Starting phenix.real_space_refine on Fri Sep 11 22:56:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6y5h_10697/09_2026/6y5h_10697.cif Found real_map, /net/cci-nas-00/data/ceres_data/6y5h_10697/09_2026/6y5h_10697.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6y5h_10697/09_2026/6y5h_10697.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6y5h_10697/09_2026/6y5h_10697.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6y5h_10697/09_2026/6y5h_10697.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6y5h_10697/09_2026/6y5h_10697.cif" model { file = "/net/cci-nas-00/data/ceres_data/6y5h_10697/09_2026/6y5h_10697.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6y5h_10697/09_2026/6y5h_10697.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.253 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 57 5.16 5 C 7458 2.51 5 N 2055 2.21 5 O 2424 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11994 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2454 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 298} Chain: "B" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1399 Classifications: {'peptide': 172} Link IDs: {'TRANS': 171} Chain: "C" Number of atoms: 2454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2454 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 298} Chain: "E" Number of atoms: 2454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2454 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 298} Chain: "D" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1399 Classifications: {'peptide': 172} Link IDs: {'TRANS': 171} Chain: "F" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1399 Classifications: {'peptide': 172} Link IDs: {'TRANS': 171} Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "H" 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 chiralities: 2 Chain: "I" 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 chiralities: 2 Chain: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 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 chiralities: 2 Chain: "L" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 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 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 chiralities: 2 Time building chain proxies: 2.95, per 1000 atoms: 0.25 Number of scatterers: 11994 At special positions: 0 Unit cell: (86.11, 87.2, 149.33, 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 57 16.00 O 2424 8.00 N 2055 7.00 C 7458 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS B 137 " distance=2.11 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS D 137 " distance=1.96 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.03 Simple disulfide: pdb=" SG CYS E 14 " - pdb=" SG CYS F 137 " distance=2.01 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 277 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 76 " distance=2.03 Simple disulfide: pdb=" SG CYS E 97 " - pdb=" SG CYS E 139 " distance=2.03 Simple disulfide: pdb=" SG CYS E 281 " - pdb=" SG CYS E 305 " distance=2.03 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.03 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 148 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA G 3 " - " MAN G 4 " " BMA J 3 " - " MAN J 4 " " BMA L 3 " - " MAN L 4 " ALPHA1-6 " BMA G 3 " - " MAN G 5 " " BMA J 3 " - " MAN J 5 " " BMA L 3 " - " MAN L 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " 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 N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 401 " - " ASN A 38 " " NAG A 409 " - " ASN A 81 " " NAG C 401 " - " ASN C 38 " " NAG C 409 " - " ASN C 81 " " NAG E 401 " - " ASN E 38 " " NAG E 409 " - " ASN E 81 " " NAG G 1 " - " ASN A 165 " " NAG H 1 " - " ASN A 285 " " NAG I 1 " - " ASN B 154 " " NAG J 1 " - " ASN C 165 " " NAG K 1 " - " ASN C 285 " " NAG L 1 " - " ASN E 165 " " NAG M 1 " - " ASN E 285 " " NAG N 1 " - " ASN D 154 " " NAG O 1 " - " ASN F 154 " Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 492.1 milliseconds 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2706 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 33 sheets defined 26.1% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 76 through 80 removed outlier: 3.816A pdb=" N GLN A 80 " --> pdb=" O ASP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 114 Processing helix chain 'A' and resid 187 through 193 removed outlier: 3.802A pdb=" N GLN A 191 " --> pdb=" O THR A 187 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N THR A 192 " --> pdb=" O ASN A 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 56 removed outlier: 3.867A pdb=" N THR B 41 " --> pdb=" O ASP B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 126 removed outlier: 3.595A pdb=" N TYR B 94 " --> pdb=" O ASP B 90 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN B 95 " --> pdb=" O LEU B 91 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL B 100 " --> pdb=" O ALA B 96 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN B 105 " --> pdb=" O ALA B 101 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N MET B 115 " --> pdb=" O THR B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 154 removed outlier: 3.850A pdb=" N GLU B 150 " --> pdb=" O ASN B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 161 removed outlier: 3.777A pdb=" N VAL B 161 " --> pdb=" O ASP B 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 158 through 161' Processing helix chain 'B' and resid 162 through 172 removed outlier: 3.648A pdb=" N GLN B 172 " --> pdb=" O ASN B 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 76 through 80 removed outlier: 3.816A pdb=" N GLN C 80 " --> pdb=" O ASP C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 114 Processing helix chain 'C' and resid 187 through 193 removed outlier: 3.801A pdb=" N GLN C 191 " --> pdb=" O THR C 187 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N THR C 192 " --> pdb=" O ASN C 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 76 through 80 removed outlier: 3.815A pdb=" N GLN E 80 " --> pdb=" O ASP E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 114 Processing helix chain 'E' and resid 187 through 193 removed outlier: 3.802A pdb=" N GLN E 191 " --> pdb=" O THR E 187 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N THR E 192 " --> pdb=" O ASN E 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 56 removed outlier: 3.867A pdb=" N THR D 41 " --> pdb=" O ASP D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 126 removed outlier: 3.595A pdb=" N TYR D 94 " --> pdb=" O ASP D 90 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN D 95 " --> pdb=" O LEU D 91 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL D 100 " --> pdb=" O ALA D 96 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN D 105 " --> pdb=" O ALA D 101 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N