Starting phenix.real_space_refine on Thu Jun 12 17:04:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wnu_37673/06_2025/8wnu_37673.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wnu_37673/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8wnu_37673/06_2025/8wnu_37673.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wnu_37673/06_2025/8wnu_37673.map" model { file = "/net/cci-nas-00/data/ceres_data/8wnu_37673/06_2025/8wnu_37673.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wnu_37673/06_2025/8wnu_37673.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.024 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.91, per 1000 atoms: 0.70 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: 3.34 Conformation dependent library (CDL) restraints added in 3.0 seconds 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: 1.85 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: 4.69 Time building geometry restraints manager: 4.07 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: 0.03 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 18.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 35.730 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.070 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.860 ------------------------------------------------------------------------------- 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 : 9.85 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (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 TRP 0.011 0.001 TRP E 210 HIS 0.005 0.001 HIS C 199 PHE 0.020 0.001 PHE A 210 TYR 0.017 0.001 TYR F 22 ARG 0.012 0.000 ARG E 14 Details of bonding type rmsd link_NAG-ASN : bond 0.00272 ( 1) link_NAG-ASN : angle 0.71261 ( 3) hydrogen bonds : bond 0.28225 ( 367) hydrogen bonds : angle 9.69857 ( 867) SS BOND : bond 0.00186 ( 22) SS BOND : angle 0.57771 ( 44) covalent geometry : bond 0.00253 (14488) covalent geometry : angle 0.57927 (19666) *********************** 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 : 1.454 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: 0.2703 time to fit residues: 101.3136 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 : 1.522 ------------------------------------------------------------------------------- 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 151 optimal weight: 7.9990 chunk 136 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 chunk 105 optimal weight: 0.7980 chunk 163 optimal weight: 6.9990 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 39 GLN A 125 GLN A 211 ASN C 148 GLN C 161 GLN C 200 GLN C 211 ASN ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 158 HIS F 82 ASN F 253 HIS H 76 ASN H 81 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.173044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.136698 restraints weight = 27449.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.135079 restraints weight = 19930.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.136553 restraints weight = 17000.710| |-----------------------------------------------------------------------------| r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 14511 Z= 0.312 Angle : 0.907 15.065 19713 Z= 0.482 Chirality : 0.050 0.228 2143 Planarity : 0.007 0.073 2528 Dihedral : 6.643 58.170 2032 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.61 % Favored : 90.11 % Rotamer: Outliers : 4.42 % Allowed : 15.77 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.19), residues: 1800 helix: -1.58 (0.47), residues: 88 sheet: -0.07 (0.23), residues: 511 loop : -1.75 (0.17), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP H 35 HIS 0.010 0.002 HIS C 199 PHE 0.024 0.003 PHE A 72 TYR 0.034 0.003 TYR F 22 ARG 0.009 0.001 ARG F 276 Details of bonding type rmsd link_NAG-ASN : bond 0.00140 ( 1) link_NAG-ASN : angle 1.41018 ( 3) hydrogen bonds : bond 0.05809 ( 367) hydrogen bonds : angle 6.80769 ( 867) SS BOND : bond 0.00944 ( 22) SS BOND : angle 2.04849 ( 44) covalent geometry : bond 0.00710 (14488) covalent geometry : angle 0.90223 (19666) *********************** 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 311 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 242 time to evaluate : 1.585 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: 0.5957 (tpp) cc_final: 0.5663 (tpp) REVERT: A 15 SER cc_start: 0.7621 (t) cc_final: 0.7264 (m) REVERT: A 18 ASP cc_start: 0.7255 (t0) cc_final: 0.6993 (t0) REVERT: A 82 GLU cc_start: 0.8136 (mp0) cc_final: 0.7888 (mp0) REVERT: B 12 LEU cc_start: 0.8396 (pt) cc_final: 0.7883 (tt) REVERT: B 214 LYS cc_start: 0.7259 (tptt) cc_final: 0.7020 (tptt) REVERT: C 18 ASP cc_start: 0.7811 (t0) cc_final: 0.7566 (t0) REVERT: C 146 LYS cc_start: 0.6786 (ttpp) cc_final: 0.6340 (ttpt) REVERT: E 61 SER cc_start: 0.7525 (p) cc_final: 0.7313 (t) REVERT: F 20 PHE cc_start: 0.7310 (OUTLIER) cc_final: 0.6462 (m-80) REVERT: F 50 TRP cc_start: 0.7843 (t60) cc_final: 0.7595 (t-100) REVERT: F 70 SER cc_start: 0.9046 (m) cc_final: 0.8765 (t) REVERT: F 209 THR cc_start: 0.8345 (p) cc_final: 0.8108 (p) REVERT: F 349 MET cc_start: 0.5757 (ppp) cc_final: 0.2929 (mmm) REVERT: G 35 TRP cc_start: 0.6594 (t-100) cc_final: 0.6177 (t-100) REVERT: G 72 ASP cc_start: 0.7388 (t70) cc_final: 0.6879 (t70) REVERT: G 112 GLN cc_start: 0.7634 (mm-40) cc_final: 0.6998 (pm20) REVERT: H 35 TRP cc_start: 0.6673 (m100) cc_final: 0.6335 (m100) outliers start: 