Starting phenix.real_space_refine on Mon Dec 30 22:13:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wnu_37673/12_2024/8wnu_37673.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wnu_37673/12_2024/8wnu_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_37673/12_2024/8wnu_37673.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wnu_37673/12_2024/8wnu_37673.map" model { file = "/net/cci-nas-00/data/ceres_data/8wnu_37673/12_2024/8wnu_37673.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wnu_37673/12_2024/8wnu_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-5532/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: 8.82, per 1000 atoms: 0.62 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: 3.51 Conformation dependent library (CDL) restraints added in 1.9 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: 1.90 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: 3.94 Time building geometry restraints manager: 3.91 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 32.960 Find NCS groups from input model: 0.400 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: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.500 ------------------------------------------------------------------------------- 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 14488 Z= 0.160 Angle : 0.579 11.687 19666 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 *********************** 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 : 1.408 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: 0.2857 time to fit residues: 107.4203 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 : 1.551 ------------------------------------------------------------------------------- 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: 5.9990 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6653 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 14488 Z= 0.460 Angle : 0.902 15.065 19666 Z= 0.480 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 *********************** 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 : 1.554 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: 0.5727 (tpp) cc_final: 0.5379 (tpp) REVERT: A 15 SER cc_start: 0.7659 (t) cc_final: 0.7340 (m) REVERT: A 18 ASP cc_start: 0.6734 (t0) cc_final: 0.6528 (t0) REVERT: B 12 LEU cc_start: 0.8369 (pt) cc_final: 0.7864 (tt) REVERT: C 18 ASP cc_start: 0.7480 (t0) cc_final: 0.7245 (t0) REVERT: C 211 ASN cc_start: 0.1328 (OUTLIER) cc_final: 0.1075 (m110) REVERT: E 61 SER cc_start: 0.7408 (p) cc_final: 0.7145 (t) REVERT: F 20 PHE cc_start: 0.7343 (OUTLIER) cc_final: 0.6499 (m-80) REVERT: F 50 TRP cc_start: 0.7810 (t60) cc_final: 0.7563 (t-100) REVERT: F 70 SER cc_start: 0.9077 (m) cc_final: 0.8826 (t) REVERT: F 209 THR cc_start: 0.8406 (p) cc_final: 0.8178 (p) REVERT: F 349 MET cc_start: 0.5752 (ppp) cc_final: 0.2914 (mmm) REVERT: G 35 TRP cc_start: 0.6611 (t-100) cc_final: 0.6199 (t-100) REVERT: G 72 ASP cc_start: 0.7322 (t70) cc_final: 0.6824 (t70) REVERT: G 112 GLN cc_start: 0.7708 (mm-40) cc_final: 0.7043 (pm20) REVERT: H 35 TRP cc_start: 0.6785 (m100) cc_final: 0.6397 (m100) outliers start: 69 outliers final: 44 residues processed: 294 average time/residue: 0.2619 time to fit residues: 113.0312 Evaluate side-chains 243 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 197 time to evaluate : 1.752 ------------------------------------------------------------------------------- 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 C residue 211 ASN Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 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 90 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 136 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 163 optimal weight: 8.9990 chunk 176 optimal weight: 10.0000 chunk 145 optimal weight: 0.8980 chunk 162 