 through 302 Processing sheet with id=AB9, first strand: chain 'C' and resid 309 through 310 Processing sheet with id=AC1, first strand: chain 'E' and resid 14 through 17 Processing sheet with id=AC2, first strand: chain 'E' and resid 29 through 31 Processing sheet with id=AC3, first strand: chain 'E' and resid 43 through 44 removed outlier: 6.028A pdb=" N AASN E 43 " --> pdb=" O ALA E 293 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'E' and resid 49 through 50 Processing sheet with id=AC5, first strand: chain 'E' and resid 116 through 119 removed outlier: 7.448A pdb=" N VAL E 190 " --> pdb=" O PRO E 270 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ILE E 267 " --> pdb=" O ALA E 159 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 116 through 119 Processing sheet with id=AC7, first strand: chain 'E' and resid 173 through 177 Processing sheet with id=AC8, first strand: chain 'E' and resid 301 through 302 Processing sheet with id=AC9, first strand: chain 'E' and resid 309 through 310 Processing sheet with id=AD1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AD2, first strand: chain 'H' and resid 65 through 67 removed outlier: 5.137A pdb=" N TRP H 52 " --> pdb=" O ARG H 43 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ARG H 43 " --> pdb=" O TRP H 52 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VAL H 117 " --> pdb=" O ARG H 106 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 65 through 67 removed outlier: 5.137A pdb=" N TRP H 52 " --> pdb=" O ARG H 43 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ARG H 43 " --> pdb=" O TRP H 52 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR H 102 " --> pdb=" O THR H 122 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 20 through 23 removed outlier: 3.836A pdb=" N GLU L 86 " --> pdb=" O SER L 83 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER L 83 " --> pdb=" O GLU L 86 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 66 through 67 removed outlier: 6.359A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AD7, first strand: chain 'G' and resid 65 through 67 removed outlier: 5.125A pdb=" N TRP G 52 " --> pdb=" O ARG G 43 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ARG G 43 " --> pdb=" O TRP G 52 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N CYS G 104 " --> pdb=" O TRP G 118 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N TRP G 118 " --> pdb=" O CYS G 104 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ARG G 106 " --> pdb=" O ASP G 116 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 10 through 11 removed outlier: 6.349A pdb=" N TRP I 41 " --> pdb=" O LEU I 53 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 20 through 23 removed outlier: 3.910A pdb=" N GLU I 86 " --> pdb=" O SER I 83 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER I 83 " --> pdb=" O GLU I 86 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AE2, first strand: chain 'J' and resid 65 through 67 removed outlier: 5.131A pdb=" N TRP J 52 " --> pdb=" O ARG J 43 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ARG J 43 " --> pdb=" O TRP J 52 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N CYS J 104 " --> pdb=" O TRP J 118 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N TRP J 118 " --> pdb=" O CYS J 104 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ARG J 106 " --> pdb=" O ASP J 116 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 65 through 67 removed outlier: 5.131A pdb=" N TRP J 52 " --> pdb=" O ARG J 43 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ARG J 43 " --> pdb=" O TRP J 52 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR J 102 " --> pdb=" O THR J 122 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 10 through 11 removed outlier: 6.329A pdb=" N TRP K 41 " --> pdb=" O LEU K 53 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 20 through 23 removed outlier: 3.898A pdb=" N GLU K 86 " --> pdb=" O SER K 83 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER K 83 " --> pdb=" O GLU K 86 " (cutoff:3.500A) 517 hydrogen bonds defined for protein. 1341 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.94 Time building geometry restraints manager: 1.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4811 1.33 - 1.46: 4144 1.46 - 1.59: 7143 1.59 - 1.72: 0 1.72 - 1.85: 102 Bond restraints: 16200 Sorted by residual: bond pdb=" C ASN E 320 " pdb=" N CYS E 321 " ideal model delta sigma weight residual 1.331 1.255 0.076 2.07e-02 2.33e+03 1.36e+01 bond pdb=" CG LEU J 112C" pdb=" CD2 LEU J 112C" ideal model delta sigma weight residual 1.521 1.404 0.117 3.30e-02 9.18e+02 1.26e+01 bond pdb=" CG ARG A 245 " pdb=" CD ARG A 245 " ideal model delta sigma weight residual 1.520 1.437 0.083 3.00e-02 1.11e+03 7.62e+00 bond pdb=" CG ARG C 245 " pdb=" CD ARG C 245 " ideal model delta sigma weight residual 1.520 1.438 0.082 3.00e-02 1.11e+03 7.43e+00 bond pdb=" C1 NAG A 404 " pdb=" O5 NAG A 404 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.36e+00 ... (remaining 16195 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.70: 21303 2.70 - 5.40: 596 5.40 - 8.09: 73 8.09 - 10.79: 13 10.79 - 13.49: 2 Bond angle restraints: 21987 Sorted by residual: angle pdb=" C ALA H 111B" pdb=" N MET H 111C" pdb=" CA MET H 111C" ideal model delta sigma weight residual 121.54 132.11 -10.57 1.91e+00 2.74e-01 3.06e+01 angle pdb=" C ALA G 111B" pdb=" N MET G 111C" pdb=" CA MET G 111C" ideal model delta sigma weight residual 121.54 131.28 -9.74 1.91e+00 2.74e-01 2.60e+01 angle pdb=" C ASP F 418 " pdb=" N GLU F 419 " pdb=" CA GLU F 419 " ideal model delta sigma weight residual 121.54 130.61 -9.07 1.91e+00 2.74e-01 2.26e+01 angle pdb=" C ALA J 111B" pdb=" N MET J 111C" pdb=" CA MET J 111C" ideal model delta sigma weight