Starting phenix.real_space_refine on Sun May 11 23:16:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bbc_44417/05_2025/9bbc_44417.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bbc_44417/05_2025/9bbc_44417.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bbc_44417/05_2025/9bbc_44417.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bbc_44417/05_2025/9bbc_44417.map" model { file = "/net/cci-nas-00/data/ceres_data/9bbc_44417/05_2025/9bbc_44417.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bbc_44417/05_2025/9bbc_44417.cif" } resolution = 3.3 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= -0.001 sd= 0.034 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 50 5.16 5 C 5385 2.51 5 N 1347 2.21 5 O 1658 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8440 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1932 Classifications: {'peptide': 253} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 240} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 2206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2206 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 268} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 810 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 100} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 930 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 113} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ASP:plan': 3} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 936 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 113} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 888 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 111} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Chain: "X" Number of atoms: 219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 219 Classifications: {'peptide': 30} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 1, 'TRANS': 28} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "Y" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 220 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 26} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 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: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 84 Unusual residues: {'CLR': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.73, per 1000 atoms: 0.92 Number of scatterers: 8440 At special positions: 0 Unit cell: (88.56, 101.52, 138.24, 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 50 16.00 O 1658 8.00 N 1347 7.00 C 5385 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 109 " distance=2.03 Simple disulfide: pdb=" SG CYS A 156 " - pdb=" SG CYS A 206 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS B 263 " distance=2.04 Simple disulfide: pdb=" SG CYS B 42 " - pdb=" SG CYS B 110 " distance=2.03 Simple disulfide: pdb=" SG CYS B 163 " - pdb=" SG CYS B 228 " distance=2.03 Simple disulfide: pdb=" SG CYS D 37 " - pdb=" SG CYS D 73 " distance=2.03 Simple disulfide: pdb=" SG CYS D 93 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 49 " - pdb=" SG CYS E 98 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 122 " distance=2.03 Simple disulfide: pdb=" SG CYS F 49 " - pdb=" SG CYS F 98 " distance=2.03 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 122 " distance=2.03 Simple disulfide: pdb=" SG CYS G 46 " - pdb=" SG CYS G 87 " distance=2.04 Simple disulfide: pdb=" SG CYS G 104 " - pdb=" SG CYS G 107 " distance=2.03 Simple disulfide: pdb=" SG CYS X 32 " - pdb=" SG CYS Y 32 " 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 BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A 301 " - " ASN A 82 " " NAG A 302 " - " ASN A 166 " " NAG A 303 " - " ASN A 200 " " NAG A 304 " - " ASN A 211 " " NAG C 1 " - " ASN D 38 " " NAG G 201 " - " ASN G 92 " " NAG H 1 " - " ASN D 74 " " NAG I 1 " - " ASN A 41 " " NAG O 1 " - " ASN B 84 " " NAG R 1 " - " ASN G 52 " Time building additional restraints: 2.74 Conformation dependent library (CDL) restraints added in 1.1 seconds 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1962 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 17 sheets defined 28.1% alpha, 31.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 100 through 104 Processing helix chain 'A' and resid 205 through 210 removed outlier: 3.685A pdb=" N ALA A 209 " --> pdb=" O ALA A 205 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N PHE A 210 " --> pdb=" O CYS A 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 205 through 210' Processing helix chain 'A' and resid 229 through 235 removed outlier: 3.661A pdb=" N VAL A 233 " --> pdb=" O ASP A 229 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS A 235 " --> pdb=" O LYS A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 273 Processing helix chain 'B' and resid 101 through 105 removed outlier: 3.503A pdb=" N THR B 105 " --> pdb=" O PRO B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 138 removed outlier: 3.980A pdb=" N ASN B 137 " --> pdb=" O ASP B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 156 removed outlier: 3.517A pdb=" N ILE B 153 " --> pdb=" O SER B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 220 Processing helix chain 'B' and resid 266 through 305 Processing helix chain 'D' and resid 64 through 66 No H-bonds generated for 'chain 'D' and resid 64 through 66' Processing helix chain 'D' and resid 100 through 126 Processing helix chain 'E' and resid 88 through 93 removed outlier: 3.653A pdb=" N SER E 93 " --> pdb=" O GLU E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 149 removed outlier: 3.957A pdb=" N