Starting phenix.real_space_refine on Tue Jun 10 08:27:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bto_44894/06_2025/9bto_44894.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bto_44894/06_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_44894/06_2025/9bto_44894.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bto_44894/06_2025/9bto_44894.map" model { file = "/net/cci-nas-00/data/ceres_data/9bto_44894/06_2025/9bto_44894.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bto_44894/06_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-5710/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: 9.61, per 1000 atoms: 0.83 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: 3.49 Conformation dependent library (CDL) restraints added in 1.6 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: 1.72 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: 3.74 Time building geometry restraints manager: 4.04 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: 11.560 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: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.150 Process input model: 32.680 Find NCS groups from input model: 0.540 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: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.500 ------------------------------------------------------------------------------- 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 : 1.408 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: 0.2944 time to fit residues: 91.0286 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 : 1.773 ------------------------------------------------------------------------------- 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 = 0.3689 r_free = 0.3689 target = 0.115006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.080900 restraints weight = 20403.075| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.66 r_work: 0.2986 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 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 : 1.246 Fit side-chains revert: symmetry clash REVERT: A 253 LYS cc_start: 0.9140 (mmtt) cc_final: 0.8856 (mmtp) REVERT: B 50 LYS cc_start: 0.8517 (mttt) cc_final: 0.8198 (mmmt) REVERT: B 81 ASP cc_start: 0.9082 (t0) cc_final: 0.8849 (t0) REVERT: B 85 ASP cc_start: 0.8467 (m-30) cc_final: 0.8242 (m-30) REVERT: B 86 ASP cc_start: 0.8963 (t0) cc_final: 0.8455 (t0) REVERT: B 125 MET cc_start: 0.8234 (mtm) cc_final: 0.8001 (mtp) REVERT: C 253 LYS cc_start: 0.9114 (mmtt) cc_final: 0.8824 (mmtm) REVERT: D 50 LYS cc_start: 0.8478 (mttt) cc_final: 0.8192 (mmmt) REVERT: D 86 ASP cc_start: 0.8905 (t70) cc_final: 0.8183 (t0) REVERT: F 21 TRP cc_start: 0.6770 (m100) cc_final: 0.6491 (m100) REVERT: F 50 LYS cc_start: 0.8514 (mttt) cc_final: 0.8167 (mmmt) REVERT: F 61 LYS cc_start: 0.9099 (mtpp) cc_final: 0.8747 (mtpp) REVERT: F 81 ASP cc_start: 0.9042 (t0) cc_final: 0.8795 (t0) REVERT: F 85 ASP cc_start: 0.8351 (m-30) cc_final: 0.8089 (m-30) REVERT: F 86 ASP cc_start: 0.8919 (t70) cc_final: 0.8494 (t0) REVERT: F 125 MET cc_start: 0.8250 (mtm) cc_final: 0.8003 (mtp) outliers start: 14 outliers final: 6 residues processed: 133 average time/residue: 0.2912 time to fit residues: 52.4479 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: 0.0070 chunk 3 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 80 optimal weight: 10.0000 chunk 13 optimal weight: 0.4980 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: 0.9002 ------------------------------------------------------------------------------- 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 = 0.3669 r_free = 0.3669 target = 0.113546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.078610 restraints weight = 20478.513| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.71 r_work: 0.2945 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11802 Z= 0.179 Angle : 0.648 7.997 16086 Z= 0.306 Chirality : 0.043 0.172 1938 Planarity : 0.004 0.032 1992 Dihedral : 7.085 37.040 2442 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.33 % Allowed : 6.48 % Favored : 92.19 % 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: 0.65 (0.21), residues: 1425 helix: 2.55 (0.28), residues: 327 sheet: -0.10 (0.30), residues: 258 loop : -0.22 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 21 HIS 0.006 0.001 HIS B 22 PHE 0.010 0.002 PHE A 192 TYR 0.018 0.002 TYR A 135 ARG 0.003 0.000 ARG C 278 Details of bonding type rmsd link_NAG-ASN : bond 0.00504 ( 21) link_NAG-ASN : angle 2.85807 ( 63) link_BETA1-4 : bond 0.00849 ( 24) link_BETA1-4 : angle 2.49667 ( 72) hydrogen bonds : bond 0.04163 ( 435) hydrogen bonds : angle 5.16903 ( 1242) SS BOND : bond 0.00259 ( 18) SS BOND : angle 0.72139 ( 36) covalent geometry : bond 0.00414 (11739) covalent geometry : angle 0.60192 (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 120 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 1.288 Fit side-chains REVERT: B 50 LYS cc_start: 0.8499 (mttt) cc_final: 0.8186 (mmmt) REVERT: B 86 ASP cc_start: 0.9008 (t0) cc_final: 0.8570 (t0) REVERT: B 125 MET cc_start: 0.8184 (mtm) cc_final: 0.7819 (mtp) REVERT: C 164 ASN cc_start: 0.8244 (t0) cc_final: 0.8000 (t0) REVERT: D 50 LYS cc_start: 0.8476 (mttt) cc_final: 0.8187 (mmmt) REVERT: D 86 ASP cc_start: 0.8987 (t70) cc_final: 0.8522 (t0) REVERT: F 50 LYS cc_start: 0.8531 (mttt) cc_final: 0.8182 (mmmt) REVERT: F 64 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.8387 (mt0) REVERT: F 86 ASP cc_start: 0.8914 (t70) cc_final: 0.8526 (t0) outliers start: 16 outliers final: 11 residues processed: 116 average time/residue: 0.2835 time to fit residues: 45.7821 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 : 1.353 ------------------------------------------------------------------------------- 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 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 C residue 279 SER Chi-restraints excluded: chain D residue 62 ASN 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: 2.9990 chunk 108 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 123 optimal weight: 3.9990 chunk 140 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 ASN 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 = 0.3582 r_free = 0.3582 target = 0.109294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.074434 restraints weight = 20914.530| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.71 r_work: 0.2823 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.076 11802 Z= 0.319 Angle : 0.703 8.814 16086 Z= 0.338 Chirality : 0.044 0.216 1938 Planarity : 0.004 0.036 1992 Dihedral : 5.438 28.331 2442 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.75 % Allowed : 7.07 % Favored : 91.19 % 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: 0.30 (0.21), residues: 1425 helix: 2.42 (0.28), residues: 324 sheet: -0.26 (0.31), residues: 258 loop : -0.53 (0.19), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 21 HIS 0.007 0.001 HIS B 22 PHE 0.013 0.002 PHE A 192 TYR 0.022 0.002 TYR A 135 ARG 0.002 0.000 ARG E 69 Details of bonding type rmsd link_NAG-ASN : bond 0.00390 ( 21) link_NAG-ASN : angle 2.90983 ( 63) link_BETA1-4 : bond 0.00572 ( 24) link_BETA1-4 : angle 2.21677 ( 72) hydrogen bonds : bond 0.04332 ( 435) hydrogen bonds : angle 5.08872 ( 1242) SS BOND : bond 0.00449 ( 18) SS BOND : angle 0.82669 ( 36) covalent geometry : bond 0.00765 (11739) covalent geometry : angle 0.66529 (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 114 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 1.337 Fit side-chains REVERT: B 50 LYS cc_start: 0.8470 (mttt) cc_final: 0.8128 (mmmt) REVERT: B 86 ASP cc_start: 0.9062 (t0) cc_final: 0.8592 (t0) REVERT: C 164 ASN cc_start: 0.8240 (t0) cc_final: 0.8004 (t0) REVERT: D 50 LYS cc_start: 0.8390 (mttt) cc_final: 0.8099 (mmmt) REVERT: D 86 ASP cc_start: 0.9031 (t70) cc_final: 0.8518 (t0) REVERT: F 50 LYS cc_start: 0.8440 (mttt) cc_final: 0.8138 (mmmt) REVERT: F 86 ASP cc_start: 0.8997 (t70) cc_final: 0.8641 (t0) outliers start: 21 outliers final: 15 residues processed: 108 average time/residue: 0.2871 