Starting phenix.real_space_refine on Wed May 14 06:25:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bto_44894/05_2025/9bto_44894.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bto_44894/05_2025/9bto_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9bto_44894/05_2025/9bto_44894.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bto_44894/05_2025/9bto_44894.map" model { file = "/net/cci-nas-00/data/ceres_data/9bto_44894/05_2025/9bto_44894.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bto_44894/05_2025/9bto_44894.cif" } resolution = 3.1 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= 0.008 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 8.86, per 1000 atoms: 0.77 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: 3.07 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.42 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: 3.13 Time building geometry restraints manager: 3.55 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: 0.07 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: 7.320 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: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 28.990 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 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 (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: 0.65 (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 TRP 0.048 0.008 TRP F 21 HIS 0.013 0.002 HIS A 85 PHE 0.020 0.006 PHE A 192 TYR 0.061 0.010 TYR A 135 ARG 0.009 0.001 ARG B 88 Details of bonding type rmsd link_NAG-ASN : bond 0.07604 ( 21) link_NAG-ASN : angle 2.51805 ( 63) link_BETA1-4 : bond 0.07015 ( 24) link_BETA1-4 : angle 4.79440 ( 72) hydrogen bonds : bond 0.15987 ( 435) hydrogen bonds : angle 7.48181 ( 1242) SS BOND : bond 0.01175 ( 18) SS BOND : angle 3.01052 ( 36) covalent geometry : bond 0.02324 (11739) covalent geometry : angle 1.74309 (15915) *********************** 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 : 1.189 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: 0.2661 time to fit residues: 82.1454 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 : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 119 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 110 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 chunk 82 optimal weight: 5.9990 chunk 128 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3681 r_free = 0.3681 target = 0.115244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.081159 restraints weight = 20662.722| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.65 r_work: 0.2986 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11802 Z= 0.178 Angle : 0.759 6.751 16086 Z= 0.358 Chirality : 0.045 0.177 1938 Planarity : 0.005 0.033 1992 Dihedral : 11.311 64.267 2442 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.16 % Allowed : 5.32 % Favored : 93.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.61 (0.20), residues: 1425 helix: 2.02 (0.28), residues: 327 sheet: 0.02 (0.30), residues: 258 loop : -0.06 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 21 HIS 0.006 0.001 HIS E 85 PHE 0.010 0.002 PHE A 192 TYR 0.024 0.002 TYR A 135 ARG 0.004 0.001 ARG C 278 Details of bonding type rmsd link_NAG-ASN : bond 0.00435 ( 21) link_NAG-ASN : angle 3.13687 ( 63) link_BETA1-4 : bond 0.00507 ( 24) link_BETA1-4 : angle 3.44871 ( 72) hydrogen bonds : bond 0.05103 ( 435) hydrogen bonds : angle 5.62278 ( 1242) SS BOND : bond 0.00209 ( 18) SS BOND : angle 1.19918 ( 36) covalent geometry : bond 0.00399 (11739) covalent geometry : angle 0.69725 (15915) *********************** 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 136 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 1.385 Fit side-chains revert: symmetry clash REVERT: A 253 LYS cc_start: 0.9140 (mmtt) cc_final: 0.8857 (mmtp) REVERT: B 50 LYS cc_start: 0.8514 (mttt) cc_final: 0.8196 (mmmt) REVERT: B 81 ASP cc_start: 0.9080 (t0) cc_final: 0.8847 (t0) REVERT: B 85 ASP cc_start: 0.8467 (m-30) cc_final: 0.8241 (m-30) REVERT: B 86 ASP cc_start: 0.8963 (t0) cc_final: 0.8454 (t0) REVERT: B 125 MET cc_start: 0.8229 (mtm) cc_final: 0.7995 (mtp) REVERT: C 253 LYS cc_start: 0.9114 (mmtt) cc_final: 0.8824 (mmtm) REVERT: D 50 LYS cc_start: 0.8475 (mttt) cc_final: 0.8190 (mmmt) REVERT: D 86 ASP cc_start: 0.8902 (t70) cc_final: 0.8180 (t0) REVERT: F 21 TRP cc_start: 0.6778 (m100) cc_final: 0.6493 (m100) REVERT: F 50 LYS cc_start: 0.8510 (mttt) cc_final: 0.8164 (mmmt) REVERT: F 61 LYS cc_start: 0.9101 (mtpp) cc_final: 0.8751 (mtpp) REVERT: F 81 ASP cc_start: 0.9043 (t0) cc_final: 0.8798 (t0) REVERT: F 85 ASP cc_start: 0.8349 (m-30) cc_final: 0.8084 (m-30) REVERT: F 86 ASP cc_start: 0.8915 (t70) cc_final: 0.8490 (t0) REVERT: F 125 MET cc_start: 0.8245 (mtm) cc_final: 0.7998 (mtp) outliers start: 14 outliers final: 6 residues processed: 133 average time/residue: 0.2864 time to fit residues: 52.0455 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 : 1.221 ------------------------------------------------------------------------------- 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 8 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 17 optimal weight: 0.4980 chunk 80 optimal weight: 9.9990 chunk 13 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 81 optimal weight: 9.9990 chunk 127 optimal weight: 8.9990 chunk 34 optimal weight: 20.0000 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 46 ASN C 99 HIS D 46 ASN F 22 HIS F 46 ASN F 64 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.113529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.078697 restraints weight = 20738.348| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.70 r_work: 0.2935 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11802 Z= 0.188 Angle : 0.643 8.324 16086 Z= 0.308 Chirality : 0.043 0.172 1938 Planarity : 0.004 0.033 1992 Dihedral : 6.258 29.507 2442 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.33 % Allowed : 6.57 % Favored : 92.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.62 (0.21), residues: 1425 helix: 2.54 (0.28), residues: 327 sheet: -0.09 (0.30), residues: 258 loop : -0.25 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 21 HIS 0.020 0.001 HIS B 22 PHE 0.010 0.002 PHE E 41 TYR 0.020 0.002 TYR A 135 ARG 0.004 0.000 ARG C 278 Details of bonding type rmsd link_NAG-ASN : bond 0.00519 ( 21) link_NAG-ASN : angle 2.77160 ( 63) link_BETA1-4 : bond 0.00866 ( 24) link_BETA1-4 : angle 2.30605 ( 72) hydrogen bonds : bond 0.04105 ( 435) hydrogen bonds : angle 5.11212 ( 1242) SS BOND : bond 0.00263 ( 18) SS BOND : angle 0.73867 ( 36) covalent geometry : bond 0.00439 (11739) covalent geometry : angle 0.60129 (15915) *********************** 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 119 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 1.282 Fit side-chains REVERT: B 50 LYS cc_start: 0.8527 (mttt) cc_final: 0.8214 (mmmt) REVERT: B 86 ASP cc_start: 0.8987 (t0) cc_final: 0.8525 (t0) REVERT: B 125 MET cc_start: 0.8140 (mtm) cc_final: 0.7762 (mtp) REVERT: C 164 ASN cc_start: 0.8250 (t0) cc_final: 0.8037 (t0) REVERT: D 50 LYS cc_start: 0.8485 (mttt) cc_final: 0.8193 (mmmt) REVERT: D 86 ASP cc_start: 0.8976 (t70) cc_final: 0.8527 (t0) REVERT: F 50 LYS cc_start: 0.8517 (mttt) cc_final: 0.8161 (mmmt) REVERT: F 64 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.8406 (mt0) REVERT: F 86 ASP cc_start: 0.8929 (t70) cc_final: 0.8548 (t0) REVERT: F 125 MET cc_start: 0.8187 (mtm) cc_final: 0.7979 (mtm) outliers start: 16 outliers final: 11 residues processed: 116 average time/residue: 0.2845 time to fit residues: 45.9992 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 : 1.235 ------------------------------------------------------------------------------- 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 