ILE E 133 " --> pdb=" O SER E 129 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N VAL E 134 " --> pdb=" O VAL E 130 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE E 135 " --> pdb=" O ALA E 131 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU E 147 " --> pdb=" O GLY E 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 93 removed outlier: 3.587A pdb=" N SER F 93 " --> pdb=" O GLU F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 108 Processing helix chain 'F' and resid 126 through 151 removed outlier: 3.636A pdb=" N ALA F 131 " --> pdb=" O VAL F 127 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR F 132 " --> pdb=" O MET F 128 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE F 133 " --> pdb=" O SER F 129 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL F 134 " --> pdb=" O VAL F 130 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE F 135 " --> pdb=" O ALA F 131 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE F 138 " --> pdb=" O VAL F 134 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY F 143 " --> pdb=" O CYS F 139 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU F 144 " --> pdb=" O ILE F 140 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU F 146 " --> pdb=" O GLY F 142 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU F 147 " --> pdb=" O GLY F 143 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL F 148 " --> pdb=" O LEU F 144 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 28 Processing helix chain 'G' and resid 78 through 80 No H-bonds generated for 'chain 'G' and resid 78 through 80' Processing helix chain 'G' and resid 111 through 137 Processing helix chain 'X' and resid 28 through 33 removed outlier: 3.947A pdb=" N CYS X 32 " --> pdb=" O ASP X 28 " (cutoff:3.500A) Processing helix chain 'X' and resid 36 through 47 removed outlier: 4.388A pdb=" N TYR X 42 " --> pdb=" O ILE X 38 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE X 45 " --> pdb=" O ILE X 41 " (cutoff:3.500A) Processing helix chain 'X' and resid 48 through 51 Processing helix chain 'Y' and resid 29 through 55 Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 26 removed outlier: 3.601A pdb=" N ASN A 41 " --> pdb=" O ILE A 26 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 33 removed outlier: 6.441A pdb=" N LEU A 30 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N HIS A 132 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL A 32 " --> pdb=" O HIS A 132 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 141 through 145 removed outlier: 4.407A pdb=" N VAL A 155 " --> pdb=" O LEU A 145 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 141 through 145 removed outlier: 4.407A pdb=" N VAL A 155 " --> pdb=" O LEU A 145 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 23 through 26 Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 33 removed outlier: 3.531A pdb=" N VAL B 107 " --> pdb=" O GLN B 56 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TRP B 53 " --> pdb=" O HIS B 66 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N HIS B 66 " --> pdb=" O TRP B 53 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ARG B 55 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N LEU B 64 " --> pdb=" O ARG B 55 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ASP B 57 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N LEU B 62 " --> pdb=" O ASP B 57 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 33 Processing sheet with id=AA8, first strand: chain 'B' and resid 142 through 146 removed outlier: 5.723A pdb=" N TYR B 206 " --> pdb=" O GLY B 167 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 142 through 146 removed outlier: 5.723A pdb=" N TYR B 206 " --> pdb=" O GLY B 167 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 182 through 183 Processing sheet with id=AB2, first strand: chain 'D' and resid 26 through 27 removed outlier: 5.670A pdb=" N VAL D 33 " --> pdb=" O LEU D 60 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 42 through 46 removed outlier: 4.121A pdb=" N ILE D 70 " --> pdb=" O VAL D 44 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N GLY D 46 " --> pdb=" O ARG D 68 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ARG D 68 " --> pdb=" O GLY D 46 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N THR D 85 " --> pdb=" O TYR E 111 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N TYR E 113 " --> pdb=" O THR D 85 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLN D 87 " --> pdb=" O TYR E 113 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N ARG E 115 " --> pdb=" O GLN D 87 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N HIS D 89 " --> pdb=" O ARG E 115 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N PHE E 110 " --> pdb=" O CYS E 98 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N CYS E 98 " --> pdb=" O PHE E 110 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 96 through 98 removed outlier: 3.961A pdb=" N VAL D 97 " --> pdb=" O MET E 123 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N MET E 123 " --> pdb=" O VAL D 97 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'E' and resid 37 through 41 Processing sheet with id=AB6, first strand: chain 'F' and resid 37 through 41 Processing sheet with id=AB7, first strand: chain 'F' and resid 64 through 66 removed outlier: 3.952A pdb=" N TRP F 59 " --> pdb=" O ILE F 66 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N TYR F 111 " --> pdb=" O GLN G 98 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N TYR G 100 " --> pdb=" O TYR F 