Starting phenix.real_space_refine on Wed Jul 30 07:20:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6y5h_10697/07_2025/6y5h_10697.cif Found real_map, /net/cci-nas-00/data/ceres_data/6y5h_10697/07_2025/6y5h_10697.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6y5h_10697/07_2025/6y5h_10697.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6y5h_10697/07_2025/6y5h_10697.map" model { file = "/net/cci-nas-00/data/ceres_data/6y5h_10697/07_2025/6y5h_10697.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6y5h_10697/07_2025/6y5h_10697.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.45, per 1000 atoms: 0.70 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: 3.45 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.44 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: 4.31 Time building geometry restraints manager: 4.08 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.230 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: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 32.090 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:15.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.540 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.005 0.001 TRP E 84 HIS 0.004 0.001 HIS F 142 PHE 0.007 0.001 PHE F 9 TYR 0.005 0.001 TYR C 161 ARG 0.004 0.000 ARG D 124 Details of bonding type rmsd link_NAG-ASN : bond 0.00135 ( 15) link_NAG-ASN : angle 1.28466 ( 45) 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_ALPHA1-3 : bond 0.06432 ( 3) link_ALPHA1-3 : angle 32.18866 ( 9) hydrogen bonds : bond 0.16874 ( 427) hydrogen bonds : angle 6.01772 ( 1173) SS BOND : bond 0.02536 ( 18) SS BOND : angle 1.09557 ( 36) covalent geometry : bond 0.00351 (12234) covalent geometry : angle 0.65518 (16590) *********************** 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 : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 274 average time/residue: 1.0037 time to fit residues: 302.4784 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 : 1.177 ------------------------------------------------------------------------------- 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 121 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 68 optimal weight: 0.3980 chunk 84 optimal weight: 0.4980 chunk 130 optimal weight: 0.3980 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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 18 HIS C 54 ASN C 132 GLN C 197 GLN C 211 GLN C 295 GLN E 54 ASN E 132 GLN D 142 HIS D 146 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.149729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.129456 restraints weight = 13466.848| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.85 r_work: 0.3255 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.6986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 12285 Z= 0.288 Angle : 1.058 18.088 16725 Z= 0.509 Chirality : 0.064 0.746 1920 Planarity : 0.007 0.062 2127 Dihedral : 9.544 70.280 2262 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 6.32 % Allowed : 18.19 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.19), residues: 1458 helix: -0.22 (0.25), residues: 360 sheet: -0.05 (0.33), residues: 258 loop : -2.13 (0.17), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP E 153 HIS 0.011 0.002 HIS C 75 PHE 0.029 0.004 PHE F 138 TYR 0.041 0.003 TYR B 162 ARG 0.014 0.001 ARG F 153 Details of bonding type rmsd link_NAG-ASN : bond 0.01035 ( 15) link_NAG-ASN : angle 4.32218 ( 45) link_ALPHA1-6 : bond 0.00982 ( 3) link_ALPHA1-6 : angle 3.91075 ( 9) link_BETA1-4 : bond 0.01247 ( 12) link_BETA1-4 : angle 3.55968 ( 36) link_ALPHA1-3 : bond 0.05869 ( 3) link_ALPHA1-3 : angle 3.65461 ( 9) hydrogen bonds : bond 0.06958 ( 427) hydrogen bonds : angle 5.49428 ( 1173) SS BOND : bond 0.00591 ( 18) SS BOND : angle 1.92249 ( 36) covalent geometry : bond 0.00626 (12234) covalent geometry : angle 1.01311 (16590) *********************** 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 321 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 240 time to evaluate : 1.260 Fit side-chains revert: symmetry clash REVERT: A 241 ASP cc_start: 0.8145 (OUTLIER) cc_final: 0.7931 (t0) REVERT: A 307 LYS cc_start: 0.8547 (mtmm) cc_final: 0.8136 (mtpt) REVERT: B 42 GLN cc_start: 0.7271 (tp40) cc_final: 0.7012 (tp40) REVERT: B 65 GLN cc_start: 0.8323 (mt0) cc_final: 0.8056 (mt0) REVERT: B 121 LYS cc_start: 0.8191 (ttmt) cc_final: 0.7879 (ttpt) REVERT: B 123 ARG cc_start: 0.8644 (ttp80) cc_final: 0.8437 (ttp-170) REVERT: C 241 ASP cc_start: 0.7967 (OUTLIER) cc_final: 0.7724 (t0) REVERT: C 260 MET cc_start: 0.7666 (mmm) cc_final: 0.7384 (mtp) REVERT: C 295 GLN cc_start: 0.9329 (OUTLIER) cc_final: 0.8858 (pp30) REVERT: E 62 ILE cc_start: 0.6817 (OUTLIER) cc_final: 0.6471 (pt) REVERT: E 104 ASP cc_start: 0.7676 (OUTLIER) cc_final: 0.7467 (OUTLIER) REVERT: E 168 MET cc_start: 0.8158 (OUTLIER) cc_final: 0.7788 (tpt) REVERT: E 207 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7116 (mtt180) REVERT: E 216 ASN cc_start: 0.7367 (m-40) cc_final: 0.7003 (OUTLIER) REVERT: E 241 ASP cc_start: 0.8160 (OUTLIER) cc_final: 0.7813 (t0) REVERT: E 280 GLU cc_start: 0.7221 (mm-30) cc_final: 0.6946 (mm-30) REVERT: E 292 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8480 (mttm) REVERT: D 62 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.6985 (mtpp) REVERT: D 65 GLN cc_start: 0.8611 (mt0) cc_final: 0.8367 (mt0) REVERT: D 111 THR cc_start: 0.7835 (p) cc_final: 0.7574 (p) REVERT: F 17 MET cc_start: 0.8405 (tpp) cc_final: 0.8147 (ttm) REVERT: F 45 ILE cc_start: 0.8186 (tt) cc_final: 0.7640 (pp) REVERT: F 59 THR cc_start: 0.3875 (OUTLIER) cc_final: 0.3489 (p) REVERT: F 139 LYS cc_start: 0.8346 (tttp) cc_final: 0.8011 (tptm) outliers start: 81 outliers final: 18 residues processed: 303 average time/residue: 1.2795 time to fit residues: 420.3175 Evaluate side-chains 185 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 158 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain C residue 110 SER 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 295 GLN Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 168 MET Chi-restraints excluded: chain E residue 201 ARG Chi-restraints excluded: chain E residue 207 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 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 115 optimal weight: 0.8980 chunk 139 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 132 optimal weight: 0.2980 chunk 99 optimal weight: 0.8980 chunk 140 optimal weight: 0.0570 chunk 16 optimal weight: 0.2980 chunk 15 optimal weight: 0.3980 chunk 96 optimal weight: 0.3980 chunk 34 optimal weight: 1.9990 chunk 133 optimal weight: 0.8980 overall best weight: 0.2898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN B 28 ASN B 34 GLN ** B 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 HIS C 44 GLN C 248 ASN C 295 GLN C 312 ASN E 18 HIS E 33 GLN E 191 GLN E 246 ASN D 47 GLN D 78 GLN D 105 GLN D 125 GLN D 146 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.140190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.118662 restraints weight = 13533.239| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.83 r_work: 0.3134 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.7584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 12285 Z= 0.122 Angle : 0.571 10.223 16725 Z= 0.288 Chirality : 0.044 0.219 1920 Planarity : 0.004 0.054 2127 Dihedral : 8.553 73.739 2262 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.67 % Allowed : 23.81 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.21), residues: 1458 helix: 1.18 (0.28), residues: 360 sheet: -0.12 (0.30), residues: 288 loop : -1.74 (0.19), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.007 0.001 HIS C 18 PHE 0.013 0.002 PHE B 24 TYR 0.011 0.001 TYR D 162 ARG 0.008 0.000 ARG C 141 Details of bonding type rmsd link_NAG-ASN : bond 0.00721 ( 15) link_NAG-ASN : angle 2.56295 ( 45) link_ALPHA1-6 : bond 0.00276 ( 3) link_ALPHA1-6 : angle 1.75626 ( 9) link_BETA1-4 : bond 0.00792 ( 12) link_BETA1-4 : angle 2.13982 ( 36) link_ALPHA1-3 : bond 0.01253 ( 3) link_ALPHA1-3 : angle 1.55240 ( 9) hydrogen bonds : bond 0.05345 ( 427) hydrogen bonds : angle 4.58104 ( 1173) SS BOND : bond 0.00429 ( 18) SS BOND : angle 1.82393 ( 36) covalent geometry : bond 0.00264 (12234) covalent geometry : angle 0.53888 (16590) *********************** 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 214 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 167 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 243 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8559 (tp) REVERT: A 251 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8217 (tp) REVERT: A 275 ASP cc_start: 0.6837 (m-30) cc_final: 0.6456 (t0) REVERT: B 46 ASP cc_start: 0.7237 (m-30) cc_final: 0.6973 (m-30) REVERT: B 65 GLN cc_start: 0.8325 (mt0) cc_final: 0.8074 (mt0) REVERT: B 115 MET cc_start: 0.8705 (OUTLIER) cc_final: 0.8067 (tpt) REVERT: B 121 LYS cc_start: 0.8225 (ttmt) cc_final: 0.7964 (ttpt) REVERT: C 118 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.7960 (mp) REVERT: C 210 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.8688 (tt0) REVERT: C 260 MET cc_start: 0.7884 (mmm) cc_final: 0.7645 (mtp) REVERT: E 168 MET cc_start: 0.8293 (mmt) cc_final: 0.7975 (mmt) REVERT: E 207 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7794 (mtt-85) REVERT: D 65 GLN cc_start: 0.8653 (mt0) cc_final: 0.8430 (mt0) REVERT: F 17 MET cc_start: 0.8549 (tpp) cc_final: 0.8293 (ttm) REVERT: F 18 ILE cc_start: 0.7634 (tp) cc_final: 0.7414 (pt) outliers start: 47 outliers final: 11 residues processed: 204 average time/residue: 1.3339 time to fit residues: 298.6241 Evaluate side-chains 164 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 147 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain B residue 115 MET 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 243 