Starting phenix.real_space_refine on Wed Mar 4 08:18:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6y5h_10697/03_2026/6y5h_10697.cif Found real_map, /net/cci-nas-00/data/ceres_data/6y5h_10697/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/6y5h_10697/03_2026/6y5h_10697.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6y5h_10697/03_2026/6y5h_10697.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6y5h_10697/03_2026/6y5h_10697.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6y5h_10697/03_2026/6y5h_10697.map" } 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-dev-5986/lib/python3.9/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 dihedrals: 15 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 15 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 dihedrals: 6 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 dihedrals: 15 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.15, per 1000 atoms: 0.26 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: 1.13 Conformation dependent library (CDL) restraints added in 612.5 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: 0.34 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: 1.97 Time building geometry restraints manager: 1.49 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 - 22.03: 7103 22.03 - 44.07: 529 44.07 - 66.10: 75 66.10 - 88.14: 39 88.14 - 110.17: 18 Dihedral angle restraints: 7764 sinusoidal: 3546 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 7761 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: 6.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.860 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 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:8.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5413 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 : 16.337 110.171 5004 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 covalent geometry : bond 0.00351 (12234) covalent geometry : angle 0.65518 (16590) SS BOND : bond 0.02536 ( 18) SS BOND : angle 1.09557 ( 36) hydrogen bonds : bond 0.16874 ( 427) hydrogen bonds : angle 6.01772 ( 1173) link_ALPHA1-3 : bond 0.06432 ( 3) link_ALPHA1-3 : angle 32.18866 ( 9) link_ALPHA1-6 : bond 0.06413 ( 3) link_ALPHA1-6 : angle 13.07044 ( 9) link_BETA1-4 : bond 0.06469 ( 12) link_BETA1-4 : angle 17.79502 ( 36) link_NAG-ASN : bond 0.00135 ( 15) link_NAG-ASN : angle 1.28466 ( 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 : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 274 average time/residue: 0.4674 time to fit residues: 140.2424 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... Flipped N/Q/H residues before XYZ refinement: 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 60 ASN D 142 HIS D 146 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.148280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.127713 restraints weight = 13550.755| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.86 r_work: 0.3220 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.8081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 12285 Z= 0.334 Angle : 1.106 21.700 16725 Z= 0.535 Chirality : 0.065 0.650 1920 Planarity : 0.008 0.067 2127 Dihedral : 9.844 73.986 2262 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 6.64 % Allowed : 18.50 % Favored : 74.86 % 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: -1.97 (0.19), residues: 1458 helix: -0.41 (0.25), residues: 360 sheet: -0.12 (0.33), residues: 258 loop : -2.21 (0.17), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.002 ARG F 153 TYR 0.042 0.004 TYR B 162 PHE 0.027 0.004 PHE D 63 TRP 0.033 0.003 TRP E 153 HIS 0.013 0.002 HIS C 75 Details of bonding type rmsd covalent geometry : bond 0.00741 (12234) covalent geometry : angle 1.05425 (16590) SS BOND : bond 0.01604 ( 18) SS BOND : angle 1.97606 ( 36) hydrogen bonds : bond 0.07695 ( 427) hydrogen bonds : angle 5.55658 ( 1173) link_ALPHA1-3 : bond 0.03475 ( 3) link_ALPHA1-3 : angle 3.54988 ( 9) link_ALPHA1-6 : bond 0.01031 ( 3) link_ALPHA1-6 : angle 4.40115 ( 9) link_BETA1-4 : bond 0.01931 ( 12) link_BETA1-4 : angle 3.83690 ( 36) link_NAG-ASN : bond 0.01490 ( 15) link_NAG-ASN : angle 4.89253 ( 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 327 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 242 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 ARG cc_start: 0.7849 (ttt90) cc_final: 0.7543 (ttt180) REVERT: A 241 ASP cc_start: 0.8295 (OUTLIER) cc_final: 0.8085 (t0) REVERT: A 275 ASP cc_start: 0.7093 (m-30) cc_final: 0.6666 (m-30) REVERT: A 307 LYS cc_start: 0.8573 (mtmm) cc_final: 0.8214 (mtpt) REVERT: B 42 GLN cc_start: 0.7576 (tp40) cc_final: 0.7275 (tp40) REVERT: B 65 GLN cc_start: 0.8592 (mt0) cc_final: 0.8361 (mt0) REVERT: B 121 LYS cc_start: 0.8221 (ttmt) cc_final: 0.7978 (ttpt) REVERT: C 28 THR cc_start: 0.9235 (OUTLIER) cc_final: 0.9031 (m) REVERT: C 241 ASP cc_start: 0.8103 (OUTLIER) cc_final: 0.7468 (t0) REVERT: C 242 VAL cc_start: 0.8120 (t) cc_final: 0.7583 (p) REVERT: C 260 MET cc_start: 0.8006 (mmm) cc_final: 0.7697 (mtp) REVERT: C 295 GLN cc_start: 0.9365 (OUTLIER) cc_final: 0.8952 (pp30) REVERT: E 88 VAL cc_start: 0.8138 (OUTLIER) cc_final: 0.7913 (t) REVERT: E 168 MET