111 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N TYR F 113 " --> pdb=" O TYR G 100 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ARG G 102 " --> pdb=" O TYR F 113 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ARG F 115 " --> pdb=" O ARG G 102 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR G 54 " --> pdb=" O LYS G 88 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE G 53 " --> pdb=" O LEU G 65 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY G 63 " --> pdb=" O TRP G 55 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N LYS G 57 " --> pdb=" O MET G 61 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N MET G 61 " --> pdb=" O LYS G 57 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 31 through 34 removed outlier: 5.784A pdb=" N VAL G 42 " --> pdb=" O LEU G 74 " (cutoff:3.500A) 402 hydrogen bonds defined for protein. 1065 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: 2.64 Time building geometry restraints manager: 3.11 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: 2645 1.34 - 1.46: 2087 1.46 - 1.58: 3821 1.58 - 1.71: 0 1.71 - 1.83: 68 Bond restraints: 8621 Sorted by residual: bond pdb=" CA ASP D 31 " pdb=" CB ASP D 31 " ideal model delta sigma weight residual 1.530 1.558 -0.027 1.69e-02 3.50e+03 2.63e+00 bond pdb=" CG1 ILE B 283 " pdb=" CD1 ILE B 283 " ideal model delta sigma weight residual 1.513 1.452 0.061 3.90e-02 6.57e+02 2.43e+00 bond pdb=" CG1 ILE D 108 " pdb=" CD1 ILE D 108 " ideal model delta sigma weight residual 1.513 1.454 0.059 3.90e-02 6.57e+02 2.28e+00 bond pdb=" C TYR F 52 " pdb=" O TYR F 52 " ideal model delta sigma weight residual 1.235 1.228 0.007 4.70e-03 4.53e+04 2.26e+00 bond pdb=" CB CYS G 104 " pdb=" SG CYS G 104 " ideal model delta sigma weight residual 1.808 1.761 0.047 3.30e-02 9.18e+02 2.02e+00 ... (remaining 8616 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 11398 2.41 - 4.82: 251 4.82 - 7.23: 60 7.23 - 9.64: 17 9.64 - 12.05: 8 Bond angle restraints: 11734 Sorted by residual: angle pdb=" C GLU D 30 " pdb=" N ASP D 31 " pdb=" CA ASP D 31 " ideal model delta sigma weight residual 121.54 133.59 -12.05 1.91e+00 2.74e-01 3.98e+01 angle pdb=" CB LYS A 149 " pdb=" CG LYS A 149 " pdb=" CD LYS A 149 " ideal model delta sigma weight residual 111.30 120.54 -9.24 2.30e+00 1.89e-01 1.61e+01 angle pdb=" N PHE Y 50 " pdb=" CA PHE Y 50 " pdb=" CB PHE Y 50 " ideal model delta sigma weight residual 110.40 116.78 -6.38 1.63e+00 3.76e-01 1.53e+01 angle pdb=" C LEU Y 49 " pdb=" N PHE Y 50 " pdb=" CA PHE Y 50 " ideal model delta sigma weight residual 121.14 114.35 6.79 1.75e+00 3.27e-01 1.51e+01 angle pdb=" N ILE D 107 " pdb=" CA ILE D 107 " pdb=" CB ILE D 107 " ideal model delta sigma weight residual 110.57 115.53 -4.96 1.28e+00 6.10e-01 1.50e+01 ... (remaining 11729 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 4807 17.68 - 35.35: 506 35.35 - 53.03: 127 53.03 - 70.71: 23 70.71 - 88.38: 7 Dihedral angle restraints: 5470 sinusoidal: 2415 harmonic: 3055 Sorted by residual: dihedral pdb=" CA CYS G 104 " pdb=" C CYS G 104 " pdb=" N GLN G 105 " pdb=" CA GLN G 105 " ideal model delta harmonic sigma weight residual 180.00 144.55 35.45 0 5.00e+00 4.00e-02 5.03e+01 dihedral pdb=" CA GLN G 91 " pdb=" C GLN G 91 " pdb=" N ASN G 92 " pdb=" CA ASN G 92 " ideal model delta harmonic sigma weight residual 180.00 153.53 26.47 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" CA LYS A 201 " pdb=" C LYS A 201 " pdb=" N SER A 202 " pdb=" CA SER A 202 " ideal model delta harmonic sigma weight residual 180.00 153.59 26.41 0 5.00e+00 4.00e-02 2.79e+01 ... (remaining 5467 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1248 0.084 - 0.169: 135 0.169 - 0.253: 6 0.253 - 0.337: 3 0.337 - 0.421: 1 Chirality restraints: 1393 Sorted by residual: chirality pdb=" C2 NAG G 201 " pdb=" C1 NAG G 201 " pdb=" C3 NAG G 201 " pdb=" N2 NAG G 201 " both_signs ideal model delta sigma weight residual False -2.49 -2.07 -0.42 2.00e-01 2.50e+01 4.44e+00 chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN B 84 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" CG LEU G 129 " pdb=" CB LEU G 129 " pdb=" CD1 LEU G 129 " pdb=" CD2 LEU G 129 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 1390 not shown) Planarity restraints: 1474 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU D 30 " -0.015 2.00e-02 2.50e+03 3.06e-02 9.38e+00 pdb=" C GLU D 30 " 0.053 2.00e-02 2.50e+03 pdb=" O GLU D 30 " -0.021 2.00e-02 2.50e+03 pdb=" N ASP D 31 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE X 40 " 0.009 2.00e-02 2.50e+03 1.51e-02 4.01e+00 pdb=" CG PHE X 40 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE X 40 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE X 40 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE X 40 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE X 40 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE X 40 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 74 " -0.019 2.00e-02 2.50e+03 1.75e-02 3.85e+00 pdb=" CG ASN D 74 " 0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN D 74 " -0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN D 74 " 0.018 2.00e-02 2.50e+03 pdb=" C1 NAG H 1 " -0.019 2.00e-02 2.50e+03 ... (remaining 1471 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 847 2.74 - 3.28: 8677 3.28 - 3.82: 13853 3.82 - 4.36: 15506 4.36 - 4.90: 26845 Nonbonded interactions: 65728 Sorted by model distance: nonbonded pdb=" N GLU E 91 " pdb=" OE1 GLU E 91 " model vdw 2.206 3.120 nonbonded pdb=" O THR D 47 " pdb=" OH TYR D 71 " model vdw 2.211 3.040 