LEU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 207 ARG Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain F residue 46 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 99 optimal weight: 0.2980 chunk 128 optimal weight: 0.3980 chunk 112 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 1 optimal weight: 0.0470 chunk 98 optimal weight: 0.5980 chunk 135 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 overall best weight: 0.4078 ------------------------------------------------------------------------------- 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 78 GLN D 105 GLN D 142 HIS F 28 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.134908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.113595 restraints weight = 13667.951| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.86 r_work: 0.3100 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.8231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12285 Z= 0.136 Angle : 0.594 13.790 16725 Z= 0.297 Chirality : 0.045 0.252 1920 Planarity : 0.004 0.040 2127 Dihedral : 7.764 67.890 2259 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 4.61 % Allowed : 22.72 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.21), residues: 1458 helix: 1.55 (0.28), residues: 360 sheet: -0.21 (0.29), residues: 306 loop : -1.62 (0.19), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 234 HIS 0.019 0.002 HIS C 18 PHE 0.016 0.002 PHE B 138 TYR 0.012 0.001 TYR A 308 ARG 0.006 0.000 ARG C 141 Details of bonding type rmsd link_NAG-ASN : bond 0.00736 ( 15) link_NAG-ASN : angle 3.34623 ( 45) link_ALPHA1-6 : bond 0.00588 ( 3) link_ALPHA1-6 : angle 1.78750 ( 9) link_BETA1-4 : bond 0.00652 ( 12) link_BETA1-4 : angle 2.15713 ( 36) link_ALPHA1-3 : bond 0.01370 ( 3) link_ALPHA1-3 : angle 1.06602 ( 9) hydrogen bonds : bond 0.05342 ( 427) hydrogen bonds : angle 4.39748 ( 1173) SS BOND : bond 0.00640 ( 18) SS BOND : angle 2.00290 ( 36) covalent geometry : bond 0.00305 (12234) covalent geometry : angle 0.55110 (16590) *********************** 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 213 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 154 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ARG cc_start: 0.7777 (ttm-80) cc_final: 0.7518 (mtp85) REVERT: A 243 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8583 (tp) REVERT: A 251 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8408 (tp) REVERT: B 46 ASP cc_start: 0.7381 (m-30) cc_final: 0.7123 (m-30) REVERT: B 65 GLN cc_start: 0.8514 (mt0) cc_final: 0.8297 (mt0) REVERT: B 67 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.6907 (mp0) REVERT: B 115 MET cc_start: 0.8931 (OUTLIER) cc_final: 0.8202 (tpt) REVERT: B 121 LYS cc_start: 0.8221 (ttmt) cc_final: 0.8004 (ttpt) REVERT: C 260 MET cc_start: 0.8149 (mmm) cc_final: 0.7912 (mtp) REVERT: E 104 ASP cc_start: 0.7889 (OUTLIER) cc_final: 0.7659 (m-30) REVERT: E 168 MET cc_start: 0.8355 (mmt) cc_final: 0.8060 (mmt) REVERT: E 207 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7625 (tpp-160) REVERT: E 223 VAL cc_start: 0.8376 (OUTLIER) cc_final: 0.8160 (m) REVERT: E 241 ASP cc_start: 0.8569 (OUTLIER) cc_final: 0.8275 (t0) REVERT: D 65 GLN cc_start: 0.8768 (mt0) cc_final: 0.8566 (mt0) REVERT: F 17 MET cc_start: 0.8584 (tpp) cc_final: 0.8301 (ttm) REVERT: F 151 SER cc_start: 0.6780 (t) cc_final: 0.5963 (p) outliers start: 59 outliers final: 26 residues processed: 202 average time/residue: 1.0628 time to fit residues: 236.8646 Evaluate side-chains 173 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 139 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 104 ASP 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 207 ARG Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain F residue 30 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 107 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 135 optimal weight: 0.9990 chunk 3 optimal weight: 0.0980 chunk 17 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 197 GLN E 295 GLN D 47 GLN D 105 GLN D 146 ASN F 28 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.127980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.106616 restraints weight = 13618.391| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 1.82 r_work: 0.2983 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 1.0018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12285 Z= 0.174 Angle : 0.683 14.995 16725 Z= 0.343 Chirality : 0.048 0.271 1920 Planarity : 0.005 0.077 2127 Dihedral : 7.747 65.867 2259 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 5.31 % Allowed : 22.01 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.20), residues: 1458 helix: 1.63 (0.28), residues: 357 sheet: 0.23 (0.33), residues: 234 loop : -1.63 (0.18), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 234 HIS 0.011 0.002 HIS C 18 PHE 0.019 0.002 PHE C 125 TYR 0.020 0.002 TYR A 308 ARG 0.011 0.001 ARG E 224 Details of bonding type rmsd link_NAG-ASN : bond 0.00654 ( 15) link_NAG-ASN : angle 3.64167 ( 45) link_ALPHA1-6 : bond 0.00386 ( 3) link_ALPHA1-6 : angle 1.73478 ( 9) link_BETA1-4 : bond 0.00638 ( 12) link_BETA1-4 : angle 2.12425 ( 36) link_ALPHA1-3 : bond 0.01193 ( 3) link_ALPHA1-3 : angle 1.10566 ( 9) hydrogen bonds : bond 0.06582 ( 427) hydrogen bonds : angle 4.50155 ( 1173) SS BOND : bond 0.00656 ( 18) SS BOND : angle 2.12388 ( 36) covalent geometry : bond 0.00411 (12234) covalent geometry : angle 0.64272 (16590) *********************** 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 249 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 181 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8704 (tp) REVERT: B 34 GLN cc_start: 0.8644 (tt0) cc_final: 0.8383 (tt0) REVERT: B 47 GLN cc_start: 0.7772 (OUTLIER) cc_final: 0.7493 (mt0) REVERT: B 67 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.7215 (mp0) REVERT: B 121 LYS cc_start: 0.8304 (ttmt) cc_final: 0.8020 (tttt) REVERT: B 125 GLN cc_start: 0.7900 (tt0) cc_final: 0.7582 (mt0) REVERT: C 118 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8362 (mp) REVERT: C 145 SER cc_start: 0.8044 (OUTLIER) cc_final: 0.7736 (p) REVERT: C 291 ASP cc_start: 0.8076 (OUTLIER) cc_final: 0.7744 (p0) REVERT: E 52 CYS cc_start: 0.7877 (m) cc_final: 0.7548 (m) REVERT: E 62 ILE cc_start: 0.8490 (OUTLIER) cc_final: 0.8200 (mp) REVERT: E 168 MET cc_start: 0.8553 (mmt) cc_final: 0.8216 (tpt) REVERT: E 280 GLU cc_start: 0.8494 (mm-30) cc_final: 0.7878 (mm-30) REVERT: D 17 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.8387 (ttp) REVERT: D 128 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7466 (tp30) REVERT: F 151 SER cc_start: 0.8268 (t) cc_final: 0.7493 (p) outliers start: 68 outliers final: 28 residues processed: 233 average time/residue: 1.1300 time to fit residues: 288.2272 Evaluate side-chains 180 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 143 time to evaluate : 1.237 ------------------------------------------------------------------------------- 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 219 SER Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 243 LEU 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 47 GLN Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 291 ASP Chi-restraints excluded: chain E residue 28 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 190 GLU Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain D residue 17 MET Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 128 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 95 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 118 optimal weight: 0.3980 chunk 28 optimal weight: 0.3980 chunk 47 optimal weight: 1.9990 chunk 86 optimal weight: 0.0270 chunk 91 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 55 optimal weight: 0.3980 chunk 24 optimal weight: 1.9990 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 18 HIS C 33 GLN C 312 ASN E 18 HIS E 33 GLN E 312 ASN D 47 GLN D 146 ASN F 28 ASN F 105 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.128424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.106834 restraints weight = 13750.528| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 1.84 r_work: 0.2999 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 1.0143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12285 Z= 0.126 Angle : 0.571 10.474 16725 Z= 0.289 Chirality : 0.044 0.226 1920 Planarity : 0.004 0.038 2127 Dihedral : 7.199 61.210 2259 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 4.22 % Allowed : 24.12 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.21), residues: 1458 helix: 1.99 (0.28), residues: 354 sheet: 0.26 (0.31), residues: 264 loop : -1.61 (0.18), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 234 HIS 0.004 0.001 HIS C 18 PHE 0.013 0.001 PHE F 24 TYR 0.010 0.001 TYR B 162 ARG 0.011 0.000 ARG C 141 Details of bonding type rmsd link_NAG-ASN : bond 0.00331 ( 15) link_NAG-ASN : angle 3.01103 ( 45) link_ALPHA1-6 : bond 0.00591 ( 3) link_ALPHA1-6 : angle 1.56126 ( 9) link_BETA1-4 : bond 0.00577 ( 12) link_BETA1-4 : angle 1.88215 ( 36) link_ALPHA1-3 : bond 0.01327 ( 3) link_ALPHA1-3 : angle 0.99025 ( 9) hydrogen bonds : bond 0.05586 ( 427) hydrogen bonds : angle 4.35416 ( 1173) SS BOND : bond 0.00540 ( 18) SS BOND : angle 1.83133 ( 36) covalent geometry : bond 0.00287 (12234) covalent geometry : angle 0.53577 (16590) *********************** 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 204 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 150 time to evaluate : 1.