cc_start: 0.8379 (OUTLIER) cc_final: 0.8078 (tpt) REVERT: E 241 ASP cc_start: 0.8412 (OUTLIER) cc_final: 0.8090 (t0) REVERT: E 280 GLU cc_start: 0.7375 (mm-30) cc_final: 0.7142 (mm-30) REVERT: E 292 LYS cc_start: 0.9035 (OUTLIER) cc_final: 0.8663 (mttm) REVERT: D 62 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7120 (mtpp) REVERT: D 65 GLN cc_start: 0.8735 (mt0) cc_final: 0.8534 (mt0) REVERT: F 17 MET cc_start: 0.8525 (tpp) cc_final: 0.8220 (ttm) REVERT: F 18 ILE cc_start: 0.7865 (tp) cc_final: 0.7440 (pt) REVERT: F 45 ILE cc_start: 0.8355 (tt) cc_final: 0.7700 (pp) outliers start: 85 outliers final: 21 residues processed: 310 average time/residue: 0.5306 time to fit residues: 178.5090 Evaluate side-chains 191 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 161 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU 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 241 ASP 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 14 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 45 optimal weight: 0.0870 chunk 109 optimal weight: 0.6980 chunk 87 optimal weight: 0.7980 chunk 85 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 90 optimal weight: 0.3980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3452 r_free = 0.3452 target = 0.136900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.115492 restraints weight = 13290.197| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.82 r_work: 0.3040 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.8729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12285 Z= 0.158 Angle : 0.638 10.903 16725 Z= 0.319 Chirality : 0.047 0.287 1920 Planarity : 0.005 0.049 2127 Dihedral : 8.808 76.165 2262 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 5.23 % Allowed : 22.17 % 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: -1.16 (0.20), residues: 1458 helix: 1.10 (0.28), residues: 357 sheet: 0.16 (0.32), residues: 264 loop : -2.04 (0.17), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 141 TYR 0.015 0.002 TYR A 308 PHE 0.016 0.002 PHE B 24 TRP 0.013 0.001 TRP A 234 HIS 0.007 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00354 (12234) covalent geometry : angle 0.59741 (16590) SS BOND : bond 0.00620 ( 18) SS BOND : angle 2.07734 ( 36) hydrogen bonds : bond 0.06056 ( 427) hydrogen bonds : angle 4.64241 ( 1173) link_ALPHA1-3 : bond 0.01100 ( 3) link_ALPHA1-3 : angle 1.78327 ( 9) link_ALPHA1-6 : bond 0.00201 ( 3) link_ALPHA1-6 : angle 2.10309 ( 9) link_BETA1-4 : bond 0.00844 ( 12) link_BETA1-4 : angle 2.50054 ( 36) link_NAG-ASN : bond 0.00595 ( 15) link_NAG-ASN : angle 3.14163 ( 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 228 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 161 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ARG cc_start: 0.7990 (ttt90) cc_final: 0.7769 (ttt-90) REVERT: A 73 ASP cc_start: 0.7856 (OUTLIER) cc_final: 0.7633 (t0) REVERT: B 67 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.7161 (mp0) REVERT: B 121 LYS cc_start: 0.8310 (ttmt) cc_final: 0.8032 (ttpt) REVERT: B 123 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.8500 (ttp-110) REVERT: C 118 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8264 (mp) REVERT: C 188 ASN cc_start: 0.8607 (t0) cc_final: 0.8392 (t0) REVERT: C 210 GLN cc_start: 0.9016 (OUTLIER) cc_final: 0.8711 (tt0) REVERT: C 245 ILE cc_start: 0.8434 (OUTLIER) cc_final: 0.7810 (mt) REVERT: E 62 ILE cc_start: 0.8126 (OUTLIER) cc_final: 0.7788 (mp) REVERT: E 168 MET cc_start: 0.8531 (mmt) cc_final: 0.8314 (tpt) REVERT: E 280 GLU cc_start: 0.7497 (mm-30) cc_final: 0.7291 (mm-30) REVERT: F 17 MET cc_start: 0.8632 (tpp) cc_final: 0.8224 (ttm) REVERT: F 151 SER cc_start: 0.6886 (t) cc_final: 0.6244 (p) outliers start: 67 outliers final: 28 residues processed: 211 average time/residue: 0.4929 time to fit residues: 113.7725 Evaluate side-chains 176 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 141 time to evaluate : 0.407 ------------------------------------------------------------------------------- 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 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 59 THR Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain C residue 18 HIS 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 195 TYR Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 247 SER 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: 0.0980 chunk 14 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 18 HIS C 312 ASN E 18 HIS D 47 GLN D 125 GLN D 142 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.129356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.107697 restraints weight = 13746.562| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.87 r_work: 0.2961 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.9345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12285 Z= 0.166 Angle : 0.663 20.408 16725 Z= 0.327 Chirality : 0.047 0.282 1920 Planarity : 0.005 0.045 2127 Dihedral : 8.050 69.216 2259 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 5.31 % Allowed : 21.94 % 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: -0.93 (0.20), residues: 1458 helix: 1.44 (0.28), residues: 357 sheet: 0.45 (0.33), residues: 