nonbonded pdb=" O ASP D 100 " pdb=" OG1 THR D 103 " model vdw 2.218 3.040 nonbonded pdb=" O ASP F 137 " pdb=" OG1 THR F 141 " model vdw 2.228 3.040 nonbonded pdb=" OE1 GLU E 120 " pdb=" ND2 ASN E 121 " model vdw 2.230 3.120 ... (remaining 65723 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: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'O' } ncs_group { reference = (chain 'E' and ((resid 33 and (name N or name CA or name C or name O or name CB \ )) or resid 34 through 151)) selection = (chain 'F' and (resid 33 through 54 or (resid 55 and (name N or name CA or name \ C or name O or name CB )) or resid 56 through 62 or (resid 63 and (name N or nam \ e CA or name C or name O or name CB )) or resid 64 through 68 or (resid 69 and ( \ name N or name CA or name C or name O or name CB )) or resid 70 or (resid 71 and \ (name N or name CA or name C or name O or name CB )) or resid 72 through 151)) } ncs_group { reference = chain 'I' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.190 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 25.460 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 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 : 0.003 0.061 8653 Z= 0.153 Angle : 0.972 14.169 11816 Z= 0.450 Chirality : 0.051 0.421 1393 Planarity : 0.004 0.067 1464 Dihedral : 15.190 88.382 3466 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.67 % Favored : 96.24 % Rotamer: Outliers : 0.56 % Allowed : 25.65 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.51 (0.26), residues: 1036 helix: 0.63 (0.34), residues: 214 sheet: 1.85 (0.32), residues: 286 loop : -0.64 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 59 HIS 0.006 0.001 HIS B 225 PHE 0.034 0.002 PHE X 40 TYR 0.022 0.001 TYR A 119 ARG 0.012 0.001 ARG E 115 Details of bonding type rmsd link_NAG-ASN : bond 0.00688 ( 10) link_NAG-ASN : angle 5.03027 ( 30) link_BETA1-4 : bond 0.00642 ( 8) link_BETA1-4 : angle 3.45839 ( 24) hydrogen bonds : bond 0.21260 ( 368) hydrogen bonds : angle 8.23393 ( 1065) SS BOND : bond 0.00237 ( 14) SS BOND : angle 2.06553 ( 28) covalent geometry : bond 0.00343 ( 8621) covalent geometry : angle 0.92323 (11734) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 187 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 MET cc_start: 0.8676 (mmp) cc_final: 0.8091 (mmp) REVERT: B 169 TYR cc_start: 0.8760 (t80) cc_final: 0.8537 (t80) REVERT: D 30 GLU cc_start: 0.8565 (pt0) cc_final: 0.8169 (pp20) REVERT: E 91 GLU cc_start: 0.8624 (pm20) cc_final: 0.8311 (pm20) REVERT: X 30 LYS cc_start: 0.9520 (mtmt) cc_final: 0.8992 (mmmt) REVERT: X 46 LEU cc_start: 0.7927 (pp) cc_final: 0.7703 (pt) outliers start: 5 outliers final: 4 residues processed: 190 average time/residue: 0.2041 time to fit residues: 52.6112 Evaluate side-chains 172 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 168 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 73 CYS Chi-restraints excluded: chain D residue 93 CYS Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain Y residue 30 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 0.6980 chunk 76 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 51 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 91 optimal weight: 0.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 48 HIS F 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.061536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.049082 restraints weight = 39820.291| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 5.26 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 8653 Z= 0.183 Angle : 0.841 12.967 11816 Z= 0.395 Chirality : 0.049 0.361 1393 Planarity : 0.004 0.032 1464 Dihedral : 8.961 59.350 1638 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.67 % Favored : 96.24 % Rotamer: Outliers : 3.94 % Allowed : 18.67 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.20 % 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 (0.26), residues: 1036 helix: 0.82 (0.33), residues: 234 sheet: 1.84 (0.32), residues: 259 loop : -0.72 (0.25), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 198 HIS 0.006 0.001 HIS B 225 PHE 0.045 0.002 PHE Y 50 TYR 0.028 0.001 TYR Y 33 ARG 0.002 0.000 ARG D 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00537 ( 10) link_NAG-ASN : angle 4.23098 ( 30) link_BETA1-4 : bond 0.00570 ( 8) link_BETA1-4 : angle 3.45873 ( 24) hydrogen bonds : bond 0.04396 ( 368) hydrogen bonds : angle 5.69619 ( 1065) SS BOND : bond 0.00208 ( 14) SS BOND : angle 1.26468 ( 28) covalent geometry : bond 0.00407 ( 8621) covalent geometry : angle 0.79872 (11734) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 175 time to evaluate : 0.926 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: symmetry clash revert: symmetry clash REVERT: A 134 TYR cc_start: 0.8802 (t80) cc_final: 0.8577 (t80) REVERT: A 267 MET cc_start: 0.8754 (mmp) cc_final: 0.8546 (mmm) REVERT: B 46 MET cc_start: 0.9163 (OUTLIER) cc_final: 0.8675 (ptm) REVERT: D 27 GLU cc_start: 0.8484 (pm20) cc_final: 0.8269 (pm20) REVERT: G 38 GLU cc_start: 0.9002 (pm20) cc_final: 0.8761 (pm20) REVERT: G 103 MET cc_start: 0.9305 (mmp) cc_final: 0.9087 (mmp) REVERT: X 30 LYS cc_start: 0.9570 (mtmt) cc_final: 0.9053 (mmmt) outliers start: 35 outliers final: 20 residues processed: 197 average time/residue: 0.2032 time to fit residues: 54.4837 Evaluate side-chains 183 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 162 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain D residue 73 CYS Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 93 CYS Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 