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8448 (mp) REVERT: B 34 GLN cc_start: 0.8670 (tt0) cc_final: 0.8423 (tt0) REVERT: B 46 ASP cc_start: 0.7681 (m-30) cc_final: 0.7426 (m-30) REVERT: B 47 GLN cc_start: 0.7821 (tt0) cc_final: 0.7583 (mt0) REVERT: B 67 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.7248 (mp0) REVERT: C 145 SER cc_start: 0.8095 (OUTLIER) cc_final: 0.7800 (p) REVERT: C 210 GLN cc_start: 0.9030 (OUTLIER) cc_final: 0.8542 (tt0) REVERT: C 275 ASP cc_start: 0.7778 (m-30) cc_final: 0.7565 (m-30) REVERT: C 291 ASP cc_start: 0.8024 (m-30) cc_final: 0.7685 (p0) REVERT: E 62 ILE cc_start: 0.8473 (OUTLIER) cc_final: 0.8205 (mp) REVERT: E 168 MET cc_start: 0.8516 (mmt) cc_final: 0.8204 (tpt) REVERT: E 195 TYR cc_start: 0.8295 (OUTLIER) cc_final: 0.6055 (m-80) REVERT: E 261 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.7633 (mmm-85) REVERT: E 276 THR cc_start: 0.8358 (OUTLIER) cc_final: 0.8025 (p) REVERT: E 280 GLU cc_start: 0.8415 (mm-30) cc_final: 0.7818 (mm-30) REVERT: D 17 MET cc_start: 0.8567 (tpp) cc_final: 0.8244 (ttp) REVERT: D 74 GLU cc_start: 0.7250 (mm-30) cc_final: 0.6566 (tt0) REVERT: F 47 GLN cc_start: 0.7701 (mt0) cc_final: 0.7427 (mt0) REVERT: F 151 SER cc_start: 0.8256 (t) cc_final: 0.7468 (p) outliers start: 54 outliers final: 28 residues processed: 193 average time/residue: 1.1423 time to fit residues: 242.3852 Evaluate side-chains 179 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 143 time to evaluate : 1.524 ------------------------------------------------------------------------------- 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 121 ILE Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 312 ASN 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 161 VAL Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain E residue 110 SER 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 261 ARG Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain F residue 143 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 36 optimal weight: 0.9990 chunk 136 optimal weight: 0.8980 chunk 118 optimal weight: 0.1980 chunk 12 optimal weight: 0.2980 chunk 7 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 142 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 GLN E 246 ASN E 312 ASN D 47 GLN F 28 ASN F 105 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.126297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.104799 restraints weight = 13860.349| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.83 r_work: 0.2961 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 1.0291 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 : 0.620 10.885 16725 Z= 0.312 Chirality : 0.046 0.244 1920 Planarity : 0.004 0.039 2127 Dihedral : 7.223 61.349 2259 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 4.76 % Allowed : 23.50 % Favored : 71.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.21), residues: 1458 helix: 2.07 (0.28), residues: 354 sheet: 0.30 (0.31), residues: 264 loop : -1.59 (0.18), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 234 HIS 0.021 0.002 HIS C 18 PHE 0.016 0.002 PHE F 24 TYR 0.015 0.002 TYR A 308 ARG 0.009 0.000 ARG C 141 Details of bonding type rmsd link_NAG-ASN : bond 0.00395 ( 15) link_NAG-ASN : angle 2.97756 ( 45) link_ALPHA1-6 : bond 0.00464 ( 3) link_ALPHA1-6 : angle 1.68348 ( 9) link_BETA1-4 : bond 0.00559 ( 12) link_BETA1-4 : angle 1.92266 ( 36) link_ALPHA1-3 : bond 0.01261 ( 3) link_ALPHA1-3 : angle 1.05971 ( 9) hydrogen bonds : bond 0.06035 ( 427) hydrogen bonds : angle 4.33329 ( 1173) SS BOND : bond 0.00636 ( 18) SS BOND : angle 2.08200 ( 36) covalent geometry : bond 0.00399 (12234) covalent geometry : angle 0.58652 (16590) *********************** 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 203 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 142 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.8442 (mp) REVERT: B 34 GLN cc_start: 0.8718 (tt0) cc_final: 0.8462 (tt0) REVERT: B 47 GLN cc_start: 0.7881 (OUTLIER) cc_final: 0.7620 (mt0) REVERT: B 67 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.7268 (mp0) REVERT: B 121 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.8160 (tttt) REVERT: B 125 GLN cc_start: 0.7938 (tt0) cc_final: 0.7656 (mt0) REVERT: C 118 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8356 (mp) REVERT: C 119 GLU cc_start: 0.8925 (tt0) cc_final: 0.8712 (tt0) REVERT: C 145 SER cc_start: 0.8221 (OUTLIER) cc_final: 0.7927 (p) REVERT: C 201 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7924 (ptt90) REVERT: C 210 GLN cc_start: 0.9045 (OUTLIER) cc_final: 0.8547 (tt0) REVERT: C 214 ILE cc_start: 0.8758 (tt) cc_final: 0.8470 (mt) REVERT: C 291 ASP cc_start: 0.8031 (m-30) cc_final: 0.7681 (p0) REVERT: C 325 GLU cc_start: 0.6429 (mp0) cc_final: 0.6167 (mp0) REVERT: E 62 ILE cc_start: 0.8529 (OUTLIER) cc_final: 0.8266 (mp) REVERT: E 168 MET cc_start: 0.8584 (mmt) cc_final: 0.8291 (tpt) REVERT: E 195 TYR cc_start: 0.8335 (OUTLIER) cc_final: 0.6256 (m-80) REVERT: E 261 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.7693 (mmm-85) REVERT: E 276 THR cc_start: 0.8326 (OUTLIER) cc_final: 0.7949 (p) REVERT: E 280 GLU cc_start: 0.8470 (mm-30) cc_final: 0.7855 (mm-30) REVERT: D 17 MET cc_start: 0.8661 (tpp) cc_final: 0.8371 (ttp) REVERT: D 72 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7546 (mt-10) REVERT: D 74 GLU