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 131 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6592 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 14488 Z= 0.256 Angle : 0.717 14.349 19666 Z= 0.376 Chirality : 0.045 0.231 2143 Planarity : 0.006 0.093 2528 Dihedral : 5.747 55.008 2030 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.39 % Favored : 91.39 % Rotamer: Outliers : 4.04 % Allowed : 19.23 % Favored : 76.73 % 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: -1.57 (0.46), residues: 93 sheet: -0.05 (0.24), residues: 461 loop : -1.70 (0.17), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 225 HIS 0.006 0.001 HIS C 199 PHE 0.022 0.002 PHE A 210 TYR 0.024 0.002 TYR C 141 ARG 0.005 0.001 ARG C 19 *********************** 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 293 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 230 time to evaluate : 1.658 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 188 GLU cc_start: 0.6714 (tp30) cc_final: 0.6431 (tp30) REVERT: B 12 LEU cc_start: 0.8388 (pt) cc_final: 0.7919 (tt) REVERT: C 88 TYR cc_start: 0.5726 (OUTLIER) cc_final: 0.3885 (p90) REVERT: D 95 TYR cc_start: 0.7072 (OUTLIER) cc_final: 0.5583 (p90) REVERT: E 67 MET cc_start: 0.9056 (tmm) cc_final: 0.8750 (tmm) REVERT: E 349 MET cc_start: 0.5565 (ttt) cc_final: 0.4430 (ptt) REVERT: F 28 TRP cc_start: 0.4860 (OUTLIER) cc_final: 0.3471 (m-90) REVERT: F 70 SER cc_start: 0.8900 (m) cc_final: 0.8696 (t) REVERT: G 112 GLN cc_start: 0.7591 (mm-40) cc_final: 0.6984 (pm20) REVERT: H 12 GLN cc_start: 0.8404 (pp30) cc_final: 0.8196 (tm-30) REVERT: H 36 PHE cc_start: 0.7934 (m-80) cc_final: 0.7588 (t80) REVERT: H 82 MET cc_start: 0.8712 (ptp) cc_final: 0.8135 (tmm) outliers start: 63 outliers final: 45 residues processed: 273 average time/residue: 0.2622 time to fit residues: 105.5427 Evaluate side-chains 248 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 200 time to evaluate : 1.613 ------------------------------------------------------------------------------- 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 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 23 THR 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 33 ASN Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 216 HIS Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 7 ASP Chi-restraints excluded: chain F residue 28 TRP Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 146 GLU Chi-restraints excluded: chain F residue 216 HIS Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 221 LYS Chi-restraints excluded: chain F residue 239 SER 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 34 SER 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 161 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 84 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 109 optimal weight: 0.9990 chunk 164 optimal weight: 10.0000 chunk 173 optimal weight: 0.0050 chunk 85 optimal weight: 5.9990 chunk 155 optimal weight: 0.0470 chunk 46 optimal weight: 0.9990 overall best weight: 0.5696 ------------------------------------------------------------------------------- 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 90 GLN D 201 ASN G 76 ASN H 2 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6519 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 14488 Z= 0.191 Angle : 0.702 18.660 19666 Z= 0.361 Chirality : 0.044 0.227 2143 Planarity : 0.005 0.078 2528 Dihedral : 5.444 54.594 2030 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.72 % Favored : 92.06 % Rotamer: Outliers : 3.85 % Allowed : 20.90 % Favored : 75.26 % 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: -1.16 (0.49), residues: 87 sheet: -0.07 (0.24), residues: 465 loop : -1.54 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 35 HIS 0.003 0.001 HIS C 199 PHE 0.021 0.001 PHE A 210 TYR 0.024 0.001 TYR C 141 ARG 0.005 0.000 ARG C 19 *********************** 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 276 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 216 time to evaluate : 1.