Starting phenix.real_space_refine on Thu Jul 31 10:33:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ce4_16598/07_2025/8ce4_16598.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ce4_16598/07_2025/8ce4_16598.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ce4_16598/07_2025/8ce4_16598.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ce4_16598/07_2025/8ce4_16598.map" model { file = "/net/cci-nas-00/data/ceres_data/8ce4_16598/07_2025/8ce4_16598.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ce4_16598/07_2025/8ce4_16598.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 70 5.16 5 C 8515 2.51 5 N 2280 2.21 5 O 2570 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13435 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 1728 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 207, 1721 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 13, 'TRANS': 193} Conformer: "B" Number of residues, atoms: 207, 1721 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 13, 'TRANS': 193} bond proxies already assigned to first conformer: 1767 Chain: "B" Number of atoms: 1728 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 207, 1721 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 13, 'TRANS': 193} Conformer: "B" Number of residues, atoms: 207, 1721 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 13, 'TRANS': 193} bond proxies already assigned to first conformer: 1767 Chain: "C" Number of atoms: 1728 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 207, 1721 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 13, 'TRANS': 193} Conformer: "B" Number of residues, atoms: 207, 1721 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 13, 'TRANS': 193} bond proxies already assigned to first conformer: 1767 Chain: "D" Number of atoms: 1728 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 207, 1721 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 13, 'TRANS': 193} Conformer: "B" Number of residues, atoms: 207, 1721 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 13, 'TRANS': 193} bond proxies already assigned to first conformer: 1767 Chain: "E" Number of atoms: 1728 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 207, 1721 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 13, 'TRANS': 193} Conformer: "B" Number of residues, atoms: 207, 1721 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 13, 'TRANS': 193} bond proxies already assigned to first conformer: 1767 Chain: "F" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 903 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "G" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 903 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "H" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 903 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "I" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 903 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "J" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 903 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} 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: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 13.08, per 1000 atoms: 0.97 Number of scatterers: 13435 At special positions: 0 Unit cell: (90.644, 92.106, 113.305, 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 70 16.00 O 2570 8.00 N 2280 7.00 C 8515 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 127 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 190 " distance=2.04 Simple disulfide: pdb=" SG CYS B 127 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS C 127 " - pdb=" SG CYS C 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 127 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 127 " - pdb=" SG CYS E 141 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 95 " - pdb=" SG CYS F 114 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 95 " - pdb=" SG CYS G 114 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 95 " - pdb=" SG CYS H 114 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 95 " - pdb=" SG CYS I 114 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 95 " - pdb=" SG CYS J 114 " 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 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-ASN " NAG A 401 " - " ASN A 23 " " NAG A 402 " - " ASN A 67 " " NAG B 401 " - " ASN B 23 " " NAG B 402 " - " ASN B 67 " " NAG C 401 " - " ASN C 23 " " NAG C 402 " - " ASN C 67 " " NAG D 401 " - " ASN D 23 " " NAG D 402 " - " ASN D 67 " " NAG E 401 " - " ASN E 23 " " NAG E 402 " - " ASN E 67 " " NAG P 1 " - " ASN A 110 " " NAG Q 1 " - " ASN B 110 " " NAG R 1 " - " ASN C 110 " " NAG S 1 " - " ASN D 110 " " NAG T 1 " - " ASN E 110 " Time building additional restraints: 3.35 Conformation dependent library (CDL) restraints added in 2.6 seconds 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3050 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 30 sheets defined 8.2% alpha, 42.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.94 Creating SS restraints... Processing helix chain 'A' and resid 1 through 11 removed outlier: 3.662A pdb=" N LYS A 5 " --> pdb=" O GLU A 1 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL A 11 " --> pdb=" O TYR A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 136 Processing helix chain 'B' and resid 2 through 11 Processing helix chain 'C' and resid 2 through 11 Processing helix chain 'D' and resid 2 through 11 removed outlier: 3.758A pdb=" N VAL D 11 " --> pdb=" O TYR D 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 11 Processing helix chain 'E' and resid 133 through 136 Processing helix chain 'F' and resid 28 through 30 No H-bonds generated for 'chain 'F' and resid 28 through 30' Processing helix chain 'F' and resid 62 through 65 Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'F' and resid 107 through 111 removed outlier: 3.742A pdb=" N GLU F 110 " --> pdb=" O ALA F 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 30 No H-bonds generated for 'chain 'G' and resid 28 through 30' Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'G' and resid 107 through 111 Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 107 through 111 removed outlier: 3.663A pdb=" N GLU H 110 " --> pdb=" O ALA H 107 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 30 No H-bonds generated for 'chain 'I' and resid 28 through 30' Processing helix chain 'I' and resid 62 through 65 Processing helix chain 'I' and resid 107 through 111 removed outlier: 3.588A pdb=" N GLU I 110 " --> pdb=" O ALA I 107 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 30 No H-bonds generated for 'chain 'J' and resid 28 through 30' Processing helix chain 'J' and resid 62 through 65 Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'J' and resid 107 through 111 Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 79 removed outlier: 4.051A pdb=" N HIS A 114 " --> pdb=" O ASN A 110 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 79 removed outlier: 4.051A pdb=" N HIS A 114 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ASN A 52 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ILE A 39 " --> pdb=" O ASN A 52 " (cutoff:3.500A) removed outlier: 8.715A pdb=" N TRP A 54 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N LEU A 37 " --> pdb=" O TRP A 54 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N GLN A 56 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N SER A 35 " --> pdb=" O GLN A 56 