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 110 LEU Chi-restraints excluded: chain C residue 312 GLU Chi-restraints excluded: chain D residue 56 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 134 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 86 optimal weight: 0.6980 chunk 123 optimal weight: 0.8980 chunk 140 optimal weight: 0.0980 chunk 47 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 GLN 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 = 0.3631 r_free = 0.3631 target = 0.111851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.076980 restraints weight = 20375.206| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.71 r_work: 0.2902 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11802 Z= 0.166 Angle : 0.591 8.803 16086 Z= 0.281 Chirality : 0.041 0.173 1938 Planarity : 0.004 0.033 1992 Dihedral : 5.115 26.405 2442 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.25 % Allowed : 7.23 % Favored : 91.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.58 (0.21), residues: 1425 helix: 2.69 (0.28), residues: 327 sheet: -0.15 (0.30), residues: 258 loop : -0.36 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 21 HIS 0.007 0.001 HIS D 22 PHE 0.010 0.001 PHE A 192 TYR 0.015 0.001 TYR A 135 ARG 0.002 0.000 ARG F 65 Details of bonding type rmsd link_NAG-ASN : bond 0.00432 ( 21) link_NAG-ASN : angle 2.71953 ( 63) link_BETA1-4 : bond 0.00583 ( 24) link_BETA1-4 : angle 2.01566 ( 72) hydrogen bonds : bond 0.03772 ( 435) hydrogen bonds : angle 4.93327 ( 1242) SS BOND : bond 0.00239 ( 18) SS BOND : angle 0.59911 ( 36) covalent geometry : bond 0.00391 (11739) covalent geometry : angle 0.55204 (15915) *********************** 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: 15 poor density : 101 time to evaluate : 1.200 Fit side-chains REVERT: B 50 LYS cc_start: 0.8444 (mttt) cc_final: 0.8124 (mmmt) REVERT: B 86 ASP cc_start: 0.8986 (t0) cc_final: 0.8486 (t0) REVERT: C 164 ASN cc_start: 0.8213 (t0) cc_final: 0.7952 (t0) REVERT: D 50 LYS cc_start: 0.8411 (mttt) cc_final: 0.8119 (mmmt) REVERT: D 86 ASP cc_start: 0.8926 (t70) cc_final: 0.8437 (t0) REVERT: F 50 LYS cc_start: 0.8426 (mttt) cc_final: 0.8066 (mmmt) REVERT: F 86 ASP cc_start: 0.8880 (t70) cc_final: 0.8438 (t0) REVERT: F 125 MET cc_start: 0.8167 (mtm) cc_final: 0.7809 (mtp) outliers start: 15 outliers final: 11 residues processed: 110 average time/residue: 0.2912 time to fit residues: 44.2395 Evaluate side-chains 101 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 1.300 ------------------------------------------------------------------------------- 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 250 MET 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 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 20 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 22 optimal weight: 0.0770 chunk 12 optimal weight: 0.0010 chunk 28 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 overall best weight: 0.4544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 HIS B 75 ASN C 14 HIS ** D 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 ASN E 14 HIS ** F 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.112789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.078182 restraints weight = 20285.032| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.75 r_work: 0.2934 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 11802 Z= 0.115 Angle : 0.534 9.015 16086 Z= 0.253 Chirality : 0.040 0.171 1938 Planarity : 0.004 0.032 1992 Dihedral : 4.546 24.265 2442 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.08 % Allowed : 7.98 % Favored : 90.