122 CYS Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain F residue 126 ASP Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain X residue 23 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 65 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 64 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.061804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.049288 restraints weight = 39691.064| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 5.27 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8653 Z= 0.138 Angle : 0.800 14.674 11816 Z= 0.368 Chirality : 0.048 0.334 1393 Planarity : 0.003 0.031 1464 Dihedral : 8.470 59.508 1632 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.05 % Favored : 95.85 % Rotamer: Outliers : 2.92 % Allowed : 19.57 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.20 % 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: 0.43 (0.26), residues: 1036 helix: 0.85 (0.33), residues: 234 sheet: 1.77 (0.32), residues: 259 loop : -0.74 (0.25), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 198 HIS 0.002 0.001 HIS B 225 PHE 0.013 0.001 PHE A 263 TYR 0.015 0.001 TYR B 270 ARG 0.003 0.000 ARG A 186 Details of bonding type rmsd link_NAG-ASN : bond 0.00332 ( 10) link_NAG-ASN : angle 4.25689 ( 30) link_BETA1-4 : bond 0.00705 ( 8) link_BETA1-4 : angle 3.45035 ( 24) hydrogen bonds : bond 0.04132 ( 368) hydrogen bonds : angle 5.32435 ( 1065) SS BOND : bond 0.00303 ( 14) SS BOND : angle 0.97004 ( 28) covalent geometry : bond 0.00307 ( 8621) covalent geometry : angle 0.75632 (11734) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 178 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 TYR cc_start: 0.8816 (t80) cc_final: 0.8553 (t80) REVERT: A 267 MET cc_start: 0.8751 (mmp) cc_final: 0.8541 (mmm) REVERT: B 46 MET cc_start: 0.9163 (mtp) cc_final: 0.8726 (ptm) REVERT: B 301 MET cc_start: 0.9078 (ppp) cc_final: 0.8872 (ppp) REVERT: X 30 LYS cc_start: 0.9565 (mtmt) cc_final: 0.9092 (mmmt) outliers start: 26 outliers final: 17 residues processed: 195 average time/residue: 0.2079 time to fit residues: 55.4335 Evaluate side-chains 177 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 160 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 93 CYS Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 122 CYS Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain F residue 126 ASP Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 68 ASP Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain X residue 23 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 88 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.060235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.047924 restraints weight = 39925.202| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 5.18 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 8653 Z= 0.221 Angle : 0.808 12.717 11816 Z= 0.380 Chirality : 0.048 0.419 1393 Planarity : 0.004 0.034 1464 Dihedral : 8.365 59.863 1631 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.44 % Favored : 95.46 % Rotamer: Outliers : 3.82 % Allowed : 21.03 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.20 % 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: 0.33 (0.26), residues: 1036 helix: 0.76 (0.33), residues: 230 sheet: 1.61 (0.31), residues: 269 loop : -0.78 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 198 HIS 0.004 0.001 HIS B 225 PHE 0.036 0.002 PHE Y 50 TYR 0.016 0.001 TYR D 79 ARG 0.003 0.000 ARG A 186 Details of bonding type rmsd link_NAG-ASN : bond 0.00585 ( 10) link_NAG-ASN : angle 4.48703 ( 30) link_BETA1-4 : bond 0.00608 ( 8) link_BETA1-4 : angle 3.43842 ( 24) hydrogen bonds : bond 0.04139 ( 368) hydrogen bonds : angle 5.25184 ( 1065) SS BOND : bond 0.00209 ( 14) SS BOND : angle 0.92881 ( 28) covalent geometry : bond 0.00490 ( 8621) covalent geometry : angle 0.76116 (11734) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 163 time to evaluate : 1.048 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: symmetry clash REVERT: A 213 SER cc_start: 0.8622 (OUTLIER) cc_final: 0.8219 (m) REVERT: A 266 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8047 (tt) REVERT: A 267 MET cc_start: 0.8756 (mmp) cc_final: 0.8279 (mmm) REVERT: B 46 MET cc_start: 0.9135 (OUTLIER) cc_final: 0.8812 (ptm) REVERT: D 28 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7933 (mt-10) REVERT: E 120 GLU cc_start: 0.9065 (tm-30) cc_final: 0.8631 (tm-30) REVERT: G 37 GLN cc_start: 0.7221 (tm-30) cc_final: 0.6759 (tm-30) REVERT: X 30 LYS cc_start: 0.9574 (mtmt) cc_final: 0.9119 (mmmt) outliers start: 34 outliers final: 22 residues processed: 184 average time/residue: 0.1946 time to fit residues: 49.7491 Evaluate side-chains 183 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 93 CYS Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 98 CYS Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 122 CYS Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain F residue 126 ASP Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain X residue 23 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 1 optimal weight: 0.0770 chunk 67 optimal weight: 9.9990 chunk 44 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 97 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 GLN ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.061341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.048945 restraints weight = 39041.776| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 5.23 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 8653 Z= 0.133 Angle : 0.811 