Starting phenix.real_space_refine on Fri Jun 5 23:13:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9x5w_66599/06_2026/9x5w_66599.cif Found real_map, /net/cci-nas-00/data/ceres_data/9x5w_66599/06_2026/9x5w_66599.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 { model { file = "/net/cci-nas-00/data/ceres_data/9x5w_66599/06_2026/9x5w_66599.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9x5w_66599/06_2026/9x5w_66599.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9x5w_66599/06_2026/9x5w_66599.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9x5w_66599/06_2026/9x5w_66599.map" } 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= 0.075 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 10051 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 69 5.16 5 C 9984 2.51 5 N 2742 2.21 5 O 3183 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 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: 15978 Number of models: 1 Model: "" Number of chains: 27 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: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 988 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 2, 'TRANS': 122} Chain: "L" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 807 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "G" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 988 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 2, 'TRANS': 122} Chain: "I" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 807 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "J" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 988 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 2, 'TRANS': 122} Chain: "K" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 807 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} 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: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 5.50, per 1000 atoms: 0.34 Number of scatterers: 15978 At special positions: 0 Unit cell: (136.95, 148.57, 163.51, 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 69 16.00 O 3183 8.00 N 2742 7.00 C 9984 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 57 " distance=2.04 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 104 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 104 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 104 " distance=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 104 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 104 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 104 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG 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 V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG A 401 " - " ASN A 233 " " NAG A 402 " - " ASN A 25 " " NAG A 403 " - " ASN A 59 " " NAG C 401 " - " ASN C 233 " " NAG C 402 " - " ASN C 25 " " NAG C 403 " - " ASN C 59 " " NAG E 401 " - " ASN E 233 " " NAG E 402 " - " ASN E 25 " " NAG E 403 " - " ASN E 59 " " NAG M 1 " - " ASN A 145 " " NAG N 1 " - " ASN A 304 " " NAG O 1 " - " ASN A 333 " " NAG P 1 " - " ASN A 197 " " NAG Q 1 " - " ASN C 145 " " NAG R 1 " - " ASN C 304 " " NAG S 1 " - " ASN C 333 " " NAG T 1 " - " ASN C 197 " " NAG U 1 " - " ASN E 145 " " NAG V 1 " - " ASN E 304 " " NAG W 1 " - " ASN E 333 " " NAG X 1 " - " ASN E 197 " Time building additional restraints: 1.58 Conformation dependent library (CDL) restraints added in 984.8 milliseconds 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3666 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 42 sheets defined 15.9% alpha, 26.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 61 through 68 Processing helix chain 'A' and resid 98 through 102 removed outlier: 3.501A pdb=" N ARG A 101 " --> pdb=" O MET A 98 " (cutoff:3.500A) removed outlier: 3.731A 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 126 through 130 removed outlier: 3.653A pdb=" N ALA A 130 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 205 Processing helix chain 'B' and resid 387 through 404 removed outlier: 3.900A pdb=" N ILE B 395 " --> pdb=" O ALA B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 460 removed outlier: 3.950A pdb=" N SER B 457 " --> pdb=" O GLY B 453 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU B 458 " --> pdb=" O ILE B 454 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ASP B 459 " --> pdb=" O ILE B 455 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU B 460 " --> pdb=" O ASN B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 471 removed outlier: 4.121A pdb=" N GLU B 466 " --> pdb=" O LEU B 462 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS B 471 " --> pdb=" O ARG B 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 68 Processing helix chain 'C' and resid 98 through 102 removed outlier: 3.501A pdb=" N ARG C 101 " --> pdb=" O MET C 98 " (cutoff:3.500A) removed outlier: 3.732A 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 126 through 130 removed outlier: 3.653A pdb=" N ALA C 130 " --> pdb=" O ALA C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 205 Processing helix chain 'D' and resid 387 through 404 removed outlier: 3.900A pdb=" N ILE D 395 " --> pdb=" O ALA D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 460 removed outlier: 3.948A pdb=" N SER D 457 " --> pdb=" O GLY D 453 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU D 458 " --> pdb=" O ILE D 454 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASP D 459 " --> pdb=" O ILE D 455 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU D 460 " --> pdb=" O ASN D 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 471 removed outlier: 4.121A pdb=" N GLU D 466 " --> pdb=" O LEU D 462 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS D 471 " --> pdb=" O ARG D 467 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 68 Processing helix chain 'E' and resid 98 through 102 removed outlier: 3.501A pdb=" N ARG E 101 " --> pdb=" O MET E 98 " (cutoff:3.500A) removed outlier: 3.731A 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 126 through 130 removed outlier: 3.654A pdb=" N ALA E 130 " --> pdb=" O ALA E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 205 Processing helix chain 'F' and resid 387 through 404 removed outlier: 3.900A pdb=" N ILE F 395 " --> pdb=" O ALA F 391 " (cutoff:3.500A) Processing helix chain 'F' and resid 421 through 460 removed outlier: 3.949A pdb=" N SER F 457 " --> pdb=" O GLY F 453 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU F 458 " --> pdb=" O ILE F 454 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASP F 459 " --> pdb=" O ILE F 455 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU F 460 " --> pdb=" O ASN F 456 " (cutoff:3.500A) Processing helix chain 'F' and resid 460 through 471 removed outlier: 4.121A pdb=" N GLU F 466 " --> pdb=" O LEU F 462 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS F 471 " --> pdb=" O ARG F 467 " (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 30 through 31 Processing sheet with id=AA3, first strand: chain 'A' and resid 43 through 44 removed outlier: 5.912A 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: 7.364A pdb=" N