234 loop : -1.95 (0.17), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 141 TYR 0.015 0.002 TYR E 308 PHE 0.016 0.002 PHE B 138 TRP 0.008 0.001 TRP A 234 HIS 0.028 0.002 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00387 (12234) covalent geometry : angle 0.59953 (16590) SS BOND : bond 0.00582 ( 18) SS BOND : angle 2.28322 ( 36) hydrogen bonds : bond 0.06021 ( 427) hydrogen bonds : angle 4.52132 ( 1173) link_ALPHA1-3 : bond 0.01637 ( 3) link_ALPHA1-3 : angle 1.10264 ( 9) link_ALPHA1-6 : bond 0.00631 ( 3) link_ALPHA1-6 : angle 1.82953 ( 9) link_BETA1-4 : bond 0.00585 ( 12) link_BETA1-4 : angle 2.28224 ( 36) link_NAG-ASN : bond 0.00612 ( 15) link_NAG-ASN : angle 4.64290 ( 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 224 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 156 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 CYS cc_start: 0.8177 (m) cc_final: 0.7823 (m) REVERT: A 73 ASP cc_start: 0.8129 (OUTLIER) cc_final: 0.7868 (t0) REVERT: B 47 GLN cc_start: 0.7668 (tt0) cc_final: 0.7393 (mt0) REVERT: B 67 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.7241 (mp0) REVERT: B 121 LYS cc_start: 0.8309 (ttmt) cc_final: 0.8029 (ttpt) REVERT: B 123 ARG cc_start: 0.8801 (OUTLIER) cc_final: 0.8542 (ttp-110) REVERT: C 118 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8334 (mp) REVERT: C 145 SER cc_start: 0.8047 (m) cc_final: 0.7570 (p) REVERT: C 210 GLN cc_start: 0.9058 (OUTLIER) cc_final: 0.8674 (tt0) REVERT: E 57 ARG cc_start: 0.7610 (ttt180) cc_final: 0.7322 (ttt180) REVERT: E 62 ILE cc_start: 0.8310 (OUTLIER) cc_final: 0.8016 (mp) REVERT: E 168 MET cc_start: 0.8603 (mmt) cc_final: 0.8318 (tpt) REVERT: E 195 TYR cc_start: 0.8139 (OUTLIER) cc_final: 0.5701 (m-80) REVERT: E 280 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7653 (mt-10) REVERT: F 17 MET cc_start: 0.8550 (tpp) cc_final: 0.8166 (ttm) REVERT: F 151 SER cc_start: 0.7943 (t) cc_final: 0.7177 (p) outliers start: 68 outliers final: 32 residues processed: 211 average time/residue: 0.4718 time to fit residues: 109.0696 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 : 0.422 ------------------------------------------------------------------------------- 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 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 59 THR Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 123 ARG 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 118 LEU 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 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 247 SER 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 F residue 30 GLU Chi-restraints excluded: chain F residue 47 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 142 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 84 optimal weight: 0.3980 chunk 64 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 80 optimal weight: 0.4980 chunk 137 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 312 ASN ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 ASN E 248 ASN E 295 GLN D 47 GLN F 28 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.128133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.106151 restraints weight = 13598.667| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 1.85 r_work: 0.2935 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 1.0137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12285 Z= 0.169 Angle : 0.649 15.051 16725 Z= 0.322 Chirality : 0.047 0.256 1920 Planarity : 0.005 0.043 2127 Dihedral : 7.739 65.646 2259 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 5.62 % Allowed : 22.87 % Favored : 71.51 % 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: -0.72 (0.20), residues: 1458 helix: 1.72 (0.28), residues: 357 sheet: 0.52 (0.33), residues: 234 loop : -1.85 (0.17), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 141 TYR 0.016 0.002 TYR E 308 PHE 0.016 0.002 PHE B 24 TRP 0.009 0.001 TRP A 234 HIS 0.012 0.002 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00400 (12234) covalent geometry : angle 0.59771 (16590) SS BOND : bond 0.00520 ( 18) SS BOND : angle 1.95661 ( 36) hydrogen bonds : bond 0.06210 ( 427) hydrogen bonds : angle 4.43553 ( 1173) link_ALPHA1-3 : bond 0.01176 ( 3) link_ALPHA1-3 : angle 1.19599 ( 9) link_ALPHA1-6 : bond 0.00285 ( 3) link_ALPHA1-6 : angle 1.73249 ( 9) link_BETA1-4 : bond 0.00765 ( 12) link_BETA1-4 : angle 2.06402 ( 36) link_NAG-ASN : bond 0.00745 ( 15) link_NAG-ASN : angle 4.20923 ( 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 232 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 160 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ILE cc_start: 0.8702 (OUTLIER) cc_final: 0.8466 (mp) REVERT: A 259 LYS cc_start: 0.9087 (OUTLIER) cc_final: 0.8659 (mtmt) REVERT: B 34 GLN cc_start: 0.8714 (tt0) cc_final: 0.8395 (tt0) REVERT: B 47 GLN cc_start: 0.7891 (tt0) cc_final: 0.7630 (mt0) REVERT: B 67 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.7251 (mp0) REVERT: B 121 LYS cc_start: 0.8226 (ttmt) cc_final: 0.7917 (tttt) REVERT: B 123 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8493 (ttp-110) REVERT: C 118 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8383 (mp) REVERT: C 119 GLU cc_start: 