69 outliers final: 44 residues processed: 294 average time/residue: 0.2489 time to fit residues: 107.3761 Evaluate side-chains 243 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 198 time to evaluate : 1.678 ------------------------------------------------------------------------------- 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 B residue 199 ILE Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 21 THR 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 116 VAL Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain D residue 33 ASN 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 165 SER Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain E residue 55 CYS 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 236 VAL Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 7 ASP Chi-restraints excluded: chain F residue 20 PHE 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 90 THR Chi-restraints excluded: chain H residue 27 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 1 optimal weight: 3.9990 chunk 169 optimal weight: 0.2980 chunk 74 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 211 ASN G 76 ASN ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.178183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.142135 restraints weight = 27358.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.141447 restraints weight = 18438.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.143110 restraints weight = 16048.650| |-----------------------------------------------------------------------------| r_work (final): 0.4051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6873 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 14511 Z= 0.148 Angle : 0.692 14.252 19713 Z= 0.360 Chirality : 0.044 0.229 2143 Planarity : 0.005 0.093 2528 Dihedral : 5.502 54.307 2030 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.33 % Favored : 92.44 % Rotamer: Outliers : 2.82 % Allowed : 19.94 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.19), residues: 1800 helix: -1.39 (0.47), residues: 87 sheet: 0.03 (0.25), residues: 464 loop : -1.56 (0.17), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 225 HIS 0.005 0.001 HIS C 199 PHE 0.020 0.001 PHE A 210 TYR 0.025 0.002 TYR C 141 ARG 0.004 0.000 ARG C 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00327 ( 1) link_NAG-ASN : angle 1.08069 ( 3) hydrogen bonds : bond 0.04054 ( 367) hydrogen bonds : angle 5.95735 ( 867) SS BOND : bond 0.00798 ( 22) SS BOND : angle 1.65076 ( 44) covalent geometry : bond 0.00317 (14488) covalent geometry : angle 0.68779 (19666) *********************** 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 277 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 233 time to evaluate : 1.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ASP cc_start: 0.7123 (t0) cc_final: 0.6889 (m-30) REVERT: B 12 LEU cc_start: 0.8381 (pt) cc_final: 0.7894 (tt) REVERT: C 146 LYS cc_start: 0.6490 (ttpp) cc_final: 0.6090 (ttpt) REVERT: D 95 TYR cc_start: 0.6984 (OUTLIER) cc_final: 0.5396 (p90) REVERT: E 67 MET cc_start: 0.9016 (tmm) cc_final: 0.8717 (tmm) REVERT: E 349 MET cc_start: 0.5620 (ttt) cc_final: 0.4434 (ptt) REVERT: F 28 TRP cc_start: 0.4854 (OUTLIER) cc_final: 0.3280 (m-90) REVERT: F 70 SER cc_start: 0.8827 (m) cc_final: 0.8596 (t) REVERT: G 112 GLN cc_start: 0.7566 (mm-40) cc_final: 0.6988 (pm20) REVERT: H 12 GLN cc_start: 0.8348 (pp30) cc_final: 0.8148 (tm-30) REVERT: H 36 PHE cc_start: 0.7922 (m-80) cc_final: 0.7669 (t80) outliers start: 44 outliers final: 30 residues processed: 265 average time/residue: 0.2565 time to fit residues: 99.2701 Evaluate side-chains 229 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 197 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 23 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 208 LYS Chi-restraints excluded: chain B residue 21 LEU 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 170 PHE Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain D residue 163 LEU 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 F residue 2 VAL 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 216 HIS Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 221 LYS Chi-restraints excluded: chain G residue 30 ARG Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain H residue 30 ARG 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 50 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 152 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 101 optimal weight: 4.9990 chunk 170 optimal weight: 10.0000 chunk 61 optimal weight: 8.9990 chunk 151 optimal weight: 0.5980 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 B 201 ASN C 39 GLN C 90 GLN C 211 ASN D 201 ASN F 95 ASN F 147 HIS G 76 ASN ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.167453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.123287 restraints weight = 27748.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.127061 restraints weight = 16362.