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 GLU cc_start: 0.6817 (tp30) cc_final: 0.6502 (tp30) REVERT: B 12 LEU cc_start: 0.8390 (pt) cc_final: 0.7960 (tt) REVERT: D 95 TYR cc_start: 0.6763 (OUTLIER) cc_final: 0.4873 (p90) REVERT: E 67 MET cc_start: 0.9124 (tmm) cc_final: 0.8909 (tmm) REVERT: E 349 MET cc_start: 0.5515 (ttt) cc_final: 0.4402 (ptt) REVERT: F 22 TYR cc_start: 0.6950 (m-80) cc_final: 0.6701 (m-80) REVERT: F 28 TRP cc_start: 0.4707 (OUTLIER) cc_final: 0.3431 (m-90) REVERT: F 50 TRP cc_start: 0.7822 (t60) cc_final: 0.7591 (t-100) REVERT: F 97 MET cc_start: 0.7262 (mtt) cc_final: 0.7002 (mtt) REVERT: F 165 THR cc_start: 0.5570 (p) cc_final: 0.5334 (p) REVERT: G 76 ASN cc_start: 0.1677 (OUTLIER) cc_final: 0.1457 (t0) REVERT: G 112 GLN cc_start: 0.7525 (mm-40) cc_final: 0.7018 (pm20) REVERT: H 12 GLN cc_start: 0.8383 (pp30) cc_final: 0.8173 (tm-30) REVERT: H 36 PHE cc_start: 0.7901 (m-80) cc_final: 0.7608 (t80) REVERT: H 82 MET cc_start: 0.8808 (ptp) cc_final: 0.8354 (tmm) outliers start: 60 outliers final: 37 residues processed: 264 average time/residue: 0.2495 time to fit residues: 98.5307 Evaluate side-chains 241 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 201 time to evaluate : 1.583 ------------------------------------------------------------------------------- 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 67 GLU Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 170 PHE Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 4 CYS Chi-restraints excluded: chain F residue 15 CYS Chi-restraints excluded: chain F residue 28 TRP Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 216 HIS Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 221 LYS Chi-restraints excluded: chain F residue 233 THR Chi-restraints excluded: chain F residue 329 CYS 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 2 GLN Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 chunk 2 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 156 optimal weight: 20.0000 chunk 43 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 39 GLN C 90 GLN 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6682 moved from start: 0.4876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 14488 Z= 0.294 Angle : 0.753 18.846 19666 Z= 0.395 Chirality : 0.045 0.233 2143 Planarity : 0.006 0.070 2528 Dihedral : 5.812 56.748 2030 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.11 % Favored : 90.67 % Rotamer: Outliers : 5.45 % Allowed : 20.32 % Favored : 74.23 % 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: -1.81 (0.19), residues: 1800 helix: -1.25 (0.49), residues: 87 sheet: -0.09 (0.24), residues: 454 loop : -1.75 (0.17), residues: 1259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 35 HIS 0.005 0.001 HIS C 199 PHE 0.024 0.002 PHE A 210 TYR 0.025 0.002 TYR F 331 ARG 0.004 0.001 ARG C 19 *********************** 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 311 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 226 time to evaluate : 1.580 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 32 SER cc_start: 0.7845 (OUTLIER) cc_final: 0.7323 (t) REVERT: A 168 ASP cc_start: 0.7544 (t0) cc_final: 0.7185 (t0) REVERT: A 188 GLU cc_start: 0.6696 (tp30) cc_final: 0.6443 (tp30) REVERT: B 12 LEU cc_start: 0.8407 (pt) cc_final: 0.7915 (tt) REVERT: C 88 TYR cc_start: 0.5673 (OUTLIER) cc_final: 0.3274 (p90) REVERT: C 90 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.8091 (tm130) REVERT: D 20 ARG cc_start: 0.7308 (ttt-90) cc_final: 0.7086 (ttm-80) REVERT: D 95 TYR cc_start: 0.6994 (OUTLIER) cc_final: 0.5343 (p90) REVERT: D 106 TYR cc_start: 0.4667 (OUTLIER) cc_final: 0.2908 (m-80) REVERT: E 