residual 121.54 130.53 -8.99 1.91e+00 2.74e-01 2.21e+01 angle pdb=" C ILE K 29 " pdb=" N SER K 36 " pdb=" CA SER K 36 " ideal model delta sigma weight residual 121.54 129.84 -8.30 1.91e+00 2.74e-01 1.89e+01 ... (remaining 21982 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 9192 17.93 - 35.86: 781 35.86 - 53.78: 138 53.78 - 71.71: 34 71.71 - 89.64: 16 Dihedral angle restraints: 10161 sinusoidal: 4401 harmonic: 5760 Sorted by residual: dihedral pdb=" CA SER C 140 " pdb=" C SER C 140 " pdb=" N GLY C 141 " pdb=" CA GLY C 141 " ideal model delta harmonic sigma weight residual 180.00 141.32 38.68 0 5.00e+00 4.00e-02 5.98e+01 dihedral pdb=" CA SER E 140 " pdb=" C SER E 140 " pdb=" N GLY E 141 " pdb=" CA GLY E 141 " ideal model delta harmonic sigma weight residual 180.00 141.98 38.02 0 5.00e+00 4.00e-02 5.78e+01 dihedral pdb=" CB CYS E 60 " pdb=" SG CYS E 60 " pdb=" SG CYS E 72 " pdb=" CB CYS E 72 " ideal model delta sinusoidal sigma weight residual -86.00 -143.47 57.47 1 1.00e+01 1.00e-02 4.44e+01 ... (remaining 10158 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1945 0.069 - 0.138: 543 0.138 - 0.207: 72 0.207 - 0.276: 15 0.276 - 0.345: 2 Chirality restraints: 2577 Sorted by residual: chirality pdb=" CG LEU H 112C" pdb=" CB LEU H 112C" pdb=" CD1 LEU H 112C" pdb=" CD2 LEU H 112C" both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.37 -0.03 2.00e-02 2.50e+03 2.97e+00 chirality pdb=" CG LEU G 112C" pdb=" CB LEU G 112C" pdb=" CD1 LEU G 112C" pdb=" CD2 LEU G 112C" both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.59e+00 ... (remaining 2574 not shown) Planarity restraints: 2814 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL K 71 " -0.047 5.00e-02 4.00e+02 7.15e-02 8.18e+00 pdb=" N PRO K 72 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO K 72 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO K 72 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL I 71 " 0.047 5.00e-02 4.00e+02 7.05e-02 7.96e+00 pdb=" N PRO I 72 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO I 72 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO I 72 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL L 71 " -0.046 5.00e-02 4.00e+02 6.95e-02 7.74e+00 pdb=" N PRO L 72 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO L 72 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO L 72 " -0.038 5.00e-02 4.00e+02 ... (remaining 2811 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2118 2.75 - 3.29: 13760 3.29 - 3.83: 26268 3.83 - 4.36: 32326 4.36 - 4.90: 56894 Nonbonded interactions: 131366 Sorted by model distance: nonbonded pdb=" OG SER H 7 " pdb=" OG SER H 22 " model vdw 2.213 3.040 nonbonded pdb=" OG SER G 7 " pdb=" OG SER G 22 " model vdw 2.226 3.040 nonbonded pdb=" OG SER J 7 " pdb=" OG SER J 22 " model vdw 2.243 3.040 nonbonded pdb=" OH TYR E 224 " pdb=" OD2 ASP E 249 " model vdw 2.264 3.040 nonbonded pdb=" OG SER E 195 " pdb=" O GLN E 227 " model vdw 2.272 3.040 ... (remaining 131361 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 38 or resid 40 through 42 or resid 44 through 30 \ 5 or resid 307 through 404)) selection = (chain 'C' and (resid 5 through 38 or resid 40 through 42 or resid 44 through 30 \ 5 or resid 307 through 404)) selection = (chain 'E' and (resid 5 through 38 or resid 40 through 42 or resid 44 through 30 \ 5 or resid 307 through 404)) } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'I' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.900 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 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:8.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 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 : 0.011 0.117 16248 Z= 0.445 Angle : 1.095 13.491 22113 Z= 0.577 Chirality : 0.063 0.345 2577 Planarity : 0.008 0.071 2793 Dihedral : 14.073 89.640 6435 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.85 % Favored : 93.00 % Rotamer: Outliers : 0.47 % Allowed : 5.09 % Favored : 94.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % 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: -3.21 (0.16), residues: 2013 helix: -2.77 (0.23), residues: 267 sheet: -1.22 (0.23), residues: 525 loop : -2.51 (0.14), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 108 TYR 0.026 0.003 TYR E 263 PHE 0.036 0.004 PHE C 193 TRP 0.018 0.003 TRP A 158 HIS 0.010 0.002 HIS D 421 Details of bonding type rmsd/Z covalent geometry : bond 0.01074 / 0.45 (16200) covalent geometry : angle 1.07417 / 0.57 (21987) SS BOND : bond 0.00805 / 0.49 ( 18) SS BOND : angle 2.86648 / 2.07 ( 36) hydrogen bonds : bond 0.13966 / 9.60 ( 469) hydrogen bonds : angle 6.99234 / 4.97 ( 1341) link_BETA1-4 : bond 0.00850 / 0.44 ( 9) link_BETA1-4 : angle 2.38704 / 1.54 ( 27) link_NAG-ASN : bond 0.00567 / 0.36 ( 21) link_NAG-ASN : angle 3.27325 / 2.12 ( 63) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 210 time to evaluate : 0.696 Fit side-chains REVERT: A 75 LYS cc_start: 0.8116 (tmtt) cc_final: 0.7722 (ttpt) REVERT: A 186 ASP cc_start: 0.8231 (m-30) cc_final: 0.7919 (m-30) REVERT: B 433 ASP cc_start: 0.6755 (m-30) cc_final: 0.6488 (m-30) REVERT: C 75 LYS cc_start: 0.8156 (tmtt) cc_final: 0.7685 (ttpt) REVERT: C 330 LYS cc_start: 0.8325 (mptt) cc_final: 0.8095 (mptm) REVERT: D 396 THR cc_start: 0.8455 (p) cc_final: 0.8179 (m) REVERT: D 433 ASP cc_start: 0.6438 (m-30) cc_final: 0.6232 (m-30) REVERT: E 75 LYS cc_start: 0.8158 (tmtt) cc_final: 0.7740 (ttpt) REVERT: E 221 THR cc_start: 0.7955 (p) cc_final: 0.7619 (m) REVERT: E 222 THR cc_start: 0.8642 (p) cc_final: 0.8396 (p) REVERT: H 116 ASP cc_start: 0.7837 (OUTLIER) cc_final: 0.7366 (m-30) REVERT: G 116 ASP cc_start: 0.7784 (OUTLIER) cc_final: 0.7267 (m-30) REVERT: I 26 SER cc_start: 0.8186 (m) cc_final: 0.7969 (m) REVERT: J 122 THR