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.129587 restraints weight = 11590.054| |-----------------------------------------------------------------------------| r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 14511 Z= 0.198 Angle : 0.779 18.940 19713 Z= 0.405 Chirality : 0.046 0.230 2143 Planarity : 0.006 0.077 2528 Dihedral : 5.870 56.572 2030 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.06 % Favored : 90.72 % Rotamer: Outliers : 5.77 % Allowed : 19.42 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.19), residues: 1800 helix: -1.40 (0.48), residues: 87 sheet: -0.20 (0.24), residues: 480 loop : -1.69 (0.17), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 35 HIS 0.006 0.001 HIS C 199 PHE 0.024 0.002 PHE A 210 TYR 0.024 0.002 TYR C 88 ARG 0.005 0.001 ARG F 338 Details of bonding type rmsd link_NAG-ASN : bond 0.00119 ( 1) link_NAG-ASN : angle 1.17289 ( 3) hydrogen bonds : bond 0.04399 ( 367) hydrogen bonds : angle 6.05852 ( 867) SS BOND : bond 0.00894 ( 22) SS BOND : angle 3.53099 ( 44) covalent geometry : bond 0.00450 (14488) covalent geometry : angle 0.76189 (19666) *********************** 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 309 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 219 time to evaluate : 1.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ASP cc_start: 0.7757 (t0) cc_final: 0.7037 (m-30) REVERT: B 12 LEU cc_start: 0.8601 (pt) cc_final: 0.8012 (tt) REVERT: D 95 TYR cc_start: 0.7133 (OUTLIER) cc_final: 0.5210 (p90) REVERT: D 113 VAL cc_start: 0.7968 (OUTLIER) cc_final: 0.7682 (t) REVERT: E 349 MET cc_start: 0.5575 (ttt) cc_final: 0.4538 (ptm) REVERT: F 28 TRP cc_start: 0.4836 (OUTLIER) cc_final: 0.3693 (m-90) REVERT: F 318 MET cc_start: 0.5707 (OUTLIER) cc_final: 0.4793 (tmm) REVERT: G 76 ASN cc_start: 0.2385 (OUTLIER) cc_final: 0.2164 (t0) REVERT: G 82 MET cc_start: 0.7957 (ptp) cc_final: 0.7116 (tmm) REVERT: G 112 GLN cc_start: 0.7662 (mm-40) cc_final: 0.6972 (pm20) REVERT: H 12 GLN cc_start: 0.8411 (pp30) cc_final: 0.8199 (tm-30) REVERT: H 31 TYR cc_start: 0.6839 (m-80) cc_final: 0.6622 (m-80) REVERT: H 36 PHE cc_start: 0.8459 (m-80) cc_final: 0.7880 (t80) REVERT: H 112 GLN cc_start: 0.6353 (mm-40) cc_final: 0.5817 (pp30) outliers start: 90 outliers final: 57 residues processed: 285 average time/residue: 0.2369 time to fit residues: 101.2059 Evaluate side-chains 268 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 206 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 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 130 THR Chi-restraints excluded: chain A residue 133 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 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 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 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 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 113 VAL Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 223 THR 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 262 THR Chi-restraints excluded: chain E residue 287 VAL 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 24 ASP Chi-restraints excluded: chain F residue 28 TRP 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 221 LYS Chi-restraints excluded: chain F residue 233 THR Chi-restraints excluded: chain F residue 239 SER Chi-restraints excluded: chain F residue 318 MET Chi-restraints excluded: chain G residue 30 ARG Chi-restraints excluded: chain G residue 76 ASN Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain H residue 17 LEU 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 119 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 170 optimal weight: 20.0000 chunk 107 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 C 211 ASN D 201 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.165435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.121318 restraints weight = 28012.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.125075 restraints weight = 16533.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.127540 restraints weight = 11722.756| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.5139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 14511 Z= 0.201 Angle : 0.767 17.164 19713 Z= 0.400 Chirality : 0.045 0.243 2143 Planarity : 0.006 0.069 2528 Dihedral : 5.908 56.272 2030 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.06 % Favored : 90.67 % Rotamer: Outliers : 5.32 % Allowed : 21.73 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.19), residues: 1800 helix: -1.10 (0.52), residues: 87 sheet: -0.11 (0.24), residues: 453 loop : -1.83 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 35 HIS 0.005 0.001 HIS F 229 PHE 0.022 0.002 PHE A 210 TYR 0.023 0.002 TYR C 141 ARG 0.004 0.001 ARG C 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00098 ( 1) link_NAG-ASN : angle 0.92750 ( 3) hydrogen bonds : bond 0.04263 ( 367) hydrogen bonds : angle 5.99450 ( 867) SS BOND : bond 0.00686 ( 22) SS BOND : angle 3.00975 ( 44) covalent geometry : bond 0.00455 (14488) covalent geometry : angle 0.75442 (19666) *********************** 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 310 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 227 time to evaluate : 1.596 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 18 ASP cc_start: 0.8069 (t0) cc_final: 0.7389 (t0) REVERT: A 32 SER cc_start: 0.8169 (OUTLIER) cc_final: 0.7523 (t) REVERT: A 168 ASP cc_start: 0.8146 (t0) cc_final: 0.7717 (t0) REVERT: B 12 LEU cc_start: 0.8652 (pt) cc_final: 0.8034 (tt) REVERT: B 82 GLN cc_start: 0.6709 (tp-100) cc_final: 0.6503 (mm-40) REVERT: B 199 ILE cc_start: 0.7701 (mt) cc_final: 0.7479 (mm) REVERT: C 88 TYR cc_start: 0.5775 (OUTLIER) cc_final: 0.3658 (p90) REVERT: C 90 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.8088 (tm130) REVERT: C 143 ARG cc_start: 0.7173 (OUTLIER) cc_final: 0.6851 (tmt-80) REVERT: D 20 ARG cc_start: 0.7448 (ttt-90) cc_final: 0.6994 (ttm-80) REVERT: D 95 TYR cc_start: 0.7269 (OUTLIER) cc_final: 0.5796 (p90) REVERT: D 106 TYR cc_start: 0.4884 (OUTLIER) cc_final: 0.3107 (m-80) REVERT: E 349 MET cc_start: 0.5556 (ttt) cc_final: 0.5070 (tmm) REVERT: F 5 SER cc_start: 0.8963 (OUTLIER) cc_final: 0.8753 (p) REVERT: F 28 TRP cc_start: 0.4859 (OUTLIER) cc_final: 0.3679 (m-90) REVERT: F 210 TRP cc_start: 0.8274 (m100) cc_final: 0.8066 (m100) REVERT: F 349 MET cc_start: 0.7161 (ppp) cc_final: 0.6839 (ppp) REVERT: G 18 ARG cc_start: 0.8282 (tpp-160) cc_final: 0.7786 (tpt170) REVERT: G 59 TYR cc_start: 0.6565 (m-10) cc_final: 0.6363 (m-10) REVERT: G 82 MET cc_start: 0.8106 (ptp) cc_final: 0.7267 (tmm) REVERT: G 85 LEU cc_start: 0.7960 (mt) cc_final: 0.7214 (mt) REVERT: G 112 GLN cc_start: 0.7582 (mm-40) cc_final: 0.7038 (pm20) REVERT: H 12 GLN cc_start: 0.8456 (pp30) cc_final: 0.8164 (tm-30) REVERT: H 19 LEU cc_start: 0.9115 (tt) cc_final: 0.8769 (mm) REVERT: H 31 TYR cc_start: 0.6874 (m-80) cc_final: 0.6503 (m-80) REVERT: H 36 PHE cc_start: 0.8443 (m-80) cc_final: 0.7796 (t80) outliers start: 83 outliers final: 58 residues processed: 288 average time/residue: 0.2514 time to fit residues: 107.4557 Evaluate side-chains 281 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 215 time to evaluate : 1.581 ------------------------------------------------------------------------------- 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 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 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 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 47 LEU Chi-restraints excluded: chain C residue 88 TYR Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain C residue 103 THR 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 32 SER 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 106 TYR Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 176 SER 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 262 THR Chi-restraints excluded: chain E residue 287 VAL 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 28 TRP Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 76 ASN 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 90 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 52 optimal weight: 0.7980 chunk 61 optimal weight: 9.9990 chunk 115 optimal weight: 0.2980 chunk 140 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 169 optimal weight: 7.9990 chunk 93 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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** C 211 ASN H 2 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.165121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.121337 restraints weight = 27615.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.125052 restraints weight = 16048.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.127581 restraints weight = 11324.034| |-----------------------------------------------------------------------------| r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.5389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14511 Z= 0.161 Angle : 0.730 15.225 19713 Z= 0.377 Chirality : 0.044 0.243 2143 Planarity : 0.005 0.072 2528 Dihedral : 5.635 55.226 2030 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.61 % Favored : 91.11 % Rotamer: Outliers : 4.49 % Allowed : 22.76 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.19), residues: 1800 helix: -1.21 (0.49), residues: 87 sheet: -0.03 (0.24), residues: 453 loop : -1.73 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 35 HIS 0.004 0.001 HIS F 229 PHE 0.022 0.002 PHE A 210 TYR 0.026 0.002 TYR C 141 ARG 0.006 0.000 ARG C 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00132 ( 1) link_NAG-ASN : angle 0.90357 ( 3) hydrogen bonds : bond 0.03853 ( 367) hydrogen bonds : angle 5.76191 ( 867) SS BOND : bond 0.00588 ( 22) SS BOND : angle 2.89532 ( 44) covalent geometry : bond 0.00363 (14488) covalent geometry : angle 0.71816 (19666) *********************** 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 294 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 224 time to evaluate : 1.486 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 18 ASP cc_start: 0.8107 (t0) cc_final: 0.7277 (m-30) REVERT: A 32 SER cc_start: 0.8118 (OUTLIER) cc_final: 0.7531 (t) REVERT: B 12 LEU cc_start: 0.8601 (pt) cc_final: 0.8046 (tt) REVERT: C 88 TYR cc_start: 0.5741 (OUTLIER) cc_final: 0.4262 (p90) REVERT: C 143 ARG cc_start: 0.7128 (OUTLIER) cc_final: 0.6561 (tmt-80) REVERT: D 20 ARG cc_start: 0.7200 (ttt-90) cc_final: 0.6980 (ttm-80) REVERT: D 95 TYR cc_start: 0.7059 (OUTLIER) cc_final: 0.5308 (p90) REVERT: D 180 TYR cc_start: 0.7550 (m-80) cc_final: 0.7218 (m-10) REVERT: E 85 GLN cc_start: 0.7510 (tp40) cc_final: 0.7169 (tp40) REVERT: E 349 MET cc_start: 0.5763 (ttt) cc_final: 0.5060 (tmm) REVERT: F 5 SER cc_start: 0.8997 (OUTLIER) cc_final: 0.8778 (p) REVERT: F 28 TRP cc_start: 0.4838 (OUTLIER) cc_final: 0.3689 (m-90) REVERT: F 318 MET cc_start: 0.6931 (tmm) cc_final: 0.6227 (tmm) REVERT: F 349 MET cc_start: 0.7110 (ppp) cc_final: 0.6866 (ppp) REVERT: G 18 ARG cc_start: 0.8260 (tpp-160) cc_final: 0.8013 (tpt170) REVERT: G 59 TYR cc_start: 0.6584 (m-10) cc_final: 0.6266 (m-10) REVERT: G 112 GLN cc_start: 0.7505 (mm-40) cc_final: 