Starting phenix.real_space_refine on Sat Oct 11 11:08:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wnu_37673/10_2025/8wnu_37673.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wnu_37673/10_2025/8wnu_37673.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wnu_37673/10_2025/8wnu_37673.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wnu_37673/10_2025/8wnu_37673.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wnu_37673/10_2025/8wnu_37673.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wnu_37673/10_2025/8wnu_37673.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.024 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 74 5.16 5 C 8864 2.51 5 N 2436 2.21 5 O 2778 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 69 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14152 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1660 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 203} Chain breaks: 1 Chain: "B" Number of atoms: 1661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1661 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 213} Chain breaks: 1 Chain: "C" Number of atoms: 1660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1660 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 203} Chain breaks: 1 Chain: "D" Number of atoms: 1661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1661 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 213} Chain breaks: 1 Chain: "E" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2818 Classifications: {'peptide': 352} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 332} Chain: "F" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2818 Classifications: {'peptide': 352} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 332} Chain: "G" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 923 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "H" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 923 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "E" 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: "F" 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 Time building chain proxies: 3.25, per 1000 atoms: 0.23 Number of scatterers: 14152 At special positions: 0 Unit cell: (127.28, 109.22, 132.44, 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 74 16.00 O 2778 8.00 N 2436 7.00 C 8864 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=22, symmetry=0 Simple disulfide: pdb=" SG CYS A 24 " - pdb=" SG CYS A 89 " distance=2.04 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 195 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 200 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 89 " distance=2.03 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 195 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 200 " distance=2.03 Simple disulfide: pdb=" SG CYS E 4 " - pdb=" SG CYS F 4 " distance=2.03 Simple disulfide: pdb=" SG CYS E 55 " - pdb=" SG CYS E 143 " distance=2.03 Simple disulfide: pdb=" SG CYS E 179 " - pdb=" SG CYS E 223 " distance=2.03 Simple disulfide: pdb=" SG CYS E 280 " - pdb=" SG CYS E 329 " distance=2.03 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 312 " distance=2.03 Simple disulfide: pdb=" SG CYS E 313 " - pdb=" SG CYS E 316 " distance=2.03 Simple disulfide: pdb=" SG CYS F 4 " - pdb=" SG CYS F 15 " distance=2.03 Simple disulfide: pdb=" SG CYS F 55 " - pdb=" SG CYS F 143 " distance=2.03 Simple disulfide: pdb=" SG CYS F 179 " - pdb=" SG CYS F 223 " distance=2.03 Simple disulfide: pdb=" SG CYS F 280 " - pdb=" SG CYS F 329 " distance=2.03 Simple disulfide: pdb=" SG CYS F 291 " - pdb=" SG CYS F 312 " distance=2.03 Simple disulfide: pdb=" SG CYS F 313 " - pdb=" SG CYS F 316 " distance=2.03 Simple disulfide: pdb=" SG CYS G 21 " - pdb=" SG CYS G 95 " distance=2.03 Simple disulfide: pdb=" SG CYS H 21 " - pdb=" SG CYS H 95 " 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 NAG-ASN " NAG E 401 " - " ASN E 207 " Time building additional restraints: 1.21 Conformation dependent library (CDL) restraints added in 527.9 milliseconds Enol-peptide restraints added in 1.2 microseconds 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3356 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 31 sheets defined 11.2% alpha, 26.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 80 through 84 removed outlier: 4.299A pdb=" N PHE A 84 " --> pdb=" O PRO A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 127 Processing helix chain 'A' and resid 184 through 188 Processing helix chain 'B' and resid 29 through 33 removed outlier: 3.763A pdb=" N SER B 32 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASN B 33 " --> pdb=" O VAL B 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 29 through 33' Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'B' and resid 160 through 162 No H-bonds generated for 'chain 'B' and resid 160 through 162' Processing helix chain 'B' and resid 189 through 193 Processing helix chain 'B' and resid 206 through 208 No H-bonds generated for 'chain 'B' and resid 206 through 208' Processing helix chain 'C' and resid 80 through 84 removed outlier: 4.005A pdb=" N PHE C 84 " --> pdb=" O PRO C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 128 removed outlier: 3.540A pdb=" N LYS C 127 " --> pdb=" O ASP C 123 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N SER C 128 " --> pdb=" O GLU C 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 123 through 128' Processing helix chain 'C' and resid 151 through 154 Processing helix chain 'C' and resid 184 through 188 Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'D' and resid 160 through 162 No H-bonds generated for 'chain 'D' and resid 160 through 162' Processing helix chain 'D' and resid 189 through 193 Processing helix chain 'D' and resid 205 through 208 Processing helix chain 'E' and resid 24 through 32 removed outlier: 3.615A pdb=" N ALA E 27 " --> pdb=" O ASP E 24 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ARG E 29 " --> pdb=" O GLU E 26 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASP E 30 " --> pdb=" O ALA E 27 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG E 31 " --> pdb=" O TRP E 28 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N TYR E 32 " --> pdb=" O ARG E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 52 removed outlier: 3.628A pdb=" N LEU E 42 " --> pdb=" O SER E 38 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA E 44 " --> pdb=" O ARG E 40 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU E 52 " --> pdb=" O GLN E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 72 Processing helix chain 'E' and resid 73 through 82 removed outlier: 3.902A pdb=" N GLU E 81 " --> pdb=" O ALA E 77 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASN E 82 " --> pdb=" O ILE E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 124 removed outlier: 4.182A pdb=" N TYR E 122 " --> pdb=" O GLY E 119 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL E 124 " --> pdb=" O SER E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 146 No H-bonds generated for 'chain 'E' and resid 144 through 146' Processing helix chain 'E' and resid 180 through 183 removed outlier: 4.283A pdb=" N VAL E 183 " --> pdb=" O ASP E 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 180 through 183' Processing helix chain 'E' and resid 226 through 230 removed outlier: 3.683A pdb=" N HIS E 229 " --> pdb=" O PRO E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 341 through 345 Processing helix chain 'F' and resid 38 through 53 removed outlier: 4.295A pdb=" N ALA F 44 " --> pdb=" O ARG F 40 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA F 45 " --> pdb=" O ARG F 41 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL F 46 " --> pdb=" O LEU F 42 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS F 47 " --> pdb=" O ALA F 43 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLN F 48 " --> pdb=" O ALA F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 72 Processing helix chain 'F' and resid 72 through 83 removed outlier: 4.044A pdb=" N ASN F 76 " --> pdb=" O GLU F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 146 No H-bonds generated for 'chain 'F' and resid 144 through 146' Processing helix chain 'F' and resid 244 through 248 Processing helix chain 'G' and resid 27 through 31 removed outlier: 3.816A pdb=" N ARG G 30 " --> pdb=" O THR G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 90 Processing helix chain 'H' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 8 removed outlier: 3.620A pdb=" N SER A 8 " --> pdb=" O THR A 23 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR A 23 " --> pdb=" O SER A 8 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL A 20 " --> pdb=" O ILE A 76 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR A 73 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER A 66 " --> pdb=" O THR A 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 14 removed outlier: 3.781A pdb=" N GLU A 106 " --> pdb=" O LEU A 12 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA A 14 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N TRP A 36 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU A 48 " --> pdb=" O TRP A 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 117 through 119 removed outlier: 3.654A pdb=" N PHE A 119 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N VAL A 134 " --> pdb=" O PHE A 119 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N TYR A 174 " --> pdb=" O ASN A 139 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 154 through 155 removed outlier: 3.836A pdb=" N VAL A 151 " --> pdb=" O ALA A 154 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 4 through 8 removed outlier: 3.920A pdb=" N GLN B 4 " --> pdb=" O SER B 26 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL B 6 " --> pdb=" O ALA B 24 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER B 22 " --> pdb=" O SER B 8 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 11 through 13 removed outlier: 6.023A pdb=" N GLY B 11 " --> pdb=" O THR B 114 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA B 92 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N MET B 35 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N VAL B 51 " --> pdb=" O MET B 35 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N TRP B 37 " --> pdb=" O VAL B 49 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 124 through 126 removed outlier: 5.557A pdb=" N LEU B 145 " --> pdb=" O SER B 184 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N SER B 184 " --> pdb=" O LEU B 145 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N LYS B 147 " --> pdb=" O LEU B 182 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N LEU B 182 " --> pdb=" O LYS B 147 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR B 149 " --> pdb=" O TYR B 180 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N SER B 181 " --> pdb=" O ALA B 172 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ALA B 172 " --> pdb=" O SER B 181 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N SER B 183 " --> pdb=" O PHE B 170 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N HIS B 168 " --> pdb=" O VAL B 185 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 154 through 158 removed outlier: 4.096A pdb=" N TYR B 198 " --> pdb=" O VAL B 215 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 5 through 8 removed outlier: 3.592A pdb=" N SER C 8 " --> pdb=" O THR C 23 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR C 23 " --> pdb=" O SER C 8 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR C 73 " --> pdb=" O SER C 66 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 11 through 14 removed outlier: 3.581A pdb=" N LEU C 12 " --> pdb=" O LYS C 104 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU C 106 " --> pdb=" O LEU C 12 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR C 50 " --> pdb=" O SER C 54 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 130 through 140 removed outlier: 6.039A pdb=" N TYR C 174 " --> pdb=" O ASN C 139 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 148 through 149 Processing sheet with id=AB4, first strand: chain 'D' and resid 5 through 8 removed outlier: 3.695A pdb=" N VAL D 6 " --> pdb=" O ALA D 24 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N SER D 8 " --> pdb=" O SER D 22 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER D 22 " --> pdb=" O SER D 8 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU D 19 " --> pdb=" O MET D 83 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 11 through 13 removed outlier: 6.495A pdb=" N GLY D 11 " --> pdb=" O THR D 114 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N MET D 35 " --> pdb=" O VAL D 51 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N VAL D 51 " --> pdb=" O MET D 35 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N TRP D 37 " --> pdb=" O VAL D 49 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 124 through 126 removed outlier: 3.866A pdb=" N PHE D 126 " --> pdb=" O LEU D 145 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU D 145 " --> pdb=" O PHE D 126 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N LEU D 145 " --> pdb=" O SER D 184 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N SER D 184 " --> pdb=" O LEU D 145 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N LYS D 147 " --> pdb=" O LEU D 182 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LEU D 182 " --> pdb=" O LYS D 147 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR D 149 " --> pdb=" O TYR D 180 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 124 through 126 removed outlier: 3.866A pdb=" N PHE D 126 " --> pdb=" O LEU D 145 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU D 145 " --> pdb=" O PHE D 126 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N LEU D 145 " --> pdb=" O SER D 184 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N SER D 184 " --> pdb=" O LEU D 145 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N LYS D 147 " --> pdb=" O LEU D 182 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LEU D 182 " --> pdb=" O LYS D 147 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR D 149 " --> pdb=" O TYR D 180 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 155 through 158 removed outlier: 3.596A pdb=" N TYR D 198 " --> pdb=" O VAL D 215 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N CYS D 200 " --> pdb=" O LYS D 213 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS D 213 " --> pdb=" O CYS D 200 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 6 through 7 Processing sheet with id=AC1, first strand: chain 'E' and resid 20 through 22 removed outlier: 3.681A pdb=" N ARG F 14 " --> pdb=" O SER F 5 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 35 through 36 removed outlier: 6.638A pdb=" N HIS E 35 " --> pdb=" O LEU E 169 " (cutoff:3.500A) removed outlier: 9.187A pdb=" N VAL E 171 " --> pdb=" O HIS E 35 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS E 170 " --> pdb=" O LEU E 154 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 87 through 88 removed outlier: 5.962A pdb=" N THR E 87 " --> pdb=" O PHE E 133 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N VAL E 135 " --> pdb=" O THR E 87 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE E 57 " --> pdb=" O VAL E 134 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N GLY E 56 " --> pdb=" O ALA E 149 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'E' and resid 328 through 331 removed outlier: 3.743A pdb=" N PHE E 323 " --> pdb=" O TRP E 330 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N LEU E 212 " --> pdb=" O GLU E 205 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N GLU E 205 " --> pdb=" O LEU E 212 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG E 214 " --> pdb=" O GLU E 203 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR F 186 " --> pdb=" O VAL E 188 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA F 187 " --> pdb=" O ALA F 194 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N GLU F 205 " --> pdb=" O LEU F 212 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N LEU F 212 " --> pdb=" O GLU F 205 " (cutoff:3.500A) removed outlier: 9.145A pdb=" N LYS F 213 " --> pdb=" O PHE F 277 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N PHE F 277 " --> pdb=" O LYS F 213 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 35 through 36 removed outlier: 6.400A pdb=" N TRP F 168 " --> pdb=" O GLU F 156 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 56 through 57 removed outlier: 7.629A pdb=" N GLY F 56 " --> pdb=" O ALA F 149 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'F' and resid 87 through 90 removed outlier: 6.916A pdb=" N THR F 87 " --> pdb=" O PHE F 133 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N VAL F 135 " --> pdb=" O THR F 87 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N VAL F 89 " --> pdb=" O VAL F 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'F' and resid 284 through 287 removed outlier: 7.238A pdb=" N LYS F 284 " --> pdb=" O TRP F 311 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N CYS F 313 " --> pdb=" O LYS F 284 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N TYR F 286 " --> pdb=" O CYS F 313 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 3 through 6 removed outlier: 3.554A pdb=" N ALA G 22 " --> pdb=" O GLN G 4 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 10 through 11 removed outlier: 3.745A pdb=" N VAL G 11 " --> pdb=" O THR G 117 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG G 37 " --> pdb=" O PHE G 46 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N PHE G 46 " --> pdb=" O ARG G 37 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 2 through 6 removed outlier: 3.613A pdb=" N LEU H 17 " --> pdb=" O MET H 82 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.822A pdb=" N VAL H 11 " --> pdb=" O THR H 117 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'H' and resid 57 through 59 removed outlier: 5.095A pdb=" N PHE H 46 " --> pdb=" O ARG H 37 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ARG H 37 " --> pdb=" O PHE H 46 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N SER H 34 " --> pdb=" O ALA H 96 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA H 96 " --> pdb=" O SER H 34 " (cutoff:3.500A) 370 hydrogen bonds defined for protein. 