Starting phenix.real_space_refine on Wed Aug 5 19:43:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bto_44894/08_2026/9bto_44894.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bto_44894/08_2026/9bto_44894.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bto_44894/08_2026/9bto_44894.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bto_44894/08_2026/9bto_44894.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bto_44894/08_2026/9bto_44894.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bto_44894/08_2026/9bto_44894.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 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 60 5.16 5 C 7170 2.51 5 N 1965 2.21 5 O 2325 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11520 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 2517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2517 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 306} Chain: "B" Number of atoms: 1122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1122 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 1, 'TRANS': 145} Chain: "C" Number of atoms: 2517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2517 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 306} Chain: "D" Number of atoms: 1122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1122 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 1, 'TRANS': 145} Chain: "E" Number of atoms: 2517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2517 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 306} Chain: "F" Number of atoms: 1122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1122 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 1, 'TRANS': 145} Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" 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: "K" 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: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 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: "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: 2.22, per 1000 atoms: 0.19 Number of scatterers: 11520 At special positions: 0 Unit cell: (90.468, 93.34, 140.01, 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 60 16.00 O 2325 8.00 N 1965 7.00 C 7170 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 57 " distance=2.05 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 72 " distance=2.03 Simple disulfide: pdb=" SG CYS A 94 " - pdb=" SG CYS A 143 " distance=2.02 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 294 " - pdb=" SG CYS A 320 " distance=2.02 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.04 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 57 " distance=2.05 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 72 " distance=2.03 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 143 " distance=2.02 Simple disulfide: pdb=" SG CYS C 180 " - pdb=" SG CYS C 274 " distance=2.03 Simple disulfide: pdb=" SG CYS C 294 " - pdb=" SG CYS C 320 " distance=2.02 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.04 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 57 " distance=2.05 Simple disulfide: pdb=" SG CYS E 60 " - pdb=" SG CYS E 72 " distance=2.03 Simple disulfide: pdb=" SG CYS E 94 " - pdb=" SG CYS E 143 " distance=2.02 Simple disulfide: pdb=" SG CYS E 180 " - pdb=" SG CYS E 274 " distance=2.03 Simple disulfide: pdb=" SG CYS E 294 " - pdb=" SG CYS E 320 " distance=2.02 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 148 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A 401 " - " ASN A 59 " " NAG A 402 " - " ASN A 232 " " NAG C 401 " - " ASN C 59 " " NAG C 402 " - " ASN C 232 " " NAG E 401 " - " ASN E 59 " " NAG E 402 " - " ASN E 232 " " NAG G 1 " - " ASN A 145 " " NAG H 1 " - " ASN A 196 " " NAG I 1 " - " ASN A 303 " " NAG J 1 " - " ASN A 25 " " NAG K 1 " - " ASN A 332 " " NAG L 1 " - " ASN C 145 " " NAG M 1 " - " ASN C 196 " " NAG N 1 " - " ASN C 303 " " NAG O 1 " - " ASN C 25 " " NAG P 1 " - " ASN C 332 " " NAG Q 1 " - " ASN E 145 " " NAG R 1 " - " ASN E 196 " " NAG S 1 " - " ASN E 303 " " NAG T 1 " - " ASN E 25 " " NAG U 1 " - " ASN E 332 " Time building additional restraints: 1.05 Conformation dependent library (CDL) restraints added in 511.0 milliseconds 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2592 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 30 sheets defined 24.2% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 61 through 67 Processing helix chain 'A' and resid 98 through 102 Processing helix chain 'A' and resid 103 through 105 No H-bonds generated for 'chain 'A' and resid 103 through 105' Processing helix chain 'A' and resid 106 through 112 Processing helix chain 'A' and resid 196 through 204 Processing helix chain 'B' and resid 37 through 57 Processing helix chain 'B' and resid 74 through 109 Processing helix chain 'B' and resid 110 through 127 Processing helix chain 'B' and resid 145 through 154 Processing helix chain 'C' and resid 61 through 67 Processing helix chain 'C' and resid 98 through 102 Processing helix chain 'C' and resid 103 through 105 No H-bonds generated for 'chain 'C' and resid 103 through 105' Processing helix chain 'C' and resid 106 through 112 Processing helix chain 'C' and resid 196 through 204 Processing helix chain 'D' and resid 37 through 57 Processing helix chain 'D' and resid 74 through 109 