MET D 115 " --> pdb=" O THR D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 154 removed outlier: 3.850A pdb=" N GLU D 150 " --> pdb=" O ASN D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 161 removed outlier: 3.778A pdb=" N VAL D 161 " --> pdb=" O ASP D 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 158 through 161' Processing helix chain 'D' and resid 162 through 172 removed outlier: 3.648A pdb=" N GLN D 172 " --> pdb=" O ASN D 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 56 removed outlier: 3.867A pdb=" N THR F 41 " --> pdb=" O ASP F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 126 removed outlier: 3.595A pdb=" N TYR F 94 " --> pdb=" O ASP F 90 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN F 95 " --> pdb=" O LEU F 91 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL F 100 " --> pdb=" O ALA F 96 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN F 105 " --> pdb=" O ALA F 101 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N MET F 115 " --> pdb=" O THR F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 154 removed outlier: 3.850A pdb=" N GLU F 150 " --> pdb=" O ASN F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 161 removed outlier: 3.777A pdb=" N VAL F 161 " --> pdb=" O ASP F 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 158 through 161' Processing helix chain 'F' and resid 162 through 172 removed outlier: 3.647A pdb=" N GLN F 172 " --> pdb=" O ASN F 168 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 35 through 36 Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 52 removed outlier: 6.064A pdb=" N ILE A 51 " --> pdb=" O ASP A 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 58 through 61 removed outlier: 6.691A pdb=" N LEU A 59 " --> pdb=" O VAL A 88 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 120 through 122 removed outlier: 6.686A pdb=" N GLY A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ILE A 179 " --> pdb=" O GLY A 256 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AA9, first strand: chain 'A' and resid 151 through 153 Processing sheet with id=AB1, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB2, first strand: chain 'A' and resid 286 through 287 Processing sheet with id=AB3, first strand: chain 'D' and resid 35 through 36 removed outlier: 3.517A pdb=" N GLY D 23 " --> pdb=" O GLY C 16 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY C 16 " --> pdb=" O GLY D 23 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 24 through 26 Processing sheet with id=AB5, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AB6, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AB7, first strand: chain 'C' and resid 51 through 52 removed outlier: 6.064A pdb=" N ILE C 51 " --> pdb=" O ASP C 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 58 through 61 removed outlier: 6.691A pdb=" N LEU C 59 " --> pdb=" O VAL C 88 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 120 through 122 removed outlier: 6.686A pdb=" N GLY C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ILE C 179 " --> pdb=" O GLY C 256 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AC2, first strand: chain 'C' and resid 151 through 153 Processing sheet with id=AC3, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AC4, first strand: chain 'C' and resid 286 through 287 Processing sheet with id=AC5, first strand: chain 'F' and resid 35 through 36 Processing sheet with id=AC6, first strand: chain 'E' and resid 24 through 26 Processing sheet with id=AC7, first strand: chain 'E' and resid 39 through 41 Processing sheet with id=AC8, first strand: chain 'E' and resid 43 through 44 Processing sheet with id=AC9, first strand: chain 'E' and resid 51 through 52 removed outlier: 6.064A pdb=" N ILE E 51 " --> pdb=" O ASP E 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'E' and resid 58 through 61 removed outlier: 6.690A pdb=" N LEU E 59 " --> pdb=" O VAL E 88 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 120 through 122 removed outlier: 6.687A pdb=" N GLY E 256 " --> pdb=" O ILE E 179 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ILE E 179 " --> pdb=" O GLY E 256 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 130 through 131 Processing sheet with id=AD4, first strand: chain 'E' and resid 151 through 153 Processing sheet with id=AD5, first strand: chain 'E' and resid 164 through 169 Processing sheet with id=AD6, first strand: chain 'E' and resid 286 through 287 427 hydrogen bonds defined for protein. 1173 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.87 Time building geometry restraints manager: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3868 1.34 - 1.46: 2158 1.46 - 1.58: 6130 1.58 - 1.70: 0 1.70 - 1.81: 78 Bond restraints: 12234 Sorted by residual: bond pdb=" N PHE E 79 " pdb=" CA PHE E 79 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.10e-02 8.26e+03 7.76e+00 bond pdb=" N PHE A 79 " pdb=" CA PHE A 79 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.10e-02 8.26e+03 7.75e+00 bond pdb=" N GLN E 80 " pdb=" CA GLN E 80 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.25e-02 6.40e+03 7.55e+00 bond pdb=" N ILE C 214 " pdb=" CA ILE C 214 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.23e-02 6.61e+03 7.53e+00 bond pdb=" N GLN A 80 " pdb=" CA GLN A 80 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.25e-02 6.40e+03 7.48e+00 ... (remaining 12229 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 15655 1.24 - 2.47: 710 2.47 - 3.71: 168 3.71 - 4.95: 27 4.95 - 6.18: 30 Bond angle restraints: 16590 Sorted by residual: angle pdb=" CA ASN E 81 " pdb=" C ASN E 81 " pdb=" O ASN E 81 " ideal model delta sigma weight residual 121.28 117.58 3.70 1.19e+00 7.06e-01 9.68e+00 angle pdb=" CA ASN C 81 " pdb=" C ASN C 81 " pdb=" O ASN C 81 " ideal model delta sigma weight residual 121.28 117.60 3.68 1.19e+00 7.06e-01 9.58e+00 angle pdb=" CA ASN A 81 " pdb=" C ASN A 81 " pdb=" O ASN A 81 " ideal model delta sigma weight residual 121.28 117.60 3.68 1.19e+00 7.06e-01 9.55e+00 angle pdb=" C VAL A 78 " pdb=" N PHE A 79 " pdb=" CA PHE A 79 " ideal model delta sigma weight residual 122.83 118.65 4.18 1.54e+00 4.22e-01 7.38e+00 angle pdb=" C VAL C 78 " pdb=" N PHE C 79 " pdb=" CA PHE C 79 " ideal model delta sigma weight residual 122.83 118.66 4.17 1.54e+00 4.22e-01 7.34e+00 ... (remaining 16585 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 6363 17.89 - 35.78: 530 35.78 - 53.68: 145 53.68 - 71.57: 27 71.57 - 89.46: 24 Dihedral angle restraints: 7089 sinusoidal: 2871 harmonic: 4218 Sorted by residual: dihedral pdb=" CB CYS D 144 " pdb=" SG CYS D 144 " pdb=" SG CYS D 148 " pdb=" CB CYS D 148 " ideal model delta sinusoidal sigma weight residual 93.00 3.54 89.46 1 1.00e+01 1.00e-02 9.51e+01 dihedral pdb=" CB CYS B 144 " pdb=" SG CYS B 144 " pdb=" SG CYS B 148 " pdb=" CB CYS B 148 " ideal model