867 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: 2.35 Time building geometry restraints manager: 1.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4569 1.34 - 1.46: 3475 1.46 - 1.58: 6344 1.58 - 1.70: 0 1.70 - 1.82: 100 Bond restraints: 14488 Sorted by residual: bond pdb=" N LYS D 133 " pdb=" CA LYS D 133 " ideal model delta sigma weight residual 1.460 1.514 -0.054 2.20e-02 2.07e+03 6.04e+00 bond pdb=" C SER D 132 " pdb=" N LYS D 133 " ideal model delta sigma weight residual 1.341 1.379 -0.038 2.13e-02 2.20e+03 3.11e+00 bond pdb=" N ASP E 1 " pdb=" CA ASP E 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.91e+00 bond pdb=" N ASP F 1 " pdb=" CA ASP F 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.85e+00 bond pdb=" CA LYS B 133 " pdb=" C LYS B 133 " ideal model delta sigma weight residual 1.524 1.546 -0.022 1.47e-02 4.63e+03 2.14e+00 ... (remaining 14483 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 19466 2.34 - 4.67: 184 4.67 - 7.01: 9 7.01 - 9.35: 4 9.35 - 11.69: 3 Bond angle restraints: 19666 Sorted by residual: angle pdb=" N LYS D 133 " pdb=" CA LYS D 133 " pdb=" C LYS D 133 " ideal model delta sigma weight residual 108.53 119.80 -11.27 2.07e+00 2.33e-01 2.96e+01 angle pdb=" N GLY H 105 " pdb=" CA GLY H 105 " pdb=" C GLY H 105 " ideal model delta sigma weight residual 113.18 124.87 -11.69 2.37e+00 1.78e-01 2.43e+01 angle pdb=" C SER C 209 " pdb=" N PHE C 210 " pdb=" CA PHE C 210 " ideal model delta sigma weight residual 121.54 129.52 -7.98 1.91e+00 2.74e-01 1.75e+01 angle pdb=" C SER A 209 " pdb=" N PHE A 210 " pdb=" CA PHE A 210 " ideal model delta sigma weight residual 122.19 131.57 -9.38 2.30e+00 1.89e-01 1.66e+01 angle pdb=" N SER H 104 " pdb=" CA SER H 104 " pdb=" C SER H 104 " ideal model delta sigma weight residual 110.80 119.37 -8.57 2.13e+00 2.20e-01 1.62e+01 ... (remaining 19661 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 7686 17.57 - 35.13: 773 35.13 - 52.70: 186 52.70 - 70.26: 35 70.26 - 87.83: 12 Dihedral angle restraints: 8692 sinusoidal: 3448 harmonic: 5244 Sorted by residual: dihedral pdb=" CA PRO D 130 " pdb=" C PRO D 130 " pdb=" N SER D 131 " pdb=" CA SER D 131 " ideal model delta harmonic sigma weight residual 180.00 -143.98 -36.02 0 5.00e+00 4.00e-02 5.19e+01 dihedral pdb=" CA PRO E 320 " pdb=" C PRO E 320 " pdb=" N LEU E 321 " pdb=" CA LEU E 321 " ideal model delta harmonic sigma weight residual 180.00 147.14 32.86 0 5.00e+00 4.00e-02 4.32e+01 dihedral pdb=" CB CYS F 313 " pdb=" SG CYS F 313 " pdb=" SG CYS F 316 " pdb=" CB CYS F 316 " ideal model delta sinusoidal sigma weight residual -86.00 -137.40 51.40 1 1.00e+01 1.00e-02 3.61e+01 ... (remaining 8689 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1924 0.066 - 0.133: 210 0.133 - 0.199: 8 0.199 - 0.266: 0 0.266 - 0.332: 1 Chirality restraints: 2143 Sorted by residual: chirality pdb=" CA LYS D 133 " pdb=" N LYS D 133 " pdb=" C LYS D 133 " pdb=" CB LYS D 133 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CA PRO D 130 " pdb=" N PRO D 130 " pdb=" C PRO D 130 " pdb=" CB PRO D 130 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 9.22e-01 chirality pdb=" CA SER H 104 " pdb=" N SER H 104 " pdb=" C SER H 104 " pdb=" CB SER H 104 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.55e-01 ... (remaining 2140 not shown) Planarity restraints: 2529 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET E 318 " -0.044 5.00e-02 4.00e+02 6.83e-02 7.46e+00 pdb=" N PRO E 319 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO E 319 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO E 319 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 129 " -0.040 5.00e-02 4.00e+02 6.09e-02 5.94e+00 pdb=" N PRO B 130 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO B 130 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 130 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 152 " -0.033 5.00e-02 4.00e+02 4.93e-02 3.88e+00 pdb=" N PRO D 153 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO D 153 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 153 " -0.025 5.00e-02 4.00e+02 ... (remaining 2526 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 162 2.55 - 3.14: 11411 3.14 - 3.72: 20696 3.72 - 4.31: 27386 4.31 - 4.90: 46783 Nonbonded interactions: 106438 Sorted by model distance: nonbonded pdb=" OG SER E 5 " pdb=" OH TYR F 22 " model vdw 1.960 3.040 nonbonded pdb=" OD1 ASP C 171 " pdb=" OG1 THR C 173 " model vdw 2.004 3.040 nonbonded pdb=" OD2 ASP D 221 " pdb=" OG1 THR D 223 " model vdw 2.075 3.040 nonbonded pdb=" OG SER H 16 " pdb=" O MET H 82 " model vdw 2.078 3.040 nonbonded pdb=" OD1 ASP A 171 " pdb=" OG1 THR A 173 " model vdw 2.126 3.040 ... (remaining 106433 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } 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 group one per residue 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: 5.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.260 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6147 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 0.054 14511 Z= 0.127 Angle : 0.579 11.687 19713 Z= 0.311 Chirality : 0.042 0.332 2143 Planarity : 0.004 0.068 2528 Dihedral : 15.008 87.828 5270 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.00 % Favored : 91.78 % Rotamer: Outliers : 0.13 % Allowed : 13.53 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.20), residues: 1800 helix: 0.25 (0.57), residues: 75 sheet: 0.47 (0.26), residues: 440 loop : -1.31 (0.18), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 14 TYR 0.017 0.001 TYR F 22 PHE 0.020 0.001 PHE A 210 TRP 0.011 0.001 TRP E 210 HIS 0.005 0.001 HIS C 199 Details of bonding type rmsd covalent geometry : bond 0.00253 (14488) covalent geometry : angle 0.57927 (19666) SS BOND : bond 0.00186 ( 22) SS BOND : angle 0.57771 ( 44) hydrogen bonds : bond 0.28225 ( 367) hydrogen bonds : angle 9.69857 ( 867) link_NAG-ASN : bond 0.00272 ( 1) link_NAG-ASN : angle 0.71261 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 261 time to evaluate : 0.525 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 12 LEU cc_start: 0.8278 (pt) cc_final: 0.7886 (tt) REVERT: F 37 ASP cc_start: 0.6890 (t0) cc_final: 0.6606 (t70) REVERT: F 318 MET cc_start: 0.6461 (tpp) cc_final: 0.5642 (tpp) REVERT: G 30 ARG cc_start: 0.6190 (mtm180) cc_final: 0.5924 (ptt90) REVERT: G 94 TYR cc_start: 0.7920 (m-80) cc_final: 0.7701 (m-80) REVERT: G 112 GLN cc_start: 0.7678 (mm-40) cc_final: 0.7153 (pm20) outliers start: 2 outliers final: 1 residues processed: 262 average time/residue: 0.1297 time to fit residues: 48.9602 Evaluate side-chains 215 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 214 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 198 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.0770 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN A 125 GLN A 211 ASN B 40 GLN C 148 GLN C 161 GLN ** C 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 GLN C 211 ASN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 158 HIS ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN H 81 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.175066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.136394 restraints weight = 26572.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.137079 restraints weight = 18269.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.138361 restraints weight = 15381.