time to fit residues: 43.0237 Evaluate side-chains 99 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 1.416 ------------------------------------------------------------------------------- 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 197 GLU Chi-restraints excluded: chain B residue 60 VAL 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 312 GLU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain E residue 48 GLU Chi-restraints excluded: chain E residue 312 GLU Chi-restraints excluded: chain F residue 60 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 20 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 22 optimal weight: 0.0870 chunk 12 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 HIS B 22 HIS B 64 GLN B 75 ASN D 75 ASN E 99 HIS F 22 HIS ** F 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.111117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.076445 restraints weight = 20318.816| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 2.71 r_work: 0.2892 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11802 Z= 0.147 Angle : 0.570 8.891 16086 Z= 0.272 Chirality : 0.040 0.175 1938 Planarity : 0.005 0.076 1992 Dihedral : 4.819 25.673 2442 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.50 % Allowed : 7.98 % Favored : 90.52 % 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: 0.50 (0.21), residues: 1425 helix: 2.78 (0.28), residues: 324 sheet: -0.05 (0.31), residues: 264 loop : -0.53 (0.19), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 14 HIS 0.009 0.001 HIS D 22 PHE 0.009 0.001 PHE A 192 TYR 0.013 0.001 TYR A 135 ARG 0.002 0.000 ARG E 278 Details of bonding type rmsd link_NAG-ASN : bond 0.00471 ( 21) link_NAG-ASN : angle 2.69996 ( 63) link_BETA1-4 : bond 0.00610 ( 24) link_BETA1-4 : angle 1.66740 ( 72) hydrogen bonds : bond 0.03682 ( 435) hydrogen bonds : angle 4.86145 ( 1242) SS BOND : bond 0.00244 ( 18) SS BOND : angle 0.54604 ( 36) covalent geometry : bond 0.00342 (11739) covalent geometry : angle 0.53550 (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 116 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 1.231 Fit side-chains REVERT: A 48 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7485 (pm20) REVERT: B 50 LYS cc_start: 0.8445 (mttt) cc_final: 0.8114 (mmmt) REVERT: B 64 GLN cc_start: 0.8833 (OUTLIER) cc_final: 0.8350 (mt0) REVERT: B 86 ASP cc_start: 0.9039 (t0) cc_final: 0.8577 (t0) REVERT: B 125 MET cc_start: 0.8112 (mtm) cc_final: 0.7365 (ptp) REVERT: C 164 ASN cc_start: 0.8241 (t0) cc_final: 0.7978 (t0) REVERT: D 50 LYS cc_start: 0.8404 (mttt) cc_final: 0.8114 (mmmt) REVERT: D 86 ASP cc_start: 0.8993 (t70) cc_final: 0.8511 (t0) REVERT: F 50 LYS cc_start: 0.8431 (mttt) cc_final: 0.8086 (mmmt) REVERT: F 86 ASP cc_start: 0.8924 (t70) cc_final: 0.8535 (t0) REVERT: F 88 ARG cc_start: 0.8145 (tmt170) cc_final: 0.7888 (tpt170) REVERT: F 125 MET cc_start: 0.7791 (mtm) cc_final: 0.7374 (ptp) outliers start: 18 outliers final: 9 residues processed: 111 average time/residue: 0.2888 time to fit residues: 44.5067 Evaluate side-chains 96 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 1.200 ------------------------------------------------------------------------------- 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 250 MET Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 64 GLN 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 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: 10.0000 chunk 17 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 80 optimal weight: 0.1980 chunk 34 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 113 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 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 = 0.3621 r_free = 0.3621 target = 0.110889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.076201 restraints weight = 20466.910| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.72 r_work: 0.2896 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11802 Z= 0.137 Angle : 0.556 9.198 16086 Z= 0.263 Chirality : 0.040 0.206 