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N SER A 58 " --> pdb=" O SER A 33 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N SER A 33 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 8.856A pdb=" N THR A 60 " --> pdb=" O TYR A 31 " (cutoff:3.500A) removed outlier: 9.553A pdb=" N TYR A 31 " --> pdb=" O THR A 60 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 89 through 91 removed outlier: 4.605A pdb=" N SER A 147 " --> pdb=" O PRO A 195 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 138 through 139 Processing sheet with id=AA5, first strand: chain 'B' and resid 76 through 79 removed outlier: 3.980A pdb=" N HIS B 114 " --> pdb=" O ASN B 110 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 76 through 79 removed outlier: 3.980A pdb=" N HIS B 114 " --> pdb=" O ASN B 110 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ASN B 52 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N ILE B 39 " --> pdb=" O ASN B 52 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N TRP B 54 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N LEU B 37 " --> pdb=" O TRP B 54 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N GLN B 56 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N SER B 35 " --> pdb=" O GLN B 56 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N SER B 58 " --> pdb=" O SER B 33 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N SER B 33 " --> pdb=" O SER B 58 " (cutoff:3.500A) removed outlier: 8.917A pdb=" N THR B 60 " --> pdb=" O TYR B 31 " (cutoff:3.500A) removed outlier: 9.625A pdb=" N TYR B 31 " --> pdb=" O THR B 60 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 89 through 91 removed outlier: 4.545A pdb=" N SER B 147 " --> pdb=" O PRO B 195 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N GLU B 192 " --> pdb=" O TYR B 187 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N TYR B 187 " --> pdb=" O GLU B 192 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 138 through 139 Processing sheet with id=AA9, first strand: chain 'C' and resid 76 through 79 removed outlier: 4.143A pdb=" N HIS C 114 " --> pdb=" O ASN C 110 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 76 through 79 removed outlier: 4.143A pdb=" N HIS C 114 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL C 48 " --> pdb=" O VAL C 42 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N VAL C 42 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR C 50 " --> pdb=" O MET C 40 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN C 38 " --> pdb=" O ASN C 52 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N TRP C 54 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N LEU C 36 " --> pdb=" O TRP C 54 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N GLN C 56 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N LEU C 34 " --> pdb=" O GLN C 56 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N SER C 58 " --> pdb=" O PHE C 32 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N PHE C 32 " --> pdb=" O SER C 58 " (cutoff:3.500A) removed outlier: 8.796A pdb=" N THR C 60 " --> pdb=" O VAL C 30 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N VAL C 30 " --> pdb=" O THR C 60 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 89 through 91 removed outlier: 4.528A pdb=" N SER C 147 " --> pdb=" O PRO C 195 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N GLU C 192 " --> pdb=" O TYR C 187 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N TYR C 187 " --> pdb=" O GLU C 192 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 138 through 139 Processing sheet with id=AB4, first strand: chain 'D' and resid 76 through 79 removed outlier: 3.854A pdb=" N HIS D 114 " --> pdb=" O ASN D 110 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 76 through 79 removed outlier: 3.854A pdb=" N HIS D 114 " --> pdb=" O ASN D 110 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ASN D 52 " --> pdb=" O ILE D 39 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N ILE D 39 " --> pdb=" O ASN D 52 " (cutoff:3.500A) removed outlier: 8.773A pdb=" N TRP D 54 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N LEU D 37 " --> pdb=" O TRP D 54 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N GLN D 56 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N SER D 35 " --> pdb=" O GLN D 56 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N SER D 58 " --> pdb=" O SER D 33 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N SER D 33 " --> pdb=" O SER D 58 " (cutoff:3.500A) removed outlier: 8.875A pdb=" N THR D 60 " --> pdb=" O TYR D 31 " (cutoff:3.500A) removed outlier: 9.563A pdb=" N TYR D 31 " --> pdb=" O THR D 60 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 89 through 91 removed outlier: 4.533A pdb=" N SER D 147 " --> pdb=" O PRO D 195 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N GLU D 192 " --> pdb=" O TYR D 187 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N TYR D 187 " --> pdb=" O GLU D 192 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 138 through 139 Processing sheet with id=AB8, first strand: chain 'E' and resid 76 through 79 removed outlier: 3.982A pdb=" N HIS E 114 " --> pdb=" O ASN E 110 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 76 through 79 removed outlier: 3.982A pdb=" N HIS E 114 " --> pdb=" O ASN E 110 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ASN E 52 " --> pdb=" O ILE E 39 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ILE E 39 " --> pdb=" O ASN E 52 " (cutoff:3.500A) removed outlier: 8.801A pdb=" N TRP E 54 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N LEU E 37 " --> pdb=" O TRP E 54 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N GLN E 56 " --> pdb=" O SER E 35 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N SER E 35 " --> pdb=" O GLN E 56 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N SER E 58 " --> pdb=" O SER E 33 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N SER E 33 " --> pdb=" O SER E 58 " (cutoff:3.500A) removed outlier: 8.910A pdb=" N THR E 60 " --> pdb=" O TYR E 31 " (cutoff:3.500A) removed outlier: 9.595A pdb=" N TYR E 31 " --> pdb=" O THR E 60 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 89 through 91 removed outlier: 4.555A pdb=" N SER E 147 " --> pdb=" O PRO E 195 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N GLU E 192 " --> pdb=" O TYR E 187 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N TYR E 187 " --> pdb=" O GLU E 192 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 138 through 139 Processing sheet with id=AC3, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AC4, first strand: chain 'F' and resid 58 through 60 removed outlier: 5.553A pdb=" N PHE F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N ARG F 38 " --> pdb=" O PHE F 47 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AC6, first strand: chain 'G' and resid 58 through 60 removed outlier: 5.562A pdb=" N PHE G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ARG G 38 " --> pdb=" O PHE G 47 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AC8, first strand: chain 'H' and resid 58 through 60 removed outlier: 5.581A pdb=" N PHE H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ARG H 38 " --> pdb=" O PHE H 47 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AD1, first strand: chain 'I' and resid 58 through 60 removed outlier: 5.631A pdb=" N PHE I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N ARG I 38 " --> pdb=" O PHE I 47 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AD3, first strand: chain 'J' and resid 10 through 11 removed outlier: 6.530A pdb=" N GLY J 10 " --> pdb=" O THR J 121 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ARG J 38 " --> pdb=" O PHE J 47 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N PHE J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) 476 hydrogen bonds defined for protein. 