cc_start: 0.7300 (p) cc_final: 0.7055 (p) outliers start: 3 outliers final: 0 residues processed: 213 average time/residue: 0.6554 time to fit residues: 153.9212 Evaluate side-chains 175 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 173 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 116 ASP Chi-restraints excluded: chain G residue 116 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 ASN A 200 GLN A 253 GLN A 264 GLN C 171 ASN C 253 GLN C 264 GLN D 393 ASN D 421 HIS E 171 ASN E 234 GLN E 253 GLN E 264 GLN F 369 HIS L 114 ASN G 92 ASN I 27 GLN I 114 ASN J 44 GLN K 27 GLN K 44 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.191541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.147613 restraints weight = 68240.365| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 3.68 r_work: 0.3521 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3535 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3535 r_free = 0.3535 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3535 r_free = 0.3535 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3535 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16248 Z= 0.144 Angle : 0.660 8.277 22113 Z= 0.339 Chirality : 0.043 0.173 2577 Planarity : 0.006 0.054 2793 Dihedral : 6.807 56.214 2803 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 1.40 % Allowed : 10.53 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.17), residues: 2013 helix: -1.10 (0.30), residues: 282 sheet: -0.90 (0.24), residues: 501 loop : -2.04 (0.15), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 80 TYR 0.018 0.001 TYR H 103 PHE 0.016 0.002 PHE A 193 TRP 0.010 0.001 TRP G 52 HIS 0.005 0.001 HIS K 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (16200) covalent geometry : angle 0.64200 / 0.34 (21987) SS BOND : bond 0.00241 / 0.15 ( 18) SS BOND : angle 1.59929 / 1.17 ( 36) hydrogen bonds : bond 0.04032 / 2.72 ( 469) hydrogen bonds : angle 5.55076 / 4.01 ( 1341) link_BETA1-4 : bond 0.00419 / 0.24 ( 9) link_BETA1-4 : angle 1.33253 / 0.83 ( 27) link_NAG-ASN : bond 0.00301 / 0.18 ( 21) link_NAG-ASN : angle 2.56962 / 1.68 ( 63) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 191 time to evaluate : 0.613 Fit side-chains REVERT: A 75 LYS cc_start: 0.8263 (tmtt) cc_final: 0.7730 (ttpt) REVERT: A 221 THR cc_start: 0.8139 (p) cc_final: 0.7703 (m) REVERT: B 422 ASN cc_start: 0.7686 (OUTLIER) cc_final: 0.7336 (m110) REVERT: B 433 ASP cc_start: 0.7782 (m-30) cc_final: 0.7528 (m-30) REVERT: C 330 LYS cc_start: 0.8456 (mptt) cc_final: 0.8242 (mptm) REVERT: D 433 ASP cc_start: 0.7489 (m-30) cc_final: 0.7201 (m-30) REVERT: E 75 LYS cc_start: 0.8310 (tmtt) cc_final: 0.8081 (mptt) REVERT: E 221 THR cc_start: 0.8072 (p) cc_final: 0.7664 (m) REVERT: E 224 TYR cc_start: 0.8955 (m-80) cc_final: 0.8748 (m-80) REVERT: F 472 MET cc_start: 0.5232 (OUTLIER) cc_final: 0.4434 (tmm) REVERT: I 26 SER cc_start: 0.8054 (m) cc_final: 0.7847 (m) outliers start: 19 outliers final: 7 residues processed: 203 average time/residue: 0.7136 time to fit residues: 158.7622 Evaluate side-chains 170 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 161 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain F residue 472 MET Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 79 SER Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain I residue 79 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 165 optimal weight: 9.9990 chunk 57 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 138 optimal weight: 5.9990 chunk 148 optimal weight: 8.9990 chunk 65 optimal weight: 0.5980 chunk 4 optimal weight: 4.9990 chunk 176 optimal weight: 2.9990 chunk 190 optimal weight: 5.9990 chunk 77 optimal weight: 0.3980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 369 HIS F 421 HIS L 27 GLN ** J 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82 ASN K 105 GLN K 114 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.189865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.144477 restraints weight = 56729.998| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 3.66 r_work: 0.3499 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3380 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| r_final: 0.3380 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16248 Z= 0.209 Angle : 0.678 8.416 22113 Z= 0.347 Chirality : 0.045 0.170 2577 Planarity : 0.005 0.074 2793 Dihedral : 6.378 52.514 2799 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.34 % Favored : 93.50 % Rotamer: Outliers : 1.99 % Allowed : 13.22 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.91 (0.17), residues: 2013 helix: -0.27 (0.31), residues: 273 sheet: -0.65 (0.25), residues: 483 loop : -1.84 (0.15), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 88 TYR 0.015 0.002 TYR E 263 PHE 0.021 0.002 PHE C 193 TRP 0.011 0.002 TRP G 52 HIS 0.005 0.001 HIS A 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.21 (16200) covalent geometry : angle 0.66102 / 0.34 (21987) SS BOND : bond 0.00330 / 0.21 ( 18) SS BOND : angle 1.75764 / 1.29 ( 36) hydrogen bonds : bond 0.03932 / 2.65 ( 469) hydrogen bonds : angle 5.36358 / 3.88 ( 1341) link_BETA1-4 : bond 0.00254 / 0.13 ( 9) link_BETA1-4 : angle 1.23452 / 0.75 ( 27) link_NAG-ASN : bond 0.00285 / 0.19 ( 21) link_NAG-ASN : angle 2.57708 / 1.67 ( 63) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 178 time to evaluate : 0.676 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8152 (tmtt) cc_final: 0.7672 (ttpt) REVERT: A 75 LYS cc_start: 0.8326 (tmtt) cc_final: 0.8108 (mptt) REVERT: A 198 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7998 (pm20) REVERT: A 221 THR cc_start: 0.8161 (p) cc_final: 0.7732 (m) REVERT: B 433 ASP cc_start: 0.7722 (m-30) cc_final: 0.7482 (m-30) REVERT: C 17 