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.138769 restraints weight = 12241.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.139137 restraints weight = 11188.083| |-----------------------------------------------------------------------------| r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 14511 Z= 0.220 Angle : 0.799 15.043 19713 Z= 0.419 Chirality : 0.047 0.223 2143 Planarity : 0.006 0.076 2528 Dihedral : 5.903 57.468 2032 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.61 % Favored : 91.11 % Rotamer: Outliers : 3.53 % Allowed : 15.13 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.46 (0.19), residues: 1800 helix: -1.14 (0.49), residues: 88 sheet: 0.12 (0.24), residues: 484 loop : -1.51 (0.17), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 276 TYR 0.029 0.002 TYR F 22 PHE 0.019 0.002 PHE A 210 TRP 0.028 0.002 TRP H 35 HIS 0.008 0.002 HIS C 199 Details of bonding type rmsd covalent geometry : bond 0.00494 (14488) covalent geometry : angle 0.79586 (19666) SS BOND : bond 0.00798 ( 22) SS BOND : angle 1.75031 ( 44) hydrogen bonds : bond 0.04602 ( 367) hydrogen bonds : angle 6.37754 ( 867) link_NAG-ASN : bond 0.00247 ( 1) link_NAG-ASN : angle 1.26945 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 251 time to evaluate : 0.585 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: symmetry clash REVERT: A 5 MET cc_start: 0.5803 (tpp) cc_final: 0.5471 (tpp) REVERT: A 15 SER cc_start: 0.7584 (t) cc_final: 0.7306 (m) REVERT: A 21 THR cc_start: 0.6878 (t) cc_final: 0.6654 (t) REVERT: B 12 LEU cc_start: 0.8444 (pt) cc_final: 0.7903 (tt) REVERT: B 214 LYS cc_start: 0.7173 (tptt) cc_final: 0.6955 (tptt) REVERT: C 146 LYS cc_start: 0.6599 (ttpp) cc_final: 0.6059 (ttpt) REVERT: C 211 ASN cc_start: -0.0293 (OUTLIER) cc_final: -0.0571 (m110) REVERT: D 95 TYR cc_start: 0.6862 (OUTLIER) cc_final: 0.4454 (p90) REVERT: D 214 LYS cc_start: 0.7913 (tptt) cc_final: 0.7707 (tptt) REVERT: F 349 MET cc_start: 0.5610 (ppp) cc_final: 0.2758 (mmm) REVERT: G 35 TRP cc_start: 0.6445 (t-100) cc_final: 0.6062 (t-100) REVERT: G 94 TYR cc_start: 0.7939 (m-80) cc_final: 0.7623 (m-80) REVERT: G 112 GLN cc_start: 0.7704 (mm-40) cc_final: 0.7080 (pm20) REVERT: H 35 TRP cc_start: 0.6748 (m100) cc_final: 0.6400 (m100) REVERT: H 112 GLN cc_start: 0.6479 (mm-40) cc_final: 0.6226 (pp30) outliers start: 55 outliers final: 34 residues processed: 287 average time/residue: 0.1209 time to fit residues: 51.1536 Evaluate side-chains 252 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 216 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 88 TYR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 216 HIS Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 7 ASP Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 146 GLU Chi-restraints excluded: chain F residue 216 HIS Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 44 optimal weight: 9.9990 chunk 107 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 165 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 136 optimal weight: 5.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 GLN C 90 GLN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 ASN ** F 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 147 HIS F 253 HIS ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.163633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.121439 restraints weight = 29117.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.122835 restraints weight = 18219.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.125932 restraints weight = 13196.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.126099 restraints weight = 10857.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.126172 restraints weight = 9526.791| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.4594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 14511 Z= 0.302 Angle : 0.868 14.420 19713 Z= 0.464 Chirality : 0.049 0.230 2143 Planarity : 0.007 0.088 2528 Dihedral : 6.610 55.575 2030 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.78 % Favored : 90.00 % Rotamer: Outliers : 5.58 % Allowed : 19.42 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.14 (0.19), residues: 1800 helix: -1.88 (0.45), residues: 93 sheet: -0.35 (0.23), residues: 510 loop : -1.99 (0.17), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 40 TYR 0.041 0.003 TYR F 331 PHE 0.028 0.003 PHE A 210 TRP 0.020 0.002 TRP F 150 HIS 0.009 0.002 HIS C 199 Details of bonding type rmsd covalent geometry : bond 0.00686 (14488) covalent geometry : angle 0.86256 (19666) SS BOND : bond 0.01791 ( 22) SS BOND : angle 2.22978 ( 44) hydrogen bonds : bond 0.05615 ( 367) hydrogen bonds : angle 6.57106 ( 867) link_NAG-ASN : bond 0.00410 ( 1) link_NAG-ASN : angle 1.47943 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 233 time to evaluate : 0.544 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 15 SER cc_start: 0.7620 (t) cc_final: 0.7250 (m) REVERT: A 18 ASP cc_start: 0.7887 (t0) cc_final: 0.7437 (t0) REVERT: A 83 ASP cc_start: 0.6382 (m-30) cc_final: 0.6151 (m-30) REVERT: A 168 ASP cc_start: 0.7971 (t0) cc_final: 0.7689 (t0) REVERT: B 12 LEU cc_start: 0.8675 (pt) cc_final: 0.8027 (tt) REVERT: C 143 ARG cc_start: 0.6910 (tmt170) cc_final: 0.6528 (tmt-80) REVERT: D 106 TYR cc_start: 0.5279 (OUTLIER) cc_final: 0.3600 (m-10) REVERT: E 151 ASN cc_start: 0.8377 (t0) cc_final: 0.8156 (t0) REVERT: E 349 MET cc_start: 0.5644 (ttt) cc_final: 0.4597 (ptm) REVERT: G 72 ASP cc_start: 0.7950 (t70) cc_final: 0.7650 (t0) REVERT: G 79 TYR cc_start: 0.7575 (m-80) cc_final: 0.7298 (m-80) REVERT: G 112 GLN cc_start: 0.7755 (mm-40) cc_final: 0.7055 (pm20) REVERT: H 35 TRP cc_start: 0.7703 (m100) cc_final: 0.7479 (m100) REVERT: H 82 MET cc_start: 0.9094 (ptp) cc_final: 0.8150 (ppp) outliers start: 87 outliers final: 60 residues processed: 299 average time/residue: 0.1149 time to fit residues: 51.2551 Evaluate side-chains 268 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 207 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 170 PHE Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 88 TYR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain D residue 106 TYR Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 216 HIS Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 5 SER Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 146 GLU Chi-restraints excluded: chain F residue 216 HIS Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 239 SER Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 16 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 chunk 84 optimal weight: 9.9990 chunk 140 optimal weight: 1.9990 chunk 42 optimal weight: 9.9990 chunk 67 optimal weight: 0.9980 chunk 158 optimal weight: 9.9990 chunk 86 optimal weight: 5.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 ASN C 90 GLN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 95 ASN G 83 ASN H 2 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.165377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.121315 restraints weight = 28940.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.125009 restraints weight = 17247.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.127558 restraints weight = 12261.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.129025 restraints weight = 9828.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.130224 restraints weight = 8548.961| |-----------------------------------------------------------------------------| r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.5040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 14511 Z= 0.199 Angle : 0.784 19.068 19713 Z= 0.408 Chirality : 0.046 0.247 2143 Planarity : 0.006 0.097 2528 Dihedral : 6.049 56.308 2030 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.89 % Favored : 90.89 % Rotamer: Outliers : 6.03 % Allowed : 20.13 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.08 (0.19), residues: 1800 helix: -1.74 (0.45), residues: 93 sheet: -0.23 (0.24), residues: 451 loop : -1.93 (0.16), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 19 TYR 0.020 0.002 TYR F 331 PHE 0.021 0.002 PHE A 210 TRP 0.015 0.002 TRP E 150 HIS 0.005 0.001 HIS F 229 Details of bonding type rmsd covalent geometry : bond 0.00452 (14488) covalent geometry : angle 0.76944 (19666) SS BOND : bond 0.00722 ( 22) SS BOND : angle 3.27599 ( 44) hydrogen bonds : bond 0.04231 ( 367) hydrogen bonds : angle 6.15060 ( 867) link_NAG-ASN : bond 0.00089 ( 1) link_NAG-ASN : angle 1.00788 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 222 time to evaluate : 0.590 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 15 SER cc_start: 