1230 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: 3.90 Time building geometry restraints manager: 3.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4318 1.35 - 1.47: 3743 1.47 - 1.59: 5648 1.59 - 1.71: 1 1.71 - 1.83: 95 Bond restraints: 13805 Sorted by residual: bond pdb=" C1 NAG S 2 " pdb=" O5 NAG S 2 " ideal model delta sigma weight residual 1.406 1.491 -0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" C1 NAG Q 2 " pdb=" O5 NAG Q 2 " ideal model delta sigma weight residual 1.406 1.489 -0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" C1 NAG T 2 " pdb=" O5 NAG T 2 " ideal model delta sigma weight residual 1.406 1.477 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" C1 NAG P 2 " pdb=" O5 NAG P 2 " ideal model delta sigma weight residual 1.406 1.475 -0.069 2.00e-02 2.50e+03 1.17e+01 bond pdb=" CB PRO F 88 " pdb=" CG PRO F 88 " ideal model delta sigma weight residual 1.492 1.627 -0.135 5.00e-02 4.00e+02 7.24e+00 ... (remaining 13800 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 18328 1.88 - 3.77: 366 3.77 - 5.65: 54 5.65 - 7.53: 5 7.53 - 9.42: 2 Bond angle restraints: 18755 Sorted by residual: angle pdb=" CA PRO F 88 " pdb=" N PRO F 88 " pdb=" CD PRO F 88 " ideal model delta sigma weight residual 112.00 102.58 9.42 1.40e+00 5.10e-01 4.52e+01 angle pdb=" CA PRO D 169 " pdb=" N PRO D 169 " pdb=" CD PRO D 169 " ideal model delta sigma weight residual 112.00 104.69 7.31 1.40e+00 5.10e-01 2.73e+01 angle pdb=" C TRP E 133 " pdb=" N PHE E 134 " pdb=" CA PHE E 134 " ideal model delta sigma weight residual 121.80 130.64 -8.84 2.44e+00 1.68e-01 1.31e+01 angle pdb=" N PRO F 88 " pdb=" CD PRO F 88 " pdb=" CG PRO F 88 " ideal model delta sigma weight residual 103.20 98.02 5.18 1.50e+00 4.44e-01 1.19e+01 angle pdb=" CA PRO F 41 " pdb=" N PRO F 41 " pdb=" CD PRO F 41 " ideal model delta sigma weight residual 112.00 107.83 4.17 1.40e+00 5.10e-01 8.87e+00 ... (remaining 18750 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.07: 7563 25.07 - 50.15: 656 50.15 - 75.22: 137 75.22 - 100.29: 14 100.29 - 125.36: 8 Dihedral angle restraints: 8378 sinusoidal: 3603 harmonic: 4775 Sorted by residual: dihedral pdb=" CB CYS G 22 " pdb=" SG CYS G 22 " pdb=" SG CYS G 96 " pdb=" CB CYS G 96 " ideal model delta sinusoidal sigma weight residual -86.00 -157.08 71.08 1 1.00e+01 1.00e-02 6.49e+01 dihedral pdb=" CB CYS H 95 " pdb=" SG CYS H 95 " pdb=" SG CYS H 114 " pdb=" CB CYS H 114 " ideal model delta sinusoidal sigma weight residual 93.00 35.04 57.96 1 1.00e+01 1.00e-02 4.51e+01 dihedral pdb=" CB CYS I 95 " pdb=" SG CYS I 95 " pdb=" SG CYS I 114 " pdb=" CB CYS I 114 " ideal model delta sinusoidal sigma weight residual 93.00 37.20 55.80 1 1.00e+01 1.00e-02 4.20e+01 ... (remaining 8375 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1541 0.044 - 0.087: 344 0.087 - 0.131: 113 0.131 - 0.175: 9 0.175 - 0.218: 3 Chirality restraints: 2010 Sorted by residual: chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN E 110 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CB ILE A 178 " pdb=" CA ILE A 178 " pdb=" CG1 ILE A 178 " pdb=" CG2 ILE A 178 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.82e-01 chirality pdb=" CB ILE E 178 " pdb=" CA ILE E 178 " pdb=" CG1 ILE E 178 " pdb=" CG2 ILE E 178 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.30e-01 ... (remaining 2007 not shown) Planarity restraints: 2425 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 168 " -0.096 5.00e-02 4.00e+02 1.40e-01 3.15e+01 pdb=" N PRO D 169 " 0.242 5.00e-02 4.00e+02 pdb=" CA PRO D 169 " -0.075 5.00e-02 4.00e+02 pdb=" CD PRO D 169 " -0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS F 87 " -0.069 5.00e-02 4.00e+02 9.87e-02 1.56e+01 pdb=" N PRO F 88 " 0.170 5.00e-02 4.00e+02 pdb=" CA PRO F 88 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO F 88 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 168 " 0.061 5.00e-02 4.00e+02 9.19e-02 1.35e+01 pdb=" N PRO B 169 " -0.159 5.00e-02 4.00e+02 pdb=" CA PRO B 169 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO B 169 " 0.050 5.00e-02 4.00e+02 ... (remaining 2422 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 474 2.71 - 3.26: 12004 3.26 - 3.80: 22376 3.80 - 4.35: 30099 4.35 - 4.90: 49427 Nonbonded interactions: 114380 Sorted by model distance: nonbonded pdb=" O TYR I 32 " pdb=" NH2 ARG I 72 " model vdw 2.159 3.120 nonbonded pdb=" O TYR G 32 " pdb=" NH2 ARG G 72 " model vdw 2.170 3.120 nonbonded pdb=" O TYR H 32 " pdb=" NH2 ARG H 72 " model vdw 2.174 3.120 nonbonded pdb=" O TYR F 32 " pdb=" NH2 ARG F 72 " model vdw 2.175 3.120 nonbonded pdb=" O TYR J 32 " pdb=" NH2 ARG J 72 " model vdw 2.186 3.120 ... (remaining 114375 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 113 or resid 115 through 207 or resid 401 throug \ h 402)) selection = (chain 'B' and (resid 1 through 113 or resid 115 through 207 or resid 401 throug \ h 402)) selection = (chain 'C' and (resid 1 through 113 or resid 115 through 207 or resid 401 throug \ h 402)) selection = (chain 'D' and (resid 1 through 113 or resid 115 through 207 or resid 401 throug \ h 402)) selection = (chain 'E' and (resid 1 through 113 or resid 115 through 207 or resid 401 throug \ h 402)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } 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=0.40 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: 4.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.640 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 38.820 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.090 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:11.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 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 : 0.004 0.135 13841 Z= 0.174 Angle : 0.649 11.167 18847 Z= 0.334 Chirality : 0.043 0.218 2010 Planarity : 0.007 0.140 2410 Dihedral : 18.891 125.364 5280 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.55 % Favored : 95.38 % Rotamer: Outliers : 2.61 % Allowed : 26.69 % Favored : 70.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.19), residues: 1630 helix: 3.20 (0.66), residues: 45 sheet: -0.35 (0.19), residues: 660 loop : -0.87 (0.18), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 153 HIS 0.002 0.001 HIS B 104 PHE 0.020 0.001 PHE A 136 TYR 0.019 0.001 TYR E 128 ARG 0.006 0.001 ARG D 204 Details of bonding type rmsd link_NAG-ASN : bond 0.00164 ( 15) link_NAG-ASN : angle 2.03378 ( 45) link_BETA1-4 : bond 0.01127 ( 5) link_BETA1-4 : angle 5.20246 ( 15) hydrogen bonds : bond 0.13933 ( 421) hydrogen bonds : angle 6.67362 ( 1230) SS BOND : bond 0.00437 ( 16) SS BOND : angle 0.76058 ( 32) covalent geometry : bond 0.00424 (13805) covalent geometry : angle 0.62555 (18755) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 284 time to evaluate : 1.627 Fit side-chains revert: symmetry clash REVERT: A 191 LYS cc_start: 0.8839 (mtpt) cc_final: 0.8524 (tmtt) REVERT: I 45 ARG cc_start: 0.7793 (ttp-170) cc_final: 0.7422 (ttm-80) REVERT: J 45 ARG cc_start: 0.7975 (ttp-170) cc_final: 0.7398 (tpp80) outliers start: 37 outliers final: 27 residues processed: 321 average time/residue: 1.8932 time to fit residues: 646.9434 Evaluate side-chains 280 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 253 time to evaluate : 2.