cc_start: 0.7322 (mm-30) cc_final: 0.6661 (tt0) REVERT: F 47 GLN cc_start: 0.7768 (mt0) cc_final: 0.7551 (mt0) REVERT: F 151 SER cc_start: 0.8368 (t) cc_final: 0.7604 (p) outliers start: 61 outliers final: 31 residues processed: 189 average time/residue: 1.1062 time to fit residues: 229.6691 Evaluate side-chains 179 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 136 time to evaluate : 1.257 ------------------------------------------------------------------------------- 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 121 ILE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 47 GLN 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 161 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 201 ARG Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain E residue 28 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 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 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 F residue 18 ILE Chi-restraints excluded: chain F residue 143 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 52 optimal weight: 1.9990 chunk 20 optimal weight: 0.0870 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 11 optimal weight: 0.0010 chunk 70 optimal weight: 0.5980 chunk 96 optimal weight: 0.9980 chunk 140 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 overall best weight: 0.4164 ------------------------------------------------------------------------------- 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 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 = 0.3351 r_free = 0.3351 target = 0.128110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.106634 restraints weight = 13861.858| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.84 r_work: 0.2981 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 1.0427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12285 Z= 0.123 Angle : 0.556 9.510 16725 Z= 0.282 Chirality : 0.044 0.219 1920 Planarity : 0.004 0.036 2127 Dihedral : 6.850 57.674 2259 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 4.22 % Allowed : 24.20 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.21), residues: 1458 helix: 2.29 (0.28), residues: 354 sheet: 0.34 (0.31), residues: 264 loop : -1.50 (0.18), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 234 HIS 0.004 0.001 HIS B 106 PHE 0.012 0.001 PHE F 24 TYR 0.010 0.001 TYR B 162 ARG 0.008 0.000 ARG C 141 Details of bonding type rmsd link_NAG-ASN : bond 0.00341 ( 15) link_NAG-ASN : angle 2.63392 ( 45) link_ALPHA1-6 : bond 0.00659 ( 3) link_ALPHA1-6 : angle 1.53400 ( 9) link_BETA1-4 : bond 0.00578 ( 12) link_BETA1-4 : angle 1.73692 ( 36) link_ALPHA1-3 : bond 0.01315 ( 3) link_ALPHA1-3 : angle 1.03379 ( 9) hydrogen bonds : bond 0.05359 ( 427) hydrogen bonds : angle 4.26268 ( 1173) SS BOND : bond 0.00520 ( 18) SS BOND : angle 1.89152 ( 36) covalent geometry : bond 0.00280 (12234) covalent geometry : angle 0.52614 (16590) *********************** 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 198 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 144 time to evaluate : 1.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 34 GLN cc_start: 0.8717 (tt0) cc_final: 0.8462 (tt0) REVERT: B 47 GLN cc_start: 0.7772 (OUTLIER) cc_final: 0.7527 (mt0) REVERT: B 67 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.7238 (mp0) REVERT: B 121 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.8079 (tttt) REVERT: C 145 SER cc_start: 0.8259 (OUTLIER) cc_final: 0.8004 (p) REVERT: C 214 ILE cc_start: 0.8738 (tt) cc_final: 0.8493 (mt) REVERT: C 245 ILE cc_start: 0.8673 (OUTLIER) cc_final: 0.8005 (mt) REVERT: C 291 ASP cc_start: 0.7919 (m-30) cc_final: 0.7626 (p0) REVERT: E 51 ILE cc_start: 0.8243 (OUTLIER) cc_final: 0.7753 (mt) REVERT: E 62 ILE cc_start: 0.8490 (OUTLIER) cc_final: 0.8232 (mp) REVERT: E 168 MET cc_start: 0.8545 (mmt) cc_final: 0.8310 (tpt) REVERT: E 276 THR cc_start: 0.8237 (OUTLIER) cc_final: 0.8010 (p) REVERT: E 280 GLU cc_start: 0.8482 (mm-30) cc_final: 0.7857 (mm-30) REVERT: D 17 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.8289 (ttp) REVERT: D 72 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7532 (mt-10) REVERT: D 74 GLU cc_start: 0.7217 (mm-30) cc_final: 0.6622 (tt0) REVERT: F 47 GLN cc_start: 0.7704 (mt0) cc_final: 0.7420 (mt0) REVERT: F 151 SER cc_start: 0.8390 (t) cc_final: 0.7630 (p) outliers start: 54 outliers final: 26 residues processed: 184 average time/residue: 1.1708 time to fit residues: 235.3986 Evaluate side-chains 175 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 140 time to evaluate : 1.237 ------------------------------------------------------------------------------- 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 224 ARG Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 47 GLN 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 161 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain E residue 28 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 