0.7755 (t) cc_final: 0.7374 (m) REVERT: A 18 ASP cc_start: 0.7857 (t0) cc_final: 0.7085 (m-30) REVERT: A 32 SER cc_start: 0.8082 (OUTLIER) cc_final: 0.7413 (t) REVERT: A 83 ASP cc_start: 0.6507 (m-30) cc_final: 0.6286 (m-30) REVERT: A 168 ASP cc_start: 0.8121 (t0) cc_final: 0.7715 (t0) REVERT: B 12 LEU cc_start: 0.8563 (pt) cc_final: 0.8052 (tt) REVERT: B 89 GLU cc_start: 0.6405 (OUTLIER) cc_final: 0.5757 (mt-10) REVERT: B 199 ILE cc_start: 0.7702 (mt) cc_final: 0.7473 (mm) REVERT: C 32 SER cc_start: 0.8015 (OUTLIER) cc_final: 0.7342 (t) REVERT: C 88 TYR cc_start: 0.5869 (OUTLIER) cc_final: 0.3306 (p90) REVERT: C 90 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.8114 (tm130) REVERT: C 143 ARG cc_start: 0.6580 (OUTLIER) cc_final: 0.6266 (tmt-80) REVERT: D 32 SER cc_start: 0.7024 (OUTLIER) cc_final: 0.6789 (p) REVERT: D 82 GLN cc_start: 0.7255 (tp40) cc_final: 0.7011 (tp40) REVERT: D 95 TYR cc_start: 0.7043 (OUTLIER) cc_final: 0.5261 (p90) REVERT: E 67 MET cc_start: 0.9190 (tmm) cc_final: 0.8905 (tpp) REVERT: E 151 ASN cc_start: 0.8345 (t0) cc_final: 0.8144 (t0) REVERT: F 22 TYR cc_start: 0.7239 (m-80) cc_final: 0.7032 (m-80) REVERT: F 26 GLU cc_start: 0.7058 (mp0) cc_final: 0.6154 (pp20) REVERT: F 28 TRP cc_start: 0.5052 (OUTLIER) cc_final: 0.3506 (m-90) REVERT: F 210 TRP cc_start: 0.8195 (m100) cc_final: 0.7981 (m100) REVERT: F 233 THR cc_start: 0.8325 (OUTLIER) cc_final: 0.7773 (t) REVERT: F 318 MET cc_start: 0.6860 (tmm) cc_final: 0.6460 (tmm) REVERT: G 35 TRP cc_start: 0.7573 (t-100) cc_final: 0.7041 (m100) REVERT: G 112 GLN cc_start: 0.7718 (mm-40) cc_final: 0.7057 (pm20) REVERT: H 31 TYR cc_start: 0.6881 (m-80) cc_final: 0.6586 (m-80) REVERT: H 35 TRP cc_start: 0.7586 (m100) cc_final: 0.7366 (m100) REVERT: H 76 ASN cc_start: 0.4543 (t0) cc_final: 0.4306 (t0) REVERT: H 82 MET cc_start: 0.9175 (ptp) cc_final: 0.8450 (tmm) outliers start: 94 outliers final: 57 residues processed: 295 average time/residue: 0.1112 time to fit residues: 49.5586 Evaluate side-chains 276 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 209 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 170 PHE Chi-restraints excluded: chain B residue 213 LYS Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 88 TYR Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain C residue 143 ARG Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain E residue 55 CYS Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 216 HIS Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 4 CYS Chi-restraints excluded: chain F residue 5 SER Chi-restraints excluded: chain F residue 7 ASP Chi-restraints excluded: chain F residue 28 TRP Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 146 GLU Chi-restraints excluded: chain F residue 216 HIS Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 221 LYS Chi-restraints excluded: chain F residue 233 THR Chi-restraints excluded: chain F residue 239 SER Chi-restraints excluded: chain F residue 329 CYS Chi-restraints excluded: chain G residue 30 ARG Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain H residue 2 GLN Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 108 optimal weight: 0.9990 chunk 105 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 171 optimal weight: 9.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 GLN C 80 GLN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.165128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.122643 restraints weight = 27933.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.125486 restraints weight = 17138.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.126817 restraints weight = 11559.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.127900 restraints weight = 10675.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.128133 restraints weight = 9266.610| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.5276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14511 Z= 0.161 Angle : 0.730 15.830 19713 Z= 0.378 Chirality : 0.044 0.245 2143 Planarity : 0.006 0.077 2528 Dihedral : 5.710 55.024 2030 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.00 % Favored : 90.78 % Rotamer: Outliers : 4.55 % Allowed : 22.69 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.91 (0.19), residues: 1800 helix: -1.61 (0.45), residues: 93 sheet: -0.16 (0.24), residues: 471 loop : -1.81 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 40 TYR 0.017 0.002 TYR G 79 PHE 0.022 0.002 PHE A 210 TRP 0.019 0.001 TRP F 115 HIS 0.003 0.001 HIS F 229 Details of bonding type rmsd covalent geometry : bond 0.00360 (14488) covalent geometry : angle 0.71677 (19666) SS BOND : bond 0.00579 ( 22) SS BOND : angle 3.01956 ( 44) hydrogen bonds : bond 0.03854 ( 367) hydrogen bonds : angle 5.86648 ( 867) link_NAG-ASN : bond 0.00110 ( 1) link_NAG-ASN : angle 1.00805 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 225 time to evaluate : 0.568 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 15 SER cc_start: 0.7825 (t) cc_final: 0.7490 (m) REVERT: A 18 ASP cc_start: 0.7930 (t0) cc_final: 0.7216 (m-30) REVERT: A 32 SER cc_start: 0.8040 (OUTLIER) cc_final: 0.7423 (t) REVERT: A 83 ASP cc_start: 0.6598 (m-30) cc_final: 0.6387 (m-30) REVERT: A 168 ASP cc_start: 0.8375 (t0) cc_final: 0.7889 (t0) REVERT: B 12 LEU cc_start: 0.8581 (pt) cc_final: 0.8054 (tt) REVERT: B 89 GLU cc_start: 0.6515 (OUTLIER) cc_final: 0.5859 (mt-10) REVERT: C 32 SER cc_start: 0.7937 (OUTLIER) cc_final: 0.7335 (t) REVERT: C 88 TYR cc_start: 0.5883 (OUTLIER) cc_final: 0.4215 (p90) REVERT: C 143 ARG cc_start: 0.6477 (OUTLIER) cc_final: 0.6179 (tmt-80) REVERT: D 7 GLU cc_start: 0.7213 (mp0) cc_final: 0.6990 (mp0) REVERT: D 32 SER cc_start: 0.7040 (p) cc_final: 0.6741 (p) REVERT: D 82 GLN cc_start: 0.7354 (tp40) cc_final: 0.7094 (tp40) REVERT: D 95 TYR cc_start: 0.7163 (OUTLIER) cc_final: 0.5707 (p90) REVERT: E 67 MET cc_start: 0.9170 (tmm) cc_final: 0.8867 (tpp) REVERT: E 349 MET cc_start: 0.5795 (ttt) cc_final: 0.4804 (ptt) REVERT: F 5 SER cc_start: 0.8944 (OUTLIER) cc_final: 0.8709 (p) REVERT: F 26 GLU cc_start: 0.7076 (mp0) cc_final: 0.6219 (pp20) REVERT: F 28 TRP cc_start: 0.4936 (OUTLIER) cc_final: 0.3538 (m-90) REVERT: F 233 THR cc_start: 0.8228 (OUTLIER) cc_final: 0.7696 (t) REVERT: F 318 MET cc_start: 0.6843 (tmm) cc_final: 0.6503 (tmm) REVERT: F 349 MET cc_start: 0.7235 (ppp) cc_final: 0.6920 (ppp) REVERT: G 19 LEU cc_start: 0.9395 (tt) cc_final: 0.9035 (mm) REVERT: G 35 TRP cc_start: 0.7423 (t-100) cc_final: 0.7037 (m100) REVERT: G 94 TYR cc_start: 0.8140 (m-80) cc_final: 0.7750 (m-80) REVERT: G 112 GLN cc_start: 0.7702 (mm-40) cc_final: 0.7055 (pm20) REVERT: H 17 LEU cc_start: 0.8668 (mp) cc_final: 0.8260 (mp) REVERT: H 18 ARG cc_start: 0.8452 (mmm160) cc_final: 0.8229 (mmm160) REVERT: H 31 TYR cc_start: 0.6776 (m-80) cc_final: 0.6455 (m-80) REVERT: H 35 TRP cc_start: 0.7486 (m100) cc_final: 0.7248 (m100) REVERT: H 82 MET cc_start: 0.9097 (ptp) cc_final: 0.8452 (tmm) outliers start: 71 outliers final: 52 residues processed: 280 average time/residue: 0.1141 time to fit residues: 47.9344 Evaluate side-chains 275 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 214 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 170 PHE Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 88 TYR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 143 ARG Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain D residue 13 ILE Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain E residue 34 TYR Chi-restraints excluded: chain E residue 55 CYS Chi-restraints excluded: chain E residue 176 SER Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 216 HIS Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 4 CYS Chi-restraints excluded: chain F residue 5 SER Chi-restraints excluded: chain F residue 7 ASP Chi-restraints excluded: chain F residue 15 CYS Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 28 TRP Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 216 HIS Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 221 LYS Chi-restraints excluded: chain F residue 233 THR Chi-restraints excluded: chain F residue 239 SER Chi-restraints excluded: chain F residue 329 CYS Chi-restraints excluded: chain G residue 30 ARG Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 115 optimal weight: 0.5980 chunk 22 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 1 optimal weight: 6.9990 chunk 118 optimal weight: 0.9990 chunk 173 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 168 optimal weight: 30.