1938 Planarity : 0.004 0.062 1992 Dihedral : 4.617 24.805 2442 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.25 % Allowed : 9.23 % Favored : 89.53 % 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: 0.54 (0.21), residues: 1425 helix: 2.84 (0.28), residues: 324 sheet: 0.01 (0.31), residues: 264 loop : -0.52 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 21 HIS 0.005 0.001 HIS A 85 PHE 0.009 0.001 PHE A 192 TYR 0.012 0.001 TYR A 135 ARG 0.004 0.000 ARG B 65 Details of bonding type rmsd link_NAG-ASN : bond 0.00422 ( 21) link_NAG-ASN : angle 2.56975 ( 63) link_BETA1-4 : bond 0.00592 ( 24) link_BETA1-4 : angle 1.59080 ( 72) hydrogen bonds : bond 0.03535 ( 435) hydrogen bonds : angle 4.77397 ( 1242) SS BOND : bond 0.00322 ( 18) SS BOND : angle 0.63272 ( 36) covalent geometry : bond 0.00320 (11739) covalent geometry : angle 0.52314 (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 105 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 1.227 Fit side-chains REVERT: A 48 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7489 (pm20) REVERT: A 164 ASN cc_start: 0.7930 (t0) cc_final: 0.7726 (t0) REVERT: B 50 LYS cc_start: 0.8452 (mttt) cc_final: 0.8116 (mmmt) REVERT: B 64 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.8389 (mt0) REVERT: B 86 ASP cc_start: 0.9054 (t0) cc_final: 0.8584 (t0) REVERT: B 125 MET cc_start: 0.8085 (mtm) cc_final: 0.7307 (ptp) REVERT: C 164 ASN cc_start: 0.8268 (t0) cc_final: 0.8007 (t0) REVERT: D 50 LYS cc_start: 0.8423 (mttt) cc_final: 0.8125 (mmmt) REVERT: D 86 ASP cc_start: 0.8976 (t70) cc_final: 0.8492 (t0) REVERT: F 50 LYS cc_start: 0.8439 (mttt) cc_final: 0.8089 (mmmt) REVERT: F 86 ASP cc_start: 0.8947 (t70) cc_final: 0.8433 (t0) REVERT: F 88 ARG cc_start: 0.8161 (tmt170) cc_final: 0.7933 (tpt170) REVERT: F 125 MET cc_start: 0.7787 (mtm) cc_final: 0.7432 (ptp) outliers start: 15 outliers final: 12 residues processed: 101 average time/residue: 0.2939 time to fit residues: 40.5799 Evaluate side-chains 102 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 1.230 ------------------------------------------------------------------------------- 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 56 SER Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 64 GLN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 86 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 125 optimal weight: 0.0020 chunk 80 optimal weight: 6.9990 chunk 32 optimal weight: 0.8980 chunk 136 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 HIS B 64 GLN B 75 ASN C 14 HIS E 14 HIS F 22 HIS F 75 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.110796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.076145 restraints weight = 20635.237| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.72 r_work: 0.2895 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11802 Z= 0.145 Angle : 0.547 9.279 16086 Z= 0.259 Chirality : 0.040 0.176 1938 Planarity : 0.004 0.056 1992 Dihedral : 4.494 24.080 2442 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.50 % Allowed : 9.14 % Favored : 89.36 % 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: 0.60 (0.22), residues: 1425 helix: 2.88 (0.28), residues: 324 sheet: 0.04 (0.32), residues: 264 loop : -0.48 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 21 HIS 0.011 0.001 HIS C 85 PHE 0.009 0.001 PHE A 192 TYR 0.012 0.001 TYR C 135 ARG 0.007 0.000 ARG C 278 Details of bonding type rmsd link_NAG-ASN : bond 0.00395 ( 21) link_NAG-ASN : angle 2.46652 ( 63) link_BETA1-4 : bond 0.00564 ( 24) link_BETA1-4 : angle 1.49082 ( 72) hydrogen bonds : bond 0.03429 ( 435) hydrogen bonds : angle 4.70129 ( 1242) SS BOND : bond 0.00239 ( 18) SS BOND : angle 0.72215 ( 36) covalent geometry : bond 0.00343 (11739) covalent geometry : angle 0.51705 (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 114 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 1.362 Fit side-chains REVERT: A 48 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7500 (pm20) REVERT: A 164 ASN cc_start: 0.7922 (t0) cc_final: 