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7948 (tmtt) REVERT: D 433 ASP cc_start: 0.7526 (m-30) cc_final: 0.7268 (m-30) REVERT: E 75 LYS cc_start: 0.8341 (tmtt) cc_final: 0.8121 (mptp) REVERT: E 221 THR cc_start: 0.8141 (p) cc_final: 0.7748 (m) REVERT: F 472 MET cc_start: 0.5290 (OUTLIER) cc_final: 0.4508 (tmm) REVERT: I 26 SER cc_start: 0.8090 (m) cc_final: 0.7869 (m) REVERT: J 43 ARG cc_start: 0.8301 (ptt180) cc_final: 0.8053 (ptp-170) outliers start: 29 outliers final: 12 residues processed: 198 average time/residue: 0.6681 time to fit residues: 145.7154 Evaluate side-chains 174 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 159 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 17 LYS Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain F residue 472 MET Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 79 SER Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain I residue 27 GLN Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain J residue 59 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 85 optimal weight: 20.0000 chunk 138 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 10 optimal weight: 0.0370 chunk 71 optimal weight: 7.9990 chunk 37 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 129 optimal weight: 9.9990 chunk 109 optimal weight: 0.1980 chunk 173 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 overall best weight: 0.8062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 400 ASN B 442 GLN D 400 ASN E 200 GLN F 442 GLN L 27 GLN I 105 GLN ** J 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.192590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.148495 restraints weight = 70089.065| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 3.73 r_work: 0.3525 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3406 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3406 r_free = 0.3406 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3406 r_free = 0.3406 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| r_final: 0.3406 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16248 Z= 0.133 Angle : 0.602 8.582 22113 Z= 0.307 Chirality : 0.043 0.259 2577 Planarity : 0.005 0.050 2793 Dihedral : 5.791 45.886 2799 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.40 % Allowed : 14.50 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.54 (0.18), residues: 2013 helix: 0.53 (0.32), residues: 273 sheet: -0.60 (0.24), residues: 501 loop : -1.63 (0.16), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 80 TYR 0.014 0.001 TYR H 103 PHE 0.015 0.001 PHE C 193 TRP 0.011 0.001 TRP G 52 HIS 0.004 0.001 HIS L 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.13 (16200) covalent geometry : angle 0.58673 / 0.30 (21987) SS BOND : bond 0.00206 / 0.13 ( 18) SS BOND : angle 1.29119 / 0.95 ( 36) hydrogen bonds : bond 0.03351 / 2.26 ( 469) hydrogen bonds : angle 5.07451 / 3.68 ( 1341) link_BETA1-4 : bond 0.00323 / 0.17 ( 9) link_BETA1-4 : angle 1.22602 / 0.74 ( 27) link_NAG-ASN : bond 0.00216 / 0.13 ( 21) link_NAG-ASN : angle 2.33413 / 1.52 ( 63) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 165 time to evaluate : 0.615 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8046 (tmtt) cc_final: 0.7572 (ttpt) REVERT: A 75 LYS cc_start: 0.8319 (tmtt) cc_final: 0.8092 (mptt) REVERT: A 198 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7960 (pm20) REVERT: A 221 THR cc_start: 0.8077 (p) cc_final: 0.7656 (m) REVERT: B 433 ASP cc_start: 0.7780 (m-30) cc_final: 0.7536 (m-30) REVERT: C 17 LYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7669 (tmtt) REVERT: E 75 LYS cc_start: 0.8332 (tmtt) cc_final: 0.8112 (mptt) REVERT: E 221 THR cc_start: 0.8080 (p) cc_final: 0.7701 (m) REVERT: F 411 GLN cc_start: 0.8720 (OUTLIER) cc_final: 0.8047 (pm20) REVERT: F 472 MET cc_start: 0.5387 (OUTLIER) cc_final: 0.4615 (tmm) REVERT: H 43 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.8220 (ptp-170) REVERT: G 43 ARG cc_start: 0.8378 (ptt180) cc_final: 0.7863 (ptp-170) REVERT: J 5 VAL cc_start: 0.8051 (t) cc_final: 0.7819 (p) outliers start: 36 outliers final: 16 residues processed: 188 average time/residue: 0.6575 time to fit residues: 136.2172 Evaluate side-chains 179 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 158 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain B residue 411 GLN Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 17 LYS Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain F residue 388 THR Chi-restraints excluded: chain F residue 411 GLN Chi-restraints excluded: chain F residue 472 MET Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 43 ARG Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 79 SER Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain I residue 79 SER Chi-restraints excluded: chain K residue 27 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 174 optimal weight: 0.0670 chunk 79 optimal weight: 3.9990 chunk 42 optimal weight: 20.0000 chunk 189 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 86 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 159 optimal weight: 7.9990 chunk 129 optimal weight: 9.9990 chunk 98 optimal weight: 0.9990 overall best weight: 1.