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 GLN ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 2 GLN ** 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 = 0.4268 r_free = 0.4268 target = 0.166376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.122722 restraints weight = 27547.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.126432 restraints weight = 16219.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.129005 restraints weight = 11478.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.130698 restraints weight = 9134.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.131811 restraints weight = 7829.583| |-----------------------------------------------------------------------------| r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.5523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14511 Z= 0.143 Angle : 0.701 14.256 19713 Z= 0.363 Chirality : 0.044 0.232 2143 Planarity : 0.005 0.074 2528 Dihedral : 5.425 54.737 2030 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.94 % Favored : 91.83 % Rotamer: Outliers : 4.17 % Allowed : 23.53 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.79 (0.19), residues: 1800 helix: -1.53 (0.45), residues: 96 sheet: 0.01 (0.24), residues: 461 loop : -1.75 (0.17), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 40 TYR 0.026 0.001 TYR D 180 PHE 0.020 0.002 PHE A 210 TRP 0.013 0.001 TRP E 210 HIS 0.003 0.001 HIS F 229 Details of bonding type rmsd covalent geometry : bond 0.00318 (14488) covalent geometry : angle 0.68965 (19666) SS BOND : bond 0.00509 ( 22) SS BOND : angle 2.77375 ( 44) hydrogen bonds : bond 0.03570 ( 367) hydrogen bonds : angle 5.64207 ( 867) link_NAG-ASN : bond 0.00173 ( 1) link_NAG-ASN : angle 0.92717 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 225 time to evaluate : 0.537 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 15 SER cc_start: 0.7816 (t) cc_final: 0.7583 (m) REVERT: A 18 ASP cc_start: 0.7847 (t0) cc_final: 0.7317 (m-30) REVERT: A 32 SER cc_start: 0.7911 (OUTLIER) cc_final: 0.7320 (t) REVERT: A 168 ASP cc_start: 0.8480 (t0) cc_final: 0.8067 (t0) REVERT: B 12 LEU cc_start: 0.8525 (pt) cc_final: 0.8042 (tt) REVERT: B 82 GLN cc_start: 0.6783 (tp-100) cc_final: 0.6518 (mm-40) REVERT: B 89 GLU cc_start: 0.6504 (OUTLIER) cc_final: 0.5796 (mt-10) REVERT: C 32 SER cc_start: 0.7933 (OUTLIER) cc_final: 0.7318 (t) REVERT: C 39 GLN cc_start: 0.7055 (tt0) cc_final: 0.6577 (tt0) REVERT: C 88 TYR cc_start: 0.5788 (OUTLIER) cc_final: 0.4099 (p90) REVERT: C 143 ARG cc_start: 0.6363 (OUTLIER) cc_final: 0.6068 (tmt-80) REVERT: D 95 TYR cc_start: 0.7060 (OUTLIER) cc_final: 0.5222 (p90) REVERT: E 67 MET cc_start: 0.9107 (tmm) cc_final: 0.8860 (tpp) REVERT: E 85 GLN cc_start: 0.7498 (tp40) cc_final: 0.7137 (tp40) REVERT: E 349 MET cc_start: 0.5811 (ttt) cc_final: 0.4792 (ptt) REVERT: F 5 SER cc_start: 0.9002 (OUTLIER) cc_final: 0.8744 (p) REVERT: F 26 GLU cc_start: 0.7269 (mp0) cc_final: 0.6930 (mp0) REVERT: F 28 TRP cc_start: 0.4838 (OUTLIER) cc_final: 0.3435 (m-90) REVERT: F 233 THR cc_start: 0.8088 (OUTLIER) cc_final: 0.7554 (t) REVERT: F 318 MET cc_start: 0.6812 (tmm) cc_final: 0.6531 (tmm) REVERT: F 349 MET cc_start: 0.7142 (ppp) cc_final: 0.6896 (ppp) REVERT: G 19 LEU cc_start: 0.9358 (tt) cc_final: 0.8991 (mm) REVERT: G 35 TRP cc_start: 0.7210 (t-100) cc_final: 0.6962 (m100) REVERT: G 94 TYR cc_start: 0.8216 (m-80) cc_final: 0.7894 (m-80) REVERT: G 112 GLN cc_start: 0.7591 (mm-40) cc_final: 0.7020 (pm20) REVERT: H 17 LEU cc_start: 0.8756 (mp) cc_final: 0.8369 (mp) REVERT: H 18 ARG cc_start: 0.8538 (mmm160) cc_final: 0.8300 (mmm160) REVERT: H 31 TYR cc_start: 0.6925 (m-80) cc_final: 0.6607 (m-80) REVERT: H 35 TRP cc_start: 0.7433 (m100) cc_final: 0.7207 (m100) REVERT: H 82 MET cc_start: 0.9022 (ptp) cc_final: 0.8506 (tmm) REVERT: H 112 GLN cc_start: 0.6299 (mm-40) cc_final: 0.5821 (mp10) outliers start: 65 outliers final: 40 residues processed: 275 average time/residue: 0.1101 time to fit residues: 45.7300 Evaluate side-chains 264 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 215 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 170 PHE Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 88 TYR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 143 ARG Chi-restraints excluded: chain D residue 13 ILE Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain E residue 55 CYS Chi-restraints excluded: chain E residue 216 HIS Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 4 CYS Chi-restraints excluded: chain F residue 5 SER Chi-restraints excluded: chain F residue 7 ASP Chi-restraints excluded: chain F residue 15 CYS Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 28 TRP Chi-restraints excluded: chain F residue 216 HIS Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 221 LYS Chi-restraints excluded: chain F residue 233 THR Chi-restraints excluded: chain F residue 239 SER Chi-restraints excluded: chain F residue 329 CYS Chi-restraints excluded: chain G residue 30 ARG Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 103 optimal weight: 4.9990 chunk 161 optimal weight: 10.0000 chunk 154 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 31 optimal weight: 0.9980 chunk 131 optimal weight: 0.0980 chunk 50 optimal weight: 4.9990 chunk 114 optimal weight: 0.0970 overall best weight: 1.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 2 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 = 0.4229 r_free = 0.4229 target = 0.163009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.119418 restraints weight = 27642.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.122970 restraints weight = 16695.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.125366 restraints weight = 11917.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.126921 restraints weight = 9573.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.127977 restraints weight = 8291.484| |-----------------------------------------------------------------------------| r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.5933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 14511 Z= 0.192 Angle : 0.748 16.076 19713 Z= 0.390 Chirality : 0.045 0.234 2143 Planarity : 0.006 0.084 2528 Dihedral : 5.716 54.870 2030 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.61 % Favored : 90.22 % Rotamer: Outliers : 5.06 % Allowed : 24.04 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.88 (0.19), residues: 1800 helix: -1.66 (0.46), residues: 88 sheet: -0.02 (0.25), residues: 454 loop : -1.82 (0.17), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 40 TYR 0.027 0.002 TYR D 149 PHE 0.020 0.002 PHE A 210 TRP 0.014 0.001 TRP E 225 HIS 0.005 0.001 HIS F 164 Details of bonding type rmsd covalent geometry : bond 0.00441 (14488) covalent geometry : angle 0.73576 (19666) SS BOND : bond 0.00680 ( 22) SS BOND : angle 2.94312 ( 44) hydrogen bonds : bond 0.04027 ( 367) hydrogen bonds : angle 5.82594 ( 867) link_NAG-ASN : bond 0.00559 ( 1) link_NAG-ASN : angle 1.21274 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 216 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 SER cc_start: 0.7719 (t) cc_final: 0.7504 (m) REVERT: A 18 ASP cc_start: 0.8131 (t0) cc_final: 0.7383 (m-30) REVERT: A 32 SER cc_start: 0.8101 (OUTLIER) cc_final: 0.7500 (t) REVERT: B 12 LEU cc_start: 0.8546 (pt) cc_final: 0.8058 (tt) REVERT: B 82 GLN cc_start: 0.6728 (tp-100) cc_final: 0.6439 (mm-40) REVERT: B 89 GLU cc_start: 0.6330 (OUTLIER) cc_final: 0.5449 (mt-10) REVERT: C 32 SER cc_start: 0.8115 (OUTLIER) cc_final: 0.7475 (t) REVERT: C 143 ARG cc_start: 0.6746 (OUTLIER) cc_final: 0.6446 (tmt-80) REVERT: D 95 TYR cc_start: 0.7127 (OUTLIER) cc_final: 0.5559 (p90) REVERT: E 67 MET cc_start: 0.9072 (tmm) cc_final: 0.8825 (tpp) REVERT: E 85 GLN cc_start: 0.7662 (tp40) cc_final: 0.7254 (tp40) REVERT: E 349 MET cc_start: 0.5629 (ttt) cc_final: 0.4694 (ptm) REVERT: F 26 GLU cc_start: 0.7269 (mp0) cc_final: 0.6956 (mp0) REVERT: F 28 TRP cc_start: 0.4673 (OUTLIER) cc_final: 0.3504 (m-90) REVERT: F 318 MET cc_start: 0.6835 (tmm) cc_final: 0.6275 (tmm) REVERT: G 19 LEU cc_start: 0.9365 (tt) cc_final: 0.9021 (mm) REVERT: G 35 TRP cc_start: 0.7343 (t-100) cc_final: 0.6991 (m100) REVERT: G 112 GLN cc_start: 0.7561 (mm-40) cc_final: 0.7046 (pm20) REVERT: H 17 LEU cc_start: 0.8766 (mp) cc_final: 0.7747 (mp) REVERT: H 31 TYR cc_start: 0.7074 (m-80) cc_final: 0.6734 (m-80) REVERT: H 35 TRP cc_start: 0.7459 (m100) cc_final: 0.7050 (m100) REVERT: H 82 MET cc_start: 0.9038 (ptp) cc_final: 0.8463 (ppp) outliers start: 79 outliers final: 59 residues processed: 275 average time/residue: 0.1104 time to fit residues: 45.9626 Evaluate side-chains 271 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 206 