0.7688 (t0) REVERT: B 50 LYS cc_start: 0.8459 (mttt) cc_final: 0.8124 (mmmt) REVERT: B 86 ASP cc_start: 0.9040 (t0) cc_final: 0.8602 (t0) REVERT: B 125 MET cc_start: 0.8008 (mtm) cc_final: 0.7238 (ptp) REVERT: C 164 ASN cc_start: 0.8270 (t0) cc_final: 0.7903 (t0) REVERT: D 50 LYS cc_start: 0.8436 (mttt) cc_final: 0.8138 (mmmt) REVERT: D 86 ASP cc_start: 0.8985 (t70) cc_final: 0.8486 (t0) REVERT: F 50 LYS cc_start: 0.8448 (mttt) cc_final: 0.8094 (mmmt) REVERT: F 64 GLN cc_start: 0.8560 (mt0) cc_final: 0.8256 (mt0) REVERT: F 86 ASP cc_start: 0.8956 (t70) cc_final: 0.8445 (t0) REVERT: F 88 ARG cc_start: 0.8151 (tmt170) cc_final: 0.7919 (tpt170) REVERT: F 125 MET cc_start: 0.7789 (mtm) cc_final: 0.7463 (ptp) outliers start: 18 outliers final: 14 residues processed: 109 average time/residue: 0.2967 time to fit residues: 44.4107 Evaluate side-chains 107 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 60 VAL 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 94 CYS 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: 8.9990 chunk 76 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 chunk 96 optimal weight: 0.0270 chunk 30 optimal weight: 0.6980 overall best weight: 1.2642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 GLN 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 = 0.3593 r_free = 0.3593 target = 0.109797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.075282 restraints weight = 21030.810| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 2.71 r_work: 0.2850 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.3992 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= 0.209 Angle : 0.586 9.053 16086 Z= 0.280 Chirality : 0.041 0.174 1938 Planarity : 0.004 0.055 1992 Dihedral : 4.615 25.062 2442 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.91 % Allowed : 8.98 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.55 (0.22), residues: 1425 helix: 2.82 (0.28), residues: 324 sheet: 0.04 (0.32), residues: 264 loop : -0.52 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 21 HIS 0.010 0.001 HIS C 85 PHE 0.011 0.001 PHE A 192 TYR 0.012 0.001 TYR C 135 ARG 0.005 0.000 ARG C 278 Details of bonding type rmsd link_NAG-ASN : bond 0.00353 ( 21) link_NAG-ASN : angle 2.47551 ( 63) link_BETA1-4 : bond 0.00518 ( 24) link_BETA1-4 : angle 1.44965 ( 72) hydrogen bonds : bond 0.03644 ( 435) hydrogen bonds : angle 4.75820 ( 1242) SS BOND : bond 0.00320 ( 18) SS BOND : angle 0.88854 ( 36) covalent geometry : bond 0.00501 (11739) covalent geometry : angle 0.55787 (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 114 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 1.239 Fit side-chains REVERT: A 48 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7517 (pm20) REVERT: A 164 ASN cc_start: 0.8024 (t0) cc_final: 0.7012 (p0) REVERT: B 50 LYS cc_start: 0.8478 (mttt) cc_final: 0.8141 (mmmt) REVERT: B 64 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.8414 (mt0) REVERT: B 86 ASP cc_start: 0.9098 (t0) cc_final: 0.8617 (t0) REVERT: B 125 MET cc_start: 0.7976 (mtm) cc_final: 0.7207 (ptp) REVERT: C 164 ASN cc_start: 0.8285 (t0) cc_final: 0.7925 (t0) REVERT: D 50 LYS cc_start: 0.8439 (mttt) cc_final: 0.8145 (mmmt) REVERT: D 86 ASP cc_start: 0.9045 (t70) cc_final: 0.8578 (t0) REVERT: E 164 ASN cc_start: 0.7992 (t0) cc_final: 0.7068 (p0) REVERT: F 50 LYS cc_start: 0.8448 (mttt) cc_final: 0.8090 (mmmt) REVERT: F 64 GLN cc_start: 0.8645 (mt0) cc_final: 0.8327 (mt0) REVERT: F 86 ASP cc_start: 0.9035 (t70) cc_final: 0.8611 (t0) REVERT: F 88 ARG cc_start: 0.8195 (tmt170) cc_final: 0.7949 (tpt170) REVERT: F 125 MET cc_start: 0.7780 (mtm) cc_final: 0.7459 (ptp) outliers start: 23 outliers final: 18 residues processed: 108 average time/residue: 0.2939 time to fit residues: 43.9451 Evaluate side-chains 110 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 1.230 ------------------------------------------------------------------------------- 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 197 GLU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 64 