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.68 (0.21), residues: 1425 helix: 3.00 (0.28), residues: 324 sheet: -0.12 (0.31), residues: 258 loop : -0.37 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 21 HIS 0.008 0.001 HIS D 22 PHE 0.008 0.001 PHE A 192 TYR 0.011 0.001 TYR C 308 ARG 0.004 0.000 ARG A 278 Details of bonding type rmsd link_NAG-ASN : bond 0.00522 ( 21) link_NAG-ASN : angle 2.51575 ( 63) link_BETA1-4 : bond 0.00608 ( 24) link_BETA1-4 : angle 1.63123 ( 72) hydrogen bonds : bond 0.03411 ( 435) hydrogen bonds : angle 4.75140 ( 1242) SS BOND : bond 0.00183 ( 18) SS BOND : angle 0.49282 ( 36) covalent geometry : bond 0.00258 (11739) covalent geometry : angle 0.50085 (15915) *********************** 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 112 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 1.175 Fit side-chains REVERT: A 48 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7424 (pm20) REVERT: A 164 ASN cc_start: 0.7889 (t0) cc_final: 0.6795 (p0) REVERT: B 50 LYS cc_start: 0.8451 (mttt) cc_final: 0.8132 (mmmt) REVERT: B 64 GLN cc_start: 0.8710 (mp10) cc_final: 0.8479 (mt0) REVERT: B 86 ASP cc_start: 0.8978 (t0) cc_final: 0.8492 (t0) REVERT: B 125 MET cc_start: 0.8089 (mtm) cc_final: 0.7304 (ptp) REVERT: C 164 ASN cc_start: 0.8218 (t0) cc_final: 0.7965 (t0) REVERT: D 50 LYS cc_start: 0.8422 (mttt) cc_final: 0.8131 (mmmt) REVERT: D 70 MET cc_start: 0.8973 (mmm) cc_final: 0.8688 (mmp) REVERT: D 86 ASP cc_start: 0.8936 (t70) cc_final: 0.8455 (t0) REVERT: D 88 ARG cc_start: 0.8163 (tmt170) cc_final: 0.7832 (tpt170) REVERT: F 50 LYS cc_start: 0.8456 (mttt) cc_final: 0.8103 (mmmt) REVERT: F 64 GLN cc_start: 0.8536 (mt0) cc_final: 0.8329 (mt0) REVERT: F 86 ASP cc_start: 0.8885 (t70) cc_final: 0.8424 (t0) REVERT: F 88 ARG cc_start: 0.8106 (tmt170) cc_final: 0.7827 (tpt170) REVERT: F 125 MET cc_start: 0.8174 (mtm) cc_final: 0.7446 (ptp) outliers start: 13 outliers final: 9 residues processed: 108 average time/residue: 0.2783 time to fit residues: 41.3884 Evaluate side-chains 101 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 250 MET 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 250 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 92 optimal weight: 20.0000 chunk 17 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 80 optimal weight: 20.0000 chunk 34 optimal weight: 10.0000 chunk 98 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 51 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 = 0.3606 r_free = 0.3606 target = 0.110851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.076169 restraints weight = 20834.757| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.74 r_work: 0.2880 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 11802 Z= 0.196 Angle : 0.580 9.092 16086 Z= 0.276 Chirality : 0.041 0.175 1938 Planarity : 0.004 0.034 1992 Dihedral : 4.567 24.879 2442 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.58 % Allowed : 8.56 % 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 (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: 0.65 (0.22), residues: 1425 helix: 2.95 (0.28), residues: 324 sheet: 0.04 (0.32), residues: 264 loop : -0.45 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 21 HIS 0.009 0.001 HIS C 85 PHE 0.010 0.001 PHE A 192 TYR 0.016 0.002 TYR A 135 ARG 0.006 0.000 ARG C 278 Details of bonding type rmsd link_NAG-ASN : bond 0.00370 ( 21) link_NAG-ASN : angle 2.49711 ( 63) link_BETA1-4 : bond 0.00544 ( 24) link_BETA1-4 : angle 1.61754 ( 72) hydrogen bonds : bond 0.03634 ( 435) hydrogen bonds : angle 4.73967 ( 1242) SS BOND : bond 0.00290 ( 18) SS BOND : angle 0.59704 ( 36) covalent geometry : bond 0.00471 (11739) covalent geometry : angle 0.54973 (15915) *********************** 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 111 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 1.314 Fit side-chains REVERT: A 48 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7521 (pm20) REVERT: A 164 ASN cc_start: 0.7939 (t0) cc_final: 0.7700 (t0) REVERT: B 50 LYS cc_start: 0.8477 (mttt) cc_final: 0.8144 (mmmt) REVERT: B 64 GLN cc_start: 0.8838 (mp10) cc_final: 0.8564 (mt0) REVERT: B 86 ASP cc_start: 0.9057 (t0) cc_final: 0.8596 (t0) REVERT: B 125 MET cc_start: 0.8085 (mtm) cc_final: 0.7373 (ptp) REVERT: C 164 ASN cc_start: 0.8269 (t0) cc_final: 0.7986 (t0) REVERT: D 50 LYS cc_start: 0.8445 (mttt) cc_final: 0.8147 (mmmt) REVERT: D 86 ASP cc_start: 0.9009 (t70) cc_final: 0.8537 (t0) REVERT: F 50 LYS cc_start: 0.8454 (mttt) cc_final: 0.8103 (mmmt) REVERT: F 64 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.8175 (mt0) REVERT: F 86 ASP cc_start: 0.8995 (t70) cc_final: 0.8486 (t0) REVERT: F 88 ARG cc_start: 0.8142 (tmt170) cc_final: 0.7912 (tpt170) REVERT: F 125 MET cc_start: 0.8161 (mtm) cc_final: 0.7452 (ptp) outliers start: 19 outliers final: 12 residues processed: 108 average time/residue: 0.2756 time to fit residues: 41.3341 Evaluate side-chains 100 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 250 MET 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 D residue 56 SER Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain E residue 312 GLU Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain F residue 64 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 86 optimal weight: 1.9990 chunk 38 optimal weight: 0.0970 chunk 22 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 125 optimal weight: 0.0040 chunk 80 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 126 optimal weight: 0.9980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 HIS D 75 ASN E 99 HIS F 22 HIS F 75 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.111828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.077244 restraints weight = 20897.404| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 2.73 r_work: 0.2911 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11802 Z= 0.126 Angle : 0.531 9.128 16086 Z= 0.252 Chirality : 0.040 0.176 1938 Planarity : 0.004 0.084 1992 Dihedral : 4.425 24.443 2442 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.41 % Allowed : 8.65 % Favored : 89.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.70 (0.22), residues: 1425 helix: 3.02 (0.28), residues: 324 sheet: 0.07 (0.32), residues: 264 loop : -0.43 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 14 HIS 0.009 0.001 HIS C 85 PHE 0.009 0.001 PHE A 192 TYR 0.012 0.001 TYR C 308 ARG 0.006 0.000 ARG C 278 Details of bonding type rmsd link_NAG-ASN : bond 0.00439 ( 21) link_NAG-ASN : angle 2.40624 ( 63) link_BETA1-4 : bond 0.00543 ( 24) link_BETA1-4 : angle 1.42878 ( 72) hydrogen bonds : bond 0.03313 ( 435) hydrogen bonds : angle 4.63921 ( 1242) SS BOND : bond 0.00238 ( 18) SS BOND : angle 0.74202 ( 36) covalent geometry : bond 0.00295 (11739) covalent geometry : angle 0.50180 (15915) *********************** 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 109 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 1.201 Fit side-chains REVERT: A 48 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7495 (pm20) REVERT: A 164 ASN cc_start: 0.7965 (t0) cc_final: 0.6909 (p0) REVERT: B 50 LYS cc_start: 0.8436 (mttt) cc_final: 0.8099 (mmmt) REVERT: B 64 GLN cc_start: 0.8787 (mp10) cc_final: 0.8495 (mt0) REVERT: B 86 ASP cc_start: 0.9075 (t0) cc_final: 0.8614 (t0) REVERT: B 125 MET cc_start: 0.8013 (mtm) cc_final: 0.7261 (ptp) REVERT: C 164 ASN cc_start: 0.8286 (t0) cc_final: 0.8017 (t0) REVERT: D 50 LYS cc_start: 0.8428 (mttt) cc_final: 0.8128 (mmmt) REVERT: D 86 ASP cc_start: 0.9003 (t70) cc_final: 0.8525 (t0) REVERT: D 88 ARG cc_start: 0.8161 (tmt170) cc_final: 0.7858 (tpt170) REVERT: E 164 ASN cc_start: 0.7848 (t0) cc_final: 0.6926 (p0) REVERT: F 50 LYS cc_start: 0.8427 (mttt) cc_final: 0.8070 (mmmt) REVERT: F 86 ASP cc_start: 0.8992 (t70) cc_final: 0.8467 (t0) REVERT: F 88 ARG cc_start: 0.8115 (tmt170) cc_final: 0.7893 (tpt170) REVERT: F 125 MET cc_start: 0.8124 (mtm) cc_final: 0.7402 (ptp) outliers start: 17 outliers final: 12 residues processed: 105 average time/residue: 0.2857 time to fit