0.8997 (tt0) cc_final: 0.8755 (tt0) REVERT: C 145 SER cc_start: 0.8183 (OUTLIER) cc_final: 0.7855 (p) REVERT: C 201 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7864 (ptt90) REVERT: C 261 ARG cc_start: 0.8423 (mtp180) cc_final: 0.7974 (mtt90) REVERT: C 291 ASP cc_start: 0.8202 (m-30) cc_final: 0.7780 (p0) REVERT: E 52 CYS cc_start: 0.7826 (m) cc_final: 0.7524 (m) REVERT: E 62 ILE cc_start: 0.8517 (OUTLIER) cc_final: 0.8265 (mp) REVERT: E 223 VAL cc_start: 0.8865 (OUTLIER) cc_final: 0.8530 (t) REVERT: E 224 ARG cc_start: 0.8802 (OUTLIER) cc_final: 0.8589 (mtm180) REVERT: E 261 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.7781 (mmm-85) REVERT: E 276 THR cc_start: 0.8455 (OUTLIER) cc_final: 0.8084 (p) REVERT: D 72 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7649 (mt-10) REVERT: D 74 GLU cc_start: 0.7368 (mm-30) cc_final: 0.6606 (tm-30) REVERT: D 128 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7288 (tp30) REVERT: F 151 SER cc_start: 0.8289 (t) cc_final: 0.7540 (p) outliers start: 72 outliers final: 36 residues processed: 216 average time/residue: 0.4847 time to fit residues: 114.5830 Evaluate side-chains 194 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 145 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL 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 228 SER Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 262 THR 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 59 THR Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 123 ARG 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 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 228 SER Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 262 THR 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 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 247 SER Chi-restraints excluded: chain E residue 261 ARG 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 F residue 18 ILE 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: 0.9980 chunk 72 optimal weight: 0.8980 chunk 57 optimal weight: 0.0770 chunk 69 optimal weight: 0.9990 chunk 116 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 GLN C 312 ASN E 18 HIS E 33 GLN E 312 ASN D 47 GLN F 28 ASN F 47 GLN F 105 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.127668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.105880 restraints weight = 13599.910| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.84 r_work: 0.2953 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 1.0391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12285 Z= 0.168 Angle : 0.629 11.850 16725 Z= 0.314 Chirality : 0.046 0.233 1920 Planarity : 0.005 0.041 2127 Dihedral : 7.437 62.987 2259 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 5.31 % Allowed : 23.19 % Favored : 71.51 % 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: -0.65 (0.20), residues: 1458 helix: 1.82 (0.28), residues: 357 sheet: 0.50 (0.34), residues: 234 loop : -1.81 (0.17), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 141 TYR 0.014 0.002 TYR A 308 PHE 0.016 0.002 PHE C 125 TRP 0.008 0.001 TRP A 234 HIS 0.005 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00404 (12234) covalent geometry : angle 0.58470 (16590) SS BOND : bond 0.00671 ( 18) SS BOND : angle 2.23270 ( 36) hydrogen bonds : bond 0.06140 ( 427) hydrogen bonds : angle 4.41094 ( 1173) link_ALPHA1-3 : bond 0.01337 ( 3) link_ALPHA1-3 : angle 0.98104 ( 9) link_ALPHA1-6 : bond 0.00431 ( 3) link_ALPHA1-6 : angle 1.68614 ( 9) link_BETA1-4 : bond 0.00522 ( 12) link_BETA1-4 : angle 1.97649 ( 36) link_NAG-ASN : bond 0.00424 ( 15) link_NAG-ASN : angle 3.62297 ( 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 218 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 150 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ASP cc_start: 0.8289 (OUTLIER) cc_final: 0.7957 (t0) REVERT: A 121 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.8461 (mp) REVERT: B 34 GLN cc_start: 0.8761 (tt0) cc_final: 0.8444 (tt0) REVERT: B 47 GLN cc_start: 0.7862 (tt0) cc_final: 0.7612 (mt0) REVERT: B 65 GLN cc_start: 0.8803 (mt0) cc_final: 0.8493 (mt0) REVERT: B 67 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.7215 (mp0) REVERT: B 121 LYS cc_start: 0.8275 (ttmt) cc_final: 0.7947 (tttt) REVERT: B 123 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.8486 (ttp-110) REVERT: C 118 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8426 (mp) REVERT: C 119 GLU cc_start: 0.8982 (tt0) cc_final: 0.8753 (tt0) REVERT: C 145 SER cc_start: 0.8261 (OUTLIER) cc_final: 0.7933 (p) REVERT: C 201 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7977 (ptt90) REVERT: C 214 ILE cc_start: 0.8730 (tt) cc_final: 0.8463 (mt) REVERT: C 245 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8133 (mt) REVERT: C 261 ARG cc_start: 0.8475 (mtp180) cc_final: 0.8037 (mtt90) REVERT: C 291 ASP cc_start: 0.8150 (m-30) cc_final: 0.7750 (p0) REVERT: C 325 GLU cc_start: 0.6355 (mp0) cc_final: 0.6100 (mp0) REVERT: E 62 ILE cc_start: 0.8616 (OUTLIER) cc_final: 0.8377 (mp) REVERT: E 195 TYR cc_start: 0.8368 (OUTLIER) cc_final: 0.6242 (m-80) REVERT: E 223 VAL cc_start: 0.8911 (OUTLIER) cc_final: 0.8481 (t) REVERT: E 247 SER cc_start: 0.9214 (OUTLIER) cc_final: 0.9004 (t) REVERT: E 276 THR cc_start: 0.8427 (OUTLIER) cc_final: 0.8105 (p) REVERT: E 312 ASN cc_start: 0.8149 (t0) cc_final: 0.7645 (p0) REVERT: D 72 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7764 (mt-10) REVERT: D 74 GLU cc_start: 0.7326 (mm-30) cc_final: 0.6733 (tt0) REVERT: F 151 SER cc_start: 0.8424 (t) cc_final: 0.7705 (p) outliers start: 68 outliers final: 32 residues processed: 209 average time/residue: 0.4681 time to fit residues: 107.2825 Evaluate side-chains 194 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 149 time to evaluate : 0.459 ------------------------------------------------------------------------------- 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 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 59 THR Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 123 ARG 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 228 SER Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 262 THR 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 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 228 SER Chi-restraints excluded: chain E residue 247 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 150 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 133 optimal weight: 0.0020 chunk 65 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 61 optimal weight: 0.0770 chunk 74 optimal weight: 0.9980 chunk 137 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 116 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 overall best weight: 0.4746 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 312 ASN E 18 HIS E 33 GLN D 47 GLN D 146 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 = 0.3357 r_free = 0.3357 target = 0.129155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.107468 restraints weight = 13447.233| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 1.83 r_work: 0.2974 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 1.0510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12285 Z= 0.131 Angle : 0.582 10.307 16725 Z= 0.292 Chirality : 0.044 0.226 1920 Planarity : 0.004 0.037 2127 Dihedral : 7.105 59.849 2259 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.68 % Allowed : 23.50 % Favored : 71.82 % 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: 2.06 (0.28), residues: 357 sheet: 0.25 (0.31), residues: 264 loop : -1.62 (0.18), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 141 TYR 0.010 0.001 TYR B 162 PHE 0.012 0.002 PHE D 9 TRP 0.007 0.001 TRP A 234 HIS 0.004 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00302 (12234) covalent geometry : angle 0.54217 (16590) SS BOND : bond 0.00582 ( 18) SS BOND : angle 1.90311 ( 36) hydrogen bonds : bond 0.05602 ( 427) hydrogen bonds : angle 4.32496 ( 1173) link_ALPHA1-3 : bond 0.01290 ( 3) link_ALPHA1-3 : angle 1.07152 ( 9) link_ALPHA1-6 : bond 0.00576 ( 3) link_ALPHA1-6 : angle 1.58435 ( 9) link_BETA1-4 : bond 0.00576 ( 12) link_BETA1-4 : angle 1.80037 ( 36) link_NAG-ASN : bond 0.00373 ( 15) link_NAG-ASN : angle 3.34939 ( 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 209 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 149 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ASP cc_start: 0.8229 (OUTLIER) cc_final: 0.7905 (t0) REVERT: A 197 GLN cc_start: 0.8610 (mp-120) cc_final: 0.8401 (mp10) REVERT: A 325 GLU cc_start: 0.6572 (OUTLIER) cc_final: 0.5802 (mp0) REVERT: B 34 GLN cc_start: 0.8762 (tt0) cc_final: 0.8436 (tt0) REVERT: B 47 GLN cc_start: 0.7852 (tt0) cc_final: 0.7598 (mt0) REVERT: B 67 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.7230 (mp0) REVERT: B 123 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.8516 (ttp-110) REVERT: B 125 GLN cc_start: 0.8035 (tt0) cc_final: 0.7685 (mt0) REVERT: C 118 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8396 (mp) REVERT: C 119 GLU cc_start: 0.8952 (tt0) cc_final: 0.8730 (tt0) REVERT: C 145 SER cc_start: 0.8311 (OUTLIER) cc_final: 0.8011 (p) REVERT: C 214 ILE cc_start: 0.8718 (tt) cc_final: 0.8490 (mt) REVERT: C 245 ILE cc_start: 0.8771 (OUTLIER) cc_final: 0.8142 (mt) REVERT: C 261 ARG cc_start: 0.8453 (mtp180) cc_final: 0.8035 (mtt90) REVERT: C 291 ASP cc_start: 0.8064 (m-30) cc_final: 0.7673 (p0) REVERT: C 325 GLU cc_start: 0.6348 (mp0) cc_final: 0.6119 (mp0) REVERT: E 62 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8366 (mp) REVERT: E 179 ILE cc_start: 0.9085 (OUTLIER) cc_final: 0.8771 (mp) REVERT: E 223 VAL cc_start: 0.8863 (OUTLIER) cc_final: 0.8515 (t) REVERT: E 276 THR cc_start: 0.8225 (OUTLIER) cc_final: 0.7944 (p) REVERT: D 72 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7801 (mt-10) REVERT: D 74 GLU cc_start: 0.7260 (mm-30) cc_final: 0.6688 (tt0) REVERT: F 47 GLN cc_start: 0.7812 (mt0) cc_final: 0.7492 (mt0) REVERT: F 151 SER cc_start: 0.8449 (t) cc_final: 0.7744 (p) outliers start: 60 outliers final: 27 residues processed: 198 average time/residue: 0.4960 time to fit residues: 107.1569 Evaluate side-chains 184 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 146 time to evaluate : 0.305 ------------------------------------------------------------------------------- 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 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 