190 GLU Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain D residue 17 MET Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 110 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 140 optimal weight: 0.6980 chunk 99 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 125 optimal weight: 0.9980 chunk 138 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 GLN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.124035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.102368 restraints weight = 13804.894| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.84 r_work: 0.2932 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 1.0603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 12285 Z= 0.198 Angle : 0.668 11.257 16725 Z= 0.335 Chirality : 0.048 0.246 1920 Planarity : 0.005 0.040 2127 Dihedral : 7.210 59.091 2259 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 4.37 % Allowed : 23.65 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.21), residues: 1458 helix: 2.09 (0.28), residues: 354 sheet: 0.25 (0.32), residues: 264 loop : -1.55 (0.18), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 234 HIS 0.007 0.001 HIS A 75 PHE 0.019 0.002 PHE C 125 TYR 0.017 0.002 TYR A 308 ARG 0.007 0.001 ARG C 141 Details of bonding type rmsd link_NAG-ASN : bond 0.00369 ( 15) link_NAG-ASN : angle 3.28797 ( 45) link_ALPHA1-6 : bond 0.00439 ( 3) link_ALPHA1-6 : angle 1.66031 ( 9) link_BETA1-4 : bond 0.00600 ( 12) link_BETA1-4 : angle 1.95919 ( 36) link_ALPHA1-3 : bond 0.01135 ( 3) link_ALPHA1-3 : angle 1.16655 ( 9) hydrogen bonds : bond 0.06570 ( 427) hydrogen bonds : angle 4.39928 ( 1173) SS BOND : bond 0.00685 ( 18) SS BOND : angle 2.14834 ( 36) covalent geometry : bond 0.00486 (12234) covalent geometry : angle 0.63206 (16590) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 152 time to evaluate : 1.294 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: B 34 GLN cc_start: 0.8790 (tt0) cc_final: 0.8528 (tt0) REVERT: B 47 GLN cc_start: 0.7866 (OUTLIER) cc_final: 0.7612 (mt0) REVERT: B 67 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.7338 (mp0) REVERT: B 121 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8154 (tttt) REVERT: B 125 GLN cc_start: 0.8069 (tt0) cc_final: 0.7771 (mt0) REVERT: C 145 SER cc_start: 0.8394 (OUTLIER) cc_final: 0.8142 (p) REVERT: C 214 ILE cc_start: 0.8798 (tt) cc_final: 0.8508 (mt) REVERT: C 245 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8201 (mt) REVERT: C 291 ASP cc_start: 0.7976 (m-30) cc_final: 0.7619 (p0) REVERT: E 51 ILE cc_start: 0.8256 (OUTLIER) cc_final: 0.7833 (mt) REVERT: E 62 ILE cc_start: 0.8537 (OUTLIER) cc_final: 0.8310 (mt) REVERT: E 168 MET cc_start: 0.8670 (mmt) cc_final: 0.8432 (tpt) REVERT: E 208 ARG cc_start: 0.8165 (ptt90) cc_final: 0.7951 (ptt-90) REVERT: E 223 VAL cc_start: 0.8835 (OUTLIER) cc_final: 0.8498 (t) REVERT: E 276 THR cc_start: 0.8467 (OUTLIER) cc_final: 0.8122 (p) REVERT: E 280 GLU cc_start: 0.8499 (mm-30) cc_final: 0.7885 (mm-30) REVERT: E 312 ASN cc_start: 0.8157 (t0) cc_final: 0.7684 (p0) REVERT: D 74 GLU cc_start: 0.7425 (mm-30) cc_final: 0.6791 (tt0) REVERT: F 47 GLN cc_start: 0.7795 (mt0) cc_final: 0.7563 (mt0) REVERT: F 114 GLU cc_start: 0.7956 (tp30) cc_final: 0.7640 (tp30) REVERT: F 151 SER cc_start: 0.8518 (t) cc_final: 0.7873 (p) outliers start: 56 outliers final: 28 residues processed: 192 average time/residue: 1.3471 time to fit residues: 281.8257 Evaluate side-chains 183 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 146 time to evaluate : 1.316 ------------------------------------------------------------------------------- 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 224 ARG Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain B residue 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 161 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain E residue 28 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 190 GLU Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain F residue 18 ILE Chi-restraints excluded: chain F residue 143 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 9 optimal weight: 0.9980 chunk 63 optimal weight: 0.4980 chunk 88 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 43 optimal weight: 0.1980 chunk 140 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN 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 = 0.3324 r_free = 0.3324 target = 0.126074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.104729 restraints weight = 13624.952| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 1.81 r_work: 0.2961 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 1.0669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12285 Z= 0.144 Angle : 0.588 10.134 16725 Z= 0.298 Chirality : 0.045 0.231 1920 Planarity : 0.004 0.037 2127 Dihedral : 6.911 55.815 2259 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.36 % Allowed : 24.43 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.21), residues: 