residues: 41.1821 Evaluate side-chains 101 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 1.171 ------------------------------------------------------------------------------- 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 125 ILE Chi-restraints excluded: chain A residue 250 MET 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 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 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 0 optimal weight: 8.9990 chunk 82 optimal weight: 40.0000 chunk 76 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 chunk 78 optimal weight: 0.1980 chunk 138 optimal weight: 0.7980 chunk 56 optimal weight: 0.3980 chunk 59 optimal weight: 0.0370 chunk 96 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 ASN F 22 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.112566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.078144 restraints weight = 20573.142| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.75 r_work: 0.2935 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 11802 Z= 0.104 Angle : 0.509 9.186 16086 Z= 0.241 Chirality : 0.039 0.179 1938 Planarity : 0.004 0.069 1992 Dihedral : 4.292 26.706 2442 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.58 % Allowed : 8.23 % Favored : 90.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.79 (0.22), residues: 1425 helix: 3.16 (0.28), residues: 324 sheet: 0.07 (0.32), residues: 264 loop : -0.39 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 14 HIS 0.007 0.001 HIS A 85 PHE 0.008 0.001 PHE A 192 TYR 0.010 0.001 TYR A 308 ARG 0.006 0.000 ARG C 278 Details of bonding type rmsd link_NAG-ASN : bond 0.00451 ( 21) link_NAG-ASN : angle 2.27806 ( 63) link_BETA1-4 : bond 0.00547 ( 24) link_BETA1-4 : angle 1.36466 ( 72) hydrogen bonds : bond 0.03090 ( 435) hydrogen bonds : angle 4.55203 ( 1242) SS BOND : bond 0.00171 ( 18) SS BOND : angle 0.84245 ( 36) covalent geometry : bond 0.00239 (11739) covalent geometry : angle 0.48091 (15915) *********************** 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 115 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 1.330 Fit side-chains REVERT: A 48 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7403 (pm20) REVERT: A 164 ASN cc_start: 0.7959 (t0) cc_final: 0.7740 (t0) REVERT: B 50 LYS cc_start: 0.8447 (mttt) cc_final: 0.8117 (mmmt) REVERT: B 64 GLN cc_start: 0.8755 (mp10) cc_final: 0.8462 (mt0) REVERT: B 86 ASP cc_start: 0.9032 (t0) cc_final: 0.8554 (t0) REVERT: B 125 MET cc_start: 0.7951 (mtm) cc_final: 0.7163 (ptp) REVERT: C 164 ASN cc_start: 0.8243 (t0) cc_final: 0.7977 (t0) REVERT: D 50 LYS cc_start: 0.8447 (mttt) cc_final: 0.8144 (mmmt) REVERT: D 70 MET cc_start: 0.8909 (mmm) cc_final: 0.8520 (mmp) REVERT: D 86 ASP cc_start: 0.8963 (t70) cc_final: 0.8501 (t0) REVERT: D 88 ARG cc_start: 0.8149 (tmt170) cc_final: 0.7841 (tpt170) REVERT: E 164 ASN cc_start: 0.7806 (t0) cc_final: 0.6918 (p0) REVERT: F 50 LYS cc_start: 0.8453 (mttt) cc_final: 0.8108 (mmmt) REVERT: F 86 ASP cc_start: 0.8944 (t70) cc_final: 0.8503 (t0) REVERT: F 88 ARG cc_start: 0.8141 (tmt170) cc_final: 0.7917 (tpt170) REVERT: F 125 MET cc_start: 0.8115 (mtm) cc_final: 0.7383 (ptp) outliers start: 19 outliers final: 16 residues processed: 110 average time/residue: 0.2738 time to fit residues: 42.0505 Evaluate side-chains 111 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 1.305 ------------------------------------------------------------------------------- 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 A residue 250 MET 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 B residue 116 LEU Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain E residue 94 CYS 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 71 optimal weight: 0.7980 chunk 110 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 120 optimal weight: 0.2980 chunk 91 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 