VAL A 190 " --> pdb=" O PRO A 270 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ILE A 267 " --> pdb=" O ALA A 159 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N TRP A 158 " --> pdb=" O GLY A 138 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 116 through 119 Processing sheet with id=AA7, first strand: chain 'A' and resid 173 through 177 Processing sheet with id=AA8, first strand: chain 'A' and resid 301 through 303 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 30 through 31 Processing sheet with id=AB3, first strand: chain 'C' and resid 43 through 44 removed outlier: 5.922A 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: 7.363A pdb=" N VAL C 190 " --> pdb=" O PRO C 270 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ILE C 267 " --> pdb=" O ALA C 159 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N TRP C 158 " --> pdb=" O GLY C 138 " (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 303 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 30 through 31 Processing sheet with id=AC3, first strand: chain 'E' and resid 43 through 44 removed outlier: 5.915A 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: 7.363A pdb=" N VAL E 190 " --> pdb=" O PRO E 270 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ILE E 267 " --> pdb=" O ALA E 159 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N TRP E 158 " --> pdb=" O GLY E 138 " (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 303 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 12 through 13 removed outlier: 6.980A pdb=" N MET H 39 " --> pdb=" O THR H 55 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N THR H 55 " --> pdb=" O MET H 39 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TRP H 41 " --> pdb=" O VAL H 53 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 12 through 13 removed outlier: 6.446A pdb=" N CYS H 104 " --> pdb=" O TRP H 118 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N TRP H 118 " --> pdb=" O CYS H 104 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ARG H 106 " --> pdb=" O ASP H 116 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AD5, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.540A pdb=" N GLU L 125 " --> pdb=" O VAL L 11 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR L 122 " --> pdb=" O TYR L 102 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N GLN L 43 " --> pdb=" O LEU L 52 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N LEU L 52 " --> pdb=" O GLN L 43 " (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 12 through 13 removed outlier: 6.980A pdb=" N MET G 39 " --> pdb=" O THR G 55 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N THR G 55 " --> pdb=" O MET G 39 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N TRP G 41 " --> pdb=" O VAL G 53 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 12 through 13 removed outlier: 6.446A pdb=" N CYS G 104 " --> pdb=" O TRP G 118 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N TRP G 118 " --> pdb=" O CYS G 104 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ARG G 106 " --> pdb=" O ASP G 116 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 5 through 6 Processing sheet with id=AE1, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.540A pdb=" N GLU I 125 " --> pdb=" O VAL I 11 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR I 122 " --> pdb=" O TYR I 102 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N GLN I 43 " --> pdb=" O LEU I 52 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N LEU I 52 " --> pdb=" O GLN I 43 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AE3, first strand: chain 'J' and resid 12 through 13 removed outlier: 6.980A pdb=" N MET J 39 " --> pdb=" O THR J 55 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N THR J 55 " --> pdb=" O MET J 39 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N TRP J 41 " --> pdb=" O VAL J 53 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 12 through 13 removed outlier: 6.445A pdb=" N CYS J 104 " --> pdb=" O TRP J 118 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N TRP J 118 " --> pdb=" O CYS J 104 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ARG J 106 " --> pdb=" O ASP J 116 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 5 through 6 Processing sheet with id=AE6, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.540A pdb=" N GLU K 125 " --> pdb=" O VAL K 11 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR K 122 " --> pdb=" O TYR K 102 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N GLN K 43 " --> pdb=" O LEU K 52 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N LEU K 52 " --> pdb=" O GLN K 43 " (cutoff:3.500A) 564 hydrogen bonds defined for protein. 1458 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: 2.89 Time building geometry restraints manager: 2.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5162 1.34 - 1.47: 3911 1.47 - 1.59: 7136 1.59 - 1.72: 3 1.72 - 1.84: 96 Bond restraints: 16308 Sorted by residual: bond pdb=" C1 NAG X 1 " pdb=" O5 NAG X 1 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 8.01e+00 bond pdb=" C1 NAG T 1 " pdb=" O5 NAG T 1 " ideal model delta sigma weight residual 1.406 1.462 -0.056 2.00e-02 2.50e+03 7.91e+00 bond pdb=" C1 NAG P 1 " pdb=" O5 NAG P 1 " ideal model delta sigma weight residual 1.406 1.462 -0.056 2.00e-02 2.50e+03 7.72e+00 bond pdb=" CB GLU I 97 " pdb=" CG GLU I 97 " ideal model delta sigma weight residual 1.520 1.595 -0.075 3.00e-02 1.11e+03 6.30e+00 bond pdb=" CB GLU K 97 " pdb=" CG GLU K 97 " ideal model delta sigma weight residual 1.520 1.595 -0.075 3.00e-02 1.11e+03 6.24e+00 ... (remaining 16303 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.86: 21882 3.86 - 7.71: 205 7.71 - 11.57: 17 11.57 - 15.43: 9 15.43 - 19.28: 6 Bond angle restraints: 22119 Sorted by residual: angle pdb=" CA GLU L 97 " pdb=" CB GLU L 97 " pdb=" CG GLU L 97 " ideal model delta sigma weight residual 114.10 133.38 -19.28 2.00e+00 2.50e-01 9.30e+01 angle pdb=" CA GLU K 97 " pdb=" CB GLU K 97 " pdb=" CG GLU K 97 " ideal model delta sigma weight residual 114.10 133.33 -19.23 2.00e+00 2.50e-01 9.25e+01 angle pdb=" CA GLU I 97 " pdb=" CB GLU I 97 " pdb=" CG GLU I 97 " ideal model delta sigma weight residual 114.10 133.30 -19.20 2.00e+00 2.50e-01 9.22e+01 angle pdb=" CA GLU J 97 " pdb=" CB GLU J 97 " pdb=" CG GLU J 97 " ideal model delta sigma weight residual 114.10 131.58 -17.48 2.00e+00 2.50e-01 7.64e+01 angle pdb=" CA GLU G 97 " pdb=" CB GLU G 97 " pdb=" CG GLU G 97 " ideal model delta sigma weight residual 114.10 131.57 -17.47 2.00e+00 2.50e-01 7.63e+01 ... (remaining 22114 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 9267 17.58 - 35.17: 771 35.17 - 52.75: 192 52.75 - 70.33: 18 70.33 - 87.92: 9 Dihedral angle restraints: 10257 sinusoidal: 4503 harmonic: 5754 Sorted by residual: dihedral pdb=" CB CYS A 60 " pdb=" SG CYS A 60 " pdb=" SG CYS A 72 " pdb=" CB CYS A 72 " ideal model delta sinusoidal sigma weight residual -86.00 -140.28 54.28 1 1.00e+01 1.00e-02 4.00e+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 -140.26 54.26 1 1.00e+01 1.00e-02 3.99e+01 dihedral pdb=" CB CYS C 60 " pdb=" SG CYS C 60 " pdb=" SG CYS C 72 " pdb=" CB CYS C 72 " ideal model delta sinusoidal sigma weight residual -86.00 -140.25 54.25 1 1.00e+01 1.00e-02 3.99e+01 ... (remaining 10254 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2125 0.071 - 0.142: 390 0.142 - 0.213: 44 0.213 - 0.283: 0 0.283 - 0.354: 3 Chirality restraints: 2562 Sorted by residual: chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN C 197 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.75 0.35 2.00e-01 2.50e+01 3.14e+00 chirality pdb=" C1 NAG X 1 " pdb=" ND2 ASN E 197 " pdb=" C2 NAG X 1 " pdb=" O5 NAG X 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.75 0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN A 197 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.75 0.35 2.00e-01 2.50e+01 3.10e+00 ... (remaining 2559 not shown) Planarity restraints: 2829 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER J 110 " -0.015 2.00e-02 2.50e+03 2.92e-02 8.53e+00 pdb=" C SER J 110 " 0.051 2.00e-02 2.50e+03 pdb=" O SER J 110 " -0.018 2.00e-02 2.50e+03 pdb=" N TYR J 111 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER H 110 " -0.015 2.00e-02 2.50e+03 2.91e-02 8.48e+00 pdb=" C SER H 110 " 0.050 2.00e-02 2.50e+03 pdb=" O SER H 110 " -0.018 2.00e-02 2.50e+03 pdb=" N TYR H 111 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER G 110 " -0.015 2.00e-02 2.50e+03 2.88e-02 8.32e+00 pdb=" C SER G 110 " 0.050 2.00e-02 2.50e+03 pdb=" O SER G 110 " -0.018 2.00e-02 2.50e+03 pdb=" N TYR G 111 " -0.017 2.00e-02 2.50e+03 ... (remaining 2826 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.27: 5 2.27 - 2.93: 6456 2.93 - 3.59: 20583 3.59 - 4.24: 38505 4.24 - 4.90: 64097 Nonbonded interactions: 129646 Sorted by model distance: nonbonded pdb=" OE2 GLU G 6 " pdb=" CB CYS G 104 " model vdw 1.615 3.440 nonbonded pdb=" OE2 GLU J 6 " pdb=" CB CYS J 104 " model vdw 1.615 3.440 nonbonded pdb=" OE2 GLU H 6 " pdb=" CB CYS H 104 " model vdw 1.616 3.440 nonbonded pdb=" O SER I 7 " pdb=" OG SER I 22 " model vdw 2.024 3.040 nonbonded pdb=" O SER K 7 " pdb=" OG SER K 22 " model vdw 2.026 3.040 ... (remaining 129641 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: 0.03 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 403)) selection = (chain 'C' and (resid 5 through 38 or resid 40 through 42 or resid 44 through 30 \ 5 or resid 307 through 403)) selection = (chain 'E' and (resid 5 through 38 or resid 40 through 42 or resid 44 through 30 \ 5 or resid 307 through 403)) } 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' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 4.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.450 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:6.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 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 : 0.006 0.075 16362 Z= 0.286 Angle : 1.078 19.285 22260 Z= 0.561 Chirality : 0.055 0.354 2562 Planarity : 0.007 0.056 2808 Dihedral : 13.372 87.918 6528 Min Nonbonded Distance : 1.615 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.57 % Allowed : 4.72 % Favored : 93.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.69 (0.16), residues: 2010 helix: -2.16 (0.23), residues: 276 sheet: -0.89 (0.23), residues: 456 loop : -2.14 (0.14), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG H 95 TYR 0.018 0.002 TYR K 107 PHE 0.022 0.003 PHE A 193 TRP 0.015 0.002 TRP J 57 HIS 0.009 0.002 HIS H 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00642 / 0.29 (16308) covalent geometry : angle 1.04474 / 0.55 (22119) SS BOND : bond 0.00643 / 0.45 ( 21) SS BOND : angle 2.34304 / 1.65 ( 42) hydrogen bonds : bond 0.12507 / 8.43 ( 525) hydrogen bonds : angle 7.21562 / 4.99 ( 1458) link_BETA1-4 : bond 0.01017 / 0.65 ( 12) link_BETA1-4 : angle 1.53792 / 1.00 ( 36) link_NAG-ASN : bond 0.00790 / 0.45 ( 21) link_NAG-ASN : angle 4.71854 / 2.70 ( 63) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 270 time to evaluate : 0.636 Fit side-chains REVERT: A 64 ASP cc_start: 0.8547 (m-30) cc_final: 0.8334 (m-30) REVERT: C 45 LYS cc_start: 0.7821 (mttt) cc_final: 0.7553 (mmtp) REVERT: E 251 MET cc_start: 0.9116 (ptt) cc_final: 0.8866 (ptt) REVERT: H 39 MET cc_start: 0.8369 (mmm) cc_final: 0.8095 (mmm) REVERT: H 88 PHE cc_start: 0.8548 (m-80) cc_final: 0.8250 (m-80) REVERT: J 67 TYR cc_start: 0.8631 (m-80) cc_final: 0.8415 (m-80) REVERT: K 107 TYR cc_start: 0.7932 (p90) cc_final: 0.7724 (p90) outliers start: 27 outliers final: 14 residues processed: 294 average time/residue: 0.6221 time to fit residues: 201.6522 Evaluate side-chains 210 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 196 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.0040 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 HIS A 150 ASN A 171 ASN A 200 GLN A 218 ASN A 234 GLN A 253 GLN A 264 GLN C 40 HIS C 116 HIS C 171 ASN C 200 GLN C 218 ASN C 234 GLN C 253 GLN C 264 GLN E 166 ASN E 171 ASN E 218 ASN E 234 GLN E 253 GLN E 264 GLN H 38 ASN H 40 HIS H 58 ASN G 58 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.189528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.131576 restraints weight = 68496.866| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 4.82 r_work: 0.3155 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3263 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3263 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16362 Z= 0.136 Angle : 0.624 11.726 22260 Z= 0.313 Chirality : 0.043 0.191 2562 Planarity : 0.005 0.038 2808 Dihedral : 5.796 46.385 2878 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.10 % Allowed : 11.83 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.17), residues: 2010 helix: 0.23 (0.30), residues: 279 sheet: -0.60 (0.23), residues: 468 loop : -1.62 (0.15), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 88 TYR 0.020 0.002 TYR J 112C PHE 0.013 0.001 PHE E 193 TRP 0.011 0.001 TRP G 52 HIS 0.008 0.001 HIS H 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (16308) covalent geometry : angle 0.59380 / 0.31 (22119) SS BOND : bond 0.00370 / 0.25 ( 21) SS BOND : angle 1.66219 / 1.17 ( 42) hydrogen bonds : bond 0.03544 / 2.36 ( 525) hydrogen bonds : angle 5.69490 / 3.96 ( 1458) link_BETA1-4 : bond 0.00310 / 0.19 ( 12) link_BETA1-4 : angle 1.22263 / 0.81 ( 36) link_NAG-ASN : bond 0.00199 / 0.14 ( 21) link_NAG-ASN : angle 3.33258 / 1.91 ( 63) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 206 time to evaluate : 0.645 Fit side-chains revert: symmetry clash REVERT: A 64 ASP cc_start: 0.8642 (m-30) cc_final: 0.8252 (m-30) REVERT: A 146 ILE cc_start: 0.8310 (OUTLIER) cc_final: 0.8012 (pp) REVERT: A 234 GLN cc_start: 0.8299 (mt0) cc_final: 0.7952 (mt0) REVERT: A 313 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7660 (tm-30) REVERT: B 394 LYS cc_start: 0.7823 (mtpp) cc_final: 0.7444 (ttmm) REVERT: B 452 GLU cc_start: 0.7900 (tp30) cc_final: 0.7647 (tp30) REVERT: C 13 PRO cc_start: 0.6602 (Cg_endo) cc_final: 0.6385 (Cg_exo) REVERT: C 64 ASP cc_start: 0.8591 (m-30) cc_final: 0.8095 (m-30) REVERT: E 20 THR cc_start: 0.7845 (p) cc_final: 0.7377 (t) REVERT: E 146 ILE cc_start: 0.8508 (OUTLIER) cc_final: 0.8268 (pp) REVERT: E 251 