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 442 GLN E 200 GLN L 27 GLN ** J 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.189808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.145618 restraints weight = 58059.072| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 3.42 r_work: 0.3508 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3517 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3517 r_free = 0.3517 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3517 r_free = 0.3517 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.3517 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 16248 Z= 0.227 Angle : 0.677 8.819 22113 Z= 0.344 Chirality : 0.045 0.155 2577 Planarity : 0.005 0.083 2793 Dihedral : 5.891 36.950 2799 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.94 % Favored : 93.91 % Rotamer: Outliers : 2.63 % Allowed : 15.20 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.51 (0.18), residues: 2013 helix: 0.61 (0.32), residues: 273 sheet: -0.57 (0.25), residues: 477 loop : -1.61 (0.16), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 80 TYR 0.015 0.002 TYR E 263 PHE 0.022 0.002 PHE C 193 TRP 0.012 0.002 TRP G 52 HIS 0.006 0.001 HIS A 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00550 / 0.23 (16200) covalent geometry : angle 0.65925 / 0.34 (21987) SS BOND : bond 0.00344 / 0.22 ( 18) SS BOND : angle 1.80570 / 1.31 ( 36) hydrogen bonds : bond 0.03793 / 2.56 ( 469) hydrogen bonds : angle 5.21816 / 3.79 ( 1341) link_BETA1-4 : bond 0.00267 / 0.15 ( 9) link_BETA1-4 : angle 1.16690 / 0.71 ( 27) link_NAG-ASN : bond 0.00288 / 0.19 ( 21) link_NAG-ASN : angle 2.56171 / 1.66 ( 63) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 164 time to evaluate : 0.591 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8112 (tmtt) cc_final: 0.7693 (ttpt) REVERT: A 75 LYS cc_start: 0.8330 (tmtt) cc_final: 0.8113 (mptt) REVERT: A 221 THR cc_start: 0.8136 (p) cc_final: 0.7716 (m) REVERT: B 433 ASP cc_start: 0.7655 (m-30) cc_final: 0.7436 (m-30) REVERT: C 17 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7872 (tmtt) REVERT: C 198 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.6833 (pm20) REVERT: D 433 ASP cc_start: 0.7569 (m-30) cc_final: 0.7352 (m-30) REVERT: D 435 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.7647 (tmm-80) REVERT: E 221 THR cc_start: 0.8135 (p) cc_final: 0.7752 (m) REVERT: F 472 MET cc_start: 0.5288 (OUTLIER) cc_final: 0.4534 (tmm) REVERT: G 23 CYS cc_start: 0.8081 (OUTLIER) cc_final: 0.7545 (t) REVERT: I 26 SER cc_start: 0.8091 (m) cc_final: 0.7877 (m) REVERT: J 5 VAL cc_start: 0.8087 (t) cc_final: 0.7859 (p) REVERT: K 122 THR cc_start: 0.8307 (OUTLIER) cc_final: 0.7865 (m) outliers start: 40 outliers final: 19 residues processed: 194 average time/residue: 0.6103 time to fit residues: 131.0877 Evaluate side-chains 186 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 161 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain B residue 411 GLN Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 17 LYS Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain D residue 435 ARG Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain F residue 388 THR Chi-restraints excluded: chain F residue 472 MET Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 116 ASP Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 79 SER Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 122 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 100 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 121 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 191 optimal weight: 10.0000 chunk 193 optimal weight: 4.9990 chunk 7 optimal weight: 0.0980 chunk 82 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 442 GLN C 200 GLN E 200 GLN L 27 GLN ** J 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.193362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.148124 restraints weight = 69934.461| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 3.89 r_work: 0.3533 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3564 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3564 r_free = 0.3564 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3564 r_free = 0.3564 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.3564 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16248 Z= 0.120 Angle : 0.578 7.695 22113 Z= 0.295 Chirality : 0.042 0.152 2577 Planarity : 0.004 0.050 2793 Dihedral : 5.332 32.192 2799 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.69 % Allowed : 15.73 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.15 (0.18), residues: 2013 helix: 1.25 (0.33), residues: 273 sheet: -0.46 (0.24), residues: 498 loop : -1.41 (0.16), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 88 TYR 0.016 0.001 TYR J 37 PHE 0.014 0.001 PHE C 193 TRP 0.011 0.001 TRP G 52 HIS 0.003 0.001 HIS C 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (16200) covalent geometry : angle 0.56279 / 0.29 (21987) SS BOND : bond 0.00230 / 0.13 ( 18) SS BOND : angle 1.25911 / 0.93 ( 36) hydrogen bonds : bond 0.03149 / 2.13 ( 469) hydrogen bonds : angle 4.91941 / 3.58 ( 1341) link_BETA1-4 : bond 0.00313 / 0.17 ( 9) link_BETA1-4 : angle 1.17036 / 0.71 ( 27) link_NAG-ASN : bond 0.00234 / 0.14 ( 21) link_NAG-ASN : angle 2.29527 / 1.50 ( 63) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 166 time to evaluate : 0.647 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7638 (ttpt) REVERT: A 221 THR cc_start: 0.8089 (p) cc_final: 0.7676 (m) REVERT: B 422 ASN cc_start: 0.7559 (OUTLIER) cc_final: 0.7257 (m110) REVERT: B 433 ASP cc_start: 0.7798 (m-30) cc_final: 0.7564 (m-30) REVERT: E 221 THR cc_start: 0.8097 (p) cc_final: 0.7694 (m) REVERT: F 411 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.7958 (pm20) REVERT: F 472 MET cc_start: 0.5253 (OUTLIER) cc_final: 0.4503 (tmm) REVERT: G 12 VAL cc_start: 0.8015 (t) cc_final: 0.7784 (m) REVERT: K 122 THR cc_start: 0.8326 (OUTLIER) cc_final: 0.7959 (m) outliers start: 41 outliers final: 15 residues processed: 197 average time/residue: 0.6181 time to fit residues: 135.1185 Evaluate side-chains 177 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 157 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain B residue 411 GLN Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain F residue 411 GLN Chi-restraints excluded: chain