323 VAL Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 167 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 228 SER Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 262 THR 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 205 SER Chi-restraints excluded: chain E residue 219 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 D residue 18 ILE Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain F residue 18 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 6 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 102 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 136 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS C 312 ASN ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 GLN E 312 ASN D 47 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 = 0.3344 r_free = 0.3344 target = 0.128215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.106489 restraints weight = 13483.794| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.83 r_work: 0.2889 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 1.0628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12285 Z= 0.174 Angle : 0.632 10.633 16725 Z= 0.316 Chirality : 0.046 0.236 1920 Planarity : 0.004 0.039 2127 Dihedral : 7.182 59.424 2259 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.84 % Allowed : 22.79 % Favored : 72.37 % 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: 2.00 (0.28), residues: 357 sheet: 0.53 (0.34), residues: 234 loop : -1.72 (0.17), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 141 TYR 0.014 0.002 TYR C 308 PHE 0.017 0.002 PHE C 125 TRP 0.009 0.001 TRP A 234 HIS 0.006 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00421 (12234) covalent geometry : angle 0.59185 (16590) SS BOND : bond 0.00760 ( 18) SS BOND : angle 2.24470 ( 36) hydrogen bonds : bond 0.06201 ( 427) hydrogen bonds : angle 4.35656 ( 1173) link_ALPHA1-3 : bond 0.01231 ( 3) link_ALPHA1-3 : angle 1.13279 ( 9) link_ALPHA1-6 : bond 0.00495 ( 3) link_ALPHA1-6 : angle 1.64787 ( 9) link_BETA1-4 : bond 0.00560 ( 12) link_BETA1-4 : angle 1.89063 ( 36) link_NAG-ASN : bond 0.00376 ( 15) link_NAG-ASN : angle 3.39727 ( 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 206 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 144 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8590 (mtmt) REVERT: A 325 GLU cc_start: 0.6587 (OUTLIER) cc_final: 0.5840 (mp0) REVERT: B 34 GLN cc_start: 0.8777 (tt0) cc_final: 0.8491 (tt0) REVERT: B 47 GLN cc_start: 0.7932 (tt0) cc_final: 0.7671 (mt0) REVERT: B 67 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.7238 (mp0) REVERT: B 121 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.8097 (tttt) REVERT: B 123 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.8504 (ttp-110) REVERT: B 125 GLN cc_start: 0.8105 (tt0) cc_final: 0.7751 (mt0) REVERT: B 128 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7627 (tp30) REVERT: C 118 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8392 (mp) REVERT: C 119 GLU cc_start: 0.8932 (tt0) cc_final: 0.8705 (tt0) REVERT: C 145 SER cc_start: 0.8371 (OUTLIER) cc_final: 0.8059 (p) REVERT: C 214 ILE cc_start: 0.8764 (tt) cc_final: 0.8547 (mt) REVERT: C 245 ILE cc_start: 0.8806 (OUTLIER) cc_final: 0.8164 (mt) REVERT: C 261 ARG cc_start: 0.8413 (mtp180) cc_final: 0.8038 (mtt90) REVERT: C 291 ASP cc_start: 0.8066 (m-30) cc_final: 0.7649 (p0) REVERT: C 325 GLU cc_start: 0.6352 (mp0) cc_final: 0.6106 (mp0) REVERT: E 62 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.8355 (mt) REVERT: E 179 ILE cc_start: 0.9086 (OUTLIER) cc_final: 0.8762 (mp) REVERT: E 195 TYR cc_start: 0.8405 (OUTLIER) cc_final: 0.6333 (m-80) REVERT: E 223 VAL cc_start: 0.8900 (OUTLIER) cc_final: 0.8552 (t) REVERT: E 224 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.7738 (mtp180) REVERT: E 276 THR cc_start: 0.8269 (OUTLIER) cc_final: 0.8018 (p) REVERT: E 312 ASN cc_start: 0.8099 (t0) cc_final: 0.7643 (p0) REVERT: D 72 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7823 (mt-10) REVERT: D 74 GLU cc_start: 0.7339 (mm-30) cc_final: 0.6745 (tt0) REVERT: F 47 GLN cc_start: 0.7867 (mt0) cc_final: 0.7579 (mt0) REVERT: F 151 SER cc_start: 0.8543 (t) cc_final: 0.7872 (p) outliers start: 62 outliers final: 33 residues processed: 192 average time/residue: 0.5110 time to fit residues: 107.0836 Evaluate side-chains 190 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 142 time to evaluate : 0.292 ------------------------------------------------------------------------------- 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 104 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 259 LYS 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 59 THR 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 123 ARG 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 168 MET 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 C residue 262 THR 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 D residue 18 ILE Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain F residue 18 ILE Chi-restraints excluded: chain F residue 143 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 43 optimal weight: 0.2980 chunk 62 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 