13.671 11816 Z= 0.373 Chirality : 0.049 0.372 1393 Planarity : 0.003 0.030 1464 Dihedral : 8.130 58.545 1631 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.86 % Favored : 96.04 % Rotamer: Outliers : 2.92 % Allowed : 22.38 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.20 % 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: 0.34 (0.26), residues: 1036 helix: 0.67 (0.33), residues: 233 sheet: 1.65 (0.31), residues: 269 loop : -0.75 (0.26), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 198 HIS 0.002 0.000 HIS B 66 PHE 0.020 0.001 PHE Y 50 TYR 0.014 0.001 TYR D 79 ARG 0.003 0.000 ARG A 186 Details of bonding type rmsd link_NAG-ASN : bond 0.00593 ( 10) link_NAG-ASN : angle 4.15587 ( 30) link_BETA1-4 : bond 0.00752 ( 8) link_BETA1-4 : angle 3.36135 ( 24) hydrogen bonds : bond 0.03839 ( 368) hydrogen bonds : angle 5.04108 ( 1065) SS BOND : bond 0.00182 ( 14) SS BOND : angle 0.71809 ( 28) covalent geometry : bond 0.00300 ( 8621) covalent geometry : angle 0.77032 (11734) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 166 time to evaluate : 0.940 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 134 TYR cc_start: 0.8766 (t80) cc_final: 0.8470 (t80) REVERT: A 213 SER cc_start: 0.8608 (OUTLIER) cc_final: 0.8205 (m) REVERT: A 254 ARG cc_start: 0.9086 (mtp180) cc_final: 0.8795 (mtp180) REVERT: A 267 MET cc_start: 0.8632 (mmp) cc_final: 0.8423 (mmm) REVERT: E 86 GLU cc_start: 0.8636 (mp0) cc_final: 0.8416 (mp0) REVERT: X 30 LYS cc_start: 0.9556 (mtmt) cc_final: 0.9107 (mmmt) outliers start: 26 outliers final: 20 residues processed: 182 average time/residue: 0.1925 time to fit residues: 48.0604 Evaluate side-chains 180 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 159 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 93 CYS Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain F residue 126 ASP Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain X residue 23 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 89 optimal weight: 7.9990 chunk 86 optimal weight: 0.5980 chunk 90 optimal weight: 0.1980 chunk 82 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 78 optimal weight: 0.1980 chunk 14 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.060736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.048387 restraints weight = 39796.978| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 5.21 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 8653 Z= 0.160 Angle : 0.803 14.271 11816 Z= 0.372 Chirality : 0.048 0.348 1393 Planarity : 0.003 0.031 1464 Dihedral : 8.123 58.512 1631 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.96 % Favored : 95.95 % Rotamer: Outliers : 3.71 % Allowed : 22.83 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.20 % 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: 0.35 (0.26), residues: 1036 helix: 0.75 (0.33), residues: 233 sheet: 1.64 (0.32), residues: 269 loop : -0.77 (0.26), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 198 HIS 0.003 0.001 HIS B 66 PHE 0.040 0.002 PHE Y 50 TYR 0.015 0.001 TYR D 79 ARG 0.003 0.000 ARG A 186 Details of bonding type rmsd link_NAG-ASN : bond 0.00197 ( 10) link_NAG-ASN : angle 4.50151 ( 30) link_BETA1-4 : bond 0.00698 ( 8) link_BETA1-4 : angle 3.32917 ( 24) hydrogen bonds : bond 0.03892 ( 368) hydrogen bonds : angle 5.02068 ( 1065) SS BOND : bond 0.00169 ( 14) SS BOND : angle 0.74093 ( 28) covalent geometry : bond 0.00369 ( 8621) covalent geometry : angle 0.75723 (11734) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 165 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 SER cc_start: 0.8609 (OUTLIER) cc_final: 0.8200 (m) REVERT: A 238 GLU cc_start: 0.7601 (pp20) cc_final: 0.7216 (pp20) REVERT: A 254 ARG cc_start: 0.9104 (mtp180) cc_final: 0.8812 (mtp180) REVERT: A 267 MET cc_start: 0.8617 (mmp) cc_final: 0.8179 (mmp) REVERT: D 27 GLU cc_start: 0.8483 (pm20) cc_final: 0.8254 (pm20) REVERT: D 30 GLU cc_start: 0.8928 (pt0) cc_final: 0.8330 (pt0) REVERT: F 147 LEU cc_start: 0.8525 (tp) cc_final: 0.8151 (mm) REVERT: G 37 GLN cc_start: 0.7353 (tm-30) cc_final: 0.6984 (tm-30) REVERT: X 30 LYS cc_start: 0.9563 (mtmt) cc_final: 0.9127 (mmmt) outliers start: 33 outliers final: 25 residues processed: 187 average time/residue: 0.1895 time to fit residues: 49.0249 Evaluate side-chains 183 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 157 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 93 CYS Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 98 CYS Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain F residue 126 ASP Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain X residue 23 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 17 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 28 optimal weight: 0.0770 chunk 32 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 chunk 73 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.061216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.048901 restraints weight = 39789.505| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 5.22 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 8653 Z= 0.139 Angle : 0.823 15.142 11816 Z= 0.380 Chirality : 0.048 0.350 1393 Planarity : 0.003 0.032 1464 Dihedral : 8.041 57.685 1631 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.25 % Favored : 95.66 % Rotamer: Outliers : 3.37 % Allowed : 23.40 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.20 % 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: 0.34 (0.26), residues: 1036 helix: 0.73 (0.33), residues: 233 sheet: 1.65 (0.32), residues: 269 loop : -0.77 (0.26), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 198 HIS 0.002 0.000 HIS F 61 PHE 0.051 0.001 PHE A 263 TYR 0.014 0.001 TYR D 79 ARG 0.004 0.000 ARG A 186 Details of bonding type rmsd link_NAG-ASN : bond 0.00249 ( 10) link_NAG-ASN : angle 3.69951 ( 30) link_BETA1-4 : bond 0.00580 ( 8) link_BETA1-4 : angle 3.26110 ( 24) hydrogen bonds : bond 0.03837 ( 368) hydrogen bonds : angle 4.96691 ( 1065) SS BOND : bond 0.00166 ( 14) SS BOND : angle 0.69384 ( 28) covalent geometry : bond 0.00322 ( 8621) covalent geometry : angle 0.79013 (11734) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 164 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 TYR cc_start: 0.8765 (t80) cc_final: 0.8413 (t80) REVERT: A 213 SER cc_start: 0.8605 (OUTLIER) cc_final: 0.8215 (m) REVERT: A 254 ARG cc_start: 0.9061 (mtp180) cc_final: 0.8777 (mtp180) REVERT: B 46 MET cc_start: 0.9096 (mtp) cc_final: 0.8864 (ptm) REVERT: D 30 GLU cc_start: 0.8980 (pt0) cc_final: 0.8397 (pt0) REVERT: E 86 GLU cc_start: 0.8590 (mp0) cc_final: 0.8207 (pm20) REVERT: F 147 LEU cc_start: 0.8499 (tp) cc_final: 0.8102 (mm) REVERT: X 30 LYS cc_start: 0.9560 (mtmt) cc_final: 0.9113 (mmmt) outliers start: 30 outliers final: 23 residues processed: 184 average time/residue: 0.1918 time to fit residues: 48.8642 Evaluate side-chains 177 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 153 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 93 CYS Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 98 CYS Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain F residue 126 ASP Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain X residue 23 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 31 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 84 optimal weight: 0.4980 chunk 4 optimal weight: 0.2980 chunk 33 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 1 optimal weight: 0.0970 chunk 35 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 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 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.061323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.049105 restraints weight = 40281.880| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 5.22 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 8653 Z= 0.140 Angle : 0.858 17.122 11816 Z= 0.396 Chirality : 0.049 0.334 1393 Planarity : 0.003 0.028 1464 Dihedral : 7.964 57.332 1631 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.34 % Favored : 95.56 % Rotamer: Outliers : 3.04 % Allowed : 23.85 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.20 % 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: 0.27 (0.26), residues: 1036 helix: 0.59 (0.33), residues: 235 sheet: 1.66 (0.32), residues: 269 loop : -0.81 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 43 HIS 0.002 0.000 HIS F 61 PHE 0.046 0.002 PHE A 263 TYR 0.012 0.001 TYR D 79 ARG 0.004 0.000 ARG A 186 Details of bonding type rmsd link_NAG-ASN : bond 0.00316 ( 10) link_NAG-ASN : angle 4.58885 ( 30) link_BETA1-4 : bond 0.00740 ( 8) link_BETA1-4 : angle 3.65704 ( 24) hydrogen bonds : bond 0.03814 ( 368) hydrogen bonds : angle 4.97076 ( 1065) SS BOND : bond 0.00165 ( 14) SS BOND : angle 0.72901 ( 28) covalent geometry : bond 0.00333 ( 8621) covalent geometry : angle 0.81150 (11734) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 168 time to evaluate : 0.924 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 134 TYR cc_start: 0.8764 (t80) cc_final: 0.8340 (t80) REVERT: A 213 SER cc_start: 0.8578 (OUTLIER) cc_final: 0.8186 (m) REVERT: A 254 ARG cc_start: 0.9015 (mtp180) cc_final: 0.8737 (mtp180) REVERT: A 266 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8043 (tt) REVERT: A 267 MET cc_start: 0.8393 (mmp) cc_final: 0.7993 (mmm) REVERT: B 46 MET cc_start: 0.9169 (mtp) cc_final: 0.8777 (ptp) REVERT: D 27 GLU cc_start: 0.8537 (pm20) cc_final: 0.8333 (pm20) REVERT: D 28 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7965 (mt-10) REVERT: D 30 GLU cc_start: 0.8958 (pt0) cc_final: 0.8356 (pt0) REVERT: D 92 MET cc_start: 0.9218 (mmp) cc_final: 0.8751 (mmp) REVERT: E 86 GLU cc_start: 0.8704 (mp0) cc_final: 0.8157 (pm20) REVERT: F 147 LEU cc_start: 0.8542 (tp) cc_final: 0.8136 (mm) REVERT: G 37 GLN cc_start: 0.6931 (tm-30) cc_final: 0.6723 (tm-30) REVERT: X 30 LYS cc_start: 0.9561 (mtmt) cc_final: 0.9116 (mmmt) outliers start: 27 outliers final: 20 residues processed: 188 average time/residue: 0.1947 time to fit residues: 50.1017 Evaluate side-chains 184 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 93 CYS Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 98 CYS Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 122 CYS Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain X residue 23 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 18 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 92 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 66 optimal weight: 0.0570 chunk 79 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 overall best weight: 0.9100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.060906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.048706 restraints weight = 40636.866| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 5.20 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 8653 Z= 0.149 Angle : 0.879 13.755 11816 Z= 0.405 Chirality : 0.049 0.291 1393 Planarity : 0.003 0.029 1464 Dihedral : 8.049 58.653 1631 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.92 % Allowed : 23.28 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.26), residues: 