0.6982 (pm20) REVERT: H 19 LEU cc_start: 0.9027 (tt) cc_final: 0.8671 (mm) REVERT: H 31 TYR cc_start: 0.7012 (m-80) cc_final: 0.6687 (m-80) REVERT: H 36 PHE cc_start: 0.8429 (m-80) cc_final: 0.7839 (t80) outliers start: 70 outliers final: 53 residues processed: 277 average time/residue: 0.2433 time to fit residues: 100.8397 Evaluate side-chains 267 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 208 time to evaluate : 1.464 ------------------------------------------------------------------------------- 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 49 VAL Chi-restraints excluded: chain B residue 74 ASN 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 23 THR 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 126 LEU Chi-restraints excluded: chain C residue 143 ARG Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 211 ASN 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 113 VAL Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain E residue 34 TYR 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 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 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 12 GLN Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 97 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 83 optimal weight: 20.0000 chunk 24 optimal weight: 4.9990 chunk 164 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 95 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 169 optimal weight: 6.9990 chunk 52 optimal weight: 0.0980 chunk 165 optimal weight: 5.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 GLN ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 ASN F 269 HIS ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.162202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.118697 restraints weight = 27530.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.122260 restraints weight = 16223.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.124653 restraints weight = 11533.629| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.5841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 14511 Z= 0.205 Angle : 0.776 16.879 19713 Z= 0.404 Chirality : 0.046 0.225 2143 Planarity : 0.006 0.082 2528 Dihedral : 5.902 55.592 2030 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.28 % Favored : 89.56 % Rotamer: Outliers : 5.26 % Allowed : 23.21 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.19), residues: 1800 helix: -1.64 (0.48), residues: 88 sheet: 0.00 (0.24), residues: 491 loop : -1.87 (0.17), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 35 HIS 0.004 0.001 HIS F 229 PHE 0.023 0.002 PHE A 210 TYR 0.025 0.002 TYR C 141 ARG 0.006 0.001 ARG C 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00679 ( 1) link_NAG-ASN : angle 1.21433 ( 3) hydrogen bonds : bond 0.04213 ( 367) hydrogen bonds : angle 5.96215 ( 867) SS BOND : bond 0.00763 ( 22) SS BOND : angle 3.07807 ( 44) covalent geometry : bond 0.00469 (14488) covalent geometry : angle 0.76323 (19666) *********************** 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 293 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 211 time to evaluate : 1.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ASP cc_start: 0.8267 (t0) cc_final: 0.7373 (m-30) REVERT: A 32 SER cc_start: 0.8294 (OUTLIER) cc_final: 0.7680 (t) REVERT: B 12 LEU cc_start: 0.8553 (pt) cc_final: 0.8043 (tt) REVERT: B 82 GLN cc_start: 0.6943 (tp40) cc_final: 0.6564 (mm-40) REVERT: C 88 TYR cc_start: 0.5656 (OUTLIER) cc_final: 0.3241 (p90) REVERT: C 143 ARG cc_start: 0.7409 (OUTLIER) cc_final: 0.6850 (tmt-80) REVERT: D 20 ARG cc_start: 0.7266 (ttt-90) cc_final: 0.6980 (ttm-80) REVERT: D 32 SER cc_start: 0.7280 (p) cc_final: 0.7073 (p) REVERT: D 95 TYR cc_start: 0.7026 (OUTLIER) cc_final: 0.5266 (p90) REVERT: D 106 TYR cc_start: 0.4841 (OUTLIER) cc_final: 0.3133 (m-80) REVERT: F 20 PHE cc_start: 0.7442 (OUTLIER) cc_final: 0.6357 (m-80) REVERT: F 26 GLU cc_start: 0.7193 (mp0) cc_final: 0.6240 (pp20) REVERT: F 28 TRP cc_start: 0.4721 (OUTLIER) cc_final: 0.3843 (m-90) REVERT: F 210 TRP cc_start: 0.8307 (m100) cc_final: 0.8052 (m100) REVERT: F 318 MET cc_start: 0.6953 (tmm) cc_final: 0.6245 (tmm) REVERT: G 18 ARG cc_start: 0.8228 (tpp-160) cc_final: 0.7919 (tpt170) REVERT: G 98 ASP cc_start: 0.7602 (t0) cc_final: 0.7334 (t0) REVERT: G 112 GLN cc_start: 0.7518 (mm-40) cc_final: 0.7023 (pm20) REVERT: H 2 GLN cc_start: 0.6155 (tm-30) cc_final: 0.5954 (tm-30) REVERT: H 19 LEU cc_start: 0.9038 (tt) cc_final: 0.8713 (mm) REVERT: H 31 TYR cc_start: 0.7158 (m-80) cc_final: 0.6785 (m-80) REVERT: H 36 PHE cc_start: 0.8413 (m-80) cc_final: 0.7716 (t80) outliers start: 82 outliers final: 57 residues processed: 274 average time/residue: 0.2557 time to fit residues: 103.9210 Evaluate side-chains 269 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 205 time to evaluate : 1.668 ------------------------------------------------------------------------------- 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 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 180 LEU Chi-restraints excluded: chain A residue 208 LYS 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 B residue 111 THR Chi-restraints excluded: chain C residue 11 THR 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 143 ARG 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 106 TYR Chi-restraints excluded: chain D residue 