18 optimal weight: 0.0970 chunk 109 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 55 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 120 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 18 HIS E 33 GLN D 28 ASN D 47 GLN F 105 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.128031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.106241 restraints weight = 13570.175| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.84 r_work: 0.2948 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 1.0681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12285 Z= 0.125 Angle : 0.567 9.450 16725 Z= 0.286 Chirality : 0.044 0.217 1920 Planarity : 0.004 0.036 2127 Dihedral : 6.832 56.034 2259 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % 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: -0.34 (0.21), residues: 1458 helix: 2.12 (0.28), residues: 360 sheet: 0.30 (0.31), residues: 264 loop : -1.56 (0.18), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 141 TYR 0.011 0.001 TYR B 162 PHE 0.012 0.001 PHE D 9 TRP 0.007 0.001 TRP B 92 HIS 0.004 0.001 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.00287 (12234) covalent geometry : angle 0.53184 (16590) SS BOND : bond 0.00575 ( 18) SS BOND : angle 2.02275 ( 36) hydrogen bonds : bond 0.05469 ( 427) hydrogen bonds : angle 4.29454 ( 1173) link_ALPHA1-3 : bond 0.01246 ( 3) link_ALPHA1-3 : angle 1.02156 ( 9) link_ALPHA1-6 : bond 0.00677 ( 3) link_ALPHA1-6 : angle 1.49085 ( 9) link_BETA1-4 : bond 0.00533 ( 12) link_BETA1-4 : angle 1.73148 ( 36) link_NAG-ASN : bond 0.00329 ( 15) link_NAG-ASN : angle 2.99823 ( 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 191 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 141 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 GLN cc_start: 0.8698 (mp-120) cc_final: 0.8488 (mp10) REVERT: A 325 GLU cc_start: 0.6548 (OUTLIER) cc_final: 0.5828 (mp0) REVERT: B 34 GLN cc_start: 0.8760 (tt0) cc_final: 0.8443 (tt0) REVERT: B 47 GLN cc_start: 0.7861 (tt0) cc_final: 0.7583 (mt0) REVERT: B 67 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.7239 (mp0) REVERT: B 121 LYS cc_start: 0.8381 (ttpt) cc_final: 0.8070 (tttt) REVERT: B 125 GLN cc_start: 0.8031 (tt0) cc_final: 0.7718 (mt0) REVERT: B 143 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8029 (mtmm) REVERT: C 118 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8404 (mp) REVERT: C 145 SER cc_start: 0.8349 (OUTLIER) cc_final: 0.8061 (p) REVERT: C 245 ILE cc_start: 0.8763 (OUTLIER) cc_final: 0.8158 (mt) REVERT: C 261 ARG cc_start: 0.8456 (mtp180) cc_final: 0.8060 (mtt90) REVERT: C 291 ASP cc_start: 0.7988 (m-30) cc_final: 0.7609 (p0) REVERT: C 325 GLU cc_start: 0.6393 (mp0) cc_final: 0.6127 (mp0) REVERT: E 62 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8381 (mp) REVERT: E 179 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8760 (mp) REVERT: E 223 VAL cc_start: 0.8843 (OUTLIER) cc_final: 0.8523 (t) REVERT: E 224 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.7672 (mtp180) REVERT: E 276 THR cc_start: 0.8145 (OUTLIER) cc_final: 0.7863 (p) REVERT: E 312 ASN cc_start: 0.8049 (t0) cc_final: 0.7630 (p0) REVERT: D 74 GLU cc_start: 0.7275 (mm-30) cc_final: 0.6709 (tt0) REVERT: F 47 GLN cc_start: 0.7828 (mt0) cc_final: 0.7483 (mt0) REVERT: F 151 SER cc_start: 0.8464 (t) cc_final: 0.7781 (p) outliers start: 50 outliers final: 30 residues processed: 182 average time/residue: 0.5055 time to fit residues: 100.4207 Evaluate side-chains 182 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 141 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL 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 A residue 325 GLU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 110 LEU 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 168 MET 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 C residue 262 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 110 SER 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 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 110 LEU 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: 0.5980 chunk 20 optimal weight: 0.2980 chunk 36 optimal weight: 0.2980 chunk 61 optimal weight: 1.9990 chunk 119 optimal weight: 0.5980 chunk 83 optimal weight: 0.0570 chunk 115 optimal weight: 0.7980 chunk 101 optimal weight: 0.5980 chunk 85 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 overall best weight: 0.3698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 312 ASN E 18 HIS E 33 GLN F 105 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.131074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.109456 restraints weight = 13500.841| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.83 r_work: 0.2969 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 1.0732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12285 Z= 0.116 Angle : 0.552 9.078 16725 Z= 0.278 Chirality : 0.044 0.209 1920 Planarity : 0.004 0.035 2127 Dihedral : 6.558 53.768 2259 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.28 % Allowed : 24.43 % Favored : 72.29 % 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: -0.22 (0.21), residues: 1458 helix: 2.29 (0.28), residues: 360 