Processing helix chain 'D' and resid 110 through 127 Processing helix chain 'D' and resid 145 through 154 Processing helix chain 'E' and resid 61 through 67 Processing helix chain 'E' and resid 98 through 102 Processing helix chain 'E' and resid 103 through 105 No H-bonds generated for 'chain 'E' and resid 103 through 105' Processing helix chain 'E' and resid 106 through 112 Processing helix chain 'E' and resid 196 through 204 Processing helix chain 'F' and resid 37 through 57 Processing helix chain 'F' and resid 74 through 109 Processing helix chain 'F' and resid 110 through 127 Processing helix chain 'F' and resid 145 through 154 Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 18 removed outlier: 3.876A pdb=" N GLY A 22 " --> pdb=" O THR A 18 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 31 Processing sheet with id=AA3, first strand: chain 'A' and resid 33 through 34 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 removed outlier: 6.113A pdb=" N ASN A 43 " --> pdb=" O ALA A 292 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 49 through 50 Processing sheet with id=AA6, first strand: chain 'A' and resid 116 through 119 removed outlier: 7.584A pdb=" N VAL A 189 " --> pdb=" O PRO A 269 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ILE A 266 " --> pdb=" O ALA A 159 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N TRP A 158 " --> pdb=" O GLY A 138 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 116 through 119 Processing sheet with id=AA8, first strand: chain 'A' and resid 140 through 144 removed outlier: 4.951A pdb=" N CYS A 143 " --> pdb=" O GLY A 151 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 172 through 176 Processing sheet with id=AB1, first strand: chain 'A' and resid 300 through 302 Processing sheet with id=AB2, first strand: chain 'C' and resid 14 through 18 removed outlier: 3.876A pdb=" N GLY C 22 " --> pdb=" O THR C 18 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 29 through 31 Processing sheet with id=AB4, first strand: chain 'C' and resid 33 through 34 Processing sheet with id=AB5, first strand: chain 'C' and resid 43 through 44 removed outlier: 6.113A pdb=" N ASN C 43 " --> pdb=" O ALA C 292 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 49 through 50 Processing sheet with id=AB7, first strand: chain 'C' and resid 116 through 119 removed outlier: 7.582A pdb=" N VAL C 189 " --> pdb=" O PRO C 269 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ILE C 266 " --> pdb=" O ALA C 159 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N TRP C 158 " --> pdb=" O GLY C 138 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 116 through 119 Processing sheet with id=AB9, first strand: chain 'C' and resid 140 through 144 removed outlier: 4.951A pdb=" N CYS C 143 " --> pdb=" O GLY C 151 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 172 through 176 Processing sheet with id=AC2, first strand: chain 'C' and resid 300 through 302 Processing sheet with id=AC3, first strand: chain 'E' and resid 14 through 18 removed outlier: 3.876A pdb=" N GLY E 22 " --> pdb=" O THR E 18 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 29 through 31 Processing sheet with id=AC5, first strand: chain 'E' and resid 33 through 34 Processing sheet with id=AC6, first strand: chain 'E' and resid 43 through 44 removed outlier: 6.113A pdb=" N ASN E 43 " --> pdb=" O ALA E 292 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'E' and resid 49 through 50 Processing sheet with id=AC8, first strand: chain 'E' and resid 116 through 119 removed outlier: 7.583A pdb=" N VAL E 189 " --> pdb=" O PRO E 269 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ILE E 266 " --> pdb=" O ALA E 159 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N TRP E 158 " --> pdb=" O GLY E 138 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 116 through 119 Processing sheet with id=AD1, first strand: chain 'E' and resid 140 through 144 removed outlier: 4.951A pdb=" N CYS E 143 " --> pdb=" O GLY E 151 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 172 through 176 Processing sheet with id=AD3, first strand: chain 'E' and resid 300 through 302 459 hydrogen bonds defined for protein. 1242 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: 1.97 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 3223 1.33 - 1.47: 3353 1.47 - 1.61: 5082 1.61 - 1.74: 3 1.74 - 1.88: 78 Bond restraints: 11739 Sorted by residual: bond pdb=" CB HIS B 22 " pdb=" CG HIS B 22 " ideal model delta sigma weight residual 1.497 1.400 0.097 1.40e-02 5.10e+03 4.84e+01 bond pdb=" CB HIS F 22 " pdb=" CG HIS F 22 " ideal model delta sigma weight residual 1.497 1.400 0.097 1.40e-02 5.10e+03 4.78e+01 bond pdb=" CB HIS D 22 " pdb=" CG HIS D 22 " ideal model delta sigma weight residual 1.497 1.400 0.097 1.40e-02 5.10e+03 4.77e+01 bond pdb=" CB LEU C 330 " pdb=" CG LEU C 330 " ideal model delta sigma weight residual 1.530 1.398 0.132 2.00e-02 2.50e+03 4.36e+01 bond pdb=" CB HIS E 296 " pdb=" CG HIS E 296 " ideal model delta sigma weight residual 1.497 1.405 0.092 1.40e-02 5.10e+03 4.35e+01 ... (remaining 11734 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 12452 1.92 - 3.84: 2780 3.84 - 5.75: 556 5.75 - 7.67: 101 7.67 - 9.59: 26 Bond angle restraints: 15915 Sorted by residual: angle pdb=" CA ASP F 90 " pdb=" CB ASP F 90 " pdb=" CG ASP F 90 " ideal model delta