113 VAL 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 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 262 THR Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 4 CYS Chi-restraints excluded: chain F residue 7 ASP Chi-restraints excluded: chain F residue 15 CYS Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 28 TRP Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 76 ASN 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 46 PHE 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 120 optimal weight: 10.0000 chunk 81 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 134 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 151 optimal weight: 0.0970 chunk 174 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 141 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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** ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 ASN G 83 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.164615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.121147 restraints weight = 27396.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.124809 restraints weight = 16029.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.127308 restraints weight = 11331.116| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.6019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14511 Z= 0.157 Angle : 0.727 14.427 19713 Z= 0.375 Chirality : 0.044 0.229 2143 Planarity : 0.006 0.100 2528 Dihedral : 5.598 54.694 2030 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.67 % Favored : 91.06 % Rotamer: Outliers : 4.04 % Allowed : 24.23 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.19), residues: 1800 helix: -1.42 (0.49), residues: 88 sheet: -0.02 (0.24), residues: 468 loop : -1.75 (0.17), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 35 HIS 0.003 0.001 HIS F 229 PHE 0.020 0.002 PHE A 210 TYR 0.025 0.002 TYR C 141 ARG 0.006 0.000 ARG H 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00030 ( 1) link_NAG-ASN : angle 1.09413 ( 3) hydrogen bonds : bond 0.03715 ( 367) hydrogen bonds : angle 5.71358 ( 867) SS BOND : bond 0.00591 ( 22) SS BOND : angle 2.73813 ( 44) covalent geometry : bond 0.00354 (14488) covalent geometry : angle 0.71649 (19666) *********************** 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 279 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 216 time to evaluate : 1.487 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: 0.8268 (t0) cc_final: 0.7387 (m-30) REVERT: A 21 THR cc_start: 0.7197 (OUTLIER) cc_final: 0.6919 (t) REVERT: A 32 SER cc_start: 0.8215 (OUTLIER) cc_final: 0.7650 (t) REVERT: B 12 LEU cc_start: 0.8574 (pt) cc_final: 0.8061 (tt) REVERT: B 47 GLU cc_start: 0.7098 (tp30) cc_final: 0.6056 (mt-10) REVERT: B 82 GLN cc_start: 0.6868 (tp40) cc_final: 0.6603 (mm-40) REVERT: C 2 ASP cc_start: 0.7711 (OUTLIER) cc_final: 0.7455 (m-30) REVERT: C 32 SER cc_start: 0.7957 (OUTLIER) cc_final: 0.7326 (t) REVERT: C 39 GLN cc_start: 0.6990 (tt0) cc_final: 0.6586 (tt0) REVERT: C 88 TYR cc_start: 0.5659 (OUTLIER) cc_final: 0.4423 (p90) REVERT: C 143 ARG cc_start: 0.7297 (OUTLIER) cc_final: 0.6760 (tmt-80) REVERT: D 20 ARG cc_start: 0.7241 (ttt-90) cc_final: 0.6962 (ttm-80) REVERT: D 95 TYR cc_start: 0.7078 (OUTLIER) cc_final: 0.5234 (p90) REVERT: E 85 GLN cc_start: 0.7441 (tp40) cc_final: 0.7212 (tp40) REVERT: E 349 MET cc_start: 0.5874 (ttt) cc_final: 0.5187 (ptm) REVERT: F 20 PHE cc_start: 0.7291 (OUTLIER) cc_final: 0.6154 (m-80) REVERT: F 26 GLU cc_start: 0.7248 (mp0) cc_final: 0.6342 (pp20) REVERT: F 28 TRP cc_start: 0.4789 (OUTLIER) cc_final: 0.3705 (m-90) REVERT: F 318 MET cc_start: 0.7009 (tmm) cc_final: 0.6389 (tmm) REVERT: G 18 ARG cc_start: 0.8099 (tpp-160) cc_final: 0.7759 (tpt170) REVERT: G 35 TRP cc_start: 0.7579 (OUTLIER) cc_final: 0.6065 (m-90) REVERT: G 59 TYR cc_start: 0.6626 (m-10) cc_final: 0.6181 (m-10) REVERT: G 98 ASP cc_start: 0.7567 (t0) cc_final: 0.7335 (t0) REVERT: G 112 GLN cc_start: 0.7463 (mm-40) cc_final: 0.6725 (pp30) REVERT: H 19 LEU cc_start: 0.9024 (tt) cc_final: 0.8686 (mm) REVERT: H 31 TYR cc_start: 0.7325 (m-80) cc_final: 0.6960 (m-80) outliers start: 63 outliers final: 47 residues processed: 265 average time/residue: 0.2445 time to fit residues: 96.8334 Evaluate side-chains 265 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 208 time to evaluate : 1.526 ------------------------------------------------------------------------------- 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 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 180 LEU Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain C residue 2 ASP 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 48 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 199 HIS 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 113 VAL 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 176 SER 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 307 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 4 CYS Chi-restraints excluded: chain F residue 7 ASP Chi-restraints excluded: chain F residue 15 CYS Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 28 TRP Chi-restraints excluded: chain F residue 60 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 35 TRP Chi-restraints excluded: chain G residue 106 SER 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 117 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 148 optimal weight: 0.8980 chunk 152 optimal weight: 0.9980 chunk 102 optimal weight: 6.9990 chunk 36 optimal weight: 0.5980 chunk 68 optimal weight: 0.4980 chunk 74 optimal weight: 2.9990 chunk 147 optimal weight: 0.5980 chunk 135 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN A 125 GLN ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 ASN ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.166744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.123123 restraints weight = 27050.