F residue 472 MET Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 79 SER Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain I residue 79 SER Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain K residue 122 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 17 optimal weight: 0.6980 chunk 110 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 161 optimal weight: 2.9990 chunk 153 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 126 optimal weight: 0.6980 chunk 128 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 GLN ** J 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.192131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.144580 restraints weight = 61487.151| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 4.10 r_work: 0.3515 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3412 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3412 r_free = 0.3412 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3412 r_free = 0.3412 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.3412 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16248 Z= 0.149 Angle : 0.605 7.937 22113 Z= 0.307 Chirality : 0.043 0.239 2577 Planarity : 0.005 0.060 2793 Dihedral : 5.282 32.806 2799 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.46 % Allowed : 16.90 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.09 (0.18), residues: 2013 helix: 1.55 (0.34), residues: 264 sheet: -0.41 (0.25), residues: 474 loop : -1.40 (0.16), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 88 TYR 0.020 0.002 TYR J 37 PHE 0.016 0.002 PHE C 193 TRP 0.012 0.001 TRP G 52 HIS 0.004 0.001 HIS A 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 (16200) covalent geometry : angle 0.58991 / 0.30 (21987) SS BOND : bond 0.00222 / 0.14 ( 18) SS BOND : angle 1.43415 / 1.06 ( 36) hydrogen bonds : bond 0.03286 / 2.22 ( 469) hydrogen bonds : angle 4.93953 / 3.59 ( 1341) link_BETA1-4 : bond 0.00272 / 0.15 ( 9) link_BETA1-4 : angle 1.12668 / 0.68 ( 27) link_NAG-ASN : bond 0.00215 / 0.14 ( 21) link_NAG-ASN : angle 2.31769 / 1.51 ( 63) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 158 time to evaluate : 0.570 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8076 (OUTLIER) cc_final: 0.7642 (ttpt) REVERT: A 38 LYS cc_start: 0.8161 (mtpp) cc_final: 0.7566 (ttmt) REVERT: A 221 THR cc_start: 0.8094 (p) cc_final: 0.7690 (m) REVERT: B 422 ASN cc_start: 0.7528 (OUTLIER) cc_final: 0.7200 (m110) REVERT: B 433 ASP cc_start: 0.7731 (m-30) cc_final: 0.7481 (m-30) REVERT: C 198 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6767 (pm20) REVERT: E 128 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7705 (mt-10) REVERT: E 221 THR cc_start: 0.8071 (p) cc_final: 0.7679 (m) REVERT: E 299 LYS cc_start: 0.8091 (OUTLIER) cc_final: 0.7883 (mmpt) REVERT: F 411 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.7937 (pm20) REVERT: F 472 MET cc_start: 0.5312 (OUTLIER) cc_final: 0.4535 (tmm) REVERT: H 43 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.8272 (ptp-170) REVERT: G 12 VAL cc_start: 0.8012 (t) cc_final: 0.7789 (m) REVERT: G 23 CYS cc_start: 0.8068 (OUTLIER) cc_final: 0.7491 (t) REVERT: K 122 THR cc_start: 0.8362 (OUTLIER) cc_final: 0.7986 (m) outliers start: 37 outliers final: 21 residues processed: 184 average time/residue: 0.6390 time to fit residues: 130.3123 Evaluate side-chains 185 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 155 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain B residue 411 GLN Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain E residue 299 LYS Chi-restraints excluded: chain F residue 411 GLN Chi-restraints excluded: chain F residue 472 MET Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 43 ARG Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 79 SER Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain I residue 79 SER Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 122 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 47 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 142 optimal weight: 0.8980 chunk 41 optimal weight: 9.9990 chunk 134 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 152 optimal weight: 8.9990 chunk 193 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 120 GLN J 44 GLN J 120 GLN K 105 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.190668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.144797 restraints weight = 62460.182| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 3.78 r_work: 0.3503 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3516 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3516 r_free = 0.3516 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3516 r_free = 0.3516 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| r_final: 0.3516 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 16248 Z= 0.205 Angle : 0.653 8.657 22113 Z= 0.332 Chirality : 0.045 0.199 2577 Planarity : 0.005 0.076 2793 Dihedral : 5.491 35.045 2799 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.59 % Favored : 94.36 % Rotamer: Outliers : 2.57 % Allowed : 17.08 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.09 (0.18), residues: 2013 helix: 1.19 (0.33), residues: 273 sheet: -0.42 (0.25), residues: 498 loop : -1.34 (0.16), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 88 TYR 0.019 0.002 TYR J 37 PHE 0.020 0.002 PHE C 193 TRP 0.012 0.002 TRP G 52 HIS 0.005 0.001 HIS A 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.20 (16200) covalent geometry : angle 0.63702 / 0.33 (21987) SS BOND : bond 0.00304 / 0.19 ( 18) SS BOND : angle 1.69593 / 1.25 ( 36) hydrogen bonds : bond 0.03603 / 2.44 ( 469) hydrogen bonds : angle 5.05164 / 3.67 ( 1341) link_BETA1-4 : bond 0.00240 / 0.13 ( 9) link_BETA1-4 : angle 1.13423 / 0.69 ( 27) link_NAG-ASN : bond 0.00231 / 0.15 ( 21) link_NAG-ASN : angle 2.46373 / 1.59 ( 63) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 159 time to evaluate : 0.681 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7718 (ttpt) REVERT: A 221 THR cc_start: 0.8132 (p) cc_final: 0.7723 (m) REVERT: B 422 ASN cc_start: 0.7684 (OUTLIER) cc_final: 0.7328 (m110) REVERT: B 433 ASP cc_start: 0.7737 (m-30) cc_final: 0.7503 (m-30) REVERT: C 17 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7882 (ttpt) REVERT: C 198 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.6864 (pm20) REVERT: D 390 GLU cc_start: 0.7440 (pp20) cc_final: 0.7178 (pp20) REVERT: E 128 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7729 (mt-10) REVERT: E 221 THR cc_start: 0.8141 (p) cc_final: 0.7748 (m) REVERT: E 299 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7874 (mmpt) REVERT: F 411 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.7900 (pm20) REVERT: F 472 MET cc_start: 0.5369 (OUTLIER) cc_final: 0.4587 (tmm) REVERT: G 23 CYS cc_start: 0.8089 (OUTLIER) cc_final: 0.7579 (t) REVERT: I 26 SER cc_start: 0.8074 (m) cc_final: 0.7862 (m) REVERT: J 120 GLN cc_start: 0.6915 (OUTLIER) cc_final: 0.6712 (pm20) REVERT: K 122 THR cc_start: 0.8372 (OUTLIER) cc_final: 0.7961 (m) outliers start: 39 outliers final: 21 residues processed: 186 average time/residue: 0.6571 time to fit residues: 134.9966 Evaluate side-chains 180 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 149 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain B residue 411 GLN Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 17 LYS Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain E residue 299 LYS Chi-restraints excluded: chain F residue 411 GLN Chi-restraints excluded: chain F residue 472 MET Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 79 SER Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain I residue 79 SER Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 120 GLN Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 122 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 42 optimal weight: 20.0000 chunk 137 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 49 optimal weight: 0.1980 chunk 85 optimal weight: 8.9990 chunk 169 optimal weight: 10.0000 chunk 118 optimal weight: 0.5980 chunk 194 optimal weight: 2.9990 chunk 44 optimal weight: 0.4980 chunk 186 optimal weight: 9.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 442 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.193835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.148804 restraints weight = 71436.660| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 3.90 r_work: 0.3536 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3570 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3570 r_free = 0.3570 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3570 r_free = 0.3570 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| r_final: 0.3570 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16248 Z= 0.110 Angle : 0.577 7.402 22113 Z= 0.294 Chirality : 0.042 0.214 2577 Planarity : 0.004 0.050 2793 Dihedral : 5.155 32.089 2799 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.11 % Allowed : 17.25 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.87 (0.18), residues: 2013 helix: 1.62 (0.33), residues: 273 sheet: -0.35 (0.25), residues: 498 loop : -1.22 (0.16), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 88 TYR 0.021 0.001 TYR J 37 PHE 0.012 0.001 PHE C 193 TRP 0.010 0.001 TRP G 52 HIS 0.003 0.001 HIS C 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (16200) covalent geometry : angle 0.56260 / 0.29 (21987) SS BOND : bond 0.00151 / 0.10 ( 18) SS BOND : angle 1.19797 / 0.88 ( 36) hydrogen bonds : bond 0.03063 / 2.07 ( 469) hydrogen bonds : angle 4.87775 / 3.55 ( 1341) link_BETA1-4 : bond 0.00304 / 0.17 ( 9) link_BETA1-4 : angle 1.16239 / 0.69 ( 27) link_NAG-ASN : bond 0.00216 / 0.13 ( 21) link_NAG-ASN : angle 2.24598 / 1.47 ( 63) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 149 time to evaluate : 0.700 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7720 (ttpt) REVERT: A 221 THR cc_start: 0.8088 (p) cc_final: 0.7685 (m) REVERT: B 422 ASN cc_start: 0.7541 (OUTLIER) cc_final: 0.7224 (m110) REVERT: B 433 ASP cc_start: 0.7767 (m-30) cc_final: 0.7538 (m-30) REVERT: C 17 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7857 (ttpt) REVERT: C 198 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.6772 (pm20) REVERT: D 390 GLU cc_start: 0.7416 (pp20) cc_final: 0.7147 (pp20) REVERT: E 128 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7805 (mt-10) REVERT: E 221 THR cc_start: 0.8073 (p) cc_final: 0.7672 (m) REVERT: F 411 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.7891 (pm20) REVERT: F 472 MET cc_start: 0.5425 (OUTLIER) cc_final: 0.4646 (tmm) REVERT: G 19 LEU cc_start: -0.2122 (OUTLIER) cc_final: -0.2538 (tp) REVERT: G 23 CYS cc_start: 0.8071 (OUTLIER) cc_final: 0.7497 (t) REVERT: K 122 THR cc_start: 0.8365 (OUTLIER) cc_final: 0.8015 (m) outliers start: 31 outliers final: 15 residues processed: 172 average time/residue: 0.6738 time to fit residues: 127.8288 Evaluate side-chains 170 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain B residue 411 GLN Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 17 LYS Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain D residue 411 GLN Chi-restraints excluded: chain F residue 411 GLN Chi-restraints excluded: chain F residue 472 MET Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain L residue 79 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain I residue 79 SER Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain K residue 122 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 