1036 helix: 0.62 (0.33), residues: 235 sheet: 1.68 (0.32), residues: 269 loop : -0.80 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 198 HIS 0.002 0.001 HIS F 61 PHE 0.045 0.001 PHE A 263 TYR 0.012 0.001 TYR D 71 ARG 0.004 0.000 ARG A 186 Details of bonding type rmsd link_NAG-ASN : bond 0.00198 ( 10) link_NAG-ASN : angle 5.17799 ( 30) link_BETA1-4 : bond 0.00791 ( 8) link_BETA1-4 : angle 3.47065 ( 24) hydrogen bonds : bond 0.03913 ( 368) hydrogen bonds : angle 4.98996 ( 1065) SS BOND : bond 0.00142 ( 14) SS BOND : angle 0.69576 ( 28) covalent geometry : bond 0.00346 ( 8621) covalent geometry : angle 0.82690 (11734) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 164 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 TYR cc_start: 0.8785 (t80) cc_final: 0.8341 (t80) REVERT: A 213 SER cc_start: 0.8586 (OUTLIER) cc_final: 0.8189 (m) REVERT: A 254 ARG cc_start: 0.9043 (mtp180) cc_final: 0.8747 (mtp180) REVERT: B 46 MET cc_start: 0.9202 (mtp) cc_final: 0.8800 (ptp) REVERT: B 256 GLU cc_start: 0.8685 (mp0) cc_final: 0.8472 (mp0) REVERT: D 27 GLU cc_start: 0.8459 (pm20) cc_final: 0.8234 (pm20) REVERT: D 28 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7982 (mt-10) REVERT: F 147 LEU cc_start: 0.8546 (tp) cc_final: 0.8151 (mm) REVERT: X 30 LYS cc_start: 0.9561 (mtmt) cc_final: 0.9117 (mmmt) outliers start: 26 outliers final: 24 residues processed: 182 average time/residue: 0.2029 time to fit residues: 50.5764 Evaluate side-chains 185 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 160 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 93 CYS Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 98 CYS Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain X residue 23 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 GLN ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.059275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.047048 restraints weight = 40997.087| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 5.20 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 8653 Z= 0.239 Angle : 0.910 14.557 11816 Z= 0.430 Chirality : 0.050 0.280 1393 Planarity : 0.004 0.030 1464 Dihedral : 8.304 57.812 1631 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 3.04 % Allowed : 23.40 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.20 % 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: 0.18 (0.26), residues: 1036 helix: 0.50 (0.32), residues: 235 sheet: 1.53 (0.32), residues: 269 loop : -0.82 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 151 HIS 0.003 0.001 HIS F 61 PHE 0.041 0.002 PHE Y 50 TYR 0.016 0.001 TYR D 79 ARG 0.004 0.000 ARG A 186 Details of bonding type rmsd link_NAG-ASN : bond 0.00327 ( 10) link_NAG-ASN : angle 4.44054 ( 30) link_BETA1-4 : bond 0.00749 ( 8) link_BETA1-4 : angle 3.26791 ( 24) hydrogen bonds : bond 0.04255 ( 368) hydrogen bonds : angle 5.16504 ( 1065) SS BOND : bond 0.00233 ( 14) SS BOND : angle 0.92109 ( 28) covalent geometry : bond 0.00546 ( 8621) covalent geometry : angle 0.87181 (11734) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 156 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 SER cc_start: 0.8674 (OUTLIER) cc_final: 0.8259 (m) REVERT: A 254 ARG cc_start: 0.9138 (mtp180) cc_final: 0.8825 (mtp180) REVERT: E 64 LYS cc_start: 0.8587 (pttp) cc_final: 0.8213 (ptpp) REVERT: G 37 GLN cc_start: 0.6967 (tm-30) cc_final: 0.6746 (tm-30) REVERT: X 30 LYS cc_start: 0.9549 (mtmt) cc_final: 0.9126 (mmmt) outliers start: 27 outliers final: 23 residues processed: 173 average time/residue: 0.2027 time to fit residues: 48.6964 Evaluate side-chains 178 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 154 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 93 CYS Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 98 CYS Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain F residue 126 ASP Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain X residue 23 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 100 optimal weight: 8.9990 chunk 55 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 68 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 chunk 70 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 212 ASN ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.059565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.047344 restraints weight = 41470.983| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 5.26 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 8653 Z= 0.186 Angle : 0.900 14.063 11816 Z= 0.424 Chirality : 0.050 0.261 1393 Planarity : 0.004 0.032 1464 Dihedral : 8.241 56.821 1631 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.59 % Allowed : 24.52 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.20 % 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: 0.14 (0.26), residues: 1036 helix: 0.40 (0.32), residues: 237 sheet: 1.50 (0.32), residues: 267 loop : -0.80 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 198 HIS 0.002 0.001 HIS F 61 PHE 0.037 0.001 PHE A 263 TYR 0.019 0.001 TYR D 79 ARG 0.004 0.000 ARG A 186 Details of bonding type rmsd link_NAG-ASN : bond 0.00251 ( 10) link_NAG-ASN : angle 4.08428 ( 30) link_BETA1-4 : bond 0.00731 ( 8) link_BETA1-4 : angle 3.07938 ( 24) hydrogen bonds : bond 0.04121 ( 368) hydrogen bonds : angle 5.11392 ( 1065) SS BOND : bond 0.00166 ( 14) SS BOND : angle 0.77345 ( 28) covalent geometry : bond 0.00434 ( 8621) covalent geometry : angle 0.86682 (11734) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3358.38 seconds wall clock time: 59 minutes 43.92 seconds (3583.92 seconds total)