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.126840 restraints weight = 15771.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.129404 restraints weight = 11117.473| |-----------------------------------------------------------------------------| r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 0.6161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14511 Z= 0.135 Angle : 0.706 13.210 19713 Z= 0.362 Chirality : 0.043 0.218 2143 Planarity : 0.005 0.081 2528 Dihedral : 5.326 53.693 2030 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.28 % Favored : 91.44 % Rotamer: Outliers : 3.08 % Allowed : 25.71 % Favored : 71.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.19), residues: 1800 helix: -1.23 (0.51), residues: 88 sheet: 0.10 (0.24), residues: 465 loop : -1.62 (0.17), residues: 1247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP F 210 HIS 0.003 0.001 HIS E 254 PHE 0.016 0.001 PHE A 210 TYR 0.025 0.001 TYR C 141 ARG 0.005 0.000 ARG C 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00154 ( 1) link_NAG-ASN : angle 1.13094 ( 3) hydrogen bonds : bond 0.03411 ( 367) hydrogen bonds : angle 5.47364 ( 867) SS BOND : bond 0.00514 ( 22) SS BOND : angle 2.54176 ( 44) covalent geometry : bond 0.00298 (14488) covalent geometry : angle 0.69598 (19666) *********************** 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 266 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 218 time to evaluate : 1.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ASP cc_start: 0.8208 (t0) cc_final: 0.7391 (m-30) REVERT: A 32 SER cc_start: 0.8052 (OUTLIER) cc_final: 0.7521 (t) REVERT: B 12 LEU cc_start: 0.8593 (pt) cc_final: 0.8134 (tt) REVERT: B 47 GLU cc_start: 0.7040 (tp30) cc_final: 0.6067 (mt-10) REVERT: B 82 GLN cc_start: 0.6806 (tp40) cc_final: 0.6591 (mm-40) REVERT: C 2 ASP cc_start: 0.7750 (OUTLIER) cc_final: 0.7458 (m-30) REVERT: C 32 SER cc_start: 0.7888 (OUTLIER) cc_final: 0.7313 (t) REVERT: C 39 GLN cc_start: 0.6920 (tt0) cc_final: 0.6509 (tt0) REVERT: C 88 TYR cc_start: 0.5542 (OUTLIER) cc_final: 0.4346 (p90) REVERT: D 20 ARG cc_start: 0.7127 (ttt-90) cc_final: 0.6916 (ttm-80) REVERT: D 95 TYR cc_start: 0.6924 (OUTLIER) cc_final: 0.4957 (p90) REVERT: E 85 GLN cc_start: 0.7530 (tp40) cc_final: 0.7043 (tp40) REVERT: E 220 MET cc_start: 0.8511 (mmt) cc_final: 0.8103 (mpp) REVERT: E 349 MET cc_start: 0.5898 (ttt) cc_final: 0.5086 (ptm) REVERT: F 20 PHE cc_start: 0.7166 (OUTLIER) cc_final: 0.6069 (m-80) REVERT: F 26 GLU cc_start: 0.7371 (mp0) cc_final: 0.6466 (pp20) REVERT: F 28 TRP cc_start: 0.4868 (OUTLIER) cc_final: 0.3731 (m-90) REVERT: F 318 MET cc_start: 0.7054 (tmm) cc_final: 0.6623 (tmm) REVERT: G 18 ARG cc_start: 0.8060 (tpp-160) cc_final: 0.7719 (tpt170) REVERT: G 21 CYS cc_start: 0.5455 (t) cc_final: 0.4453 (t) REVERT: G 30 ARG cc_start: 0.7713 (tpp-160) cc_final: 0.7247 (ptt90) REVERT: G 35 TRP cc_start: 0.7577 (OUTLIER) cc_final: 0.7204 (m100) REVERT: G 94 TYR cc_start: 0.8445 (m-80) cc_final: 0.8127 (m-80) REVERT: G 112 GLN cc_start: 0.7442 (mm-40) cc_final: 0.6692 (pp30) REVERT: H 19 LEU cc_start: 0.9004 (tt) cc_final: 0.8655 (mm) REVERT: H 31 TYR cc_start: 0.7463 (m-80) cc_final: 0.7078 (m-80) REVERT: H 36 PHE cc_start: 0.8220 (m-80) cc_final: 0.7379 (t80) outliers start: 48 outliers final: 33 residues processed: 255 average time/residue: 0.2393 time to fit residues: 91.7119 Evaluate side-chains 249 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 208 time to evaluate : 1.629 ------------------------------------------------------------------------------- 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 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 180 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain C residue 2 ASP 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 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 113 VAL Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 169 THR 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 F residue 2 VAL Chi-restraints excluded: chain F residue 4 CYS Chi-restraints excluded: chain F residue 7 ASP Chi-restraints excluded: chain F residue 15 CYS Chi-restraints excluded: chain F residue 20 PHE 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 35 TRP 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 98 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 117 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 102 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 ASN ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.165627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.122159 restraints weight = 26983.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.125867 restraints weight = 15824.