MET cc_start: 0.9329 (ptt) cc_final: 0.9127 (ptt) REVERT: E 313 GLU cc_start: 0.8102 (tp30) cc_final: 0.7779 (tm-30) REVERT: F 400 ASN cc_start: 0.7225 (m110) cc_final: 0.6873 (m-40) REVERT: F 404 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.6951 (pt0) REVERT: H 40 HIS cc_start: 0.8252 (m-70) cc_final: 0.7995 (m-70) REVERT: H 88 PHE cc_start: 0.7832 (m-80) cc_final: 0.7447 (m-80) REVERT: G 88 PHE cc_start: 0.7414 (m-80) cc_final: 0.7166 (m-80) REVERT: J 67 TYR cc_start: 0.7866 (m-80) cc_final: 0.7586 (m-80) REVERT: K 107 TYR cc_start: 0.6833 (p90) cc_final: 0.6318 (p90) outliers start: 36 outliers final: 13 residues processed: 229 average time/residue: 0.5788 time to fit residues: 147.3776 Evaluate side-chains 206 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 190 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain D residue 418 ASP Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 286 SER Chi-restraints excluded: chain F residue 404 GLU Chi-restraints excluded: chain F residue 418 ASP Chi-restraints excluded: chain H residue 58 ASN Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain I residue 37 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 64 optimal weight: 6.9990 chunk 147 optimal weight: 9.9990 chunk 187 optimal weight: 6.9990 chunk 120 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 50 optimal weight: 0.4980 chunk 165 optimal weight: 0.3980 chunk 84 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN B 421 HIS B 456 ASN C 234 GLN D 421 HIS D 456 ASN E 166 ASN E 234 GLN E 242 GLN F 421 HIS F 456 ASN H 58 ASN L 105 GLN G 58 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.186846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.128592 restraints weight = 76651.426| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 4.86 r_work: 0.3117 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3230 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3230 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16362 Z= 0.164 Angle : 0.631 12.182 22260 Z= 0.314 Chirality : 0.044 0.177 2562 Planarity : 0.004 0.039 2808 Dihedral : 5.231 46.602 2870 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.33 % Allowed : 13.58 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.18), residues: 2010 helix: 1.04 (0.32), residues: 279 sheet: -0.23 (0.24), residues: 459 loop : -1.34 (0.16), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 88 TYR 0.015 0.002 TYR L 107 PHE 0.014 0.001 PHE C 193 TRP 0.011 0.002 TRP J 52 HIS 0.005 0.001 HIS C 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.16 (16308) covalent geometry : angle 0.59785 / 0.31 (22119) SS BOND : bond 0.00299 / 0.19 ( 21) SS BOND : angle 1.61291 / 1.16 ( 42) hydrogen bonds : bond 0.03395 / 2.26 ( 525) hydrogen bonds : angle 5.44979 / 3.80 ( 1458) link_BETA1-4 : bond 0.00482 / 0.32 ( 12) link_BETA1-4 : angle 1.21030 / 0.80 ( 36) link_NAG-ASN : bond 0.00233 / 0.13 ( 21) link_NAG-ASN : angle 3.55562 / 2.02 ( 63) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 197 time to evaluate : 0.678 Fit side-chains revert: symmetry clash REVERT: A 64 ASP cc_start: 0.8674 (m-30) cc_final: 0.8254 (m-30) REVERT: A 146 ILE cc_start: 0.8466 (OUTLIER) cc_final: 0.8229 (pp) REVERT: A 234 GLN cc_start: 0.8191 (mt0) cc_final: 0.7835 (mt0) REVERT: A 299 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7772 (mttm) REVERT: B 394 LYS cc_start: 0.7840 (mtpp) cc_final: 0.7507 (ttmm) REVERT: B 422 ASN cc_start: 0.7667 (OUTLIER) cc_final: 0.7258 (m110) REVERT: B 435 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7432 (tmm-80) REVERT: B 452 GLU cc_start: 0.7951 (tp30) cc_final: 0.7374 (mm-30) REVERT: B 458 GLU cc_start: 0.6850 (tm-30) cc_final: 0.6648 (tm-30) REVERT: C 64 ASP cc_start: 0.8664 (m-30) cc_final: 0.8182 (m-30) REVERT: C 281 LYS cc_start: 0.8700 (mttt) cc_final: 0.8472 (mtmt) REVERT: C 313 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7640 (tm-30) REVERT: D 435 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.6349 (tmm-80) REVERT: E 20 THR cc_start: 0.7957 (p) cc_final: 0.7492 (t) REVERT: E 146 ILE cc_start: 0.8492 (OUTLIER) cc_final: 0.8280 (pp) REVERT: E 251 MET cc_start: 0.9350 (ptt) cc_final: 0.9130 (ptt) REVERT: F 400 ASN cc_start: 0.7335 (m110) cc_final: 0.6905 (m-40) REVERT: F 404 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.6955 (pt0) REVERT: H 88 PHE cc_start: 0.7798 (m-80) cc_final: 0.7412 (m-80) REVERT: G 88 PHE cc_start: 0.7427 (m-80) cc_final: 0.7222 (m-80) REVERT: I 37 SER cc_start: 0.6422 (OUTLIER) cc_final: 0.6204 (p) REVERT: J 67 TYR cc_start: 0.7921 (m-80) cc_final: 0.7569 (m-80) REVERT: K 107 TYR cc_start: 0.7004 (p90) cc_final: 0.6457 (p90) outliers start: 40 outliers final: 16 residues processed: 222 average time/residue: 0.5477 time to fit residues: 135.6333 Evaluate side-chains 207 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 182 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 435 ARG Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain D residue 418 ASP Chi-restraints excluded: chain D residue 435 ARG Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 286 SER Chi-restraints excluded: chain F residue 404 GLU Chi-restraints excluded: chain F residue 418 ASP Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain I residue 37 SER Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 110 SER Chi-restraints excluded: chain K residue 22 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 162 optimal weight: 0.9980 chunk 138 optimal weight: 10.0000 chunk 164 optimal weight: 50.0000 chunk 173 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 153 optimal weight: 0.9980 chunk 171 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 159 optimal weight: 6.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN C 234 GLN E 166 ASN E 234 GLN H 58 ASN G 35 ASN G 58 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.186831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.127725 restraints weight = 62187.798| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 4.61 r_work: 0.3140 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3244 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3244 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16362 Z= 0.144 Angle : 0.590 11.542 22260 Z= 0.293 Chirality : 0.042 0.181 2562 Planarity : 0.004 0.039 2808 Dihedral : 4.974 48.397 2866 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.04 % Allowed : 13.93 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.18), residues: 2010 helix: 1.71 (0.33), residues: 267 sheet: -0.02 (0.24), residues: 459 loop : -1.12 (0.16), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 88 TYR 0.030 0.002 TYR C 337 PHE 0.013 0.001 PHE E 193 TRP 0.011 0.001 TRP J 52 HIS 0.004 0.001 HIS G 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 (16308) covalent geometry : angle 0.55562 / 0.28 (22119) SS BOND : bond 0.00299 / 0.20 ( 21) SS BOND : angle 1.41331 / 1.03 ( 42) hydrogen bonds : bond 0.03092 / 2.07 ( 525) hydrogen bonds : angle 5.24163 / 3.65 ( 1458) link_BETA1-4 : bond 0.00458 / 0.30 ( 12) link_BETA1-4 : angle 1.15283 / 0.78 ( 36) link_NAG-ASN : bond 0.00154 / 0.11 ( 21) link_NAG-ASN : angle 3.52884 / 2.03 ( 63) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 182 time to evaluate : 0.602 Fit side-chains REVERT: A 64 ASP cc_start: 0.8610 (m-30) cc_final: 0.8177 (m-30) REVERT: A 146 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.8302 (pp) REVERT: A 234 GLN cc_start: 0.8135 (mt0) cc_final: 0.7804 (mt0) REVERT: B 394 LYS cc_start: 0.7817 (mtpp) cc_final: 0.7519 (ttmm) REVERT: B 401 SER cc_start: 0.8680 (t) cc_final: 0.8396 (m) REVERT: B 422 ASN cc_start: 0.7644 (OUTLIER) cc_final: 0.7278 (m110) REVERT: B 435 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7222 (tmm-80) REVERT: C 64 ASP cc_start: 0.8644 (m-30) cc_final: 0.8176 (m-30) REVERT: C 281 LYS cc_start: 0.8705 (mttt) cc_final: 0.8426 (mtmt) REVERT: C 313 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7791 (tm-30) REVERT: E 20 THR cc_start: 0.7974 (p) cc_final: 0.7538 (t) REVERT: E 146 ILE cc_start: 0.8529 (OUTLIER) cc_final: 0.8313 (pp) REVERT: F 400 ASN cc_start: 0.7477 (m110) cc_final: 0.7017 (m-40) REVERT: F 404 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.6878 (pt0) REVERT: F 435 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.6469 (tmm-80) REVERT: H 88 PHE cc_start: 0.7752 (m-80) cc_final: 0.7336 (m-80) REVERT: L 105 GLN cc_start: 0.7205 (tt0) cc_final: 0.6740 (tt0) REVERT: G 88 PHE cc_start: 0.7474 (m-80) cc_final: 0.7244 (m-80) REVERT: I 37 SER cc_start: 0.6416 (OUTLIER) cc_final: 0.6206 (p) outliers start: 35 outliers final: 15 residues processed: 206 average time/residue: 0.5707 time to fit residues: 131.1682 Evaluate side-chains 195 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 172 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 435 ARG Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain D residue 418 ASP Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain F residue 404 GLU Chi-restraints excluded: chain F residue 418 ASP Chi-restraints excluded: chain F residue 435 ARG Chi-restraints excluded: chain H residue 59 ASP Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 37 SER Chi-restraints excluded: chain J residue 55 THR Chi-restraints excluded: chain J residue 59 ASP Chi-restraints excluded: chain J residue 110 SER Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 22 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 137 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 166 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 157 optimal weight: 0.7980 chunk 20 optimal weight: 0.2980 chunk 66 optimal weight: 0.5980 chunk 155 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN C 166 ASN C 234 GLN E 234 GLN H 58 ASN G 35 ASN G 58 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.183307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.128063 restraints weight = 73884.605| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 4.71 r_work: 0.3057 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3140 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3140 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16362 Z= 0.166 Angle : 0.621 12.020 22260 Z= 0.305 Chirality : 0.044 0.197 2562 Planarity : 0.004 0.061 2808 Dihedral : 4.970 47.443 2866 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.91 % Allowed : 13.05 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.18), residues: 2010 helix: 1.91 (0.33), residues: 267 sheet: 0.11 (0.24), residues: 459 loop : -1.03 (0.16), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 88 TYR 0.031 0.002 TYR A 337 PHE 0.013 0.001 PHE C 193 TRP 0.010 0.002 TRP J 52 HIS 0.005 0.001 HIS G 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (16308) covalent geometry : angle 0.57855 / 0.30 (22119) SS BOND : bond 0.00265 / 0.17 ( 21) SS BOND : angle 1.49234 / 1.09 ( 42) hydrogen bonds : bond 0.03202 / 2.14 ( 525) hydrogen bonds : angle 5.23432 / 3.65 ( 1458) link_BETA1-4 : bond 0.00470 / 0.31 ( 12) link_BETA1-4 : angle 1.20816 / 0.81 ( 36) link_NAG-ASN : bond 0.00138 / 0.08 ( 21) link_NAG-ASN : angle 4.05391 / 2.41 ( 63) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 183 time to evaluate : 0.663 Fit side-chains REVERT: A 146 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.8351 (pp) REVERT: A 234 GLN cc_start: 0.8236 (mt0) cc_final: 0.7965 (mt0) REVERT: A 299 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7893 (mttm) REVERT: B 401 SER cc_start: 0.8729 (t) cc_final: 0.8434 (m) REVERT: B 422 ASN cc_start: 0.7782 (OUTLIER) cc_final: 0.7391 (m110) REVERT: B 435 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.7425 (tmm-80) REVERT: C 45 LYS cc_start: 0.7881 (mttt) cc_final: 0.7429 (mmtp) REVERT: C 64 ASP cc_start: 0.8678 (m-30) cc_final: 0.8278 (m-30) REVERT: E 20 THR cc_start: 0.8004 (p) cc_final: 0.7603 (t) REVERT: E 146 ILE cc_start: 0.8607 (OUTLIER) cc_final: 0.8391 (pp) REVERT: E 257 LYS cc_start: 0.7829 (mttp) cc_final: 0.7473 (mttt) REVERT: F 400 ASN cc_start: 0.7611 (m110) cc_final: 0.7092 (m-40) REVERT: F 404 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.6934 (pt0) REVERT: F 435 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.6672 (tmm-80) REVERT: H 88 PHE cc_start: 0.7832 (m-80) cc_final: 0.7433 (m-80) REVERT: G 88 PHE cc_start: 0.7604 (m-80) cc_final: 0.7396 (m-80) REVERT: I 37 SER cc_start: 0.6482 (OUTLIER) cc_final: 0.6274 (p) REVERT: K 107 TYR cc_start: 0.7103 (p90) cc_final: 0.6589 (p90) outliers start: 50 outliers final: 19 residues processed: 218 average time/residue: 0.5128 time to fit residues: 126.1025 Evaluate side-chains 199 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 172 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 435 ARG Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain D residue 418 ASP Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 286 SER Chi-restraints excluded: chain F residue 404 GLU Chi-restraints excluded: chain F residue 418 ASP Chi-restraints excluded: chain F residue 435 ARG Chi-restraints excluded: chain H residue 59 ASP Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain I residue 37 SER Chi-restraints excluded: chain J residue 55 THR Chi-restraints excluded: chain J residue 59 ASP Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 110 SER Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 22 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 128 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 182 optimal weight: 6.9990 chunk 99 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 79 optimal weight: 0.0070 chunk 49 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN C 234 GLN D 409 ASN H 58 ASN G 35 ASN G 58 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.186295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.130222 restraints weight = 65798.453| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 4.44 r_work: 0.3096 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3177 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3177 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16362 Z= 0.116 Angle : 0.576 11.663 22260 Z= 0.282 Chirality : 0.042 0.224 2562 Planarity : 0.004 0.038 2808 Dihedral : 4.765 47.718 2866 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.33 % Allowed : 15.09 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.18), residues: 2010 helix: 2.42 (0.33), residues: 267 sheet: 0.21 (0.24), residues: 459 loop : -0.91 (0.17), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 88 TYR 0.025 0.001 TYR E 337 PHE 0.011 0.001 PHE C 193 TRP 0.009 0.001 TRP J 52 HIS 0.004 0.001 HIS G 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (16308) covalent geometry : angle 0.53343 / 0.27 (22119) SS BOND : bond 0.00214 / 0.14 ( 21) SS BOND : angle 1.22878 / 0.91 ( 42) hydrogen bonds : bond 0.02879 / 1.93 ( 525) hydrogen bonds : angle 5.04417 / 3.53 ( 1458) link_BETA1-4 : bond 0.00519 / 0.32 ( 12) link_BETA1-4 : angle 1.09113 / 0.73 ( 36) link_NAG-ASN : bond 0.00427 / 0.24 ( 21) link_NAG-ASN : angle 3.97756 / 2.43 ( 63) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 178 time to evaluate : 0.653 Fit side-chains REVERT: A 146 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8382 (pp) REVERT: A 234 GLN cc_start: 0.8089 (mt0) cc_final: 0.7883 (mt0) REVERT: B 394 LYS cc_start: 0.7977 (mtpp) cc_final: 0.7686 (ttmm) REVERT: B 401 SER cc_start: 0.8700 (t) cc_final: 0.8403 (m) REVERT: C 45 LYS cc_start: 0.7942 (mttt) cc_final: 0.7496 (mmtp) REVERT: C 64 ASP cc_start: 0.8595 (m-30) cc_final: 0.8209 (m-30) REVERT: C 257 LYS cc_start: 0.7739 (mttt) cc_final: 0.7413 (mmtt) REVERT: C 313 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7449 (tm-30) REVERT: D 394 LYS cc_start: 0.7952 (mtpp) cc_final: 0.7648 (ttmm) REVERT: D 435 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.6588 (tmm-80) REVERT: E 20 THR cc_start: 0.7988 (p) cc_final: 0.7564 (t) REVERT: E 146 ILE cc_start: 0.8609 (OUTLIER) cc_final: 0.8403 (pp) REVERT: E 313 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7920 (tp30) REVERT: F 400 ASN cc_start: 0.7583 (m110) cc_final: 0.7088 (m-40) REVERT: F 404 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.6964 (pt0) REVERT: F 435 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.6566 (tmm-80) REVERT: H 88 PHE cc_start: 0.7757 (m-80) cc_final: 0.7342 (m-80) REVERT: L 105 GLN cc_start: 0.7316 (tt0) cc_final: 0.6864 (tt0) REVERT: G 91 MET cc_start: 0.7253 (mtp) cc_final: 0.7023 (mtm) REVERT: I 79 SER cc_start: 0.7918 (t) cc_final: 0.7508 (m) outliers start: 40 outliers final: 19 residues processed: 208 average time/residue: 0.5404 time to fit residues: 125.9924 Evaluate side-chains 195 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 171 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain D residue 418 ASP Chi-restraints excluded: chain D residue 435 ARG Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 286 SER Chi-restraints excluded: chain F residue 404 GLU Chi-restraints excluded: chain F residue 418 ASP Chi-restraints excluded: chain F residue 435 ARG Chi-restraints excluded: chain H residue 59 ASP Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain J residue 55 THR Chi-restraints excluded: chain J residue 59 ASP Chi-restraints excluded: chain J residue 110 SER Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 22 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 130 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 chunk 95 optimal weight: 0.9990 chunk 171 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 141 optimal weight: 7.9990 chunk 133 optimal weight: 0.6980 chunk 21 optimal weight: 0.0270 chunk 73 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 23 optimal weight: 0.0770 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN C 234 GLN D 409 ASN E 234 GLN H 92 ASN G 35 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.187524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.130674 restraints weight = 59187.024| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 4.48 r_work: 0.3119 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3205 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3205 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16362 Z= 0.099 Angle : 0.542 10.041 22260 Z= 0.266 Chirality : 0.041 0.165 2562 Planarity : 0.004 0.044 2808 Dihedral : 4.533 47.178 2866 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.27 % Allowed : 15.56 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.19), residues: 2010 helix: 2.79 (0.33), residues: 267 sheet: 0.34 (0.24), residues: 459 loop : -0.75 (0.17), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 88 TYR 0.021 0.001 TYR E 337 PHE 0.011 0.001 PHE E 193 TRP 0.007 0.001 TRP G 118 HIS 0.006 0.001 HIS E 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 (16308) covalent geometry : angle 0.50604 / 0.26 (22119) SS BOND : bond 0.00209 / 0.14 ( 21) SS BOND : angle 1.10110 / 0.80 ( 42) hydrogen bonds : bond 0.02715 / 1.82 ( 525) hydrogen bonds : angle 4.89211 / 3.43 ( 1458) link_BETA1-4 : bond 0.00502 / 0.33 ( 12) link_BETA1-4 : angle 1.02959 / 0.68 ( 36) link_NAG-ASN : bond 0.00197 / 0.12 ( 21) link_NAG-ASN : angle 3.55570 / 2.15 ( 63) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 180 time to evaluate : 0.540 Fit side-chains REVERT: A 146 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8380 (pp) REVERT: A 234 GLN cc_start: 0.7979 (mt0) cc_final: 0.7778 (mt0) REVERT: B 394 LYS cc_start: 0.7922 (mtpp) cc_final: 0.7611 (ttmm) REVERT: B 408 LYS cc_start: 0.8419 (ttmm) cc_final: 0.7359 (tttt) REVERT: B 422 ASN cc_start: 0.7638 (OUTLIER) cc_final: 0.7246 (m110) REVERT: B 472 MET cc_start: 0.8025 (OUTLIER) cc_final: 0.7654 (mpp) REVERT: C 45 LYS cc_start: 0.7981 (mttt) cc_final: 0.7545 (mmtp) REVERT: C 64 ASP cc_start: 0.8555 (m-30) cc_final: 0.8139 (m-30) REVERT: C 88 ARG cc_start: 0.8223 (mtm-85) cc_final: 0.7163 (ttt-90) REVERT: D 394 LYS cc_start: 0.7968 (mtpp) cc_final: 0.7669 (ttmm) REVERT: D 435 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.6579 (tmm-80) REVERT: E 20 THR cc_start: 0.7967 (p) cc_final: 0.7529 (t) REVERT: E 69 ARG cc_start: 0.8677 (ttt180) cc_final: 0.8432 (ttt180) REVERT: E 257 LYS cc_start: 0.7825 (mttp) cc_final: 0.7451 (mttt) REVERT: E 313 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7865 (tp30) REVERT: F 400 ASN cc_start: 0.7634 (m110) cc_final: 0.7165 (m-40) REVERT: F 404 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.6975 (pt0) REVERT: F 435 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.6561 (tmm-80) REVERT: H 88 PHE cc_start: 0.7691 (m-80) cc_final: 0.7308 (m-80) REVERT: L 79 SER cc_start: 0.7806 (t) cc_final: 0.7379 (m) REVERT: I 79 SER cc_start: 0.7956 (t) cc_final: 0.7580 (m) outliers start: 39 outliers final: 25 residues processed: 207 average time/residue: 0.5502 time to fit residues: 127.2886 Evaluate side-chains 207 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 176 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 472 MET Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain D residue 418 ASP Chi-restraints excluded: chain D residue 435 ARG Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 286 SER Chi-restraints excluded: chain F residue 404 GLU Chi-restraints excluded: chain F residue 418 ASP Chi-restraints excluded: chain F residue 435 ARG Chi-restraints excluded: chain H residue 59 ASP Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain J residue 55 THR