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 114 CYS Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 65 LYS Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 120 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 3.9990 chunk 121 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 125 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 145 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN A 56 GLN B 3 GLN B 46 ASN C 26 GLN C 46 ASN C 116 GLN D 46 ASN E 46 ASN F 13 GLN G 13 GLN H 13 GLN I 13 GLN I 84 ASN J 5 GLN J 13 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.075719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.054446 restraints weight = 53458.832| |-----------------------------------------------------------------------------| r_work (start): 0.2592 rms_B_bonded: 3.65 r_work: 0.2439 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2439 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2441 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2441 r_free = 0.2441 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2440 r_free = 0.2440 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2440 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9057 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13841 Z= 0.155 Angle : 0.648 8.851 18847 Z= 0.328 Chirality : 0.042 0.286 2010 Planarity : 0.006 0.098 2410 Dihedral : 11.787 115.383 2269 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.31 % Favored : 95.63 % Rotamer: Outliers : 4.01 % Allowed : 24.51 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.19), residues: 1630 helix: 1.99 (0.73), residues: 50 sheet: -0.21 (0.19), residues: 655 loop : -0.95 (0.18), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 133 HIS 0.002 0.001 HIS E 62 PHE 0.013 0.001 PHE A 136 TYR 0.015 0.001 TYR A 117 ARG 0.008 0.001 ARG J 108 Details of bonding type rmsd link_NAG-ASN : bond 0.00237 ( 15) link_NAG-ASN : angle 2.11591 ( 45) link_BETA1-4 : bond 0.01114 ( 5) link_BETA1-4 : angle 4.97770 ( 15) hydrogen bonds : bond 0.03391 ( 421) hydrogen bonds : angle 5.47603 ( 1230) SS BOND : bond 0.00319 ( 16) SS BOND : angle 0.75751 ( 32) covalent geometry : bond 0.00359 (13805) covalent geometry : angle 0.62508 (18755) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 266 time to evaluate : 1.669 Fit side-chains REVERT: A 75 LYS cc_start: 0.9407 (OUTLIER) cc_final: 0.9144 (mtmm) REVERT: A 172 GLU cc_start: 0.8956 (mt-10) cc_final: 0.8746 (tt0) REVERT: A 191 LYS cc_start: 0.9020 (OUTLIER) cc_final: 0.8152 (tmtt) REVERT: F 13 GLN cc_start: 0.7676 (mm-40) cc_final: 0.7067 (mm110) REVERT: G 13 GLN cc_start: 0.7772 (mm-40) cc_final: 0.7201 (mm110) REVERT: H 73 ASP cc_start: 0.8998 (t0) cc_final: 0.8723 (t0) REVERT: H 84 ASN cc_start: 0.7968 (m-40) cc_final: 0.7547 (m110) REVERT: I 13 GLN cc_start: 0.7744 (mm-40) cc_final: 0.7123 (mm110) REVERT: I 73 ASP cc_start: 0.8919 (t0) cc_final: 0.8699 (t0) REVERT: J 13 GLN cc_start: 0.7603 (mm-40) cc_final: 0.6986 (mm110) REVERT: J 121 THR cc_start: 0.9514 (m) cc_final: 0.9078 (p) outliers start: 57 outliers final: 22 residues processed: 308 average time/residue: 1.8624 time to fit residues: 610.0495 Evaluate side-chains 277 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 253 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain G residue 44 GLU Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 114 CYS Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 93 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 72 optimal weight: 1.9990 chunk 33 optimal weight: 0.0670 chunk 79 optimal weight: 6.9990 chunk 129 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 156 optimal weight: 4.9990 chunk 2 optimal weight: 0.0970 chunk 44 optimal weight: 0.0000 chunk 81 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 overall best weight: 0.3720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN B 3 GLN B 46 ASN C 116 GLN D 46 ASN E 46 ASN H 13 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.077108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.055680 restraints weight = 58576.841| |-----------------------------------------------------------------------------| r_work (start): 0.2626 rms_B_bonded: 3.81 r_work: 0.2472 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2472 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2470 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2470 r_free = 0.2470 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2470 r_free = 0.2470 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2470 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9038 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13841 Z= 0.119 Angle : 0.613 8.281 18847 Z= 0.309 Chirality : 0.041 0.241 2010 Planarity : 0.005 0.082 2410 Dihedral : 10.954 115.437 2249 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.59 % Allowed : 24.93 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.19), residues: 1630 helix: 2.95 (0.73), residues: 45 sheet: -0.17 (0.19), residues: 655 loop : -1.10 (0.18), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 133 HIS 0.001 0.000 HIS B 62 PHE 0.016 0.001 PHE E 136 TYR 0.015 0.001 TYR A 117 ARG 0.009 0.001 ARG B 204 Details of bonding type rmsd link_NAG-ASN : bond 0.00169 ( 15) link_NAG-ASN : angle 2.15680 ( 45) link_BETA1-4 : bond 0.01332 ( 5) link_BETA1-4 : angle 4.81807 ( 15) hydrogen bonds : bond 0.02876 ( 421) hydrogen bonds : angle 5.14244 ( 1230) SS BOND : bond 0.00320 ( 16) SS BOND : angle 0.66323 ( 32) covalent geometry : bond 0.00278 (13805) covalent geometry : angle 0.58948 (18755) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 264 time to evaluate : 1.494 Fit side-chains revert: symmetry clash REVERT: A 75 LYS cc_start: 0.9391 (OUTLIER) cc_final: 0.9148 (mtmm) REVERT: A 172 GLU cc_start: 0.8973 (mt-10) cc_final: 0.8768 (tt0) REVERT: A 191 LYS cc_start: 0.9003 (mtpt) cc_final: 0.8190 (tmtt) REVERT: B 97 GLU cc_start: 0.9065 (pt0) cc_final: 0.8770 (mp0) REVERT: D 97 GLU cc_start: 0.9132 (pt0) cc_final: 0.8754 (mp0) REVERT: D 170 ASN cc_start: 0.9114 (t0) cc_final: 0.8711 (t0) REVERT: D 192 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8126 (tp30) REVERT: E 97 GLU cc_start: 0.9050 (pt0) cc_final: 0.8708 (mp0) REVERT: F 84 ASN cc_start: 0.7750 (m-40) cc_final: 0.7485 (m110) REVERT: H 13 GLN cc_start: 0.7609 (mm-40) cc_final: 0.6973 (mm110) REVERT: H 73 ASP cc_start: 0.9023 (t0) cc_final: 0.8743 (t0) REVERT: H 84 ASN cc_start: 0.7885 (m-40) cc_final: 0.7584 (m-40) REVERT: I 45 ARG cc_start: 0.8657 (ttp80) cc_final: 0.8085 (tpp80) REVERT: I 73 ASP cc_start: 0.8942 (t0) cc_final: 0.8669 (t0) REVERT: I 87 LYS cc_start: 0.9280 (OUTLIER) cc_final: 0.8866 (mttp) outliers start: 51 outliers final: 22 residues processed: 300 average time/residue: 1.8875 time to fit residues: 602.7027 Evaluate side-chains 280 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 255 time to evaluate : 2.