delta sinusoidal sigma weight residual 93.00 3.60 89.40 1 1.00e+01 1.00e-02 9.50e+01 dihedral pdb=" CB CYS F 144 " pdb=" SG CYS F 144 " pdb=" SG CYS F 148 " pdb=" CB CYS F 148 " ideal model delta sinusoidal sigma weight residual 93.00 3.62 89.38 1 1.00e+01 1.00e-02 9.50e+01 ... (remaining 7086 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.236: 1905 0.236 - 0.472: 6 0.472 - 0.708: 6 0.708 - 0.943: 0 0.943 - 1.179: 3 Chirality restraints: 1920 Sorted by residual: chirality pdb=" C1 MAN J 4 " pdb=" O3 BMA J 3 " pdb=" C2 MAN J 4 " pdb=" O5 MAN J 4 " both_signs ideal model delta sigma weight residual False 2.40 1.22 1.18 2.00e-02 2.50e+03 3.48e+03 chirality pdb=" C1 MAN G 4 " pdb=" O3 BMA G 3 " pdb=" C2 MAN G 4 " pdb=" O5 MAN G 4 " both_signs ideal model delta sigma weight residual False 2.40 1.22 1.18 2.00e-02 2.50e+03 3.48e+03 chirality pdb=" C1 MAN L 4 " pdb=" O3 BMA L 3 " pdb=" C2 MAN L 4 " pdb=" O5 MAN L 4 " both_signs ideal model delta sigma weight residual False 2.40 1.22 1.18 2.00e-02 2.50e+03 3.46e+03 ... (remaining 1917 not shown) Planarity restraints: 2142 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 409 " -0.167 2.00e-02 2.50e+03 1.38e-01 2.38e+02 pdb=" C7 NAG E 409 " 0.045 2.00e-02 2.50e+03 pdb=" C8 NAG E 409 " -0.123 2.00e-02 2.50e+03 pdb=" N2 NAG E 409 " 0.223 2.00e-02 2.50e+03 pdb=" O7 NAG E 409 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 409 " -0.167 2.00e-02 2.50e+03 1.38e-01 2.37e+02 pdb=" C7 NAG A 409 " 0.045 2.00e-02 2.50e+03 pdb=" C8 NAG A 409 " -0.123 2.00e-02 2.50e+03 pdb=" N2 NAG A 409 " 0.222 2.00e-02 2.50e+03 pdb=" O7 NAG A 409 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 409 " -0.167 2.00e-02 2.50e+03 1.38e-01 2.37e+02 pdb=" C7 NAG C 409 " 0.045 2.00e-02 2.50e+03 pdb=" C8 NAG C 409 " -0.123 2.00e-02 2.50e+03 pdb=" N2 NAG C 409 " 0.222 2.00e-02 2.50e+03 pdb=" O7 NAG C 409 " 0.022 2.00e-02 2.50e+03 ... (remaining 2139 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1954 2.77 - 3.30: 9864 3.30 - 3.84: 18906 3.84 - 4.37: 22571 4.37 - 4.90: 40324 Nonbonded interactions: 93619 Sorted by model distance: nonbonded pdb=" N GLY F 1 " pdb=" OD2 ASP F 112 " model vdw 2.238 3.120 nonbonded pdb=" N GLY B 1 " pdb=" OD2 ASP B 112 " model vdw 2.238 3.120 nonbonded pdb=" N GLY D 1 " pdb=" OD2 ASP D 112 " model vdw 2.239 3.120 nonbonded pdb=" OD1 ASP C 68 " pdb=" OH TYR C 100 " model vdw 2.337 3.040 nonbonded pdb=" OD1 ASP E 68 " pdb=" OH TYR E 100 " model vdw 2.337 3.040 ... (remaining 93614 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' } 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: 4.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.100 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5647 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 12285 Z= 0.240 Angle : 1.328 40.189 16725 Z= 0.521 Chirality : 0.076 1.179 1920 Planarity : 0.007 0.138 2127 Dihedral : 15.257 88.687 4329 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.70 % Allowed : 16.39 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.50 (0.18), residues: 1458 helix: -0.26 (0.26), residues: 348 sheet: -0.34 (0.31), residues: 243 loop : -2.83 (0.15), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 124 TYR 0.005 0.001 TYR C 161 PHE 0.007 0.001 PHE F 9 TRP 0.005 0.001 TRP E 84 HIS 0.004 0.001 HIS F 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.20 (12234) covalent geometry : angle 0.65518 / 0.35 (16590) SS BOND : bond 0.02536 / 1.36 ( 18) SS BOND : angle 1.09557 / 0.70 ( 36) hydrogen bonds : bond 0.16874 / 11.46 ( 427) hydrogen bonds : angle 6.01772 / 4.18 ( 1173) link_ALPHA1-3 : bond 0.06432 / 3.22 ( 3) link_ALPHA1-3 : angle 32.18866 / 21.31 ( 9) link_ALPHA1-6 : bond 0.06413 / 3.22 ( 3) link_ALPHA1-6 : angle 13.07044 / 9.10 ( 9) link_BETA1-4 : bond 0.06469 / 4.02 ( 12) link_BETA1-4 : angle 17.79502 / 11.33 ( 36) link_NAG-ASN : bond 0.00135 / 0.08 ( 15) link_NAG-ASN : angle 1.28466 / 0.86 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 267 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 274 average time/residue: 0.4794 time to fit residues: 144.5723 Evaluate side-chains 140 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 139 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 295 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 170 ASN A 216 ASN B 27 GLN B 142 HIS C 54 ASN C 132 GLN C 197 GLN C 211 GLN C 295 GLN E 18 HIS E 54 ASN E 132 GLN E 188 ASN D 142 HIS D 146 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.150092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.130024 restraints weight = 13687.764| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.82 r_work: 0.3229 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.8069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 12285 Z= 0.316 Angle : 1.108 20.981 16725 Z= 0.540 Chirality : 0.065 0.669 1920 Planarity : 0.008 0.060 2127 Dihedral : 6.085 39.130 1587 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 6.64 % Allowed : 18.66 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.19), residues: 1458 helix: -0.47 (0.25), residues: 360 sheet: -0.12 (0.33), residues: 258 loop : -2.19 (0.17), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.002 ARG F 153 TYR 0.046 0.004 TYR B 162 PHE 0.027 0.004 PHE D 63 TRP 0.034 0.003 TRP E 153 HIS 0.012 0.002 HIS C 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00700 / 0.31 (12234) covalent geometry : angle 1.06126 / 0.53 (16590) SS BOND : bond 0.01527 / 1.02 ( 18) SS BOND : angle 2.21674 / 1.51 ( 36) hydrogen bonds : bond 0.07747 / 5.39 ( 427) hydrogen bonds : angle 5.64527 / 3.97 ( 1173) link_ALPHA1-3 : bond 0.02479 / 1.24 ( 3) link_ALPHA1-3 : angle 2.54613 / 1.89 ( 9) link_ALPHA1-6 : bond 0.00513 / 0.27 ( 3) link_ALPHA1-6 : angle 4.14816 / 2.72 ( 9) link_BETA1-4 : bond 0.01297 / 0.75 ( 12) link_BETA1-4 : angle 3.60075 / 2.41 ( 36) link_NAG-ASN : bond 0.01728 / 1.27 ( 15) link_NAG-ASN : angle 4.70291 / 2.97 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 245 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 ARG cc_start: 0.7836 (ttt90) cc_final: 0.7541 (ttt180) REVERT: A 275 ASP cc_start: 0.7068 (m-30) cc_final: 0.6596 (m-30) REVERT: A 307 LYS cc_start: 0.8563 (mtmm) cc_final: 0.8164 (mtpt) REVERT: B 42 GLN cc_start: 0.7621 (tp40) cc_final: 0.7333 (tp40) REVERT: B 65 GLN cc_start: 0.8567 (mt0) cc_final: 0.8340 (mt0) REVERT: C 28 THR cc_start: 0.9219 (OUTLIER) cc_final: 0.9017 (m) REVERT: C 241 ASP cc_start: 0.8104 (OUTLIER) cc_final: 0.7515 (t0) REVERT: C 242 VAL cc_start: 0.8105 (t) cc_final: 0.7647 (p) REVERT: C 260 MET cc_start: 0.8016 (mmm) cc_final: 0.7681 (mtp) REVERT: C 295 GLN cc_start: 0.9345 (OUTLIER) cc_final: 0.8954 (pp30) REVERT: E 88 VAL cc_start: 0.8087 (OUTLIER) cc_final: 0.7812 (t) REVERT: E 168 MET cc_start: 0.8302 (OUTLIER) cc_final: 0.7989 (tpt) REVERT: E 241 ASP cc_start: 0.8365 (OUTLIER) cc_final: 0.8049 (t0) REVERT: E 280 GLU cc_start: 0.7336 (mm-30) cc_final: 0.7134 (mm-30) REVERT: E 292 LYS cc_start: 0.9038 (OUTLIER) cc_final: 0.8673 (mttm) REVERT: D 62 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7132 (mtpp) REVERT: D 65 GLN cc_start: 0.8743 (mt0) cc_final: 0.8504 (mt0) REVERT: F 17 MET cc_start: 0.8535 (tpp) cc_final: 0.8283 (ttm) REVERT: F 18 ILE cc_start: 0.7921 (tp) cc_final: 0.7478 (pt) REVERT: F 45 ILE cc_start: 0.8372 (tt) cc_final: 0.7758 (pp) REVERT: F 139 LYS cc_start: 0.8542 (tttp) cc_final: 0.8341 (tmtp) REVERT: F 151 SER cc_start: 0.6052 (OUTLIER) cc_final: 0.5850 (t) outliers start: 85 outliers final: 21 residues processed: 312 average time/residue: 0.5227 time to fit residues: 177.6554 Evaluate side-chains 202 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 172 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 241 ASP Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 295 GLN Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 168 MET Chi-restraints excluded: chain E residue 201 ARG Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 292 LYS Chi-restraints excluded: chain D residue 62 LYS Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 151 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 14 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 109 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 85 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 90 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 54 ASN B 34 GLN C 18 HIS C 248 ASN C 295 GLN C 312 ASN E 18 HIS E 33 GLN E 197 GLN E 246 ASN D 47 GLN D 125 GLN F 28 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.132632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.110791 restraints weight = 13615.489| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.84 r_work: 0.2952 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.8829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 12285 Z= 0.180 Angle : 0.670 11.584 16725 Z= 0.335 Chirality : 0.047 0.278 1920 Planarity : 0.005 0.050 2127 Dihedral : 5.012 43.241 1587 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 5.31 % Allowed : 21.86 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.20), residues: 1458 helix: 1.05 (0.28), residues: 357 sheet: 0.29 (0.33), residues: 234 loop : -2.08 (0.17), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 141 TYR 0.018 0.002 TYR A 308 PHE 0.018 0.002 PHE B 24 TRP 0.013 0.001 TRP A 234 HIS 0.007 0.002 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (12234) covalent geometry : angle 0.62521 / 0.32 (16590) SS BOND : bond 0.00836 / 0.53 ( 18) SS BOND : angle 2.38412 / 1.63 ( 36) hydrogen bonds : bond 0.06434 / 4.49 ( 427) hydrogen bonds : angle 4.65360 / 3.30 ( 1173) link_ALPHA1-3 : bond 0.00484 / 0.25 ( 3) link_ALPHA1-3 : angle 1.96919 / 1.49 ( 9) link_ALPHA1-6 : bond 0.00054 / 0.03 ( 3) link_ALPHA1-6 : angle 2.02878 / 1.28 ( 9) link_BETA1-4 : bond 0.00743 / 0.50 ( 12) link_BETA1-4 : angle 2.45933 / 1.56 ( 36) link_NAG-ASN : bond 0.00916 / 0.69 ( 15) link_NAG-ASN : angle 3.39538 / 2.25 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 165 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 CYS cc_start: 0.8167 (m) cc_final: 0.7808 (m) REVERT: A 73 ASP cc_start: 0.7986 (OUTLIER) cc_final: 0.7760 (t0) REVERT: B 67 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7213 (mp0) REVERT: B 121 LYS cc_start: 0.8393 (ttpt) cc_final: 0.8175 (tttt) REVERT: C 73 ASP cc_start: 0.8052 (OUTLIER) cc_final: 0.7612 (t0) REVERT: C 118 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8277 (mp) REVERT: C 210 GLN cc_start: 0.9042 (OUTLIER) cc_final: 0.8739 (tt0) REVERT: C 245 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.7894 (mt) REVERT: E 62 ILE cc_start: 0.8218 (OUTLIER) cc_final: 0.7876 (mp) REVERT: E 104 ASP cc_start: 0.7956 (t0) cc_final: 0.7598 (m-30) REVERT: E 168 MET cc_start: 0.8528 (mmt) cc_final: 0.8287 (tpt) REVERT: E 280 GLU cc_start: 0.7696 (mm-30) cc_final: 0.7457 (mm-30) REVERT: F 17 MET cc_start: 0.8638 (tpp) cc_final: 0.8193 (ttm) REVERT: F 151 SER cc_start: 0.7444 (t) cc_final: 0.6618 (p) outliers start: 68 outliers final: 28 residues processed: 215 average time/residue: 0.5036 time to fit residues: 118.9756 Evaluate side-chains 178 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 143 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain F residue 47 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 52 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 88 optimal weight: 0.3980 chunk 40 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 18 HIS E 18 HIS E 295 GLN D 47 GLN D 142 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.127838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.105871 restraints weight = 13784.241| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.89 r_work: 0.2898 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.9589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12285 Z= 0.185 Angle : 0.687 21.420 16725 Z= 0.342 Chirality : 0.047 0.280 1920 Planarity : 0.005 0.046 2127 Dihedral : 4.676 19.098 1584 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 5.31 % Allowed : 21.78 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.20), residues: 1458 helix: 1.35 (0.28), residues: 357 sheet: 0.46 (0.34), residues: 234 loop : -2.00 (0.17), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 54 TYR 0.018 0.002 TYR E 308 PHE 0.017 0.002 PHE C 125 TRP 0.010 0.001 TRP A 234 HIS 0.035 0.002 HIS C 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.18 (12234) covalent geometry : angle 0.63271 / 0.33 (16590) SS BOND : bond 0.00721 / 0.45 ( 18) SS BOND : angle 2.36018 / 1.53 ( 36) hydrogen bonds : bond 0.06421 / 4.47 ( 427) hydrogen bonds : angle 4.50784 / 3.21 ( 1173) link_ALPHA1-3 : bond 0.00610 / 0.30 ( 3) link_ALPHA1-3 : angle 1.38654 / 1.00 ( 9) link_ALPHA1-6 : bond 0.00453 / 0.23 ( 3) link_ALPHA1-6 : angle 1.50908 / 1.02 ( 9) link_BETA1-4 : bond 0.00425 / 0.27 ( 12) link_BETA1-4 : angle 2.06515 / 1.29 ( 36) link_NAG-ASN : bond 0.00860 / 0.63 ( 15) link_NAG-ASN : angle 4.38098 / 3.75 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 165 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ASP cc_start: 0.8318 (OUTLIER) cc_final: 0.8043 (t0) REVERT: B 47 GLN cc_start: 0.7715 (tt0) cc_final: 0.7404 (mt0) REVERT: B 67 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.7241 (mp0) REVERT: B 121 LYS cc_start: 0.8437 (ttpt) cc_final: 0.8207 (tttt) REVERT: B 160 ASP cc_start: 0.7962 (m-30) cc_final: 0.7743 (t0) REVERT: C 118 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8359 (mp) REVERT: C 119 GLU cc_start: 0.8998 (tt0) cc_final: 0.8747 (tt0) REVERT: C 145 SER cc_start: 0.8093 (m) cc_final: 0.7633 (p) REVERT: C 159 SER cc_start: 0.7714 (t) cc_final: 0.7360 (p) REVERT: C 210 GLN cc_start: 0.9073 (OUTLIER) cc_final: 0.8668 (tt0) REVERT: C 243 