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.128321 restraints weight = 11166.426| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.6316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14511 Z= 0.141 Angle : 0.718 13.478 19713 Z= 0.370 Chirality : 0.043 0.215 2143 Planarity : 0.005 0.077 2528 Dihedral : 5.314 54.403 2030 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.39 % Favored : 91.33 % Rotamer: Outliers : 3.01 % Allowed : 25.83 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.19), residues: 1800 helix: -1.17 (0.50), residues: 88 sheet: 0.18 (0.25), residues: 451 loop : -1.57 (0.17), residues: 1261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP F 210 HIS 0.004 0.001 HIS F 195 PHE 0.014 0.001 PHE C 119 TYR 0.026 0.002 TYR C 141 ARG 0.004 0.000 ARG C 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00176 ( 1) link_NAG-ASN : angle 1.20220 ( 3) hydrogen bonds : bond 0.03443 ( 367) hydrogen bonds : angle 5.45140 ( 867) SS BOND : bond 0.00537 ( 22) SS BOND : angle 2.59141 ( 44) covalent geometry : bond 0.00316 (14488) covalent geometry : angle 0.70787 (19666) ********************** 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 256 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 209 time to evaluate : 2.650 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: 0.8216 (t0) cc_final: 0.7394 (m-30) REVERT: A 32 SER cc_start: 0.8106 (OUTLIER) cc_final: 0.7565 (t) REVERT: B 12 LEU cc_start: 0.8587 (pt) cc_final: 0.8136 (tt) REVERT: B 47 GLU cc_start: 0.7074 (tp30) cc_final: 0.6100 (mt-10) REVERT: B 82 GLN cc_start: 0.6798 (tp40) cc_final: 0.6598 (mm-40) REVERT: C 2 ASP cc_start: 0.7686 (OUTLIER) cc_final: 0.7347 (m-30) REVERT: C 32 SER cc_start: 0.7965 (OUTLIER) cc_final: 0.7370 (t) REVERT: C 88 TYR cc_start: 0.5631 (OUTLIER) cc_final: 0.4226 (p90) REVERT: D 20 ARG cc_start: 0.7199 (ttt-90) cc_final: 0.6953 (ttm-80) REVERT: D 95 TYR cc_start: 0.6888 (OUTLIER) cc_final: 0.4762 (p90) REVERT: E 85 GLN cc_start: 0.7556 (tp40) cc_final: 0.7294 (tp40) REVERT: E 220 MET cc_start: 0.8452 (mmt) cc_final: 0.8087 (mpp) REVERT: E 349 MET cc_start: 0.5954 (ttt) cc_final: 0.5067 (ptm) REVERT: F 20 PHE cc_start: 0.7209 (OUTLIER) cc_final: 0.6043 (m-80) REVERT: F 26 GLU cc_start: 0.7380 (mp0) cc_final: 0.6535 (pp20) REVERT: F 28 TRP cc_start: 0.4857 (OUTLIER) cc_final: 0.3706 (m-90) REVERT: F 318 MET cc_start: 0.7100 (tmm) cc_final: 0.6650 (tmm) REVERT: G 21 CYS cc_start: 0.5232 (t) cc_final: 0.4370 (t) REVERT: G 35 TRP cc_start: 0.7754 (OUTLIER) cc_final: 0.6147 (m-90) REVERT: G 112 GLN cc_start: 0.7372 (mm-40) cc_final: 0.6628 (pp30) REVERT: H 19 LEU cc_start: 0.9004 (tt) cc_final: 0.8644 (mm) REVERT: H 31 TYR cc_start: 0.7511 (m-80) cc_final: 0.7151 (m-80) REVERT: H 36 PHE cc_start: 0.8277 (m-80) cc_final: 0.7335 (t80) outliers start: 47 outliers final: 34 residues processed: 247 average time/residue: 0.2950 time to fit residues: 109.5142 Evaluate side-chains 246 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 204 time to evaluate : 2.035 ------------------------------------------------------------------------------- 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 103 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain C residue 2 ASP 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 199 HIS Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain E residue 34 TYR 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 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 20 PHE Chi-restraints excluded: chain F residue 28 TRP Chi-restraints excluded: chain F residue 60 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 35 TRP 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 178 optimal weight: 9.9990 chunk 117 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 28 optimal weight: 0.1980 chunk 153 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 147 optimal weight: 0.5980 chunk 155 optimal weight: 10.0000 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN A 39 GLN B 40 GLN ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 ASN ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.164139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.120662 restraints weight = 27443.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.124299 restraints weight = 16011.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.126756 restraints weight = 11324.315| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.6553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14511 Z= 0.155 Angle : 0.728 14.201 19713 Z= 0.374 Chirality : 0.044 0.215 2143 Planarity : 0.005 0.074 2528 Dihedral : 5.405 54.557 2030 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.78 % Favored : 90.94 % Rotamer: Outliers : 3.21 % Allowed : 25.90 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.19), residues: 1800 helix: -1.24 (0.50), residues: 88 sheet: 0.28 (0.25), residues: 450 loop : -1.60 (0.17), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP F 210 HIS 0.003 0.001 HIS F 229 PHE 0.016 0.002 PHE C 119 TYR 0.029 0.002 TYR B 149 ARG 0.004 0.000 ARG C 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00107 ( 1) link_NAG-ASN : angle 1.11660 ( 3) hydrogen bonds : bond 0.03587 ( 367) hydrogen bonds : angle 5.50502 ( 867) SS BOND : bond 0.00591 ( 22) SS BOND : angle 2.68257 ( 44) covalent geometry : bond 0.00353 (14488) covalent geometry : angle 0.71722 (19666) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5349.52 seconds wall clock time: 94 minutes 30.26 seconds (5670.26 seconds total)