13 optimal weight: 0.0470 chunk 70 optimal weight: 1.9990 chunk 85 optimal weight: 0.0020 chunk 4 optimal weight: 0.9980 overall best weight: 0.4286 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 ASN F 22 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.112787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.078693 restraints weight = 20614.441| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.73 r_work: 0.2941 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.4129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 11802 Z= 0.104 Angle : 0.504 9.138 16086 Z= 0.237 Chirality : 0.039 0.181 1938 Planarity : 0.004 0.061 1992 Dihedral : 4.198 27.491 2442 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.58 % Allowed : 8.40 % 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 (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: 0.87 (0.22), residues: 1425 helix: 3.27 (0.28), residues: 324 sheet: 0.13 (0.32), residues: 264 loop : -0.36 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 14 HIS 0.007 0.001 HIS A 85 PHE 0.008 0.001 PHE A 192 TYR 0.010 0.001 TYR C 135 ARG 0.007 0.000 ARG C 278 Details of bonding type rmsd link_NAG-ASN : bond 0.00429 ( 21) link_NAG-ASN : angle 2.18434 ( 63) link_BETA1-4 : bond 0.00520 ( 24) link_BETA1-4 : angle 1.31650 ( 72) hydrogen bonds : bond 0.03009 ( 435) hydrogen bonds : angle 4.50786 ( 1242) SS BOND : bond 0.00169 ( 18) SS BOND : angle 0.75399 ( 36) covalent geometry : bond 0.00239 (11739) covalent geometry : angle 0.47787 (15915) *********************** 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 113 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 1.251 Fit side-chains REVERT: A 48 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7420 (pm20) REVERT: A 164 ASN cc_start: 0.7978 (t0) cc_final: 0.6939 (p0) REVERT: B 50 LYS cc_start: 0.8443 (mttt) cc_final: 0.8108 (mmmt) REVERT: B 64 GLN cc_start: 0.8761 (mp10) cc_final: 0.8461 (mt0) REVERT: B 86 ASP cc_start: 0.9028 (t0) cc_final: 0.8551 (t0) REVERT: B 125 MET cc_start: 0.7977 (mtm) cc_final: 0.7180 (ptp) REVERT: C 164 ASN cc_start: 0.8229 (t0) cc_final: 0.7967 (t0) REVERT: D 50 LYS cc_start: 0.8442 (mttt) cc_final: 0.8139 (mmmt) REVERT: D 86 ASP cc_start: 0.8965 (t70) cc_final: 0.8507 (t0) REVERT: D 88 ARG cc_start: 0.8151 (tmt170) cc_final: 0.7812 (tpt170) REVERT: E 164 ASN cc_start: 0.7785 (t0) cc_final: 0.6911 (p0) REVERT: F 50 LYS cc_start: 0.8461 (mttt) cc_final: 0.8111 (mmmt) REVERT: F 86 ASP cc_start: 0.8922 (t70) cc_final: 0.8459 (t0) REVERT: F 88 ARG cc_start: 0.8186 (tmt170) cc_final: 0.7942 (tpt170) REVERT: F 125 MET cc_start: 0.8095 (mtm) cc_final: 0.7374 (ptp) outliers start: 19 outliers final: 14 residues processed: 107 average time/residue: 0.2633 time to fit residues: 39.3204 Evaluate side-chains 108 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 1.209 ------------------------------------------------------------------------------- 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 A residue 250 MET Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain E residue 94 CYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 113 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 46 optimal weight: 7.9990 chunk 106 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 48 optimal weight: 7.9990 chunk 140 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3605 r_free = 0.3605 target = 0.110667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.076088 restraints weight = 20880.453| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.71 r_work: 0.2882 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11802 Z= 0.201 Angle : 0.560 8.750 16086 Z= 0.268 Chirality : 0.041 0.174 1938 Planarity : 0.004 0.060 1992 Dihedral : 4.387 26.065 2442 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.08 % Allowed : 9.14 % 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 (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: 0.71 (0.22), residues: 1425 helix: 3.03 (0.27), residues: 324 sheet: 0.10 (0.32), residues: 264 loop : -0.44 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 21 HIS 0.008 0.001 HIS A 85 PHE 0.011 0.001 PHE A 192 TYR 0.014 0.002 TYR A 135 ARG 0.006 0.000 ARG C 278 Details of bonding type rmsd link_NAG-ASN : bond 0.00349 ( 21) link_NAG-ASN : angle 2.27822 ( 63) link_BETA1-4 : bond 0.00493 ( 24) link_BETA1-4 : angle 1.36763 ( 72) hydrogen bonds : bond 0.03403 ( 435) hydrogen bonds : angle 4.62668 ( 1242) SS BOND : bond 0.00298 ( 18) SS BOND : angle 0.85532 ( 36) covalent geometry : bond 0.00482 (11739) covalent geometry : angle 0.53537 (15915) ********************** 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: 13 poor density : 96 time to evaluate : 1.191 Fit side-chains REVERT: A 48 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7533 (pm20) REVERT: A 164 ASN cc_start: 0.8076 (t0) cc_final: 0.6999 (p0) REVERT: B 50 LYS cc_start: 0.8460 (mttt) cc_final: 0.8123 (mmmt) REVERT: B 64 GLN cc_start: 0.8861 (mp10) cc_final: 0.8517 (mt0) REVERT: B 86 ASP cc_start: 0.9098 (t0) cc_final: 0.8630 (t0) REVERT: B 125 MET cc_start: 0.7920 (mtm) cc_final: 0.7163 (ptp) REVERT: C 164 ASN cc_start: 0.8288 (t0) cc_final: 0.7951 (t0) REVERT: D 50 LYS cc_start: 0.8426 (mttt) cc_final: 0.8123 (mmmt) REVERT: D 86 ASP cc_start: 0.9057 (t70) cc_final: 0.8605 (t0) REVERT: E 164 ASN cc_start: 0.7954 (t0) cc_final: 0.7059 (p0) REVERT: F 50 LYS cc_start: 0.8440 (mttt) cc_final: 0.8075 (mmmt) REVERT: F 86 ASP cc_start: 0.9031 (t70) cc_final: 0.8624 (t0) REVERT: F 88 ARG cc_start: 0.8189 (tmt170) cc_final: 0.7954 (tpt170) REVERT: F 125 MET cc_start: 0.8104 (mtm) cc_final: 0.7416 (ptp) outliers start: 13 outliers final: 10 residues processed: 106 average time/residue: 0.2739 time to fit residues: 40.1639 Evaluate side-chains 106 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 1.219 ------------------------------------------------------------------------------- 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 B residue 116 LEU Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain D residue 62 ASN 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 116 optimal weight: 0.3980 chunk 64 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 96 optimal weight: 0.9980 chunk 125 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 54 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 ASN B 75 ASN D 75 ASN F 22 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.110783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.076403 restraints weight = 20545.745| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.70 r_work: 0.2898 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11802 Z= 0.170 Angle : 0.540 9.079 16086 Z= 0.257 Chirality : 0.040 0.174 1938 Planarity : 0.004 0.059 1992 Dihedral : 4.404 26.930 2442 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.16 % Allowed : 9.14 % 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 (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: 0.72 (0.22), residues: 1425 helix: 3.11 (0.28), residues: 324 sheet: 0.06 (0.32), residues: 264 loop : -0.44 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 21 HIS 0.007 0.001 HIS A 85 PHE 0.011 0.001 PHE A 192 TYR 0.012 0.001 TYR A 135 ARG 0.006 0.000 ARG C 278 Details of bonding type rmsd link_NAG-ASN : bond 0.00362 ( 21) link_NAG-ASN : angle 2.28236 ( 63) link_BETA1-4 : bond 0.00509 ( 24) link_BETA1-4 : angle 1.29014 ( 72) hydrogen bonds : bond 0.03276 ( 435) hydrogen bonds : angle 4.58848 ( 1242) SS BOND : bond 0.00255 ( 18) SS BOND : angle 0.76849 ( 36) covalent geometry : bond 0.00407 (11739) covalent geometry : angle 0.51502 (15915) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6219.84 seconds wall clock time: 108 minutes 46.87 seconds (6526.87 seconds total)