sigma weight residual 112.60 120.90 -8.30 1.00e+00 1.00e+00 6.89e+01 angle pdb=" CA ASP D 90 " pdb=" CB ASP D 90 " pdb=" CG ASP D 90 " ideal model delta sigma weight residual 112.60 120.89 -8.29 1.00e+00 1.00e+00 6.87e+01 angle pdb=" CA ASP B 90 " pdb=" CB ASP B 90 " pdb=" CG ASP B 90 " ideal model delta sigma weight residual 112.60 120.88 -8.28 1.00e+00 1.00e+00 6.85e+01 angle pdb=" C PHE A 230 " pdb=" N PRO A 231 " pdb=" CA PRO A 231 " ideal model delta sigma weight residual 119.92 127.20 -7.28 1.07e+00 8.73e-01 4.63e+01 angle pdb=" C PHE E 230 " pdb=" N PRO E 231 " pdb=" CA PRO E 231 " ideal model delta sigma weight residual 119.92 127.18 -7.26 1.07e+00 8.73e-01 4.60e+01 ... (remaining 15910 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.09: 7377 21.09 - 42.19: 165 42.19 - 63.28: 54 63.28 - 84.37: 57 84.37 - 105.47: 45 Dihedral angle restraints: 7698 sinusoidal: 3639 harmonic: 4059 Sorted by residual: dihedral pdb=" O4 BMA M 3 " pdb=" C4 BMA M 3 " pdb=" C5 BMA M 3 " pdb=" O5 BMA M 3 " ideal model delta sinusoidal sigma weight residual -71.29 -176.76 105.47 1 3.00e+01 1.11e-03 1.35e+01 dihedral pdb=" O4 BMA H 3 " pdb=" C4 BMA H 3 " pdb=" C5 BMA H 3 " pdb=" O5 BMA H 3 " ideal model delta sinusoidal sigma weight residual -71.29 -176.76 105.47 1 3.00e+01 1.11e-03 1.35e+01 dihedral pdb=" O4 BMA R 3 " pdb=" C4 BMA R 3 " pdb=" C5 BMA R 3 " pdb=" O5 BMA R 3 " ideal model delta sinusoidal sigma weight residual -71.29 -176.74 105.45 1 3.00e+01 1.11e-03 1.35e+01 ... (remaining 7695 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1218 0.093 - 0.187: 446 0.187 - 0.280: 145 0.280 - 0.374: 84 0.374 - 0.467: 45 Chirality restraints: 1938 Sorted by residual: chirality pdb=" C1 NAG U 2 " pdb=" O4 NAG U 1 " pdb=" C2 NAG U 2 " pdb=" O5 NAG U 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.52e+02 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.49e+02 chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.44e+02 ... (remaining 1935 not shown) Planarity restraints: 2013 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 25 " -0.052 2.00e-02 2.50e+03 5.39e-02 3.63e+01 pdb=" CG ASN C 25 " 0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN C 25 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN C 25 " 0.083 2.00e-02 2.50e+03 pdb=" C1 NAG O 1 " -0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 25 " -0.052 2.00e-02 2.50e+03 5.37e-02 3.60e+01 pdb=" CG ASN E 25 " 0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN E 25 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN E 25 " 0.083 2.00e-02 2.50e+03 pdb=" C1 NAG T 1 " -0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 25 " -0.052 2.00e-02 2.50e+03 5.33e-02 3.55e+01 pdb=" CG ASN A 25 " 0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN A 25 " 0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN A 25 " 0.082 2.00e-02 2.50e+03 pdb=" C1 NAG J 1 " -0.064 2.00e-02 2.50e+03 ... (remaining 2010 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.93: 5261 2.93 - 3.42: 10513 3.42 - 3.91: 19675 3.91 - 4.41: 22081 4.41 - 4.90: 35560 Nonbonded interactions: 93090 Sorted by model distance: nonbonded pdb=" NZ LYS B 61 " pdb=" OD2 ASP D 86 " model vdw 2.436 3.120 nonbonded pdb=" NZ LYS D 61 " pdb=" OD2 ASP F 86 " model vdw 2.437 3.120 nonbonded pdb=" OD2 ASP B 86 " pdb=" NZ LYS F 61 " model vdw 2.438 3.120 nonbonded pdb=" O5 NAG J 1 " pdb=" O6 NAG J 1 " model vdw 2.444 2.432 nonbonded pdb=" O5 NAG T 1 " pdb=" O6 NAG T 1 " model vdw 2.444 2.432 ... (remaining 93085 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'O' selection = chain 'P' selection = chain 'T' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.000 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: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 10.990 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 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 : 0.024 0.132 11802 Z= 1.289 Angle : 1.776 9.589 16086 Z= 1.141 Chirality : 0.136 0.467 1938 Planarity : 0.008 0.038 1992 Dihedral : 15.344 105.468 5052 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 0.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.20), residues: 1425 helix: 0.94 (0.27), residues: 321 sheet: 0.60 (0.33), residues: 234 loop : 0.30 (0.19), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 88 TYR 0.061 0.010 TYR A 135 PHE 0.020 0.006 PHE A 192 TRP 0.048 0.008 TRP F 21 HIS 0.013 0.002 HIS A 85 Details of bonding type rmsd/Z covalent geometry : bond 0.02324 / 1.27 (11739) covalent geometry : angle 1.74309 / 1.14 (15915) SS BOND : bond 0.01175 / 0.70 ( 18) SS BOND : angle 3.01052 / 2.10 ( 36) hydrogen bonds : bond 0.15987 / 10.88 ( 435) hydrogen bonds : angle 7.48181 / 5.26 ( 1242) link_BETA1-4 : bond 0.07015 / 4.71 ( 24) link_BETA1-4 : angle 4.79440 / 3.52 ( 72) link_NAG-ASN : bond 0.07604 / 4.94 ( 21) link_NAG-ASN : angle 2.51805 / 1.65 ( 63) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.426 Fit side-chains REVERT: B 22 HIS cc_start: 0.4073 (t-90) cc_final: 0.3859 (p-80) REVERT: B 47 LYS cc_start: 0.8254 (tttt) cc_final: 0.8034 (ttmt) REVERT: B 50 LYS cc_start: 0.8664 (mttt) cc_final: 0.8347 (mmmt) REVERT: B 86 ASP cc_start: 0.8555 (t70) cc_final: 0.8296 (t0) REVERT: B 125 MET cc_start: 0.7565 (mtm) cc_final: 0.7347 (mtp) REVERT: D 22 HIS cc_start: 0.4279 (t-90) cc_final: 0.3889 (p-80) REVERT: D 50 LYS cc_start: 0.8665 (mttt) cc_final: 0.8347 (mmmt) REVERT: D 86 ASP cc_start: 0.8627 (t70) cc_final: 0.8010 (t0) REVERT: F 50 LYS cc_start: 0.8700 (mttt) cc_final: 0.8317 (mmmt) REVERT: F 86 ASP cc_start: 0.8567 (t70) cc_final: 0.8045 (t0) REVERT: F 125 MET cc_start: 0.7550 (mtm) cc_final: 0.7312 (mtp) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.1143 time to fit residues: 35.7305 Evaluate side-chains 97 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 51 ASN B 74 HIS ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 ASN D 74 HIS ** D 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 51 ASN F 74 HIS ** F 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.115390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.081416 restraints weight = 20649.210| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.68 r_work: 0.2988 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11802 Z= 0.177 Angle : 0.755 6.458 16086 Z= 0.358 Chirality : 0.045 0.194 1938 Planarity : 0.004 0.033 1992 Dihedral : 11.341 64.743 2442 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.08 % Allowed : 5.32 % Favored : 93.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.21), residues: 1425 helix: 2.07 (0.28), residues: 327 sheet: 0.05 (0.30), residues: 258 loop : -0.04 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 278 TYR 0.021 0.002 TYR A 135 PHE 0.010 0.002 PHE A 192 TRP 0.011 0.001 TRP F 21 HIS 0.006 0.001 HIS D 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.18 (11739) covalent geometry : angle 0.69445 / 0.35 (15915) SS BOND : bond 0.00216 / 0.16 ( 18) SS BOND : angle 1.20670 / 0.85 ( 36) hydrogen bonds : bond 0.05188 / 3.63 ( 435) hydrogen bonds : angle 5.62527 / 3.94 ( 1242) link_BETA1-4 : bond 0.00805 / 0.55 ( 24) link_BETA1-4 : angle 3.40996 / 2.44 ( 72) link_NAG-ASN : bond 0.00429 / 0.29 ( 21) link_NAG-ASN : angle 3.08238 / 2.19 ( 63) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: A 253 LYS cc_start: 0.9139 (mmtt) cc_final: 0.8855 (mmtp) REVERT: B 50 LYS cc_start: 0.8536 (mttt) cc_final: 0.8220 (mmmt) REVERT: B 86 ASP cc_start: 0.8967 (t70) cc_final: 0.8465 (t0) REVERT: B 125 MET cc_start: 0.8213 (mtm) cc_final: 0.7978 (mtp) REVERT: C 253 LYS cc_start: 0.9114 (mmtt) cc_final: 0.8807 (mmtm) REVERT: D 50 LYS cc_start: 0.8511 (mttt) cc_final: 0.8228 (mmmt) REVERT: D 85 ASP cc_start: 0.8430 (m-30) cc_final: 0.8222 (m-30) REVERT: D 86 ASP cc_start: 0.8896 (t70) cc_final: 0.8173 (t0) REVERT: F 21 TRP cc_start: 0.6797 (m100) cc_final: 0.6499 (m100) REVERT: F 50 LYS cc_start: 0.8530 (mttt) cc_final: 0.8187 (mmmt) REVERT: F 61 LYS cc_start: 0.9092 (mtpp) cc_final: 0.8757 (mtpp) REVERT: F 81 ASP cc_start: 0.9043 (t0) cc_final: 0.8792 (t0) REVERT: F 85 ASP cc_start: 0.8357 (m-30) cc_final: 0.8084 (m-30) REVERT: F 86 ASP cc_start: 0.8907 (t70) cc_final: 0.8492 (t0) REVERT: F 125 MET cc_start: 0.8248 (mtm) cc_final: 0.8000 (mtp) outliers start: 13 outliers final: 6 residues processed: 136 average time/residue: 0.1327 time to fit residues: 24.9170 Evaluate side-chains 95 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain E residue 48 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 17 optimal weight: 0.5980 chunk 7 optimal weight: 5.9990 chunk 111 optimal weight: 0.2980 chunk 31 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 82 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 46 ASN C 99 HIS D 46 ASN E 99 HIS F 22 HIS F 46 ASN F 64 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.113930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.079229 restraints weight = 20521.012| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.72 r_work: 0.2953 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 11802 Z= 0.164 Angle : 0.632 8.101 16086 Z= 0.300 Chirality : 0.043 0.174 1938 Planarity : 0.004 0.031 1992 Dihedral : 6.706 33.848 2442 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.16 % Allowed : 6.48 % Favored : 92.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.21), residues: 1425 helix: 2.59 (0.28), residues: 327 sheet: -0.09 (0.30), residues: 258 loop : -0.19 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 278 TYR 0.017 0.001 TYR A 135 PHE 0.008 0.001 PHE A 192 TRP 0.008 0.001 TRP D 14 HIS 0.011 0.001 HIS B 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (11739) covalent geometry : angle 0.58794 / 0.29 (15915) SS BOND : bond 0.00212 / 0.15 ( 18) SS BOND : angle 0.72976 / 0.50 ( 36) hydrogen bonds : bond 0.04085 / 2.85 ( 435) hydrogen bonds : angle 5.14155 / 3.58 ( 1242) link_BETA1-4 : bond 0.00833 / 0.56 ( 24) link_BETA1-4 : angle 2.43129 / 1.77 ( 72) link_NAG-ASN : bond 0.00553 / 0.37 ( 21) link_NAG-ASN : angle 2.74210 / 1.95 ( 63) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.562 Fit side-chains REVERT: B 50 LYS cc_start: 0.8496 (mttt) cc_final: 0.8185 (mmmt) REVERT: B 86 ASP cc_start: 0.8980 (t0) cc_final: 0.8521 (t0) REVERT: B 125 MET cc_start: 0.8185 (mtm) cc_final: 0.7813 (mtp) REVERT: C 164 ASN cc_start: 0.8239 (t0) cc_final: 0.7985 (t0) REVERT: D 50 LYS cc_start: 0.8474 (mttt) cc_final: 0.8191 (mmmt) REVERT: D 81 ASP cc_start: 0.8909 (t0) cc_final: 0.8643 (t0) REVERT: D 86 ASP cc_start: 0.8948 (t70) cc_final: 0.8498 (t0) REVERT: F 50 LYS cc_start: 0.8529 (mttt) cc_final: 0.8171 (mmmt) REVERT: F 64 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.8381 (mt0) REVERT: F 86 ASP cc_start: 0.8896 (t70) cc_final: 0.8501 (t0) outliers start: 14 outliers final: 9 residues processed: 116 average time/residue: 0.1273 time to fit residues: 20.6023 Evaluate side-chains 103 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain E residue 48 GLU Chi-restraints excluded: chain E residue 279 SER Chi-restraints excluded: chain F residue 64 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 59 optimal weight: 0.0870 chunk 90 optimal weight: 0.9980 chunk 139 optimal weight: 20.0000 chunk 89 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 47 optimal weight: 7.9990 chunk 98 optimal weight: 4.