1458 helix: 2.14 (0.28), residues: 357 sheet: 0.29 (0.32), residues: 264 loop : -1.49 (0.18), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 234 HIS 0.005 0.001 HIS B 106 PHE 0.014 0.002 PHE F 24 TYR 0.011 0.001 TYR B 162 ARG 0.007 0.000 ARG C 141 Details of bonding type rmsd link_NAG-ASN : bond 0.00287 ( 15) link_NAG-ASN : angle 2.84510 ( 45) link_ALPHA1-6 : bond 0.00661 ( 3) link_ALPHA1-6 : angle 1.48875 ( 9) link_BETA1-4 : bond 0.00525 ( 12) link_BETA1-4 : angle 1.74842 ( 36) link_ALPHA1-3 : bond 0.01250 ( 3) link_ALPHA1-3 : angle 1.02714 ( 9) hydrogen bonds : bond 0.05740 ( 427) hydrogen bonds : angle 4.31701 ( 1173) SS BOND : bond 0.00584 ( 18) SS BOND : angle 2.03178 ( 36) covalent geometry : bond 0.00342 (12234) covalent geometry : angle 0.55599 (16590) ********************** 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 182 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 139 time to evaluate : 1.471 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 325 GLU cc_start: 0.6640 (OUTLIER) cc_final: 0.5881 (mp0) REVERT: B 34 GLN cc_start: 0.8762 (tt0) cc_final: 0.8500 (tt0) REVERT: B 47 GLN cc_start: 0.7839 (OUTLIER) cc_final: 0.7605 (mt0) REVERT: B 67 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.7232 (mp0) REVERT: B 121 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8156 (tttt) REVERT: B 125 GLN cc_start: 0.8016 (tt0) cc_final: 0.7739 (mt0) REVERT: C 118 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8349 (mp) REVERT: C 145 SER cc_start: 0.8366 (OUTLIER) cc_final: 0.8127 (p) REVERT: C 214 ILE cc_start: 0.8773 (tt) cc_final: 0.8564 (mt) REVERT: C 245 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8184 (mt) REVERT: C 291 ASP cc_start: 0.7991 (m-30) cc_final: 0.7633 (p0) REVERT: E 51 ILE cc_start: 0.8211 (OUTLIER) cc_final: 0.7886 (mt) REVERT: E 62 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.8318 (mp) REVERT: E 168 MET cc_start: 0.8627 (mmt) cc_final: 0.8418 (tpt) REVERT: E 276 THR cc_start: 0.8198 (OUTLIER) cc_final: 0.7998 (p) REVERT: E 280 GLU cc_start: 0.8482 (mm-30) cc_final: 0.7856 (mm-30) REVERT: D 74 GLU cc_start: 0.7299 (mm-30) cc_final: 0.6778 (tt0) REVERT: F 47 GLN cc_start: 0.7822 (mt0) cc_final: 0.7558 (mt0) REVERT: F 151 SER cc_start: 0.8525 (t) cc_final: 0.7876 (p) outliers start: 43 outliers final: 27 residues processed: 172 average time/residue: 1.1764 time to fit residues: 221.5928 Evaluate side-chains 174 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 137 time to evaluate : 1.195 ------------------------------------------------------------------------------- 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 224 ARG Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 47 GLN 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 161 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain E residue 28 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 190 GLU Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 18 optimal weight: 0.9990 chunk 57 optimal weight: 0.0060 chunk 75 optimal weight: 0.0070 chunk 59 optimal weight: 0.7980 chunk 137 optimal weight: 0.3980 chunk 91 optimal weight: 0.3980 chunk 72 optimal weight: 0.0980 chunk 9 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 overall best weight: 0.1814 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN C 312 ASN E 18 HIS E 33 GLN E 312 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 = 0.3364 r_free = 0.3364 target = 0.129272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.107806 restraints weight = 13711.660| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.84 r_work: 0.2940 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 1.0705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12285 Z= 0.099 Angle : 0.513 8.520 16725 Z= 0.261 Chirality : 0.042 0.196 1920 Planarity : 0.004 0.034 2127 Dihedral : 6.327 51.562 2259 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.89 % Allowed : 25.06 % Favored : 72.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.21), residues: 1458 helix: 2.50 (0.28), residues: 357 sheet: 0.12 (0.32), residues: 276 loop : -1.30 (0.19), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 92 HIS 0.004 0.001 HIS F 142 PHE 0.010 0.001 PHE F 24 TYR 0.010 0.001 TYR B 162 ARG 0.006 0.000 ARG C 141 Details of bonding type rmsd link_NAG-ASN : bond 0.00251 ( 15) link_NAG-ASN : angle 2.38737 ( 45) link_ALPHA1-6 : bond 0.00849 ( 3) link_ALPHA1-6 : angle 1.43286 ( 9) link_BETA1-4 : bond 0.00513 ( 12) link_BETA1-4 : angle 1.52624 ( 36) link_ALPHA1-3 : bond 0.01304 ( 3) link_ALPHA1-3 : angle 1.03246 ( 9) hydrogen bonds : bond 0.04703 ( 427) hydrogen bonds : angle 4.13551 ( 1173) SS BOND : bond 0.00471 ( 18) SS BOND : angle 1.69005 ( 36) covalent geometry : bond 0.00211 (12234) covalent geometry : angle 0.48692 (16590) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8427.15 seconds wall clock time: 149 minutes 12.14 seconds (8952.14 seconds total)