GLN 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 E residue 312 GLU 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: 0.9990 chunk 110 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 95 optimal weight: 0.1980 chunk 13 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 4 optimal weight: 0.0170 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 GLN 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 = 0.3622 r_free = 0.3622 target = 0.110906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.076173 restraints weight = 20611.645| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.76 r_work: 0.2899 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.4080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11802 Z= 0.120 Angle : 0.537 9.155 16086 Z= 0.255 Chirality : 0.039 0.175 1938 Planarity : 0.004 0.052 1992 Dihedral : 4.462 25.346 2442 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.25 % Allowed : 9.56 % Favored : 89.19 % 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: 0.68 (0.22), residues: 1425 helix: 3.04 (0.28), residues: 324 sheet: 0.08 (0.32), residues: 264 loop : -0.47 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 21 HIS 0.010 0.001 HIS C 85 PHE 0.009 0.001 PHE A 192 TYR 0.010 0.001 TYR A 135 ARG 0.006 0.000 ARG C 278 Details of bonding type rmsd link_NAG-ASN : bond 0.00421 ( 21) link_NAG-ASN : angle 2.36494 ( 63) link_BETA1-4 : bond 0.00555 ( 24) link_BETA1-4 : angle 1.33113 ( 72) hydrogen bonds : bond 0.03256 ( 435) hydrogen bonds : angle 4.64465 ( 1242) SS BOND : bond 0.00218 ( 18) SS BOND : angle 0.73073 ( 36) covalent geometry : bond 0.00279 (11739) covalent geometry : angle 0.51031 (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 109 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 1.271 Fit side-chains REVERT: A 48 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7490 (pm20) REVERT: A 164 ASN cc_start: 0.8003 (t0) cc_final: 0.6991 (p0) REVERT: B 50 LYS cc_start: 0.8466 (mttt) cc_final: 0.8126 (mmmt) REVERT: B 64 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.8479 (mt0) REVERT: B 86 ASP cc_start: 0.9058 (t0) cc_final: 0.8574 (t0) REVERT: B 125 MET cc_start: 0.7944 (mtm) cc_final: 0.7179 (ptp) REVERT: C 48 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7415 (pm20) REVERT: C 164 ASN cc_start: 0.8293 (t0) cc_final: 0.7937 (t0) REVERT: D 50 LYS cc_start: 0.8443 (mttt) cc_final: 0.8146 (mmmt) REVERT: D 86 ASP cc_start: 0.8991 (t70) cc_final: 0.8516 (t0) REVERT: D 107 ILE cc_start: 0.7005 (mm) cc_final: 0.6733 (mm) REVERT: E 164 ASN cc_start: 0.7968 (t0) cc_final: 0.7035 (p0) REVERT: F 50 LYS cc_start: 0.8456 (mttt) cc_final: 0.8102 (mmmt) REVERT: F 64 GLN cc_start: 0.8553 (mt0) cc_final: 0.8239 (mt0) REVERT: F 86 ASP cc_start: 0.8997 (t70) cc_final: 0.8575 (t0) REVERT: F 88 ARG cc_start: 0.8135 (tmt170) cc_final: 0.7919 (tpt170) REVERT: F 125 MET cc_start: 0.7782 (mtm) cc_final: 0.7483 (ptp) outliers start: 15 outliers final: 12 residues processed: 104 average time/residue: 0.2828 time to fit residues: 40.8446 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 : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 60 VAL Chi-restraints excluded: chain B residue 64 GLN 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 94 CYS Chi-restraints excluded: chain E residue 250 MET 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: 0.7980 chunk 86 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 46 optimal weight: 6.9990 chunk 106 optimal weight: 0.0970 chunk 93 optimal weight: 9.9990 chunk 107 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 140 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** F 22 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.110769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.076333 restraints weight = 20468.648| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.73 r_work: 0.2886 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11802 Z= 0.131 Angle : 0.534 9.119 16086 Z= 0.252 Chirality : 0.039 0.175 1938 Planarity : 0.004 0.053 