Chi-restraints excluded: chain J residue 59 ASP Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 110 SER Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 22 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 108 optimal weight: 0.0370 chunk 45 optimal weight: 2.9990 chunk 148 optimal weight: 5.9990 chunk 81 optimal weight: 0.5980 chunk 7 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 173 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 192 optimal weight: 10.0000 overall best weight: 1.1062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN C 234 GLN D 409 ASN E 234 GLN H 58 ASN G 35 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.184245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.127238 restraints weight = 70030.078| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 4.48 r_work: 0.3063 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3146 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16362 Z= 0.161 Angle : 0.617 11.726 22260 Z= 0.302 Chirality : 0.044 0.180 2562 Planarity : 0.004 0.040 2808 Dihedral : 4.627 47.652 2864 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.45 % Allowed : 16.08 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.19), residues: 2010 helix: 2.43 (0.33), residues: 270 sheet: 0.38 (0.24), residues: 459 loop : -0.79 (0.17), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 88 TYR 0.017 0.002 TYR A 224 PHE 0.013 0.001 PHE E 193 TRP 0.010 0.002 TRP J 52 HIS 0.006 0.001 HIS A 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 (16308) covalent geometry : angle 0.57323 / 0.29 (22119) SS BOND : bond 0.00288 / 0.18 ( 21) SS BOND : angle 1.51534 / 1.11 ( 42) hydrogen bonds : bond 0.03156 / 2.11 ( 525) hydrogen bonds : angle 5.03732 / 3.53 ( 1458) link_BETA1-4 : bond 0.00489 / 0.33 ( 12) link_BETA1-4 : angle 1.16790 / 0.78 ( 36) link_NAG-ASN : bond 0.00147 / 0.10 ( 21) link_NAG-ASN : angle 4.11655 / 2.46 ( 63) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 180 time to evaluate : 0.752 Fit side-chains REVERT: A 146 ILE cc_start: 0.8666 (OUTLIER) cc_final: 0.8433 (pp) REVERT: A 234 GLN cc_start: 0.8213 (mt0) cc_final: 0.7962 (mt0) REVERT: B 394 LYS cc_start: 0.8018 (mtpp) cc_final: 0.7765 (ttmm) REVERT: B 408 LYS cc_start: 0.8479 (ttmm) cc_final: 0.7402 (tttt) REVERT: B 422 ASN cc_start: 0.7758 (OUTLIER) cc_final: 0.7380 (m110) REVERT: C 45 LYS cc_start: 0.7949 (mttt) cc_final: 0.7523 (mmtp) REVERT: C 64 ASP cc_start: 0.8652 (m-30) cc_final: 0.8252 (m-30) REVERT: C 313 GLU cc_start: 0.8094 (tm-30) cc_final: 0.7621 (tm-30) REVERT: D 435 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.6659 (tmm-80) REVERT: E 20 THR cc_start: 0.8031 (p) cc_final: 0.7608 (t) REVERT: E 146 ILE cc_start: 0.8525 (OUTLIER) cc_final: 0.8307 (pp) REVERT: E 257 LYS cc_start: 0.7819 (mttp) cc_final: 0.7452 (mttt) REVERT: E 313 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7958 (tp30) REVERT: F 400 ASN cc_start: 0.7671 (m110) cc_final: 0.7166 (m-40) REVERT: F 404 GLU cc_start: 0.7578 (mt-10) cc_final: 0.6959 (pt0) REVERT: F 435 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.6639 (tmm-80) REVERT: H 88 PHE cc_start: 0.7797 (m-80) cc_final: 0.7396 (m-80) REVERT: L 79 SER cc_start: 0.7991 (t) cc_final: 0.7570 (m) REVERT: I 79 SER cc_start: 0.7964 (t) cc_final: 0.7562 (m) REVERT: I 105 GLN cc_start: 0.7277 (OUTLIER) cc_final: 0.6672 (tt0) REVERT: K 79 SER cc_start: 0.8357 (t) cc_final: 0.7959 (m) REVERT: K 107 TYR cc_start: 0.7030 (p90) cc_final: 0.6571 (p90) outliers start: 42 outliers final: 26 residues processed: 209 average time/residue: 0.5448 time to fit residues: 127.7503 Evaluate side-chains 208 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 176 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain D residue 418 ASP Chi-restraints excluded: chain D residue 435 ARG Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 286 SER Chi-restraints excluded: chain F residue 418 ASP Chi-restraints excluded: chain F residue 435 ARG Chi-restraints excluded: chain H residue 59 ASP Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 105 GLN Chi-restraints excluded: chain J residue 55 THR Chi-restraints excluded: chain J residue 59 ASP Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 110 SER Chi-restraints excluded: chain K residue 10 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 37 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 52 optimal weight: 0.0870 chunk 192 optimal weight: 8.9990 chunk 163 optimal weight: 8.9990 chunk 105 optimal weight: 2.9990 chunk 145 optimal weight: 0.1980 chunk 172 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 81 optimal weight: 0.6980 chunk 149 optimal weight: 1.9990 overall best weight: 1.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN D 409 ASN E 234 GLN H 58 ASN G 35 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.184007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.126400 restraints weight = 59636.787| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 4.48 r_work: 0.3059 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3143 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3143 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16362 Z= 0.172 Angle : 0.628 11.966 22260 Z= 0.308 Chirality : 0.044 0.188 2562 Planarity : 0.004 0.041 2808 Dihedral : 4.754 47.184 2864 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.10 % Allowed : 16.61 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.18), residues: 2010 helix: 2.25 (0.33), residues: 276 sheet: 0.40 (0.24), residues: 459 loop : -0.84 (0.16), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 88 TYR 0.021 0.002 TYR J 112C PHE 0.013 0.001 PHE E 193 TRP 0.010 0.002 TRP J 52 HIS 0.005 0.001 HIS J 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.17 (16308) covalent geometry : angle 0.58485 / 0.30 (22119) SS BOND : bond 0.00250 / 0.16 ( 21) SS BOND : angle 1.58445 / 1.18 ( 42) hydrogen bonds : bond 0.03209 / 2.14 ( 525) hydrogen bonds : angle 5.06706 / 3.55 ( 1458) link_BETA1-4 : bond 0.00466 / 0.31 ( 12) link_BETA1-4 : angle 1.17195 / 0.78 ( 36) link_NAG-ASN : bond 0.00178 / 0.12 ( 21) link_NAG-ASN : angle 4.09855 / 2.45 ( 63) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 176 time to evaluate : 0.674 Fit side-chains revert: symmetry clash REVERT: A 146 ILE cc_start: 0.8652 (OUTLIER) cc_final: 0.8432 (pp) REVERT: A 234 GLN cc_start: 0.8211 (mt0) cc_final: 0.7966 (mt0) REVERT: B 394 LYS cc_start: 0.8020 (mtpp) cc_final: 0.7787 (ttmm) REVERT: B 422 ASN cc_start: 0.7766 (OUTLIER) cc_final: 0.7393 (m110) REVERT: C 45 LYS cc_start: 0.7941 (mttt) cc_final: 0.7510 (mmtp) REVERT: C 64 ASP cc_start: 0.8650 (m-30) cc_final: 0.8244 (m-30) REVERT: C 257 LYS cc_start: 0.7738 (mmtt) cc_final: 0.7533 (mmtt) REVERT: C 313 GLU cc_start: 0.8106 (tm-30) cc_final: 0.7614 (tm-30) REVERT: D 394 LYS cc_start: 0.7969 (mtpp) cc_final: 0.7684 (ttmm) REVERT: D 435 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.6621 (tmm-80) REVERT: E 20 THR cc_start: 0.8050 (p) cc_final: 0.7637 (t) REVERT: E 146 ILE cc_start: 0.8517 (OUTLIER) cc_final: 0.8316 (pp) REVERT: E 257 LYS cc_start: 0.7811 (mttp) cc_final: 0.7437 (mttt) REVERT: E 313 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7928 (tp30) REVERT: F 400 ASN cc_start: 0.7668 (m110) cc_final: 0.7156 (m-40) REVERT: F 404 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.6953 (pt0) REVERT: F 435 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.6639 (tmm-80) REVERT: H 88 PHE cc_start: 0.7826 (m-80) cc_final: 0.7412 (m-80) REVERT: L 79 SER cc_start: 0.8055 (t) cc_final: 0.7646 (m) REVERT: L 105 GLN cc_start: 0.7351 (tt0) cc_final: 0.6829 (tt0) REVERT: I 79 SER cc_start: 0.7922 (t) cc_final: 0.7513 (m) REVERT: K 107 TYR cc_start: 0.7008 (p90) cc_final: 0.6531 (p90) outliers start: 36 outliers final: 25 residues processed: 200 average time/residue: 0.5422 time to fit residues: 121.4658 Evaluate side-chains 201 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 170 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain D residue 418 ASP Chi-restraints excluded: chain D residue 435 ARG Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 286 SER Chi-restraints excluded: chain F residue 404 GLU Chi-restraints excluded: chain F residue 418 ASP Chi-restraints excluded: chain F residue 435 ARG Chi-restraints excluded: chain H residue 59 ASP Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain J residue 59 ASP Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 110 SER Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 22 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 125 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 187 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 161 optimal weight: 0.0980 chunk 183 optimal weight: 3.9990 chunk 113 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 71 optimal weight: 5.9990 chunk 119 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN D 409 ASN H 58 ASN G 35 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.185633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.133880 restraints weight = 78011.676| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 4.46 r_work: 0.3084 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3152 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3152 r_free = 0.3152 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3152 r_free = 0.3152 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3152 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16362 Z= 0.124 Angle : 0.581 10.986 22260 Z= 0.286 Chirality : 0.042 0.176 2562 Planarity : 0.004 0.040 2808 Dihedral : 4.626 47.352 2864 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.92 % Allowed : 17.13 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.18), residues: 2010 helix: 2.47 (0.33), residues: 276 sheet: 0.37 (0.24), residues: 465 loop : -0.82 (0.16), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 88 TYR 0.017 0.002 TYR J 112C PHE 0.011 0.001 PHE E 193 TRP 0.009 0.001 TRP J 52 HIS 0.005 0.001 HIS H 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.12 (16308) covalent geometry : angle 0.54046 / 0.28 (22119) SS BOND : bond 0.00213 / 0.14 ( 21) SS BOND : angle 1.32296 / 0.98 ( 42) hydrogen bonds : bond 0.02943 / 1.96 ( 525) hydrogen bonds : angle 4.96383 / 3.48 ( 1458) link_BETA1-4 : bond 0.00475 / 0.31 ( 12) link_BETA1-4 : angle 1.08353 / 0.72 ( 36) link_NAG-ASN : bond 0.00185 / 0.15 ( 21) link_NAG-ASN : angle 3.83922 / 2.31 ( 63) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 170 time to evaluate : 0.751 Fit side-chains revert: symmetry clash REVERT: A 146 ILE cc_start: 0.8636 (OUTLIER) cc_final: 0.8424 (pp) REVERT: A 234 GLN cc_start: 0.8035 (mt0) cc_final: 0.7802 (mt0) REVERT: B 394 LYS cc_start: 0.8005 (mtpp) cc_final: 0.7786 (ttmm) REVERT: B 422 ASN cc_start: 0.7681 (OUTLIER) cc_final: 0.7293 (m110) REVERT: C 64 ASP cc_start: 0.8577 (m-30) cc_final: 0.8178 (m-30) REVERT: C 313 GLU cc_start: 0.8015 (tm-30) cc_final: 0.7521 (tm-30) REVERT: D 394 LYS cc_start: 0.7935 (mtpp) cc_final: 0.7653 (ttmm) REVERT: D 435 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.6504 (tmm-80) REVERT: E 20 THR cc_start: 0.8009 (p) cc_final: 0.7590 (t) REVERT: E 146 ILE cc_start: 0.8534 (OUTLIER) cc_final: 0.8324 (pp) REVERT: E 257 LYS cc_start: 0.7771 (mttp) cc_final: 0.7400 (mttt) REVERT: F 400 ASN cc_start: 0.7631 (m110) cc_final: 0.7123 (m-40) REVERT: F 404 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.6937 (pt0) REVERT: F 435 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.6500 (tmm-80) REVERT: H 88 PHE cc_start: 0.7735 (m-80) cc_final: 0.7297 (m-80) REVERT: L 79 SER cc_start: 0.8222 (t) cc_final: 0.7826 (m) REVERT: L 105 GLN cc_start: 0.7288 (tt0) cc_final: 0.6780 (tt0) REVERT: I 79 SER cc_start: 0.7895 (t) cc_final: 0.7463 (m) outliers start: 33 outliers final: 23 residues processed: 192 average time/residue: 0.5608 time to fit residues: 120.2718 Evaluate side-chains 198 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 169 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain D residue 418 ASP Chi-restraints excluded: chain D residue 435 ARG Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 286 SER Chi-restraints excluded: chain F residue 404 GLU Chi-restraints excluded: chain F residue 418 ASP Chi-restraints excluded: chain F residue 435 ARG Chi-restraints excluded: chain H residue 59 ASP Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain J residue 55 THR Chi-restraints excluded: chain J residue 59 ASP Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 110 SER Chi-restraints excluded: chain K residue 10 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 162 optimal weight: 0.8980 chunk 36 optimal weight: 0.0070 chunk 84 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 181 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 409 ASN E 234 GLN G 35 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.184711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.132218 restraints weight = 75618.363| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 4.37 r_work: 0.3088 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3151 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16362 Z= 0.126 Angle : 0.580 10.833 22260 Z= 0.285 Chirality : 0.042 0.171 2562 Planarity : 0.004 0.043 2808 Dihedral : 4.564 47.304 2864 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.92 % Allowed : 17.02 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.18), residues: 2010 helix: 2.50 (0.33), residues: 276 sheet: 0.47 (0.25), residues: 429 loop : -0.74 (0.16), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 88 TYR 0.017 0.002 TYR J 112C PHE 0.012 0.001 PHE E 193 TRP 0.009 0.001 TRP J 52 HIS 0.004 0.001 HIS J 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (16308) covalent geometry : angle 0.53886 / 0.28 (22119) SS BOND : bond 0.00227 / 0.14 ( 21) SS BOND : angle 1.34781 / 1.00 ( 42) hydrogen bonds : bond 0.02929 / 1.96 ( 525) hydrogen bonds : angle 4.92689 / 3.46 ( 1458) link_BETA1-4 : bond 0.00477 / 0.31 ( 12) link_BETA1-4 : angle 1.06938 / 0.71 ( 36) link_NAG-ASN : bond 0.00189 / 0.16 ( 21) link_NAG-ASN : angle 3.86162 / 2.32 ( 63) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7353.97 seconds wall clock time: 125 minutes 43.15 seconds (7543.15 seconds total)