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 192 GLU Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 114 CYS Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 87 LYS Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 16 ASP Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 120 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 107 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 122 optimal weight: 8.9990 chunk 147 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 139 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN B 3 GLN B 46 ASN ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 GLN ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 ASN F 13 GLN G 13 GLN I 13 GLN J 13 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.073844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.052489 restraints weight = 55578.476| |-----------------------------------------------------------------------------| r_work (start): 0.2557 rms_B_bonded: 3.68 r_work: 0.2406 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2406 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2401 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2401 r_free = 0.2401 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2401 r_free = 0.2401 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2401 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9085 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13841 Z= 0.206 Angle : 0.652 7.943 18847 Z= 0.326 Chirality : 0.043 0.227 2010 Planarity : 0.005 0.076 2410 Dihedral : 10.786 115.477 2246 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.52 % Allowed : 25.07 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.19), residues: 1630 helix: 1.89 (0.76), residues: 50 sheet: -0.10 (0.19), residues: 650 loop : -1.15 (0.18), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 133 HIS 0.003 0.001 HIS E 62 PHE 0.014 0.001 PHE C 2 TYR 0.012 0.001 TYR E 128 ARG 0.008 0.001 ARG B 204 Details of bonding type rmsd link_NAG-ASN : bond 0.00318 ( 15) link_NAG-ASN : angle 2.25254 ( 45) link_BETA1-4 : bond 0.00850 ( 5) link_BETA1-4 : angle 4.91033 ( 15) hydrogen bonds : bond 0.03248 ( 421) hydrogen bonds : angle 5.20809 ( 1230) SS BOND : bond 0.00456 ( 16) SS BOND : angle 0.83970 ( 32) covalent geometry : bond 0.00471 (13805) covalent geometry : angle 0.62803 (18755) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 254 time to evaluate : 2.155 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.9420 (OUTLIER) cc_final: 0.9158 (mtmm) REVERT: A 97 GLU cc_start: 0.9067 (pt0) cc_final: 0.8729 (mp0) REVERT: A 172 GLU cc_start: 0.9003 (mt-10) cc_final: 0.8780 (tt0) REVERT: A 191 LYS cc_start: 0.9002 (mtpt) cc_final: 0.8165 (tmtt) REVERT: B 97 GLU cc_start: 0.9069 (pt0) cc_final: 0.8764 (mp0) REVERT: B 192 GLU cc_start: 0.8467 (tp30) cc_final: 0.8189 (tp30) REVERT: C 192 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8116 (tp30) REVERT: D 40 MET cc_start: 0.9298 (OUTLIER) cc_final: 0.8999 (mtm) REVERT: D 97 GLU cc_start: 0.9168 (pt0) cc_final: 0.8768 (mp0) REVERT: D 192 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8136 (tp30) REVERT: E 97 GLU cc_start: 0.9056 (pt0) cc_final: 0.8716 (mp0) REVERT: F 43 LYS cc_start: 0.9253 (ttmm) cc_final: 0.9041 (mppt) REVERT: G 87 LYS cc_start: 0.9325 (mttt) cc_final: 0.9100 (mttt) REVERT: H 73 ASP cc_start: 0.9080 (t0) cc_final: 0.8657 (t0) REVERT: H 84 ASN cc_start: 0.7972 (m-40) cc_final: 0.7614 (m-40) REVERT: I 73 ASP cc_start: 0.9004 (t0) cc_final: 0.8669 (t0) REVERT: I 84 ASN cc_start: 0.7903 (m-40) cc_final: 0.7667 (m-40) REVERT: I 87 LYS cc_start: 0.9296 (OUTLIER) cc_final: 0.8972 (mttp) outliers start: 50 outliers final: 21 residues processed: 290 average time/residue: 2.5132 time to fit residues: 773.0781 Evaluate side-chains 274 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 248 time to evaluate : 1.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 192 GLU Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 114 CYS Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain I residue 76 LYS Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 87 LYS Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 120 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 101 optimal weight: 8.9990 chunk 56 optimal weight: 0.9980 chunk 154 optimal weight: 0.0270 chunk 46 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 109 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 2 optimal weight: 0.0970 chunk 117 optimal weight: 0.1980 chunk 89 optimal weight: 5.9990 chunk 121 optimal weight: 0.7980 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN B 3 GLN B 46 ASN ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 GLN ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 ASN F 13 GLN H 13 GLN I 13 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.076598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.055309 restraints weight = 57163.473| |-----------------------------------------------------------------------------| r_work (start): 0.2621 rms_B_bonded: 3.77 r_work: 0.2468 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2468 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2464 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2464 r_free = 0.2464 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2464 r_free = 0.2464 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2464 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9042 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13841 Z= 0.118 Angle : 0.614 9.076 18847 Z= 0.307 Chirality : 0.041 0.206 2010 Planarity : 0.005 0.069 2410 Dihedral : 10.340 115.003 2245 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.54 % Allowed : 26.41 % Favored : 71.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.19), residues: 1630 helix: 2.80 (0.75), residues: 45 sheet: -0.13 (0.19), residues: 655 loop : -1.22 (0.18), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 133 HIS 0.001 0.000 HIS B 62 PHE 0.009 0.001 PHE E 136 TYR 0.012 0.001 TYR C 117 ARG 0.008 0.001 ARG A 204 Details of bonding type rmsd link_NAG-ASN : bond 0.00157 ( 15) link_NAG-ASN : angle 2.10728 ( 45) link_BETA1-4 : bond 0.01275 ( 5) link_BETA1-4 : angle 4.68921 ( 15) hydrogen bonds : bond 0.02630 ( 421) hydrogen bonds : angle 4.95800 ( 1230) SS BOND : bond 0.00280 ( 16) SS BOND : angle 0.68431 ( 32) covalent geometry : bond 0.00274 (13805) covalent geometry : angle 0.59153 (18755) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 254 time to evaluate : 1.502 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.9077 (pt0) cc_final: 0.8731 (mp0) REVERT: A 191 LYS cc_start: 0.8947 (mtpt) cc_final: 0.8152 (tmtt) REVERT: B 97 GLU cc_start: 0.9069 (pt0) cc_final: 0.8750 (mp0) REVERT: C 181 LYS cc_start: 0.9419 (OUTLIER) cc_final: 0.9154 (ptmm) REVERT: D 40 MET cc_start: 0.9247 (OUTLIER) cc_final: 0.8940 (mtm) REVERT: D 43 ASP cc_start: 0.9315 (t0) cc_final: 0.8851 (t0) REVERT: D 46 ASN cc_start: 0.9312 (m110) cc_final: 0.8948 (m110) REVERT: D 97 GLU cc_start: 0.9146 (pt0) cc_final: 0.8720 (mp0) REVERT: D 192 GLU cc_start: 0.8434 (tp30) cc_final: 0.8157 (tp30) REVERT: E 97 GLU cc_start: 0.9052 (pt0) cc_final: 0.8698 (mp0) REVERT: E 170 ASN cc_start: 0.9080 (t0) cc_final: 0.8460 (t0) REVERT: F 84 ASN cc_start: 0.7694 (m-40) cc_final: 0.7412 (m110) REVERT: G 11 LEU cc_start: 0.9559 (tt) cc_final: 0.9353 (tm) REVERT: G 87 LYS cc_start: 0.9317 (mttt) cc_final: 0.9089 (ptpt) REVERT: H 3 GLN cc_start: 0.8706 (mt0) cc_final: 0.8488 (tt0) REVERT: H 73 ASP cc_start: 0.9065 (t0) cc_final: 0.8572 (t0) REVERT: H 84 ASN cc_start: 0.7904 (m-40) cc_final: 0.7558 (m-40) REVERT: I 45 ARG cc_start: 0.8381 (ttp80) cc_final: 0.7901 (tpp80) REVERT: I 73 ASP cc_start: 0.8988 (t0) cc_final: 0.8623 (t0) REVERT: I 84 ASN cc_start: 0.7569 (m-40) cc_final: 0.7111 (m-40) outliers start: 36 outliers final: 17 residues processed: 284 average time/residue: 2.2088 time to fit residues: 664.9450 Evaluate side-chains 257 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 238 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 120 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 141 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 136 optimal weight: 8.9990 chunk 102 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 1 optimal weight: 0.0070 chunk 39 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 overall best weight: 1.