28 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 166 optimal weight: 0.9990 chunk 100 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 146 optimal weight: 3.9990 chunk 153 optimal weight: 7.9990 chunk 81 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 92 optimal weight: 0.5980 chunk 72 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 120 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.193402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.148801 restraints weight = 69823.135| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 3.79 r_work: 0.3532 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3568 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3568 r_free = 0.3568 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3568 r_free = 0.3568 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| r_final: 0.3568 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16248 Z= 0.131 Angle : 0.587 7.936 22113 Z= 0.298 Chirality : 0.042 0.184 2577 Planarity : 0.005 0.053 2793 Dihedral : 5.100 32.889 2799 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.87 % Allowed : 17.54 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.80 (0.18), residues: 2013 helix: 1.44 (0.33), residues: 282 sheet: -0.31 (0.24), residues: 498 loop : -1.13 (0.16), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 88 TYR 0.019 0.002 TYR G 37 PHE 0.015 0.001 PHE C 193 TRP 0.009 0.001 TRP G 52 HIS 0.004 0.001 HIS A 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 (16200) covalent geometry : angle 0.57183 / 0.29 (21987) SS BOND : bond 0.00191 / 0.12 ( 18) SS BOND : angle 1.31475 / 0.97 ( 36) hydrogen bonds : bond 0.03132 / 2.11 ( 469) hydrogen bonds : angle 4.86311 / 3.54 ( 1341) link_BETA1-4 : bond 0.00294 / 0.16 ( 9) link_BETA1-4 : angle 1.11475 / 0.67 ( 27) link_NAG-ASN : bond 0.00190 / 0.12 ( 21) link_NAG-ASN : angle 2.25817 / 1.46 ( 63) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 150 time to evaluate : 0.631 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7702 (ttpt) REVERT: A 221 THR cc_start: 0.8098 (p) cc_final: 0.7696 (m) REVERT: B 422 ASN cc_start: 0.7555 (OUTLIER) cc_final: 0.7235 (m110) REVERT: B 433 ASP cc_start: 0.7749 (m-30) cc_final: 0.7526 (m-30) REVERT: C 17 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7859 (ttpt) REVERT: C 198 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.6772 (pm20) REVERT: D 390 GLU cc_start: 0.7427 (pp20) cc_final: 0.7129 (pp20) REVERT: E 128 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7749 (mt-10) REVERT: E 221 THR cc_start: 0.8029 (p) cc_final: 0.7641 (m) REVERT: F 411 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.7896 (pm20) REVERT: F 472 MET cc_start: 0.5373 (OUTLIER) cc_final: 0.4597 (tmm) REVERT: G 19 LEU cc_start: -0.2088 (OUTLIER) cc_final: -0.2457 (tp) REVERT: G 23 CYS cc_start: 0.8031 (OUTLIER) cc_final: 0.7474 (t) REVERT: K 122 THR cc_start: 0.8372 (OUTLIER) cc_final: 0.8016 (m) outliers start: 27 outliers final: 15 residues processed: 169 average time/residue: 0.6782 time to fit residues: 126.2256 Evaluate side-chains 174 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain B residue 411 GLN Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 17 LYS Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain D residue 411 GLN Chi-restraints excluded: chain F residue 411 GLN Chi-restraints excluded: chain F residue 472 MET Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain L residue 79 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain I residue 79 SER Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain K residue 122 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 106 optimal weight: 0.1980 chunk 90 optimal weight: 4.9990 chunk 179 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 191 optimal weight: 10.0000 chunk 30 optimal weight: 0.0470 chunk 158 optimal weight: 3.9990 chunk 137 optimal weight: 0.9980 chunk 172 optimal weight: 0.7980 chunk 173 optimal weight: 10.0000 chunk 161 optimal weight: 2.9990 overall best weight: 1.0080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 105 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.192946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.147130 restraints weight = 66564.806| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 3.85 r_work: 0.3525 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3559 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3559 r_free = 0.3559 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3559 r_free = 0.3559 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| r_final: 0.3559 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16248 Z= 0.147 Angle : 0.603 8.217 22113 Z= 0.305 Chirality : 0.043 0.200 2577 Planarity : 0.005 0.058 2793 Dihedral : 5.138 32.575 2799 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.16 % Allowed : 17.31 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.79 (0.18), residues: 2013 helix: 1.40 (0.33), residues: 282 sheet: -0.30 (0.24), residues: 498 loop : -1.10 (0.16), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 88 TYR 0.018 0.002 TYR G 37 PHE 0.016 0.001 PHE C 193 TRP 0.010 0.001 TRP G 52 HIS 0.004 0.001 HIS A 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (16200) covalent geometry : angle 0.58813 / 0.30 (21987) SS BOND : bond 0.00218 / 0.14 ( 18) SS BOND : angle 1.40123 / 1.04 ( 36) hydrogen bonds : bond 0.03228 / 2.17 ( 469) hydrogen bonds : angle 4.88036 / 3.55 ( 1341) link_BETA1-4 : bond 0.00302 / 0.16 ( 9) link_BETA1-4 : angle 1.08126 / 0.65 ( 27) link_NAG-ASN : bond 0.00194 / 0.12 ( 21) link_NAG-ASN : angle 2.28709 / 1.48 ( 63) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6899.92 seconds wall clock time: 118 minutes 9.44 seconds (7089.44 seconds total)