1992 Dihedral : 4.406 26.016 2442 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.25 % Allowed : 9.64 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.07 (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 C 85 PHE 0.009 0.001 PHE A 192 TYR 0.010 0.001 TYR A 135 ARG 0.005 0.000 ARG C 278 Details of bonding type rmsd link_NAG-ASN : bond 0.00387 ( 21) link_NAG-ASN : angle 2.33828 ( 63) link_BETA1-4 : bond 0.00532 ( 24) link_BETA1-4 : angle 1.32552 ( 72) hydrogen bonds : bond 0.03217 ( 435) hydrogen bonds : angle 4.60442 ( 1242) SS BOND : bond 0.00213 ( 18) SS BOND : angle 0.75056 ( 36) covalent geometry : bond 0.00311 (11739) covalent geometry : angle 0.50711 (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 108 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 1.488 Fit side-chains REVERT: A 48 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7462 (pm20) REVERT: A 164 ASN cc_start: 0.7994 (t0) cc_final: 0.6992 (p0) REVERT: B 50 LYS cc_start: 0.8454 (mttt) cc_final: 0.8113 (mmmt) REVERT: B 64 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.8253 (mt0) REVERT: B 86 ASP cc_start: 0.9059 (t0) cc_final: 0.8567 (t0) REVERT: B 125 MET cc_start: 0.7943 (mtm) cc_final: 0.7178 (ptp) REVERT: C 48 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7382 (pm20) REVERT: C 164 ASN cc_start: 0.8295 (t0) cc_final: 0.7936 (t0) REVERT: D 50 LYS cc_start: 0.8430 (mttt) cc_final: 0.8132 (mmmt) REVERT: D 86 ASP cc_start: 0.8973 (t70) cc_final: 0.8526 (t0) REVERT: D 107 ILE cc_start: 0.7029 (mm) cc_final: 0.6771 (mm) REVERT: E 164 ASN cc_start: 0.7970 (t0) cc_final: 0.7033 (p0) REVERT: F 50 LYS cc_start: 0.8451 (mttt) cc_final: 0.8089 (mmmt) REVERT: F 64 GLN cc_start: 0.8573 (mt0) cc_final: 0.8269 (mt0) REVERT: F 86 ASP cc_start: 0.8997 (t70) cc_final: 0.8580 (t0) REVERT: F 88 ARG cc_start: 0.8158 (tmt170) cc_final: 0.7918 (tpt170) REVERT: F 125 MET cc_start: 0.7783 (mtm) cc_final: 0.7492 (ptp) outliers start: 15 outliers final: 12 residues processed: 103 average time/residue: 0.2942 time to fit residues: 41.8071 Evaluate side-chains 105 residues out of total 1203 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 60 VAL Chi-restraints excluded: chain B residue 64 GLN 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 94 CYS Chi-restraints excluded: chain E residue 250 MET 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: 1.9990 chunk 64 optimal weight: 1.9990 chunk 98 optimal weight: 0.0000 chunk 43 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 54 optimal weight: 0.0670 chunk 34 optimal weight: 10.0000 overall best weight: 0.9526 ------------------------------------------------------------------------------- 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 = 0.3608 r_free = 0.3608 target = 0.110799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.076466 restraints weight = 20869.131| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.70 r_work: 0.2889 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11802 Z= 0.165 Angle : 0.543 9.019 16086 Z= 0.258 Chirality : 0.040 0.174 1938 Planarity : 0.004 0.052 1992 Dihedral : 4.424 25.927 2442 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.25 % Allowed : 9.56 % Favored : 89.19 % 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: 0.67 (0.22), residues: 1425 helix: 3.04 (0.28), residues: 324 sheet: 0.05 (0.32), residues: 264 loop : -0.47 (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 C 85 PHE 0.010 0.001 PHE A 192 TYR 0.011 0.001 TYR C 135 ARG 0.005 0.000 ARG C 278 Details of bonding type rmsd link_NAG-ASN : bond 0.00357 ( 21) link_NAG-ASN : angle 2.33934 ( 63) link_BETA1-4 : bond 0.00516 ( 24) link_BETA1-4 : angle 1.32354 ( 72) hydrogen bonds : bond 0.03287 ( 435) hydrogen bonds : angle 4.60045 ( 1242) SS BOND : bond 0.00260 ( 18) SS BOND : angle 0.76493 ( 36) covalent geometry : bond 0.00396 (11739) covalent geometry : angle 0.51720 (15915) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6768.58 seconds wall clock time: 117 minutes 3.37 seconds (7023.37 seconds total)