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 ASN ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 GLN ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 ASN F 13 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.074741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.053722 restraints weight = 51291.743| |-----------------------------------------------------------------------------| r_work (start): 0.2581 rms_B_bonded: 3.56 r_work: 0.2433 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2433 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2429 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2429 r_free = 0.2429 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2429 r_free = 0.2429 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2429 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9070 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13841 Z= 0.169 Angle : 0.639 7.791 18847 Z= 0.320 Chirality : 0.042 0.201 2010 Planarity : 0.005 0.067 2410 Dihedral : 10.255 115.243 2242 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.25 % Allowed : 27.11 % Favored : 70.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.19), residues: 1630 helix: 1.73 (0.76), residues: 50 sheet: -0.09 (0.19), residues: 650 loop : -1.19 (0.18), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 133 HIS 0.002 0.001 HIS E 62 PHE 0.012 0.001 PHE C 2 TYR 0.013 0.001 TYR E 128 ARG 0.009 0.001 ARG B 204 Details of bonding type rmsd link_NAG-ASN : bond 0.00265 ( 15) link_NAG-ASN : angle 2.12528 ( 45) link_BETA1-4 : bond 0.01093 ( 5) link_BETA1-4 : angle 4.72508 ( 15) hydrogen bonds : bond 0.02977 ( 421) hydrogen bonds : angle 5.00870 ( 1230) SS BOND : bond 0.00415 ( 16) SS BOND : angle 0.85243 ( 32) covalent geometry : bond 0.00393 (13805) covalent geometry : angle 0.61636 (18755) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 244 time to evaluate : 1.685 Fit side-chains revert: symmetry clash REVERT: A 97 GLU cc_start: 0.9042 (pt0) cc_final: 0.8710 (mp0) REVERT: A 191 LYS cc_start: 0.8973 (mtpt) cc_final: 0.8164 (tmtt) REVERT: C 1 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.6955 (tt0) REVERT: C 181 LYS cc_start: 0.9419 (OUTLIER) cc_final: 0.9144 (ptmm) REVERT: C 192 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8103 (tp30) REVERT: D 40 MET cc_start: 0.9258 (OUTLIER) cc_final: 0.8945 (mtm) REVERT: D 43 ASP cc_start: 0.9312 (t0) cc_final: 0.8828 (t0) REVERT: D 70 GLU cc_start: 0.8952 (OUTLIER) cc_final: 0.8495 (mt-10) REVERT: D 97 GLU cc_start: 0.9141 (pt0) cc_final: 0.8701 (mp0) REVERT: D 192 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8192 (tp30) REVERT: E 97 GLU cc_start: 0.9046 (pt0) cc_final: 0.8708 (mp0) REVERT: F 39 GLN cc_start: 0.9074 (tp-100) cc_final: 0.8673 (tp40) REVERT: F 43 LYS cc_start: 0.8719 (mppt) cc_final: 0.8506 (mppt) REVERT: G 11 LEU cc_start: 0.9580 (tt) cc_final: 0.9364 (tm) REVERT: G 65 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8836 (mmtm) REVERT: G 87 LYS cc_start: 0.9329 (mttt) cc_final: 0.9049 (ptpt) REVERT: H 3 GLN cc_start: 0.8773 (mt0) cc_final: 0.8507 (tt0) REVERT: H 73 ASP cc_start: 0.9044 (t0) cc_final: 0.8842 (t0) REVERT: H 84 ASN cc_start: 0.7943 (m-40) cc_final: 0.7535 (m-40) REVERT: I 45 ARG cc_start: 0.8406 (ttp80) cc_final: 0.7967 (tpp80) REVERT: I 73 ASP cc_start: 0.9011 (t0) cc_final: 0.8639 (t0) REVERT: I 84 ASN cc_start: 0.7804 (m-40) cc_final: 0.7230 (m-40) REVERT: J 73 ASP cc_start: 0.9061 (t0) cc_final: 0.8844 (t0) outliers start: 32 outliers final: 18 residues processed: 268 average time/residue: 1.8467 time to fit residues: 525.8816 Evaluate side-chains 256 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 231 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 1 GLU Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 192 GLU Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain G residue 65 LYS Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain I residue 76 LYS Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 65 LYS Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 120 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 105 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 117 optimal weight: 0.5980 chunk 108 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 GLN B 46 ASN ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 ASN C 116 GLN ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.073964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.052397 restraints weight = 71620.076| |-----------------------------------------------------------------------------| r_work (start): 0.2545 rms_B_bonded: 4.00 r_work: 0.2385 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2385 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2381 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2381 r_free = 0.2381 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2381 r_free = 0.2381 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2381 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9098 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13841 Z= 0.203 Angle : 0.655 7.748 18847 Z= 0.329 Chirality : 0.043 0.200 2010 Planarity : 0.005 0.066 2410 Dihedral : 10.293 115.401 2242 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.96 % Allowed : 26.55 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.19), residues: 1630 helix: 1.60 (0.76), residues: 50 sheet: -0.14 (0.19), residues: 650 loop : -1.18 (0.18), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP E 133 HIS 0.003 0.001 HIS E 62 PHE 0.013 0.001 PHE D 2 TYR 0.012 0.001 TYR A 128 ARG 0.009 0.001 ARG B 204 Details of bonding type rmsd link_NAG-ASN : bond 0.00296 ( 15) link_NAG-ASN : angle 2.18109 ( 45) link_BETA1-4 : bond 0.01018 ( 5) link_BETA1-4 : angle 4.83209 ( 15) hydrogen bonds : bond 0.03140 ( 421) hydrogen bonds : angle 5.10578 ( 1230) SS BOND : bond 0.00379 ( 16) SS BOND : angle 1.01838 ( 32) covalent geometry : bond 0.00469 (13805) covalent geometry : angle 0.63207 (18755) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 236 time to evaluate : 1.563 Fit side-chains revert: symmetry clash REVERT: A 75 LYS cc_start: 0.9438 (OUTLIER) cc_final: 0.9177 (mtmm) REVERT: A 97 GLU cc_start: 0.9044 (pt0) cc_final: 0.8701 (mp0) REVERT: A 191 LYS cc_start: 0.8976 (mtpt) cc_final: 0.8141 (tmtt) REVERT: C 1 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7066 (tt0) REVERT: C 192 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8128 (tp30) REVERT: D 40 MET cc_start: 0.9310 (OUTLIER) cc_final: 0.9013 (mtm) REVERT: D 43 ASP cc_start: 0.9305 (t0) cc_final: 0.8862 (t0) REVERT: D 97 GLU cc_start: 0.9161 (pt0) cc_final: 0.8699 (mp0) REVERT: D 192 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8335 (tp30) REVERT: E 97 GLU cc_start: 0.9087 (pt0) cc_final: 0.8717 (mp0) REVERT: F 73 ASP cc_start: 0.9079 (t0) cc_final: 0.8667 (t0) REVERT: F 87 LYS cc_start: 0.9358 (mttt) cc_final: 0.9066 (ptpt) REVERT: G 65 LYS cc_start: 0.9115 (OUTLIER) cc_final: 0.8868 (mmtm) REVERT: G 87 LYS cc_start: 0.9348 (mttt) cc_final: 0.9077 (ptpt) REVERT: H 3 GLN cc_start: 0.8837 (mt0) cc_final: 0.8570 (tt0) REVERT: H 73 ASP cc_start: 0.9045 (t0) cc_final: 0.8820 (t0) REVERT: H 84 ASN cc_start: 0.7992 (m-40) cc_final: 0.7572 (m-40) REVERT: I 45 ARG cc_start: 0.8453 (ttp80) cc_final: 0.8004 (tpp80) REVERT: I 73 ASP cc_start: 0.9051 (t0) cc_final: 0.8667 (t0) REVERT: I 84 ASN cc_start: 0.7911 (m-40) cc_final: 0.7693 (m-40) REVERT: J 73 ASP cc_start: 0.9096 (t0) cc_final: 0.8872 (t0) outliers start: 42 outliers final: 24 residues processed: 268 average time/residue: 1.8041 time to fit residues: 514.6591 Evaluate side-chains 271 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 241 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 1 GLU Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 192 GLU Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain F residue 65 LYS Chi-restraints excluded: chain G residue 44 GLU Chi-restraints excluded: chain G residue 65 LYS Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain I residue 76 LYS Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 43 LYS Chi-restraints excluded: chain J residue 65 LYS Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 120 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 3 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 98 optimal weight: 0.4980 chunk 146 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 chunk 122 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 GLN B 46 ASN ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 GLN ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.074935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.053535 restraints weight = 67057.175| |-----------------------------------------------------------------------------| r_work (start): 0.2573 rms_B_bonded: 3.92 r_work: 0.2416 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2416 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2403 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2403 r_free = 0.2403 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2403 r_free = 0.2403 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2403 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9076 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13841 Z= 0.150 Angle : 0.645 8.178 18847 Z= 0.323 Chirality : 0.042 0.186 2010 Planarity : 0.005 0.065 2410 Dihedral : 10.192 115.124 2242 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.32 % Allowed : 27.46 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.19), residues: 1630 helix: 1.63 (0.76), residues: 50 sheet: -0.15 (0.19), residues: 650 loop : -1.17 (0.18), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP E 133 HIS 0.002 0.001 HIS A 62 PHE 0.010 0.001 PHE D 2 TYR 0.014 0.001 TYR D 128 ARG 0.008 0.001 ARG C 204 Details of bonding type rmsd link_NAG-ASN : bond 0.00221 ( 15) link_NAG-ASN : angle 2.11432 ( 45) link_BETA1-4 : bond 0.01191 ( 5) link_BETA1-4 : angle 4.73567 ( 15) hydrogen bonds : bond 0.02862 ( 421) hydrogen bonds : angle 5.02887 ( 1230) SS BOND : bond 0.00302 ( 16) SS BOND : angle 0.88127 ( 32) covalent geometry : bond 0.00350 (13805) covalent geometry : angle 0.62265 (18755) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 247 time to evaluate : 1.464 Fit side-chains revert: symmetry clash REVERT: A 75 LYS cc_start: 0.9435 (OUTLIER) cc_final: 0.9190 (mtmm) REVERT: A 97 GLU cc_start: 0.9036 (pt0) cc_final: 0.8688 (mp0) REVERT: A 191 LYS cc_start: 0.8922 (mtpt) cc_final: 0.8113 (tmtt) REVERT: C 1 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.6931 (tt0) REVERT: C 192 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8160 (tp30) REVERT: D 40 MET cc_start: 0.9288 (OUTLIER) cc_final: 0.8998 (mtm) REVERT: D 43 ASP cc_start: 0.9274 (t0) cc_final: 0.9012 (t0) REVERT: D 97 GLU cc_start: 0.9147 (pt0) cc_final: 0.8687 (mp0) REVERT: E 97 GLU cc_start: 0.9074 (pt0) cc_final: 0.8705 (mp0) REVERT: F 39 GLN cc_start: 0.9079 (tp-100) cc_final: 0.8634 (tp-100) REVERT: F 73 ASP cc_start: 0.9072 (t0) cc_final: 0.8653 (t0) REVERT: F 87 LYS cc_start: 0.9343 (mttt) cc_final: 0.9028 (ptpt) REVERT: F 108 ARG cc_start: 0.8320 (tpt170) cc_final: 0.8025 (mmt180) REVERT: G 87 LYS cc_start: 0.9327 (mttt) cc_final: 0.9046 (ptpt) REVERT: H 3 GLN cc_start: 0.8817 (mt0) cc_final: 0.8567 (tt0) REVERT: H 84 ASN cc_start: 0.8003 (m-40) cc_final: 0.7649 (m-40) REVERT: H 85 ASN cc_start: 0.9185 (p0) cc_final: 0.8840 (p0) REVERT: I 45 ARG cc_start: 0.8445 (ttp80) cc_final: 0.8032 (tpp80) REVERT: I 73 ASP cc_start: 0.9038 (t0) cc_final: 0.8635 (t0) REVERT: I 84 ASN cc_start: 0.7941 (m-40) cc_final: 0.7688 (m-40) REVERT: J 73 ASP cc_start: 0.9076 (t0) cc_final: 0.8865 (t0) outliers start: 33 outliers final: 20 residues processed: 273 average time/residue: 1.8820 time to fit residues: 545.7979 Evaluate side-chains 267 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 243 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 1 GLU Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 43 LYS Chi-restraints excluded: chain J residue 65 LYS Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 120 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 65 optimal weight: 1.9990 chunk 137 optimal weight: 8.9990 chunk 111 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 93 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 151 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 125 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 GLN B 46 ASN ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.073416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2582 r_free = 0.2582 target = 0.051935 restraints weight = 67554.333| |-----------------------------------------------------------------------------| r_work (start): 0.2535 rms_B_bonded: 3.92 r_work: 0.2376 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2376 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2374 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2374 r_free = 0.2374 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2374 r_free = 0.2374 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2374 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9098 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13841 Z= 0.215 Angle : 0.678 7.759 18847 Z= 0.340 Chirality : 0.043 0.198 2010 Planarity : 0.005 0.063 2410 Dihedral : 10.289 115.323 2242 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.54 % Allowed : 27.25 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.19), residues: 1630 helix: 1.54 (0.75), residues: 50 sheet: -0.20 (0.19), residues: 645 loop : -1.18 (0.18), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP E 133 HIS 0.003 0.001 HIS D 62 PHE 0.014 0.001 PHE D 2 TYR 0.013 0.001 TYR A 128 ARG 0.009 0.001 ARG C 204 Details of bonding type rmsd link_NAG-ASN : bond 0.00332 ( 15) link_NAG-ASN : angle 2.19239 ( 45) link_BETA1-4 : bond 0.00973 ( 5) link_BETA1-4 : angle 4.84894 ( 15) hydrogen bonds : bond 0.03225 ( 421) hydrogen bonds : angle 5.17671 ( 1230) SS BOND : bond 0.00380 ( 16) SS BOND : angle 1.00675 ( 32) covalent geometry : bond 0.00497 (13805) covalent geometry : angle 0.65553 (18755) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 248 time to evaluate : 1.505 Fit side-chains REVERT: A 75 LYS cc_start: 0.9455 (OUTLIER) cc_final: 