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 22 HIS B 75 ASN D 75 ASN F 75 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.113644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.078901 restraints weight = 20445.441| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.69 r_work: 0.2949 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11802 Z= 0.147 Angle : 0.586 8.631 16086 Z= 0.277 Chirality : 0.041 0.220 1938 Planarity : 0.004 0.032 1992 Dihedral : 5.241 26.710 2442 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.16 % Allowed : 7.48 % Favored : 91.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.21), residues: 1425 helix: 2.67 (0.28), residues: 327 sheet: -0.10 (0.30), residues: 258 loop : -0.29 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 278 TYR 0.014 0.001 TYR E 135 PHE 0.009 0.001 PHE A 192 TRP 0.008 0.001 TRP B 21 HIS 0.006 0.001 HIS A 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (11739) covalent geometry : angle 0.54540 / 0.27 (15915) SS BOND : bond 0.00207 / 0.15 ( 18) SS BOND : angle 0.57057 / 0.39 ( 36) hydrogen bonds : bond 0.03769 / 2.62 ( 435) hydrogen bonds : angle 4.97514 / 3.46 ( 1242) link_BETA1-4 : bond 0.00626 / 0.42 ( 24) link_BETA1-4 : angle 2.13434 / 1.54 ( 72) link_NAG-ASN : bond 0.00476 / 0.33 ( 21) link_NAG-ASN : angle 2.68906 / 1.89 ( 63) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.264 Fit side-chains REVERT: B 50 LYS cc_start: 0.8510 (mttt) cc_final: 0.8198 (mmmt) REVERT: B 86 ASP cc_start: 0.8976 (t0) cc_final: 0.8508 (t0) REVERT: C 164 ASN cc_start: 0.8194 (t0) cc_final: 0.7935 (t0) REVERT: D 50 LYS cc_start: 0.8504 (mttt) cc_final: 0.8216 (mmmt) REVERT: D 86 ASP cc_start: 0.8955 (t70) cc_final: 0.8503 (t0) REVERT: F 50 LYS cc_start: 0.8536 (mttt) cc_final: 0.8180 (mmmt) REVERT: F 86 ASP cc_start: 0.8899 (t70) cc_final: 0.8462 (t0) REVERT: F 125 MET cc_start: 0.7839 (mtm) cc_final: 0.7331 (ptp) outliers start: 14 outliers final: 12 residues processed: 112 average time/residue: 0.1007 time to fit residues: 15.7641 Evaluate side-chains 105 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain E residue 48 GLU Chi-restraints excluded: chain E residue 250 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 28 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 95 optimal weight: 4.9990 chunk 59 optimal weight: 0.5980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 ASN ** D 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 ASN F 75 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.111502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.076666 restraints weight = 20548.126| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 2.73 r_work: 0.2892 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11802 Z= 0.182 Angle : 0.581 8.971 16086 Z= 0.277 Chirality : 0.041 0.173 1938 Planarity : 0.004 0.033 1992 Dihedral : 4.687 25.826 2442 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.08 % Allowed : 7.81 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.21), residues: 1425 helix: 2.75 (0.28), residues: 327 sheet: -0.15 (0.31), residues: 258 loop : -0.38 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 278 TYR 0.017 0.001 TYR A 135 PHE 0.010 0.001 PHE A 192 TRP 0.010 0.001 TRP F 21 HIS 0.010 0.001 HIS D 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.18 (11739) covalent geometry : angle 0.54720 / 0.27 (15915) SS BOND : bond 0.00257 / 0.18 ( 18) SS BOND : angle 0.60127 / 0.40 ( 36) hydrogen bonds : bond 0.03714 / 2.61 ( 435) hydrogen bonds : angle 4.88632 / 3.39 ( 1242) link_BETA1-4 : bond 0.00592 / 0.40 ( 24) link_BETA1-4 : angle 1.78168 / 1.27 ( 72) link_NAG-ASN : bond 0.00404 / 0.28 ( 21) link_NAG-ASN : angle 2.60956 / 1.82 ( 63) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.455 Fit side-chains REVERT: A 48 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7497 (pm20) REVERT: A 164 ASN cc_start: 0.7915 (t0) cc_final: 0.7674 (t0) REVERT: B 50 LYS cc_start: 0.8460 (mttt) cc_final: 0.8141 (mmmt) REVERT: B 64 GLN cc_start: 0.8812 (mp10) cc_final: 0.8539 (mt0) REVERT: B 86 ASP cc_start: 0.9033 (t0) cc_final: 0.8558 (t0) REVERT: B 125 MET cc_start: 0.8107 (mtm) cc_final: 0.7339 (ptp) REVERT: C 164 ASN cc_start: 0.8206 (t0) cc_final: 0.7960 (t0) REVERT: D 50 LYS cc_start: 0.8408 (mttt) cc_final: 0.8119 (mmmt) REVERT: D 86 ASP cc_start: 0.8951 (t70) cc_final: 0.8461 (t0) REVERT: F 50 LYS cc_start: 0.8433 (mttt) cc_final: 0.8077 (mmmt) REVERT: F 86 ASP cc_start: 0.8942 (t70) cc_final: 0.8498 (t0) REVERT: F 125 MET cc_start: 0.7847 (mtm) cc_final: 0.7409 (ptp) outliers start: 13 outliers final: 10 residues processed: 102 average time/residue: 0.1282 time to fit residues: 17.8276 Evaluate side-chains 97 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain E residue 48 GLU Chi-restraints excluded: chain E residue 250 MET Chi-restraints excluded: chain F residue 60 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 64 optimal weight: 0.9980 chunk 91 optimal weight: 0.0030 chunk 53 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 85 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 14 HIS D 75 ASN E 14 HIS F 64 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.112598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.078128 restraints weight = 20698.947| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.74 r_work: 0.2949 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 11802 Z= 0.127 Angle : 0.527 9.186 16086 Z= 0.250 Chirality : 0.040 0.187 1938 Planarity : 0.004 0.032 1992 Dihedral : 4.457 23.777 2442 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.33 % Allowed : 8.40 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.22), residues: 1425 helix: 3.00 (0.28), residues: 324 sheet: -0.11 (0.31), residues: 258 loop : -0.37 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 278 TYR 0.012 0.001 TYR E 135 PHE 0.008 0.001 PHE A 192 TRP 0.005 0.001 TRP F 14 HIS 0.006 0.001 HIS A 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (11739) covalent geometry : angle 0.49650 / 0.24 (15915) SS BOND : bond 0.00195 / 0.14 ( 18) SS BOND : angle 0.47133 / 0.32 ( 36) hydrogen bonds : bond 0.03348 / 2.34 ( 435) hydrogen bonds : angle 4.72462 / 3.27 ( 1242) link_BETA1-4 : bond 0.00583 / 0.39 ( 24) link_BETA1-4 : angle 1.50398 / 1.08 ( 72) link_NAG-ASN : bond 0.00443 / 0.31 ( 21) link_NAG-ASN : angle 2.44184 / 1.69 ( 63) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.451 Fit side-chains REVERT: A 48 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7517 (pm20) REVERT: A 164 ASN cc_start: 0.7936 (t0) cc_final: 0.7699 (t0) REVERT: B 50 LYS cc_start: 0.8518 (mttt) cc_final: 0.8191 (mmmt) REVERT: B 64 GLN cc_start: 0.8728 (mp10) cc_final: 0.8444 (mt0) REVERT: B 86 ASP cc_start: 0.9013 (t0) cc_final: 0.8554 (t0) REVERT: B 125 MET cc_start: 0.8086 (mtm) cc_final: 0.7307 (ptp) REVERT: C 164 ASN cc_start: 0.8231 (t0) cc_final: 0.7991 (t0) REVERT: D 50 LYS cc_start: 0.8487 (mttt) cc_final: 0.8197 (mmmt) REVERT: D 86 ASP cc_start: 0.8950 (t70) cc_final: 0.8502 (t0) REVERT: F 50 LYS cc_start: 0.8518 (mttt) cc_final: 0.8165 (mmmt) REVERT: F 64 GLN cc_start: 0.8218 (mt0) cc_final: 0.7967 (mt0) REVERT: F 86 ASP cc_start: 0.8948 (t70) cc_final: 0.8504 (t0) REVERT: F 88 ARG cc_start: 0.8182 (tmt170) cc_final: 0.7939 (tpt170) REVERT: F 125 MET cc_start: 0.7826 (mtm) cc_final: 0.7507 (ptp) outliers start: 16 outliers final: 9 residues processed: 109 average time/residue: 0.1257 time to fit residues: 18.8319 Evaluate side-chains 100 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain E residue 250 MET Chi-restraints excluded: chain F residue 56 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 125 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 58.1205 > 50:) chunk 137 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 126 optimal weight: 0.5980 chunk 108 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 96 optimal weight: 0.9980 chunk 92 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 ASN F 75 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.110760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.075954 restraints weight = 20559.322| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.73 r_work: 0.2891 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11802 Z= 0.178 Angle : 0.561 9.126 16086 Z= 0.266 Chirality : 0.040 0.174 1938 Planarity : 0.004 0.033 1992 Dihedral : 4.457 24.368 2442 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.00 % Allowed : 8.98 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.22), residues: 1425 helix: 2.86 (0.28), residues: 324 sheet: 0.03 (0.32), residues: 264 loop : -0.43 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 278 TYR 0.014 0.001 TYR A 135 PHE 0.010 0.001 PHE A 192 TRP 0.006 0.001 TRP B 21 HIS 0.011 0.001 HIS C 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.18 (11739) covalent geometry : angle 0.53177 / 0.26 (15915) SS BOND : bond 0.00292 / 0.20 ( 18) SS BOND : angle 0.83054 / 0.55 ( 36) hydrogen bonds : bond 0.03472 / 2.43 ( 435) hydrogen bonds : angle 4.72621 / 3.28 ( 1242) link_BETA1-4 : bond 0.00535 / 0.36 ( 24) link_BETA1-4 : angle 1.50370 / 1.07 ( 72) link_NAG-ASN : bond 0.00370 / 0.26 ( 21) link_NAG-ASN : angle 2.42772 / 1.67 ( 63) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.464 Fit side-chains REVERT: A 48 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7498 (pm20) REVERT: A 164 ASN cc_start: 0.7997 (t0) cc_final: 0.7748 (t0) REVERT: B 50 LYS cc_start: 0.8464 (mttt) cc_final: 0.8128 (mmmt) REVERT: B 64 GLN cc_start: 0.8805 (mp10) cc_final: 0.8497 (mt0) REVERT: B 86 ASP cc_start: 0.9051 (t0) cc_final: 0.8579 (t0) REVERT: B 125 MET cc_start: 0.8044 (mtm) cc_final: 0.7291 (ptp) REVERT: C 164 ASN cc_start: 0.8256 (t0) cc_final: 0.7989 (t0) REVERT: D 50 LYS cc_start: 0.8437 (mttt) cc_final: 0.8143 (mmmt) REVERT: D 86 ASP cc_start: 0.8999 (t70) cc_final: 0.8525 (t0) REVERT: D 107 ILE cc_start: 0.7055 (mm) cc_final: 0.6829 (mm) REVERT: F 50 LYS cc_start: 0.8453 (mttt) cc_final: 0.8098 (mmmt) REVERT: F 86 ASP cc_start: 0.9006 (t70) cc_final: 0.8495 (t0) REVERT: F 88 ARG cc_start: 0.8139 (tmt170) cc_final: 