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 141 TYR Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 170 PHE Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 88 TYR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 143 ARG Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 199 HIS Chi-restraints excluded: chain D residue 13 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 34 TYR Chi-restraints excluded: chain E residue 55 CYS Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 216 HIS Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 4 CYS Chi-restraints excluded: chain F residue 15 CYS Chi-restraints excluded: chain F residue 28 TRP Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 216 HIS Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 221 LYS Chi-restraints excluded: chain F residue 233 THR Chi-restraints excluded: chain F residue 239 SER Chi-restraints excluded: chain F residue 329 CYS Chi-restraints excluded: chain G residue 30 ARG Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 9 optimal weight: 0.6980 chunk 22 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 115 optimal weight: 4.9990 chunk 143 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 153 optimal weight: 0.4980 chunk 81 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 74 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.166318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.126034 restraints weight = 27134.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.128904 restraints weight = 17257.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.129424 restraints weight = 11991.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.129861 restraints weight = 10133.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.130115 restraints weight = 9532.832| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.6036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14511 Z= 0.137 Angle : 0.696 13.600 19713 Z= 0.361 Chirality : 0.044 0.258 2143 Planarity : 0.005 0.075 2528 Dihedral : 5.301 54.006 2030 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.83 % Favored : 92.00 % Rotamer: Outliers : 3.78 % Allowed : 25.26 % Favored : 70.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.69 (0.19), residues: 1800 helix: -1.30 (0.49), residues: 90 sheet: 0.11 (0.24), residues: 465 loop : -1.71 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 19 TYR 0.020 0.001 TYR D 149 PHE 0.017 0.001 PHE C 119 TRP 0.017 0.001 TRP E 210 HIS 0.003 0.001 HIS F 195 Details of bonding type rmsd covalent geometry : bond 0.00302 (14488) covalent geometry : angle 0.68625 (19666) SS BOND : bond 0.00492 ( 22) SS BOND : angle 2.58939 ( 44) hydrogen bonds : bond 0.03448 ( 367) hydrogen bonds : angle 5.52386 ( 867) link_NAG-ASN : bond 0.00107 ( 1) link_NAG-ASN : angle 1.12238 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 215 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ASP cc_start: 0.8202 (t0) cc_final: 0.7405 (m-30) REVERT: A 21 THR cc_start: 0.7103 (OUTLIER) cc_final: 0.6825 (t) REVERT: A 32 SER cc_start: 0.7949 (OUTLIER) cc_final: 0.7386 (t) REVERT: B 12 LEU cc_start: 0.8609 (pt) cc_final: 0.8118 (tt) REVERT: B 89 GLU cc_start: 0.6550 (OUTLIER) cc_final: 0.5878 (mt-10) REVERT: C 32 SER cc_start: 0.7880 (OUTLIER) cc_final: 0.7307 (t) REVERT: D 95 TYR cc_start: 0.7008 (OUTLIER) cc_final: 0.5286 (p90) REVERT: E 67 MET cc_start: 0.9047 (tmm) cc_final: 0.8786 (tpp) REVERT: E 85 GLN cc_start: 0.7667 (tp40) cc_final: 0.7259 (tp40) REVERT: E 349 MET cc_start: 0.5527 (ttt) cc_final: 0.4544 (ptt) REVERT: F 26 GLU cc_start: 0.7266 (mp0) cc_final: 0.7015 (mp0) REVERT: F 28 TRP cc_start: 0.4823 (OUTLIER) cc_final: 0.3624 (m-90) REVERT: F 233 THR cc_start: 0.8088 (OUTLIER) cc_final: 0.7517 (t) REVERT: F 318 MET cc_start: 0.6894 (tmm) cc_final: 0.6652 (tmm) REVERT: G 19 LEU cc_start: 0.9314 (tt) cc_final: 0.8952 (mm) REVERT: G 21 CYS cc_start: 0.5251 (t) cc_final: 0.4051 (t) REVERT: G 98 ASP cc_start: 0.7572 (t0) cc_final: 0.7346 (t0) REVERT: G 112 GLN cc_start: 0.7506 (mm-40) cc_final: 0.6483 (pp30) REVERT: H 17 LEU cc_start: 0.8741 (mp) cc_final: 0.7599 (mp) REVERT: H 31 TYR cc_start: 0.7037 (m-80) cc_final: 0.6694 (m-80) REVERT: H 35 TRP cc_start: 0.7107 (m100) cc_final: 0.6806 (m100) REVERT: H 82 MET cc_start: 0.8882 (ptp) cc_final: 0.8384 (ppp) outliers start: 59 outliers final: 45 residues processed: 256 average time/residue: 0.1060 time to fit residues: 41.8611 Evaluate side-chains 260 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 208 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 170 PHE Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 141 TYR Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain E residue 34 TYR Chi-restraints excluded: chain E residue 55 CYS Chi-restraints excluded: chain E residue 216 HIS Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 4 CYS Chi-restraints excluded: chain F residue 15 CYS Chi-restraints excluded: chain F residue 28 TRP Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 164 HIS Chi-restraints excluded: chain F residue 216 HIS Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 221 LYS Chi-restraints excluded: chain F residue 233 THR Chi-restraints excluded: chain F residue 239 SER Chi-restraints excluded: chain H residue 55 ASP Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 80 optimal weight: 10.0000 chunk 108 optimal weight: 0.8980 chunk 165 optimal weight: 6.9990 chunk 166 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 139 optimal weight: 0.8980 chunk 115 optimal weight: 0.2980 chunk 156 optimal weight: 8.9990 chunk 119 optimal weight: 0.9980 chunk 172 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 GLN ** C 90 GLN ** 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 = 0.4263 r_free = 0.4263 target = 0.165764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.126500 restraints weight = 27361.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.129162 restraints weight = 17625.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.129813 restraints weight = 11802.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.130308 restraints weight = 10564.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.130532 restraints weight = 9823.260| |-----------------------------------------------------------------------------| r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 moved from start: 0.6234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14511 Z= 0.141 Angle : 0.708 13.478 19713 Z= 0.367 Chirality : 0.044 0.258 2143 Planarity : 0.005 0.075 2528 Dihedral : 5.276 54.277 2030 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.39 % Favored : 91.39 % Rotamer: Outliers : 3.59 % Allowed : 25.51 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.60 (0.19), residues: 1800 helix: -1.46 (0.48), residues: 90 sheet: 0.31 (0.25), residues: 438 loop : -1.65 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 19 TYR 0.017 0.001 TYR D 149 PHE 0.020 0.001 PHE H 36 TRP 0.021 0.001 TRP G 35 HIS 0.003 0.001 HIS F 195 Details of bonding type rmsd covalent geometry : bond 0.00314 (14488) covalent geometry : angle 0.69715 (19666) SS BOND : bond 0.00519 ( 22) SS BOND : angle 2.64846 ( 44) hydrogen bonds : bond 0.03430 ( 367) hydrogen bonds : angle 5.43882 ( 867) link_NAG-ASN : bond 0.00163 ( 1) link_NAG-ASN : angle 1.17402 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 214 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ASP cc_start: 0.8229 (t0) cc_final: 0.7405 (m-30) REVERT: A 21 THR cc_start: 0.7168 (OUTLIER) cc_final: 0.6881 (t) REVERT: B 5 LEU cc_start: 0.5376 (OUTLIER) cc_final: 0.5166 (mp) REVERT: B 12 LEU cc_start: 0.8614 (pt) cc_final: 0.8135 (tt) REVERT: B 47 GLU cc_start: 0.6859 (tp30) cc_final: 0.5798 (mt-10) REVERT: B 89 GLU cc_start: 0.6540 (OUTLIER) cc_final: 0.5871 (mt-10) REVERT: C 2 ASP cc_start: 0.7729 (OUTLIER) cc_final: 0.7470 (m-30) REVERT: C 32 SER cc_start: 0.7993 (OUTLIER) cc_final: 0.7379 (t) REVERT: C 39 GLN cc_start: 0.7023 (tt0) cc_final: 0.6521 (tt0) REVERT: C 88 TYR cc_start: 0.5536 (OUTLIER) cc_final: 0.4048 (p90) REVERT: D 95 TYR cc_start: 0.7028 (OUTLIER) cc_final: 0.5068 (p90) REVERT: E 67 MET cc_start: 0.9038 (tmm) cc_final: 0.8777 (tpp) REVERT: E 85 GLN cc_start: 0.7675 (tp40) cc_final: 0.7115 (tp40) REVERT: E 220 MET cc_start: 0.8521 (mmt) cc_final: 0.8130 (mpp) REVERT: E 349 MET cc_start: 0.5545 (ttt) cc_final: 0.4593 (ptm) REVERT: F 26 GLU cc_start: 0.7328 (mp0) cc_final: 0.7091 (mp0) REVERT: F 28 TRP cc_start: 0.4945 (OUTLIER) cc_final: 0.3728 (m-90) REVERT: F 318 MET cc_start: 0.6847 (tmm) cc_final: 0.6609 (tmm) REVERT: G 19 LEU cc_start: 0.9350 (tt) cc_final: 0.8990 (mm) REVERT: G 30 ARG cc_start: 0.7596 (tpp-160) cc_final: 0.7130 (ptt90) REVERT: G 98 ASP cc_start: 0.7476 (t0) cc_final: 0.7117 (t0) REVERT: G 112 GLN cc_start: 0.7384 (mm-40) cc_final: 0.6588 (pp30) REVERT: H 17 LEU cc_start: 0.8768 (mp) cc_final: 0.7645 (mp) REVERT: H 31 TYR cc_start: 0.7024 (m-80) cc_final: 0.6663 (m-80) REVERT: H 35 TRP cc_start: 0.7003 (m100) cc_final: 0.6708 (m100) REVERT: H 82 MET cc_start: 0.8783 (ptp) cc_final: 0.8382 (ppp) outliers start: 56 outliers final: 46 residues processed: 254 average time/residue: 0.1103 time to fit residues: 43.0355 Evaluate side-chains 258 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 204 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 170 PHE Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 88 TYR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 141 TYR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 199 HIS Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain E residue 34 TYR Chi-restraints excluded: chain E residue 55 CYS Chi-restraints excluded: chain E residue 216 HIS Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 4 CYS Chi-restraints excluded: chain F residue 15 CYS Chi-restraints excluded: chain F residue 28 TRP Chi-restraints excluded: chain F residue 164 HIS Chi-restraints excluded: chain F residue 216 HIS Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 221 LYS Chi-restraints excluded: chain F residue 239 SER Chi-restraints excluded: chain F residue 329 CYS Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 0.0670 chunk 100 optimal weight: 0.8980 chunk 171 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 166 optimal weight: 0.4980 chunk 31 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 167 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 122 optimal weight: 0.0970 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN A 156 GLN B 40 GLN C 90 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.168242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.125143 restraints weight = 27142.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.129507 restraints weight = 17092.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.131016 restraints weight = 10492.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.133160 restraints weight = 9368.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.133015 restraints weight = 8031.908| |-----------------------------------------------------------------------------| r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.6326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14511 Z= 0.129 Angle : 0.689 13.110 19713 Z= 0.354 Chirality : 0.043 0.235 2143 Planarity : 0.005 0.077 2528 Dihedral : 5.076 53.533 2030 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.50 % Favored : 92.28 % Rotamer: Outliers : 3.27 % Allowed : 26.15 % Favored : 70.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.45 (0.19), residues: 1800 helix: -1.41 (0.50), residues: 90 sheet: 0.37 (0.25), residues: 455 loop : -1.55 (0.17), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 19 TYR 0.016 0.001 TYR D 149 PHE 0.022 0.001 PHE H 36 TRP 0.018 0.001 TRP E 210 HIS 0.003 0.001 HIS F 113 Details of bonding type rmsd covalent geometry : bond 0.00285 (14488) covalent geometry : angle 0.67878 (19666) SS BOND : bond 0.00481 ( 22) SS BOND : angle 2.52577 ( 44) hydrogen bonds : bond 0.03278 ( 367) hydrogen bonds : angle 5.41608 ( 867) link_NAG-ASN : bond 0.00299 ( 1) link_NAG-ASN : angle 1.26171 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 214 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ASP cc_start: 0.8019 (t0) cc_final: 0.7385 (m-30) REVERT: A 19 ARG cc_start: 0.7186 (ttt-90) cc_final: 0.6812 (mmm160) REVERT: A 21 THR cc_start: 0.7198 (OUTLIER) cc_final: 0.6918 (t) REVERT: A 32 SER cc_start: 0.7789 (OUTLIER) cc_final: 0.7258 (t) REVERT: B 12 LEU cc_start: 0.8567 (pt) cc_final: 0.8153 (tt) REVERT: B 47 GLU cc_start: 0.6853 (tp30) cc_final: 0.5928 (mt-10) REVERT: B 89 GLU cc_start: 0.6522 (OUTLIER) cc_final: 0.5864 (mt-10) REVERT: C 2 ASP cc_start: 0.7642 (OUTLIER) cc_final: 0.7331 (m-30) REVERT: C 19 ARG cc_start: 0.6737 (tmm160) cc_final: 0.5487 (tpt170) REVERT: C 32 SER cc_start: 0.7898 (OUTLIER) cc_final: 0.7319 (t) REVERT: C 37 TYR cc_start: 0.7021 (m-80) cc_final: 0.6790 (m-80) REVERT: C 39 GLN cc_start: 0.6872 (tt0) cc_final: 0.6367 (tt0) REVERT: C 88 TYR cc_start: 0.5436 (OUTLIER) cc_final: 0.3899 (p90) REVERT: C 90 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.7754 (tm130) REVERT: D 21 LEU cc_start: 0.6644 (mt) cc_final: 0.6429 (mt) REVERT: D 95 TYR cc_start: 0.6623 (OUTLIER) cc_final: 0.4170 (p90) REVERT: E 67 MET cc_start: 0.9075 (tmm) cc_final: 0.8823 (tpp) REVERT: E 85 GLN cc_start: 0.7618 (tp40) cc_final: 0.7246 (tp40) REVERT: E 220 MET cc_start: 0.8512 (mmt) cc_final: 0.8148 (mpp) REVERT: E 349 MET cc_start: 0.5457 (ttt) cc_final: 0.4795 (ptm) REVERT: F 28 TRP cc_start: 0.4784 (OUTLIER) cc_final: 0.3417 (m-90) REVERT: G 19 LEU cc_start: 0.9394 (tt) cc_final: 0.9102 (mm) REVERT: G 98 ASP cc_start: 0.7591 (t0) cc_final: 0.7387 (t0) REVERT: G 112 GLN cc_start: 0.7551 (mm-40) cc_final: 0.6692 (pp30) REVERT: H 17 LEU cc_start: 0.8657 (mp) cc_final: 0.7578 (mp) REVERT: H 31 TYR cc_start: 0.7183 (m-80) cc_final: 0.6782 (m-80) REVERT: H 35 TRP cc_start: 0.7538 (m100) cc_final: 0.7058 (m100) REVERT: H 82 MET cc_start: 0.9050 (ptp) cc_final: 0.8358 (ppp) outliers start: 51 outliers final: 35 residues processed: 252 average time/residue: 0.1103 time to fit residues: 42.1365 Evaluate side-chains 250 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 206 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 88 TYR Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 141 TYR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 199 HIS Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain E residue 34 TYR Chi-restraints excluded: chain E residue 55 CYS Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 4 CYS Chi-restraints excluded: chain F residue 15 CYS Chi-restraints excluded: chain F residue 28 TRP Chi-restraints excluded: chain F residue 216 HIS Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 221 LYS Chi-restraints excluded: chain F residue 329 CYS Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 33 optimal weight: 0.7980 chunk 129 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 115 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 135 optimal weight: 0.0170 chunk 155 optimal weight: 0.0030 chunk 66 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 138 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.4228 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 90 GLN ** C 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 201 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.168057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.128434 restraints weight = 27180.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.131480 restraints weight = 17164.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.131750 restraints weight = 11638.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.132837 restraints weight = 10139.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.132922 restraints weight = 9129.507| |-----------------------------------------------------------------------------| r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.6359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.130 14511 Z= 0.165 Angle : 0.895 59.143 19713 Z= 0.493 Chirality : 0.045 0.544 2143 Planarity : 0.005 0.076 2528 Dihedral : 5.077 53.524 2030 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.44 % Favored : 92.28 % Rotamer: Outliers : 2.95 % Allowed : 26.73 % Favored : 70.32 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 15.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.44 (0.19), residues: 1800 helix: -1.40 (0.50), residues: 90 sheet: 0.39 (0.25), residues: 455 loop : -1.54 (0.17), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 19 TYR 0.040 0.001 TYR C 174 PHE 0.019 0.001 PHE H 36 TRP 0.016 0.001 TRP E 210 HIS 0.003 0.001 HIS F 113 Details of bonding type rmsd covalent geometry : bond 0.00372 (14488) covalent geometry : angle 0.88773 (19666) SS BOND : bond 0.00446 ( 22) SS BOND : angle 2.51257 ( 44) hydrogen bonds : bond 0.03290 ( 367) hydrogen bonds : angle 5.43562 ( 867) link_NAG-ASN : bond 0.00308 ( 1) link_NAG-ASN : angle 1.25388 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2650.78 seconds wall clock time: 46 minutes 44.23 seconds (2804.23 seconds total)