0.9191 (mtmm) REVERT: A 97 GLU cc_start: 0.9051 (pt0) cc_final: 0.8713 (mp0) REVERT: A 191 LYS cc_start: 0.8953 (mtpt) cc_final: 0.8101 (tmtt) REVERT: C 1 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7174 (tt0) REVERT: D 40 MET cc_start: 0.9302 (OUTLIER) cc_final: 0.9029 (mtm) REVERT: D 43 ASP cc_start: 0.9264 (t0) cc_final: 0.9037 (t0) REVERT: D 97 GLU cc_start: 0.9146 (pt0) cc_final: 0.8680 (mp0) REVERT: E 97 GLU cc_start: 0.9091 (pt0) cc_final: 0.8708 (mp0) REVERT: F 39 GLN cc_start: 0.9058 (tp-100) cc_final: 0.8676 (tp40) REVERT: F 43 LYS cc_start: 0.9256 (mtmm) cc_final: 0.8750 (mppt) REVERT: F 73 ASP cc_start: 0.9087 (t0) cc_final: 0.8647 (t0) REVERT: F 87 LYS cc_start: 0.9371 (mttt) cc_final: 0.9056 (ptpt) REVERT: G 87 LYS cc_start: 0.9352 (mttt) cc_final: 0.9148 (mttp) REVERT: H 85 ASN cc_start: 0.9222 (p0) cc_final: 0.8852 (p0) REVERT: I 45 ARG cc_start: 0.8480 (ttp80) cc_final: 0.8098 (tpp80) REVERT: I 73 ASP cc_start: 0.9048 (t0) cc_final: 0.8642 (t0) REVERT: J 73 ASP cc_start: 0.9102 (t0) cc_final: 0.8879 (t0) outliers start: 36 outliers final: 24 residues processed: 276 average time/residue: 2.0455 time to fit residues: 603.9999 Evaluate side-chains 269 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 242 time to evaluate : 1.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 1 GLU Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain G residue 44 GLU Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain I residue 76 LYS Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 43 LYS Chi-restraints excluded: chain J residue 65 LYS Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 120 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 110 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 138 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 GLN ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.073481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2590 r_free = 0.2590 target = 0.052344 restraints weight = 55355.098| |-----------------------------------------------------------------------------| r_work (start): 0.2544 rms_B_bonded: 3.64 r_work: 0.2391 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2391 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2376 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2376 r_free = 0.2376 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2376 r_free = 0.2376 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2376 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9095 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13841 Z= 0.205 Angle : 0.677 7.915 18847 Z= 0.339 Chirality : 0.043 0.192 2010 Planarity : 0.005 0.064 2410 Dihedral : 10.294 115.316 2242 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.11 % Allowed : 27.75 % Favored : 70.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.19), residues: 1630 helix: 1.52 (0.75), residues: 50 sheet: -0.23 (0.19), residues: 645 loop : -1.17 (0.18), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP E 133 HIS 0.002 0.001 HIS A 62 PHE 0.013 0.001 PHE D 2 TYR 0.015 0.001 TYR D 128 ARG 0.010 0.001 ARG B 204 Details of bonding type rmsd link_NAG-ASN : bond 0.00291 ( 15) link_NAG-ASN : angle 2.22335 ( 45) link_BETA1-4 : bond 0.01014 ( 5) link_BETA1-4 : angle 4.87710 ( 15) hydrogen bonds : bond 0.03151 ( 421) hydrogen bonds : angle 5.18135 ( 1230) SS BOND : bond 0.00349 ( 16) SS BOND : angle 0.97374 ( 32) covalent geometry : bond 0.00475 (13805) covalent geometry : angle 0.65401 (18755) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 240 time to evaluate : 1.514 Fit side-chains REVERT: A 75 LYS cc_start: 0.9452 (OUTLIER) cc_final: 0.9201 (mtmm) REVERT: A 97 GLU cc_start: 0.9026 (pt0) cc_final: 0.8717 (mp0) REVERT: A 191 LYS cc_start: 0.8950 (mtpt) cc_final: 0.8117 (tmtt) REVERT: B 172 GLU cc_start: 0.8986 (OUTLIER) cc_final: 0.8481 (tt0) REVERT: C 1 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7085 (tt0) REVERT: D 43 ASP cc_start: 0.9269 (t0) cc_final: 0.9030 (t0) REVERT: D 97 GLU cc_start: 0.9128 (pt0) cc_final: 0.8679 (mp0) REVERT: E 97 GLU cc_start: 0.9080 (pt0) cc_final: 0.8708 (mp0) REVERT: F 39 GLN cc_start: 0.9073 (tp-100) cc_final: 0.8718 (tp40) REVERT: F 43 LYS cc_start: 0.9255 (mtmm) cc_final: 0.8799 (mppt) REVERT: F 73 ASP cc_start: 0.9092 (t0) cc_final: 0.8663 (t0) REVERT: F 87 LYS cc_start: 0.9370 (mttt) cc_final: 0.9053 (ptpt) REVERT: H 3 GLN cc_start: 0.8841 (mt0) cc_final: 0.8594 (tt0) REVERT: H 85 ASN cc_start: 0.9240 (p0) cc_final: 0.8839 (p0) REVERT: I 45 ARG cc_start: 0.8526 (ttp80) cc_final: 0.8106 (tpp80) REVERT: I 73 ASP cc_start: 0.9040 (t0) cc_final: 0.8637 (t0) REVERT: J 73 ASP cc_start: 0.9106 (t0) cc_final: 0.8880 (t0) outliers start: 30 outliers final: 23 residues processed: 264 average time/residue: 2.5622 time to fit residues: 718.7297 Evaluate side-chains 265 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 239 time to evaluate : 1.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 1 GLU Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain G residue 44 GLU Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain J residue 43 LYS Chi-restraints excluded: chain J residue 65 LYS Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 120 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 155 optimal weight: 0.9990 chunk 125 optimal weight: 6.9990 chunk 104 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 113 optimal weight: 8.9990 chunk 124 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 157 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN B 3 GLN B 46 ASN ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 ASN I 84 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.072069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2549 r_free = 0.2549 target = 0.050562 restraints weight = 63994.441| |-----------------------------------------------------------------------------| r_work (start): 0.2494 rms_B_bonded: 3.82 r_work: 0.2336 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2336 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2345 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2345 r_free = 0.2345 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2345 r_free = 0.2345 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2345 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9118 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 13841 Z= 0.268 Angle : 0.711 8.280 18847 Z= 0.356 Chirality : 0.045 0.200 2010 Planarity : 0.005 0.065 2410 Dihedral : 10.422 115.434 2242 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.18 % Allowed : 27.75 % Favored : 70.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.19), residues: 1630 helix: 1.32 (0.74), residues: 50 sheet: -0.28 (0.19), residues: 635 loop : -1.16 (0.18), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP E 133 HIS 0.004 0.001 HIS E 62 PHE 0.015 0.002 PHE D 2 TYR 0.015 0.001 TYR A 128 ARG 0.010 0.001 ARG B 204 Details of bonding type rmsd link_NAG-ASN : bond 0.00398 ( 15) link_NAG-ASN : angle 2.35048 ( 45) link_BETA1-4 : bond 0.00877 ( 5) link_BETA1-4 : angle 5.06062 ( 15) hydrogen bonds : bond 0.03476 ( 421) hydrogen bonds : angle 5.34272 ( 1230) SS BOND : bond 0.00437 ( 16) SS BOND : angle 1.09624 ( 32) covalent geometry : bond 0.00620 (13805) covalent geometry : angle 0.68707 (18755) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14386.47 seconds wall clock time: 258 minutes 9.74 seconds (15489.74 seconds total)