0.7913 (tpt170) REVERT: F 125 MET cc_start: 0.7806 (mtm) cc_final: 0.7485 (ptp) outliers start: 12 outliers final: 10 residues processed: 104 average time/residue: 0.1381 time to fit residues: 19.6657 Evaluate side-chains 100 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain E residue 250 MET Chi-restraints excluded: chain F residue 56 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 29 optimal weight: 0.9990 chunk 106 optimal weight: 0.1980 chunk 16 optimal weight: 0.4980 chunk 34 optimal weight: 8.9990 chunk 116 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 55 optimal weight: 0.0170 chunk 49 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 chunk 72 optimal weight: 3.9990 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 HIS D 75 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.112937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.078363 restraints weight = 20703.631| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.76 r_work: 0.2896 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 11802 Z= 0.104 Angle : 0.512 9.381 16086 Z= 0.242 Chirality : 0.039 0.179 1938 Planarity : 0.004 0.084 1992 Dihedral : 4.305 26.593 2442 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.08 % Allowed : 9.06 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.22), residues: 1425 helix: 3.14 (0.28), residues: 324 sheet: 0.04 (0.32), residues: 264 loop : -0.40 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 278 TYR 0.012 0.001 TYR C 308 PHE 0.008 0.001 PHE A 192 TRP 0.010 0.001 TRP B 21 HIS 0.010 0.001 HIS C 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.10 (11739) covalent geometry : angle 0.48331 / 0.24 (15915) SS BOND : bond 0.00168 / 0.13 ( 18) SS BOND : angle 0.79279 / 0.53 ( 36) hydrogen bonds : bond 0.03136 / 2.19 ( 435) hydrogen bonds : angle 4.62195 / 3.20 ( 1242) link_BETA1-4 : bond 0.00572 / 0.39 ( 24) link_BETA1-4 : angle 1.34863 / 0.97 ( 72) link_NAG-ASN : bond 0.00466 / 0.32 ( 21) link_NAG-ASN : angle 2.32109 / 1.60 ( 63) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.490 Fit side-chains REVERT: A 48 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7356 (pm20) REVERT: A 164 ASN cc_start: 0.7989 (t0) cc_final: 0.7739 (t0) REVERT: B 50 LYS cc_start: 0.8428 (mttt) cc_final: 0.8088 (mmmt) REVERT: B 64 GLN cc_start: 0.8785 (mp10) cc_final: 0.8505 (mt0) REVERT: B 86 ASP cc_start: 0.9035 (t0) cc_final: 0.8564 (t0) REVERT: B 125 MET cc_start: 0.7940 (mtm) cc_final: 0.7157 (ptp) REVERT: C 164 ASN cc_start: 0.8236 (t0) cc_final: 0.7926 (t0) REVERT: D 50 LYS cc_start: 0.8405 (mttt) cc_final: 0.8102 (mmmt) REVERT: D 86 ASP cc_start: 0.8942 (t70) cc_final: 0.8482 (t0) REVERT: D 88 ARG cc_start: 0.8102 (tmt170) cc_final: 0.7784 (tpt170) REVERT: E 164 ASN cc_start: 0.7748 (t0) cc_final: 0.6893 (p0) REVERT: F 50 LYS cc_start: 0.8423 (mttt) cc_final: 0.8076 (mmmt) REVERT: F 86 ASP cc_start: 0.8946 (t70) cc_final: 0.8486 (t0) REVERT: F 88 ARG cc_start: 0.8086 (tmt170) cc_final: 0.7857 (tpt170) REVERT: F 125 MET cc_start: 0.7777 (mtm) cc_final: 0.7469 (ptp) outliers start: 13 outliers final: 8 residues processed: 108 average time/residue: 0.1353 time to fit residues: 20.0176 Evaluate side-chains 100 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain E residue 250 MET Chi-restraints excluded: chain E residue 254 SER Chi-restraints excluded: chain F residue 56 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 73 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 4 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.109514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.074933 restraints weight = 20863.530| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.68 r_work: 0.2856 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 11802 Z= 0.276 Angle : 0.616 8.798 16086 Z= 0.295 Chirality : 0.042 0.172 1938 Planarity : 0.004 0.076 1992 Dihedral : 4.637 25.643 2442 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.41 % Allowed : 8.81 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.22), residues: 1425 helix: 2.82 (0.28), residues: 324 sheet: 0.03 (0.32), residues: 264 loop : -0.53 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 278 TYR 0.015 0.002 TYR A 135 PHE 0.013 0.002 PHE A 192 TRP 0.010 0.001 TRP B 21 HIS 0.005 0.001 HIS A 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00656 / 0.28 (11739) covalent geometry : angle 0.59023 / 0.29 (15915) SS BOND : bond 0.00452 / 0.30 ( 18) SS BOND : angle 0.90271 / 0.58 ( 36) hydrogen bonds : bond 0.03758 / 2.65 ( 435) hydrogen bonds : angle 4.80703 / 3.36 ( 1242) link_BETA1-4 : bond 0.00519 / 0.35 ( 24) link_BETA1-4 : angle 1.46004 / 1.04 ( 72) link_NAG-ASN : bond 0.00403 / 0.27 ( 21) link_NAG-ASN : angle 2.44270 / 1.67 ( 63) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.330 Fit side-chains REVERT: A 48 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7583 (pm20) REVERT: A 164 ASN cc_start: 0.8079 (t0) cc_final: 0.6986 (p0) REVERT: B 50 LYS cc_start: 0.8485 (mttt) cc_final: 0.8141 (mmmt) REVERT: B 64 GLN cc_start: 0.8898 (mp10) cc_final: 0.8497 (mt0) REVERT: B 86 ASP cc_start: 0.9128 (t0) cc_final: 0.8650 (t0) REVERT: B 125 MET cc_start: 0.7951 (mtm) cc_final: 0.7199 (ptp) REVERT: C 164 ASN cc_start: 0.8307 (t0) cc_final: 0.7951 (t0) REVERT: D 50 LYS cc_start: 0.8405 (mttt) cc_final: 0.8113 (mmmt) REVERT: D 86 ASP cc_start: 