sheet: 0.31 (0.31), residues: 264 loop : -1.50 (0.19), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 141 TYR 0.010 0.001 TYR D 157 PHE 0.012 0.001 PHE F 24 TRP 0.007 0.001 TRP B 92 HIS 0.004 0.001 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.00263 (12234) covalent geometry : angle 0.51950 (16590) SS BOND : bond 0.00498 ( 18) SS BOND : angle 1.88364 ( 36) hydrogen bonds : bond 0.05260 ( 427) hydrogen bonds : angle 4.22904 ( 1173) link_ALPHA1-3 : bond 0.01253 ( 3) link_ALPHA1-3 : angle 1.06338 ( 9) link_ALPHA1-6 : bond 0.00708 ( 3) link_ALPHA1-6 : angle 1.46953 ( 9) link_BETA1-4 : bond 0.00531 ( 12) link_BETA1-4 : angle 1.65073 ( 36) link_NAG-ASN : bond 0.00316 ( 15) link_NAG-ASN : angle 2.83976 ( 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 184 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 142 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ASP cc_start: 0.8211 (OUTLIER) cc_final: 0.7875 (t0) REVERT: A 197 GLN cc_start: 0.8697 (mp-120) cc_final: 0.8483 (mp10) REVERT: A 325 GLU cc_start: 0.6465 (OUTLIER) cc_final: 0.5805 (mp0) REVERT: B 34 GLN cc_start: 0.8781 (tt0) cc_final: 0.8496 (tt0) REVERT: B 47 GLN cc_start: 0.7832 (tt0) cc_final: 0.7596 (mt0) REVERT: B 65 GLN cc_start: 0.8759 (mt0) cc_final: 0.8479 (mt0) REVERT: B 67 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.7244 (mp0) REVERT: B 121 LYS cc_start: 0.8386 (ttpt) cc_final: 0.8096 (tttt) REVERT: B 125 GLN cc_start: 0.7957 (tt0) cc_final: 0.7674 (tt0) REVERT: B 143 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8045 (mtmm) REVERT: C 145 SER cc_start: 0.8377 (OUTLIER) cc_final: 0.8107 (p) REVERT: C 245 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8096 (mt) REVERT: C 261 ARG cc_start: 0.8454 (mtp180) cc_final: 0.8047 (mtt90) REVERT: C 291 ASP cc_start: 0.7971 (m-30) cc_final: 0.7589 (p0) REVERT: E 62 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8363 (mt) REVERT: E 179 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8757 (mp) REVERT: E 223 VAL cc_start: 0.8855 (OUTLIER) cc_final: 0.8518 (t) REVERT: E 224 ARG cc_start: 0.8849 (OUTLIER) cc_final: 0.7681 (mtp180) REVERT: E 312 ASN cc_start: 0.8019 (t0) cc_final: 0.7631 (p0) REVERT: D 74 GLU cc_start: 0.7237 (mm-30) cc_final: 0.6695 (tt0) REVERT: F 47 GLN cc_start: 0.7857 (mt0) cc_final: 0.7514 (mt0) REVERT: F 151 SER cc_start: 0.8522 (t) cc_final: 0.7858 (p) outliers start: 42 outliers final: 26 residues processed: 176 average time/residue: 0.5114 time to fit residues: 98.0985 Evaluate side-chains 173 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 137 time to evaluate : 0.432 ------------------------------------------------------------------------------- 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 155 THR Chi-restraints excluded: chain A residue 228 SER 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 59 THR Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 143 LYS 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 168 MET 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 C residue 262 THR 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 155 THR Chi-restraints excluded: chain E residue 179 ILE Chi-restraints excluded: chain E residue 190 GLU 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 D residue 18 ILE Chi-restraints excluded: chain D residue 110 LEU 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: 0.7980 chunk 127 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 53 optimal weight: 0.2980 chunk 107 optimal weight: 0.0470 chunk 32 optimal weight: 2.9990 chunk 66 optimal weight: 0.4980 chunk 12 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 312 ASN E 18 HIS E 33 GLN D 47 GLN F 105 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.127550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.105375 restraints weight = 13616.771| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.87 r_work: 0.2940 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 1.0776 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= 0.123 Angle : 0.559 9.038 16725 Z= 0.282 Chirality : 0.044 0.209 1920 Planarity : 0.004 0.034 2127 Dihedral : 6.480 52.515 2259 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.36 % Allowed : 24.36 % Favored : 72.29 % 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: -0.18 (0.21), residues: 1458 helix: 2.33 (0.28), residues: 360 sheet: 0.33 (0.32), residues: 264 loop : -1.48 (0.19), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 141 TYR 0.010 0.001 TYR D 157 PHE 0.013 0.001 PHE F 24 TRP 0.008 0.001 TRP B 92 HIS 0.004 0.001 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.00283 (12234) covalent geometry : angle 0.52617 (16590) SS BOND : bond 0.00527 ( 18) SS BOND : angle 1.97291 ( 36) hydrogen bonds : bond 0.05360 ( 427) hydrogen bonds : angle 4.22694 ( 1173) link_ALPHA1-3 : bond 0.01211 ( 3) link_ALPHA1-3 : angle 1.05913 ( 9) link_ALPHA1-6 : bond 0.00717 ( 3) link_ALPHA1-6 : angle 1.44793 ( 9) link_BETA1-4 : bond 0.00520 ( 12) link_BETA1-4 : angle 1.63942 ( 36) link_NAG-ASN : bond 0.00311 ( 15) link_NAG-ASN : angle 2.84045 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3713.63 seconds wall clock time: 64 minutes 9.02 seconds (3849.02 seconds total)