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8627 (tp) REVERT: C 245 ILE cc_start: 0.8742 (OUTLIER) cc_final: 0.7996 (mt) REVERT: C 261 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.7803 (mtp85) REVERT: C 291 ASP cc_start: 0.8165 (OUTLIER) cc_final: 0.7624 (p0) REVERT: E 62 ILE cc_start: 0.8379 (OUTLIER) cc_final: 0.8127 (mp) REVERT: E 168 MET cc_start: 0.8636 (mmt) cc_final: 0.8373 (tpt) REVERT: E 195 TYR cc_start: 0.8161 (OUTLIER) cc_final: 0.5751 (m-80) REVERT: E 223 VAL cc_start: 0.8851 (OUTLIER) cc_final: 0.8455 (t) REVERT: F 151 SER cc_start: 0.8166 (t) cc_final: 0.7420 (p) outliers start: 68 outliers final: 30 residues processed: 218 average time/residue: 0.4803 time to fit residues: 114.9186 Evaluate side-chains 190 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 149 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 261 ARG Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 291 ASP Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 190 GLU Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 161 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 142 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 69 optimal weight: 0.4980 chunk 80 optimal weight: 0.9980 chunk 137 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 312 ASN ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 312 ASN D 47 GLN D 146 ASN F 28 ASN F 105 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.126348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.104092 restraints weight = 13703.787| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.91 r_work: 0.2942 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 1.0008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12285 Z= 0.167 Angle : 0.628 12.772 16725 Z= 0.316 Chirality : 0.045 0.257 1920 Planarity : 0.005 0.050 2127 Dihedral : 4.555 18.799 1584 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 5.31 % Allowed : 22.56 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.20), residues: 1458 helix: 1.63 (0.28), residues: 360 sheet: 0.40 (0.33), residues: 234 loop : -1.85 (0.17), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 141 TYR 0.016 0.002 TYR D 162 PHE 0.017 0.002 PHE F 24 TRP 0.009 0.001 TRP A 234 HIS 0.010 0.002 HIS C 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 (12234) covalent geometry : angle 0.58676 / 0.31 (16590) SS BOND : bond 0.00845 / 0.49 ( 18) SS BOND : angle 2.23531 / 1.46 ( 36) hydrogen bonds : bond 0.06132 / 4.27 ( 427) hydrogen bonds : angle 4.41152 / 3.15 ( 1173) link_ALPHA1-3 : bond 0.00646 / 0.32 ( 3) link_ALPHA1-3 : angle 1.46916 / 1.08 ( 9) link_ALPHA1-6 : bond 0.00279 / 0.14 ( 3) link_ALPHA1-6 : angle 1.61747 / 1.09 ( 9) link_BETA1-4 : bond 0.00787 / 0.53 ( 12) link_BETA1-4 : angle 1.89773 / 1.22 ( 36) link_NAG-ASN : bond 0.00681 / 0.50 ( 15) link_NAG-ASN : angle 3.40831 / 2.62 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 154 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ASP cc_start: 0.8297 (OUTLIER) cc_final: 0.7975 (t0) REVERT: A 121 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8501 (mp) REVERT: B 34 GLN cc_start: 0.8653 (tt0) cc_final: 0.8338 (tt0) REVERT: B 47 GLN cc_start: 0.7922 (tt0) cc_final: 0.7638 (mt0) REVERT: B 67 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.7292 (mp0) REVERT: B 121 LYS cc_start: 0.8532 (ttpt) cc_final: 0.8267 (tttt) REVERT: C 118 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8376 (mp) REVERT: C 119 GLU cc_start: 0.9008 (tt0) cc_final: 0.8790 (tt0) REVERT: C 145 SER cc_start: 0.8221 (OUTLIER) cc_final: 0.7848 (p) REVERT: C 201 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.7722 (ptt90) REVERT: C 245 ILE cc_start: 0.8799 (OUTLIER) cc_final: 0.8170 (mt) REVERT: C 291 ASP cc_start: 0.8253 (OUTLIER) cc_final: 0.7810 (p0) REVERT: E 52 CYS cc_start: 0.7878 (m) cc_final: 0.7568 (m) REVERT: E 62 ILE cc_start: 0.8548 (OUTLIER) cc_final: 0.8286 (mp) REVERT: E 168 MET cc_start: 0.8663 (mmt) cc_final: 0.8463 (tpt) REVERT: E 179 ILE cc_start: 0.9062 (OUTLIER) cc_final: 0.8728 (mp) REVERT: E 195 TYR cc_start: 0.8286 (OUTLIER) cc_final: 0.5969 (m-80) REVERT: E 223 VAL cc_start: 0.8855 (OUTLIER) cc_final: 0.8543 (t) REVERT: E 224 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.7679 (mtp180) REVERT: E 261 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.7814 (mmm-85) REVERT: D 17 MET cc_start: 0.8747 (tpp) cc_final: 0.8382 (ttp) REVERT: D 72 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7428 (mt-10) REVERT: D 74 GLU cc_start: 0.7470 (mm-30) cc_final: 0.6637 (tt0) REVERT: F 151 SER cc_start: 0.8267 (t) cc_final: 0.7561 (p) outliers start: 68 outliers final: 36 residues processed: 208 average time/residue: 0.4721 time to fit residues: 108.3992 Evaluate side-chains 197 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 147 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 201 ARG Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 291 ASP Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 179 ILE Chi-restraints excluded: chain E residue 190 GLU Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 224 ARG Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 261 ARG Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain F residue 18 ILE Chi-restraints excluded: chain F residue 143 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 0 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 57 optimal weight: 0.0770 chunk 69 optimal weight: 0.5980 chunk 116 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 100 optimal weight: 0.1980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 125 GLN E 18 HIS E 33 GLN E 246 ASN E 312 ASN D 47 GLN D 146 ASN F 105 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.127627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.105167 restraints weight = 13651.057| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 1.89 r_work: 0.2947 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 1.0266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12285 Z= 0.139 Angle : 0.584 11.903 16725 Z= 0.295 Chirality : 0.044 0.227 1920 Planarity : 0.004 0.038 2127 Dihedral : 4.363 17.033 1584 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 5.46 % Allowed : 22.40 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.21), residues: 1458 helix: 1.84 (0.29), residues: 360 sheet: 0.10 (0.31), residues: 264 loop : -1.63 (0.18), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 141 TYR 0.017 0.001 TYR D 162 PHE 0.013 0.002 PHE B 24 TRP 0.008 0.001 TRP A 234 HIS 0.004 0.001 HIS E 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (12234) covalent geometry : angle 0.54840 / 0.29 (16590) SS BOND : bond 0.00534 / 0.33 ( 18) SS BOND : angle 2.00318 / 1.29 ( 36) hydrogen bonds : bond 0.05741 / 4.01 ( 427) hydrogen bonds : angle 4.31840 / 3.08 ( 1173) link_ALPHA1-3 : bond 0.00653 / 0.32 ( 3) link_ALPHA1-3 : angle 1.33936 / 0.98 ( 9) link_ALPHA1-6 : bond 0.00300 / 0.15 ( 3) link_ALPHA1-6 : angle 1.47816 / 1.00 ( 9) link_BETA1-4 : bond 0.00515 / 0.36 ( 12) link_BETA1-4 : angle 1.76650 / 1.15 ( 36) link_NAG-ASN : bond 0.00402 / 0.28 ( 15) link_NAG-ASN : angle 3.07054 / 2.40 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 150 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 CYS cc_start: 0.8380 (m) cc_final: 0.7974 (m) REVERT: A 73 ASP cc_start: 0.8291 (OUTLIER) cc_final: 0.7951 (t0) REVERT: A 121 ILE cc_start: 0.8675 (OUTLIER) cc_final: 0.8457 (mp) REVERT: A 325 GLU cc_start: 0.6556 (OUTLIER) cc_final: 0.5795 (mp0) REVERT: B 34 GLN cc_start: 0.8762 (tt0) cc_final: 0.8462 (tt0) REVERT: B 47 GLN cc_start: 0.7903 (tt0) cc_final: 0.7635 (mt0) REVERT: B 65 GLN cc_start: 0.8769 (mt0) cc_final: 0.8421 (mt0) REVERT: B 67 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.7272 (mp0) REVERT: B 121 LYS cc_start: 0.8525 (ttpt) cc_final: 0.8246 (tttt) REVERT: C 119 GLU cc_start: 0.8954 (tt0) cc_final: 0.8739 (tt0) REVERT: C 145 SER cc_start: 0.8257 (OUTLIER) cc_final: 0.7903 (p) REVERT: C 214 ILE cc_start: 0.8721 (tt) cc_final: 0.8430 (mt) REVERT: C 245 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8200 (mt) REVERT: C 291 ASP cc_start: 0.8180 (m-30) cc_final: 0.7719 (p0) REVERT: C 325 GLU cc_start: 0.6307 (mp0) cc_final: 0.6035 (mp0) REVERT: E 62 ILE cc_start: 0.8567 (OUTLIER) cc_final: 0.8326 (mp) REVERT: E 179 ILE cc_start: 0.9044 (OUTLIER) cc_final: 0.8722 (mp) REVERT: E 195 TYR cc_start: 0.8303 (OUTLIER) cc_final: 0.6159 (m-80) REVERT: E 223 VAL cc_start: 0.8865 (OUTLIER) cc_final: 0.8524 (t) REVERT: E 224 ARG cc_start: 0.8830 (OUTLIER) cc_final: 0.7576 (mtp180) REVERT: E 276 THR cc_start: 0.8424 (OUTLIER) cc_final: 0.8132 (p) REVERT: D 72 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7639 (mt-10) REVERT: D 74 GLU cc_start: 0.7389 (mm-30) cc_final: 0.6692 (tt0) REVERT: F 151 SER cc_start: 0.8366 (t) cc_final: 0.7659 (p) outliers start: 70 outliers final: 27 residues processed: 206 average time/residue: 0.4926 time to fit residues: 111.4382 Evaluate side-chains 185 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 146 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 179 ILE Chi-restraints excluded: chain E residue 190 GLU Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 224 ARG Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain F residue 30 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 133 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 97 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 61 optimal weight: 0.0980 chunk 74 optimal weight: 0.8980 chunk 137 optimal weight: 0.9980 chunk 101 optimal weight: 0.6980 chunk 116 optimal weight: 0.9980 chunk 82 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 312 ASN E 18 HIS E 33 GLN E 312 ASN D 28 ASN D 47 GLN F 28 ASN F 105 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.128202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.106213 restraints weight = 13527.792| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 1.85 r_work: 0.2955 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 1.0450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12285 Z= 0.141 Angle : 0.588 10.323 16725 Z= 0.299 Chirality : 0.044 0.220 1920 Planarity : 0.004 0.038 2127 Dihedral : 4.335 19.606 1584 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.61 % Allowed : 22.64 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.21), residues: 1458 helix: 1.97 (0.28), residues: 360 sheet: 0.44 (0.33), residues: 234 loop : -1.69 (0.18), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 141 TYR 0.015 0.001 TYR D 162 PHE 0.015 0.002 PHE F 24 TRP 0.008 0.001 TRP A 234 HIS 0.004 0.001 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (12234) covalent geometry : angle 0.55610 / 0.29 (16590) SS BOND : bond 0.00632 / 0.38 ( 18) SS BOND : angle 1.97278 / 1.30 ( 36) hydrogen bonds : bond 0.05747 / 4.01 ( 427) hydrogen bonds : angle 4.29131 / 3.06 ( 1173) link_ALPHA1-3 : bond 0.00612 / 0.30 ( 3) link_ALPHA1-3 : angle 1.41105 / 1.04 ( 9) link_ALPHA1-6 : bond 0.00289 / 0.15 ( 3) link_ALPHA1-6 : angle 1.53187 / 1.04 ( 9) link_BETA1-4 : bond 0.00455 / 0.30 ( 12) link_BETA1-4 : angle 1.78020 / 1.17 ( 36) link_NAG-ASN : bond 0.00403 / 0.28 ( 15) link_NAG-ASN : angle 2.82132 / 2.17 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 147 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ASP cc_start: 0.8315 (OUTLIER) cc_final: 0.7992 (t0) REVERT: A 140 LYS cc_start: 0.7425 (mttp) cc_final: 0.7186 (mttp) REVERT: A 197 GLN cc_start: 0.8679 (mp-120) cc_final: 0.8466 (mp10) REVERT: A 325 GLU cc_start: 0.6506 (OUTLIER) cc_final: 0.5715 (mp0) REVERT: B 34 GLN cc_start: 0.8781 (tt0) cc_final: 0.8463 (tt0) REVERT: B 47 GLN cc_start: 0.7897 (tt0) cc_final: 0.7636 (mt0) REVERT: B 65 GLN cc_start: 0.8759 (mt0) cc_final: 0.8456 (mt0) REVERT: B 67 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.7199 (mp0) REVERT: B 121 LYS cc_start: 0.8446 (ttpt) cc_final: 0.8159 (tttt) REVERT: B 125 GLN cc_start: 0.8012 (tt0) cc_final: 0.7677 (mt0) REVERT: C 118 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8366 (mp) REVERT: C 119 GLU cc_start: 0.8938 (tt0) cc_final: 0.8725 (tt0) REVERT: C 145 SER cc_start: 0.8289 (OUTLIER) cc_final: 0.7971 (p) REVERT: C 210 GLN cc_start: 0.8986 (OUTLIER) cc_final: 0.8486 (tt0) REVERT: C 214 ILE cc_start: 0.8727 (tt) cc_final: 0.8466 (mt) REVERT: C 245 ILE cc_start: 0.8774 (OUTLIER) cc_final: 0.8279 (mt) REVERT: C 291 ASP cc_start: 0.8120 (m-30) cc_final: 0.7690 (p0) REVERT: C 325 GLU cc_start: 0.6371 (mp0) cc_final: 0.6123 (mp0) REVERT: E 62 ILE cc_start: 0.8600 (OUTLIER) cc_final: 0.8360 (mp) REVERT: E 179 ILE cc_start: 0.9082 (OUTLIER) cc_final: 0.8764 (mp) REVERT: E 195 TYR cc_start: 0.8328 (OUTLIER) cc_final: 0.6181 (m-80) REVERT: E 223 VAL cc_start: 0.8862 (OUTLIER) cc_final: 0.8523 (t) REVERT: E 224 ARG cc_start: 0.8818 (OUTLIER) cc_final: 0.7612 (mtp180) REVERT: E 276 THR cc_start: 0.8250 (OUTLIER) cc_final: 0.7974 (p) REVERT: E 312 ASN cc_start: 0.8099 (t0) cc_final: 0.7598 (p0) REVERT: D 72 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7756 (mt-10) REVERT: D 74 GLU cc_start: 0.7265 (mm-30) cc_final: 0.6655 (tt0) REVERT: D 128 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7361 (tp30) REVERT: F 47 GLN cc_start: 0.7748 (mt0) cc_final: 0.7458 (mt0) REVERT: F 151 SER cc_start: 0.8444 (t) cc_final: 0.7762 (p) outliers start: 59 outliers final: 30 residues processed: 192 average time/residue: 0.4729 time to fit residues: 99.5921 Evaluate side-chains 185 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 141 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 179 ILE Chi-restraints excluded: chain E residue 190 GLU Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 224 ARG Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain F residue 143 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 6 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 102 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 136 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 74 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 142 HIS C 33 GLN C 312 ASN E 18 HIS E 33 GLN F 105 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.125524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.103175 restraints weight = 13616.234| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 1.88 r_work: 0.2873 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 1.0623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12285 Z= 0.171 Angle : 0.621 9.955 16725 Z= 0.316 Chirality : 0.046 0.245 1920 Planarity : 0.004 0.039 2127 Dihedral : 4.448 18.042 1584 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.92 % Allowed : 22.17 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.21), residues: 1458 helix: 2.00 (0.28), residues: 357 sheet: 0.41 (0.33), residues: 234 loop : -1.70 (0.18), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 141 TYR 0.015 0.002 TYR D 162 PHE 0.017 0.002 PHE F 24 TRP 0.008 0.001 TRP A 234 HIS 0.005 0.001 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.17 (12234) covalent geometry : angle 0.58943 / 0.31 (16590) SS BOND : bond 0.00608 / 0.37 ( 18) SS BOND : angle 2.24679 / 1.47 ( 36) hydrogen bonds : bond 0.06209 / 4.33 ( 427) hydrogen bonds : angle 4.34274 / 3.11 ( 1173) link_ALPHA1-3 : bond 0.00499 / 0.25 ( 3) link_ALPHA1-3 : angle 1.35534 / 0.98 ( 9) link_ALPHA1-6 : bond 0.00267 / 0.13 ( 3) link_ALPHA1-6 : angle 1.54333 / 1.03 ( 9) link_BETA1-4 : bond 0.00441 / 0.29 ( 12) link_BETA1-4 : angle 1.81330 / 1.20 ( 36) link_NAG-ASN : bond 0.00396 / 0.26 ( 15) link_NAG-ASN : angle 2.81191 / 2.14 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 149 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ASP cc_start: 0.8405 (OUTLIER) cc_final: 0.8068 (t0) REVERT: B 34 GLN cc_start: 0.8785 (tt0) cc_final: 0.8474 (tt0) REVERT: B 47 GLN cc_start: 0.7916 (tt0) cc_final: 0.7649 (mt0) REVERT: B 67 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.7291 (mp0) REVERT: B 121 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8286 (tttt) REVERT: B 125 GLN cc_start: 0.8055 (tt0) cc_final: 0.7735 (mt0) REVERT: B 128 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7714 (tp30) REVERT: C 118 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8354 (mp) REVERT: C 145 SER cc_start: 0.8403 (OUTLIER) cc_final: 0.8093 (p) REVERT: C 210 GLN cc_start: 0.9031 (OUTLIER) cc_final: 0.8516 (tt0) REVERT: C 214 ILE cc_start: 0.8775 (tt) cc_final: 0.8538 (mt) REVERT: C 245 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8238 (mt) REVERT: C 275 ASP cc_start: 0.7481 (m-30) cc_final: 0.7278 (m-30) REVERT: C 291 ASP cc_start: 0.8087 (m-30) cc_final: 0.7613 (p0) REVERT: E 62 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8365 (mt) REVERT: E 179 ILE cc_start: 0.9096 (OUTLIER) cc_final: 0.8785 (mp) REVERT: E 223 VAL cc_start: 0.8876 (OUTLIER) cc_final: 0.8513 (t) REVERT: E 224 ARG cc_start: 0.8812 (OUTLIER) cc_final: 0.7574 (mtp180) REVERT: E 276 THR cc_start: 0.8194 (OUTLIER) cc_final: 0.7973 (p) REVERT: D 72 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7850 (mt-10) REVERT: D 74 GLU cc_start: 0.7448 (mm-30) cc_final: 0.6742 (tt0) REVERT: F 47 GLN cc_start: 0.7812 (mt0) cc_final: 0.7521 (mt0) REVERT: F 114 GLU cc_start: 0.7908 (tp30) cc_final: 0.7591 (tp30) REVERT: F 151 SER cc_start: 0.8533 (t) cc_final: 0.7878 (p) outliers start: 63 outliers final: 34 residues processed: 199 average time/residue: 0.5138 time to fit residues: 112.0689 Evaluate side-chains 189 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 142 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 179 ILE Chi-restraints excluded: chain E residue 190 GLU Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 224 ARG Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain F residue 18 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 43 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 109 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 120 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 18 HIS E 33 GLN E 312 ASN F 105 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.125600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.103288 restraints weight = 13579.712| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 1.88 r_work: 0.2874 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 1.0702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12285 Z= 0.169 Angle : 0.632 14.373 16725 Z= 0.318 Chirality : 0.046 0.266 1920 Planarity : 0.004 0.038 2127 Dihedral : 4.447 20.501 1584 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.68 % Allowed : 22.33 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.21), residues: 1458 helix: 1.96 (0.28), residues: 360 sheet: 0.42 (0.33), residues: 234 loop : -1.70 (0.18), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 141 TYR 0.015 0.002 TYR D 162 PHE 0.016 0.002 PHE F 24 TRP 0.008 0.001 TRP A 234 HIS 0.006 0.001 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 (12234) covalent geometry : angle 0.58992 / 0.31 (16590) SS BOND : bond 0.00662 / 0.42 ( 18) SS BOND : angle 2.16449 / 1.41 ( 36) hydrogen bonds : bond 0.06160 / 4.30 ( 427) hydrogen bonds : angle 4.34484 / 3.11 ( 1173) link_ALPHA1-3 : bond 0.00548 / 0.27 ( 3) link_ALPHA1-3 : angle 1.37053 / 1.00 ( 9) link_ALPHA1-6 : bond 0.00236 / 0.12 ( 3) link_ALPHA1-6 : angle 1.54368 / 1.03 ( 9) link_BETA1-4 : bond 0.00440 / 0.30 ( 12) link_BETA1-4 : angle 1.79015 / 1.19 ( 36) link_NAG-ASN : bond 0.00386 / 0.26 ( 15) link_NAG-ASN : angle 3.63696 / 2.81 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 148 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 34 GLN cc_start: 0.8794 (tt0) cc_final: 0.8496 (tt0) REVERT: B 47 GLN cc_start: 0.7935 (OUTLIER) cc_final: 0.7656 (mt0) REVERT: B 67 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.7288 (mp0) REVERT: B 121 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8288 (tttt) REVERT: B 125 GLN cc_start: 0.8061 (tt0) cc_final: 0.7749 (mt0) REVERT: B 128 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7717 (tp30) REVERT: B 143 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.7920 (mtmm) REVERT: C 118 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8357 (mp) REVERT: C 145 SER cc_start: 0.8421 (OUTLIER) cc_final: 0.8134 (p) REVERT: C 210 GLN cc_start: 0.9043 (OUTLIER) cc_final: 0.8518 (tt0) REVERT: C 214 ILE cc_start: 0.8797 (tt) cc_final: 0.8568 (mt) REVERT: C 245 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8238 (mt) REVERT: C 291 ASP cc_start: 0.8077 (m-30) cc_final: 0.7582 (p0) REVERT: C 325 GLU cc_start: 0.6411 (mp0) cc_final: 0.6208 (mp0) REVERT: E 62 ILE cc_start: 0.8587 (OUTLIER) cc_final: 0.8361 (mt) REVERT: E 179 ILE cc_start: 0.9082 (OUTLIER) cc_final: 0.8761 (mp) REVERT: E 223 VAL cc_start: 0.8875 (OUTLIER) cc_final: 0.8517 (t) REVERT: E 224 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.7585 (mtp180) REVERT: E 276 THR cc_start: 0.8203 (OUTLIER) cc_final: 0.7830 (p) REVERT: E 312 ASN cc_start: 0.8158 (t0) cc_final: 0.7667 (p0) REVERT: D 72 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7841 (mt-10) REVERT: D 74 GLU cc_start: 0.7490 (mm-30) cc_final: 0.6784 (tt0) REVERT: F 47 GLN cc_start: 0.7828 (mt0) cc_final: 0.7531 (mt0) REVERT: F 114 GLU cc_start: 0.7925 (tp30) cc_final: 0.7620 (tp30) REVERT: F 151 SER cc_start: 0.8580 (t) cc_final: 0.7940 (p) outliers start: 60 outliers final: 34 residues processed: 197 average time/residue: 0.5123 time to fit residues: 110.4229 Evaluate side-chains 192 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 144 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 179 ILE Chi-restraints excluded: chain E residue 190 GLU Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 224 ARG Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain F residue 18 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 105 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 115 optimal weight: 0.2980 chunk 101 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 312 ASN ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 GLN F 105 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.125730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.103401 restraints weight = 13650.278| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 1.88 r_work: 0.2875 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 1.0745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12285 Z= 0.154 Angle : 0.608 13.208 16725 Z= 0.307 Chirality : 0.045 0.231 1920 Planarity : 0.004 0.037 2127 Dihedral : 4.380 20.127 1584 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.90 % Allowed : 23.50 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.21), residues: 1458 helix: 2.11 (0.28), residues: 357 sheet: 0.44 (0.34), residues: 234 loop : -1.65 (0.18), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 141 TYR 0.014 0.002 TYR D 162 PHE 0.015 0.002 PHE F 24 TRP 0.008 0.001 TRP A 234 HIS 0.005 0.001 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.15 (12234) covalent geometry : angle 0.56848 / 0.30 (16590) SS BOND : bond 0.00576 / 0.37 ( 18) SS BOND : angle 2.11908 / 1.36 ( 36) hydrogen bonds : bond 0.05949 / 4.15 ( 427) hydrogen bonds : angle 4.32464 / 3.09 ( 1173) link_ALPHA1-3 : bond 0.00564 / 0.28 ( 3) link_ALPHA1-3 : angle 1.35985 / 0.99 ( 9) link_ALPHA1-6 : bond 0.00260 / 0.13 ( 3) link_ALPHA1-6 : angle 1.53011 / 1.02 ( 9) link_BETA1-4 : bond 0.00419 / 0.28 ( 12) link_BETA1-4 : angle 1.77951 / 1.17 ( 36) link_NAG-ASN : bond 0.00400 / 0.27 ( 15) link_NAG-ASN : angle 3.33485 / 2.59 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 144 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 34 GLN cc_start: 0.8790 (tt0) cc_final: 0.8526 (tt0) REVERT: B 47 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7677 (mt0) REVERT: B 67 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.7310 (mp0) REVERT: B 121 LYS cc_start: 0.8537 (ttpt) cc_final: 0.8287 (tttt) REVERT: B 125 GLN cc_start: 0.8044 (tt0) cc_final: 0.7729 (mt0) REVERT: B 128 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7734 (tp30) REVERT: C 145 SER cc_start: 0.8435 (OUTLIER) cc_final: 0.8151 (p) REVERT: C 210 GLN cc_start: 0.9025 (OUTLIER) cc_final: 0.8459 (tt0) REVERT: C 214 ILE cc_start: 0.8802 (tt) cc_final: 0.8572 (mt) REVERT: C 245 ILE cc_start: 0.8756 (OUTLIER) cc_final: 0.8253 (mt) REVERT: C 291 ASP cc_start: 0.8023 (m-30) cc_final: 0.7549 (p0) REVERT: C 325 GLU cc_start: 0.6380 (mp0) cc_final: 0.6148 (mp0) REVERT: E 62 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8431 (mt) REVERT: E 179 ILE cc_start: 0.9076 (OUTLIER) cc_final: 0.8754 (mp) REVERT: E 195 TYR cc_start: 0.8376 (OUTLIER) cc_final: 0.6352 (m-80) REVERT: E 223 VAL cc_start: 0.8867 (OUTLIER) cc_final: 0.8512 (t) REVERT: E 224 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.7542 (mtp180) REVERT: E 312 ASN cc_start: 0.8089 (t0) cc_final: 0.7646 (p0) REVERT: D 74 GLU cc_start: 0.7446 (mm-30) cc_final: 0.6778 (tt0) REVERT: F 47 GLN cc_start: 0.7874 (mt0) cc_final: 0.7580 (mt0) REVERT: F 114 GLU cc_start: 0.7921 (tp30) cc_final: 0.7594 (tp30) REVERT: F 151 SER cc_start: 0.8586 (t) cc_final: 0.7954 (p) outliers start: 50 outliers final: 32 residues processed: 184 average time/residue: 0.5487 time to fit residues: 110.2888 Evaluate side-chains 186 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 143 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 179 ILE Chi-restraints excluded: chain E residue 190 GLU Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 224 ARG Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain F residue 18 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 102 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 107 optimal weight: 0.0270 chunk 32 optimal weight: 2.9990 chunk 66 optimal weight: 0.0020 chunk 12 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.5046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 GLN F 105 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.126641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.104389 restraints weight = 13582.008| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.87 r_work: 0.2950 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 1.0792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12285 Z= 0.135 Angle : 0.581 12.562 16725 Z= 0.295 Chirality : 0.044 0.220 1920 Planarity : 0.004 0.036 2127 Dihedral : 4.286 19.686 1584 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.67 % Allowed : 23.58 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.21), residues: 1458 helix: 2.15 (0.28), residues: 360 sheet: 0.45 (0.34), residues: 234 loop : -1.57 (0.18), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 141 TYR 0.014 0.001 TYR D 162 PHE 0.014 0.002 PHE F 24 TRP 0.007 0.001 TRP A 234 HIS 0.005 0.001 HIS B 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.13 (12234) covalent geometry : angle 0.54489 / 0.29 (16590) SS BOND : bond 0.00558 / 0.35 ( 18) SS BOND : angle 2.01939 / 1.30 ( 36) hydrogen bonds : bond 0.05651 / 3.94 ( 427) hydrogen bonds : angle 4.27905 / 3.05 ( 1173) link_ALPHA1-3 : bond 0.00559 / 0.28 ( 3) link_ALPHA1-3 : angle 1.36161 / 1.00 ( 9) link_ALPHA1-6 : bond 0.00284 / 0.14 ( 3) link_ALPHA1-6 : angle 1.50820 / 1.01 ( 9) link_BETA1-4 : bond 0.00426 / 0.28 ( 12) link_BETA1-4 : angle 1.72148 / 1.14 ( 36) link_NAG-ASN : bond 0.00376 / 0.26 ( 15) link_NAG-ASN : angle 3.11170 / 2.44 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3925.66 seconds wall clock time: 67 minutes 49.74 seconds (4069.74 seconds total)