0.9071 (t70) cc_final: 0.8603 (t0) REVERT: D 107 ILE cc_start: 0.7050 (mm) cc_final: 0.6792 (mm) REVERT: E 164 ASN cc_start: 0.7880 (t0) cc_final: 0.7063 (p0) REVERT: F 50 LYS cc_start: 0.8442 (mttt) cc_final: 0.8084 (mmmt) REVERT: F 86 ASP cc_start: 0.9065 (t70) cc_final: 0.8636 (t0) REVERT: F 88 ARG cc_start: 0.8182 (tmt170) cc_final: 0.7960 (tpt170) REVERT: F 125 MET cc_start: 0.7816 (mtm) cc_final: 0.7512 (ptp) outliers start: 17 outliers final: 11 residues processed: 109 average time/residue: 0.1141 time to fit residues: 17.2816 Evaluate side-chains 102 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain E residue 94 CYS Chi-restraints excluded: chain E residue 312 GLU Chi-restraints excluded: chain F residue 56 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 76 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 108 optimal weight: 0.3980 chunk 60 optimal weight: 0.9980 chunk 51 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 ASN F 22 HIS F 75 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.111383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.076926 restraints weight = 20756.303| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.68 r_work: 0.2904 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11802 Z= 0.125 Angle : 0.535 9.275 16086 Z= 0.254 Chirality : 0.040 0.175 1938 Planarity : 0.004 0.098 1992 Dihedral : 4.457 26.848 2442 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.91 % Allowed : 9.31 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.22), residues: 1425 helix: 3.06 (0.28), residues: 324 sheet: 0.02 (0.32), residues: 264 loop : -0.47 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 278 TYR 0.011 0.001 TYR C 308 PHE 0.009 0.001 PHE A 192 TRP 0.013 0.001 TRP B 21 HIS 0.006 0.001 HIS C 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 (11739) covalent geometry : angle 0.50863 / 0.25 (15915) SS BOND : bond 0.00241 / 0.18 ( 18) SS BOND : angle 0.78239 / 0.53 ( 36) hydrogen bonds : bond 0.03280 / 2.31 ( 435) hydrogen bonds : angle 4.66265 / 3.24 ( 1242) link_BETA1-4 : bond 0.00547 / 0.36 ( 24) link_BETA1-4 : angle 1.29700 / 0.94 ( 72) link_NAG-ASN : bond 0.00431 / 0.30 ( 21) link_NAG-ASN : angle 2.35161 / 1.61 ( 63) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.433 Fit side-chains REVERT: A 48 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7489 (pm20) REVERT: A 164 ASN cc_start: 0.8062 (t0) cc_final: 0.6967 (p0) REVERT: B 50 LYS cc_start: 0.8446 (mttt) cc_final: 0.8110 (mmmt) REVERT: B 64 GLN cc_start: 0.8781 (mp10) cc_final: 0.8479 (mt0) REVERT: B 86 ASP cc_start: 0.9084 (t0) cc_final: 0.8604 (t0) REVERT: B 125 MET cc_start: 0.7903 (mtm) cc_final: 0.7145 (ptp) REVERT: C 164 ASN cc_start: 0.8291 (t0) cc_final: 0.7941 (t0) REVERT: D 50 LYS cc_start: 0.8424 (mttt) cc_final: 0.8125 (mmmt) REVERT: D 86 ASP cc_start: 0.9034 (t70) cc_final: 0.8545 (t0) REVERT: D 107 ILE cc_start: 0.7018 (mm) cc_final: 0.6756 (mm) REVERT: E 164 ASN cc_start: 0.7904 (t0) cc_final: 0.7065 (p0) REVERT: F 50 LYS cc_start: 0.8424 (mttt) cc_final: 0.8067 (mmmt) REVERT: F 86 ASP cc_start: 0.9006 (t70) cc_final: 0.8577 (t0) REVERT: F 88 ARG cc_start: 0.8138 (tmt170) cc_final: 0.7912 (tpt170) REVERT: F 125 MET cc_start: 0.7792 (mtm) cc_final: 0.7504 (ptp) outliers start: 11 outliers final: 10 residues processed: 108 average time/residue: 0.1200 time to fit residues: 18.1085 Evaluate side-chains 105 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain E residue 94 CYS Chi-restraints excluded: chain F residue 56 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 87 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 115 optimal weight: 0.3980 chunk 106 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 33 optimal weight: 0.0010 chunk 114 optimal weight: 0.5980 chunk 80 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 123 optimal weight: 0.0770 overall best weight: 0.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 ASN D 75 ASN F 22 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.112012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.077720 restraints weight = 20578.978| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.74 r_work: 0.2930 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 11802 Z= 0.105 Angle : 0.512 9.296 16086 Z= 0.242 Chirality : 0.039 0.179 1938 Planarity : 0.004 0.083 1992 Dihedral : 4.286 29.341 2442 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.00 % Allowed : 9.31 % Favored : 89.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.22), residues: 1425 helix: 3.19 (0.28), residues: 324 sheet: 0.03 (0.32), residues: 264 loop : -0.41 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 88 TYR 0.011 0.001 TYR C 308 PHE 0.009 0.001 PHE A 192 TRP 0.013 0.001 TRP B 21 HIS 0.007 0.001 HIS C 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.10 (11739) covalent geometry : angle 0.48704 / 0.24 (15915) SS BOND : bond 0.00179 / 0.13 ( 18) SS BOND : angle 0.72690 / 0.50 ( 36) hydrogen bonds : bond 0.03002 / 2.11 ( 435) hydrogen bonds : angle 4.54536 / 3.15 ( 1242) link_BETA1-4 : bond 0.00524 / 0.35 ( 24) link_BETA1-4 : angle 1.26697 / 0.91 ( 72) link_NAG-ASN : bond 0.00421 / 0.29 ( 21) link_NAG-ASN : angle 2.23372 / 1.53 ( 63) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2973.83 seconds wall clock time: 51 minutes 47.42 seconds (3107.42 seconds total)