349 MET cc_start: 0.5757 (ttt) cc_final: 0.4792 (ptm) REVERT: F 28 TRP cc_start: 0.4724 (OUTLIER) cc_final: 0.3577 (m-90) REVERT: F 70 SER cc_start: 0.8832 (m) cc_final: 0.8577 (t) REVERT: G 18 ARG cc_start: 0.8181 (tpp-160) cc_final: 0.7952 (tpt170) REVERT: G 82 MET cc_start: 0.7181 (ptp) cc_final: 0.6883 (tmm) REVERT: G 85 LEU cc_start: 0.7497 (mt) cc_final: 0.6974 (mt) REVERT: G 112 GLN cc_start: 0.7343 (mm-40) cc_final: 0.7013 (pm20) REVERT: H 12 GLN cc_start: 0.8449 (pp30) cc_final: 0.8154 (tm-30) REVERT: H 31 TYR cc_start: 0.6493 (m-80) cc_final: 0.6229 (m-80) REVERT: H 36 PHE cc_start: 0.7973 (m-80) cc_final: 0.7601 (t80) REVERT: H 82 MET cc_start: 0.8845 (ptp) cc_final: 0.8465 (tmm) REVERT: H 112 GLN cc_start: 0.6317 (mm-40) cc_final: 0.5903 (pp30) outliers start: 85 outliers final: 58 residues processed: 286 average time/residue: 0.2653 time to fit residues: 112.4000 Evaluate side-chains 281 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 217 time to evaluate : 1.438 ------------------------------------------------------------------------------- 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 32 SER Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain B residue 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 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 90 GLN Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 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 140 LEU 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 E residue 351 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 4 CYS Chi-restraints excluded: chain F residue 15 CYS Chi-restraints excluded: chain F residue 21 ILE 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 329 CYS Chi-restraints excluded: chain G residue 30 ARG Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 0.9990 chunk 156 optimal weight: 10.0000 chunk 34 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 174 optimal weight: 4.9990 chunk 144 optimal weight: 0.0770 chunk 80 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 91 optimal weight: 7.9990 overall best weight: 0.7344 ------------------------------------------------------------------------------- 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 14 GLN ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 201 ASN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6593 moved from start: 0.5050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14488 Z= 0.192 Angle : 0.685 14.302 19666 Z= 0.353 Chirality : 0.043 0.234 2143 Planarity : 0.005 0.067 2528 Dihedral : 5.354 54.671 2030 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.72 % Favored : 92.06 % Rotamer: Outliers : 3.72 % Allowed : 22.44 % Favored : 73.85 % 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: -0.91 (0.51), residues: 87 sheet: 0.15 (0.25), residues: 423 loop : -1.62 (0.17), residues: 1290 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 0.022 0.001 PHE A 210 TYR 0.027 0.001 TYR C 141 ARG 0.005 0.000 ARG C 19 *********************** 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 288 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 230 time to evaluate : 1.680 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 32 SER cc_start: 0.7605 (OUTLIER) cc_final: 0.7206 (t) REVERT: A 167 GLN cc_start: 0.7072 (tt0) cc_final: 0.6681 (pp30) REVERT: A 188 GLU cc_start: 0.6701 (tp30) cc_final: 0.6453 (tp30) REVERT: B 12 LEU cc_start: 0.8361 (pt) cc_final: 0.7957 (tt) REVERT: C 39 GLN cc_start: 0.6892 (tt0) cc_final: 0.6515 (tt0) REVERT: C 88 TYR cc_start: 0.5524 (OUTLIER) cc_final: 0.4174 (p90) REVERT: D 95 TYR cc_start: 0.6850 (OUTLIER) cc_final: 0.4929 (p90) REVERT: E 85 GLN cc_start: 0.7165 (tp40) cc_final: 0.6925 (tp40) REVERT: E 349 MET cc_start: 0.5597 (ttt) cc_final: 0.4759 (ptm) REVERT: F 28 TRP cc_start: 0.4663 (OUTLIER) cc_final: 0.3478 (m-90) REVERT: F 50 TRP cc_start: 0.7857 (t60) cc_final: 0.7630 (t-100) REVERT: F 70 SER cc_start: 0.8829 (m) cc_final: 0.8498 (t) REVERT: F 318 MET cc_start: 0.7076 (tmm) cc_final: 0.6667 (tmm) REVERT: G 112 GLN cc_start: 0.7293 (mm-40) cc_final: 0.6964 (pm20) REVERT: H 17 LEU cc_start: 0.8887 (mp) cc_final: 0.7693 (mp) REVERT: H 31 TYR cc_start: 0.6575 (m-80) cc_final: 0.6228 (m-80) REVERT: H 36 PHE cc_start: 0.7992 (m-80) cc_final: 0.7635 (t80) REVERT: H 82 MET cc_start: 0.8739 (ptp) cc_final: 0.8279 (ppp) REVERT: H 112 GLN cc_start: 0.6337 (mm-40) cc_final: 0.5967 (pp30) outliers start: 58 outliers final: 41 residues processed: 275 average time/residue: 0.2534 time to fit residues: 104.0240 Evaluate side-chains 267 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 222 time to evaluate : 1.635 ------------------------------------------------------------------------------- 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 208 LYS Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 170 PHE 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 D residue 32 SER Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 223 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 E residue 287 VAL Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 4 CYS Chi-restraints excluded: chain F residue 7 ASP Chi-restraints excluded: chain F residue 15 CYS Chi-restraints excluded: chain F residue 21 ILE 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 G residue 30 ARG Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain H residue 12 GLN Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 10.0000 chunk 19 optimal weight: 0.9980 chunk 99 optimal weight: 0.0470 chunk 127 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 146 optimal weight: 2.9990 chunk 97 optimal weight: 0.3980 chunk 173 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 80 optimal weight: 9.9990 overall best weight: 1.2882 ------------------------------------------------------------------------------- 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 ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6680 moved from start: 0.5458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14488 Z= 0.243 Angle : 0.715 15.884 19666 Z= 0.371 Chirality : 0.044 0.227 2143 Planarity : 0.005 0.065 2528 Dihedral : 5.523 55.737 2030 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.00 % Favored : 90.83 % Rotamer: Outliers : 3.91 % Allowed : 23.14 % 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: -1.64 (0.19), residues: 1800 helix: -1.25 (0.49), residues: 88 sheet: 0.12 (0.25), residues: 445 loop : -1.65 (0.17), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP H 35 HIS 0.003 0.001 HIS E 195 PHE 0.022 0.002 PHE A 210 TYR 0.026 0.002 TYR C 141 ARG 0.007 0.001 ARG C 19 *********************** 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 285 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 224 time to evaluate : 1.771 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 32 SER cc_start: 0.7736 (OUTLIER) cc_final: 0.7259 (t) REVERT: A 188 GLU cc_start: 0.6661 (tp30) cc_final: 0.6443 (tp30) REVERT: B 12 LEU cc_start: 0.8340 (pt) cc_final: 0.7921 (tt) REVERT: B 14 GLN cc_start: 0.8444 (mm-40) cc_final: 0.8165 (mm110) REVERT: C 88 TYR cc_start: 0.5617 (OUTLIER) cc_final: 0.3973 (p90) REVERT: C 90 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.8059 (tm130) REVERT: D 20 ARG cc_start: 0.7299 (ttt-90) cc_final: 0.7002 (ttm-80) REVERT: D 95 TYR cc_start: 0.6896 (OUTLIER) cc_final: 0.5053 (p90) REVERT: D 180 TYR cc_start: 0.7441 (m-80) cc_final: 0.6991 (m-10) REVERT: F 28 TRP cc_start: 0.4679 (OUTLIER) cc_final: 0.3491 (m-90) REVERT: F 50 TRP cc_start: 0.7845 (t60) cc_final: 0.7610 (t-100) REVERT: F 70 SER cc_start: 0.8836 (m) cc_final: 0.8592 (t) REVERT: F 318 MET cc_start: 0.7085 (tmm) cc_final: 0.6434 (tmm) REVERT: F 349 MET cc_start: 0.7015 (ppp) cc_final: 0.6805 (ppp) REVERT: G 35 TRP cc_start: 0.6691 (OUTLIER) cc_final: 0.5478 (m-90) REVERT: G 82 MET cc_start: 0.7434 (ptp) cc_final: 0.6934 (tmm) REVERT: G 112 GLN cc_start: 0.7351 (mm-40) cc_final: 0.7105 (pm20) REVERT: H 17 LEU cc_start: 0.8882 (mp) cc_final: 0.8424 (mp) REVERT: H 31 TYR cc_start: 0.6895 (m-80) cc_final: 0.6576 (m-80) REVERT: H 36 PHE cc_start: 0.8041 (m-80) cc_final: 0.7584 (t80) REVERT: H 82 MET cc_start: 0.8732 (ptp) cc_final: 0.8373 (tmm) outliers start: 61 outliers final: 47 residues processed: 268 average time/residue: 0.2585 time to fit residues: 102.4953 Evaluate side-chains 264 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 211 time to evaluate : 1.537 ------------------------------------------------------------------------------- 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 208 LYS Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 170 PHE Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 88 TYR Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 223 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 351 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 4 CYS Chi-restraints excluded: chain F residue 15 CYS Chi-restraints excluded: chain F residue 28 TRP Chi-restraints excluded: chain F residue 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 G residue 30 ARG Chi-restraints excluded: chain G residue 35 TRP Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 34 optimal weight: 8.9990 chunk 33 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 118 optimal weight: 0.0070 chunk 85 optimal weight: 10.0000 chunk 16 optimal weight: 7.9990 chunk 136 optimal weight: 4.9990 overall best weight: 1.1202 ------------------------------------------------------------------------------- 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** ** G 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6664 moved from start: 0.5694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14488 Z= 0.227 Angle : 0.704 14.491 19666 Z= 0.366 Chirality : 0.044 0.229 2143 Planarity : 0.005 0.072 2528 Dihedral : 5.431 53.936 2030 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.72 % Favored : 91.11 % Rotamer: Outliers : 3.91 % Allowed : 23.46 % Favored : 72.63 % 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: -1.61 (0.19), residues: 1800 helix: -1.34 (0.50), residues: 88 sheet: 0.04 (0.24), residues: 465 loop : -1.60 (0.17), residues: 1247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP H 35 HIS 0.003 0.001 HIS F 229 PHE 0.021 0.002 PHE A 210 TYR 0.029 0.002 TYR D 149 ARG 0.004 0.000 ARG C 19 *********************** 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 282 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 221 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 32 SER cc_start: 0.7622 (OUTLIER) cc_final: 0.7219 (t) REVERT: B 12 LEU cc_start: 0.8311 (pt) cc_final: 0.7997 (tt) REVERT: C 2 ASP cc_start: 0.7418 (OUTLIER) cc_final: 0.7208 (m-30) REVERT: C 88 TYR cc_start: 0.5663 (OUTLIER) cc_final: 0.4395 (p90) REVERT: D 20 ARG cc_start: 0.7365 (ttt-90) cc_final: 0.6992 (ttm-80) REVERT: D 32 SER cc_start: 0.6661 (p) cc_final: 0.6363 (p) REVERT: D 95 TYR cc_start: 0.6976 (OUTLIER) cc_final: 0.5139 (p90) REVERT: E 85 GLN cc_start: 0.7186 (tp40) cc_final: 0.6946 (tp40) REVERT: E 349 MET cc_start: 0.5664 (ttt) cc_final: 0.5461 (ptm) REVERT: F 26 GLU cc_start: 0.6934 (mp0) cc_final: 0.6098 (pp20) REVERT: F 28 TRP cc_start: 0.4700 (OUTLIER) cc_final: 0.3584 (m-90) REVERT: F 50 TRP cc_start: 0.7862 (t60) cc_final: 0.7634 (t-100) REVERT: F 70 SER cc_start: 0.8812 (m) cc_final: 0.8553 (t) REVERT: F 318 MET cc_start: 0.7105 (tmm) cc_final: 0.6578 (tmm) REVERT: G 35 TRP cc_start: 0.6705 (OUTLIER) cc_final: 0.5325 (m-90) REVERT: G 112 GLN cc_start: 0.7292 (mm-40) cc_final: 0.6667 (pp30) REVERT: H 17 LEU cc_start: 0.8866 (mp) cc_final: 0.8427 (mp) REVERT: H 31 TYR cc_start: 0.7032 (m-80) cc_final: 0.6654 (m-80) REVERT: H 36 PHE cc_start: 0.8023 (m-80) cc_final: 0.7569 (t80) REVERT: H 82 MET cc_start: 0.8742 (ptp) cc_final: 0.8432 (tmm) outliers start: 61 outliers final: 43 residues processed: 265 average time/residue: 0.2510 time to fit residues: 99.7397 Evaluate side-chains 262 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 213 time to evaluate : 1.682 ------------------------------------------------------------------------------- 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 180 LEU 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 89 GLU 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 2 ASP Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 23 THR 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 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 183 VAL Chi-restraints excluded: chain E residue 216 HIS Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 4 CYS Chi-restraints excluded: chain F residue 15 CYS Chi-restraints excluded: chain F residue 28 TRP Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 216 HIS Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 221 LYS Chi-restraints excluded: chain F residue 233 THR Chi-restraints excluded: chain F residue 239 SER Chi-restraints excluded: chain G residue 30 ARG Chi-restraints excluded: chain G residue 35 TRP Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 20.0000 chunk 166 optimal weight: 10.0000 chunk 151 optimal weight: 0.6980 chunk 161 optimal weight: 6.9990 chunk 97 optimal weight: 0.0050 chunk 70 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 146 optimal weight: 0.9990 chunk 152 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 overall best weight: 0.9198 ------------------------------------------------------------------------------- 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 D 201 ASN ** G 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6651 moved from start: 0.5895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14488 Z= 0.211 Angle : 0.697 13.964 19666 Z= 0.360 Chirality : 0.043 0.226 2143 Planarity : 0.005 0.071 2528 Dihedral : 5.313 54.308 2030 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.39 % Favored : 91.39 % Rotamer: Outliers : 3.59 % Allowed : 23.65 % Favored : 72.76 % 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: -1.57 (0.19), residues: 1800 helix: -1.21 (0.50), residues: 88 sheet: 0.05 (0.24), residues: 467 loop : -1.56 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP H 35 HIS 0.003 0.001 HIS F 229 PHE 0.020 0.001 PHE A 210 TYR 0.026 0.001 TYR C 141 ARG 0.004 0.000 ARG C 19 *********************** 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 274 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 218 time to evaluate : 1.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 SER cc_start: 0.7615 (OUTLIER) cc_final: 0.7204 (t) REVERT: B 12 LEU cc_start: 0.8332 (pt) cc_final: 0.7968 (tt) REVERT: B 47 GLU cc_start: 0.7009 (tp30) cc_final: 0.6053 (mt-10) REVERT: C 2 ASP cc_start: 0.7356 (OUTLIER) cc_final: 0.7012 (m-30) REVERT: C 37 TYR cc_start: 0.7130 (m-80) cc_final: 0.6911 (m-80) REVERT: C 39 GLN cc_start: 0.6956 (tt0) cc_final: 0.6584 (tt0) REVERT: C 88 TYR cc_start: 0.5529 (OUTLIER) cc_final: 0.4299 (p90) REVERT: C 90 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.8016 (tm130) REVERT: D 20 ARG cc_start: 0.7398 (ttt-90) cc_final: 0.6971 (ttm-80) REVERT: D 32 SER cc_start: 0.6619 (p) cc_final: 0.6372 (p) REVERT: D 95 TYR cc_start: 0.6912 (OUTLIER) cc_final: 0.4909 (p90) REVERT: D 112 MET cc_start: 0.7516 (tmm) cc_final: 0.7057 (pmm) REVERT: E 349 MET cc_start: 0.5885 (ttt) cc_final: 0.5378 (ptm) REVERT: F 26 GLU cc_start: 0.6878 (mp0) cc_final: 0.6196 (pp20) REVERT: F 28 TRP cc_start: 0.4723 (OUTLIER) cc_final: 0.3601 (m-90) REVERT: F 50 TRP cc_start: 0.7868 (t60) cc_final: 0.7656 (t-100) REVERT: F 70 SER cc_start: 0.8845 (m) cc_final: 0.8552 (t) REVERT: F 165 THR cc_start: 0.5755 (p) cc_final: 0.5525 (p) REVERT: F 318 MET cc_start: 0.7140 (tmm) cc_final: 0.6673 (tmm) REVERT: F 338 ARG cc_start: 0.6522 (OUTLIER) cc_final: 0.6168 (ttt180) REVERT: G 34 SER cc_start: 0.7875 (p) cc_final: 0.7318 (m) REVERT: G 35 TRP cc_start: 0.6668 (OUTLIER) cc_final: 0.5242 (m-90) REVERT: G 98 ASP cc_start: 0.7318 (t0) cc_final: 0.7072 (t0) REVERT: G 112 GLN cc_start: 0.7282 (mm-40) cc_final: 0.6703 (pp30) REVERT: H 17 LEU cc_start: 0.8846 (mp) cc_final: 0.8425 (mp) REVERT: H 31 TYR cc_start: 0.7091 (m-80) cc_final: 0.6705 (m-80) REVERT: H 82 MET cc_start: 0.8728 (ptp) cc_final: 0.8418 (tmm) outliers start: 56 outliers final: 39 residues processed: 259 average time/residue: 0.2615 time to fit residues: 100.3375 Evaluate side-chains 259 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 212 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 88 TYR Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 216 HIS Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 4 CYS Chi-restraints excluded: chain F residue 15 CYS Chi-restraints excluded: chain F residue 28 TRP Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 216 HIS Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 221 LYS Chi-restraints excluded: chain F residue 233 THR Chi-restraints excluded: chain F residue 239 SER Chi-restraints excluded: chain F residue 338 ARG Chi-restraints excluded: chain G residue 30 ARG Chi-restraints excluded: chain G residue 35 TRP Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 9.9990 chunk 104 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 118 optimal weight: 0.0980 chunk 179 optimal weight: 6.9990 chunk 165 optimal weight: 20.0000 chunk 142 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 ** G 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6680 moved from start: 0.6086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14488 Z= 0.230 Angle : 0.711 14.580 19666 Z= 0.368 Chirality : 0.044 0.225 2143 Planarity : 0.005 0.076 2528 Dihedral : 5.393 54.372 2030 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.89 % Favored : 90.89 % Rotamer: Outliers : 3.40 % Allowed : 24.10 % Favored : 72.50 % 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: -1.28 (0.49), residues: 88 sheet: 0.08 (0.25), residues: 463 loop : -1.60 (0.17), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP H 35 HIS 0.003 0.001 HIS E 195 PHE 0.026 0.002 PHE H 36 TYR 0.026 0.002 TYR C 141 ARG 0.004 0.000 ARG C 19 ********************** 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 266 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 213 time to evaluate : 1.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.5558 (tpp) cc_final: 0.5340 (tpp) REVERT: A 32 SER cc_start: 0.7719 (OUTLIER) cc_final: 0.7278 (t) REVERT: B 12 LEU cc_start: 0.8352 (pt) cc_final: 0.7974 (tt) REVERT: B 47 GLU cc_start: 0.7028 (tp30) cc_final: 0.6052 (mt-10) REVERT: C 2 ASP cc_start: 0.7303 (OUTLIER) cc_final: 0.6850 (m-30) REVERT: C 37 TYR cc_start: 0.7126 (m-80) cc_final: 0.6895 (m-80) REVERT: C 39 GLN cc_start: 0.6992 (tt0) cc_final: 0.6590 (tt0) REVERT: C 88 TYR cc_start: 0.5549 (OUTLIER) cc_final: 0.4221 (p90) REVERT: C 90 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.8032 (tm130) REVERT: D 20 ARG cc_start: 0.7482 (ttt-90) cc_final: 0.6945 (ttm-80) REVERT: D 95 TYR cc_start: 0.6966 (OUTLIER) cc_final: 0.4998 (p90) REVERT: D 112 MET cc_start: 0.7501 (tmm) cc_final: 0.6964 (pmm) REVERT: E 349 MET cc_start: 0.5929 (ttt) cc_final: 0.5350 (ptm) REVERT: F 26 GLU cc_start: 0.7008 (mp0) cc_final: 0.6327 (pp20) REVERT: F 28 TRP cc_start: 0.4688 (OUTLIER) cc_final: 0.3604 (m-90) REVERT: F 50 TRP cc_start: 0.7888 (t60) cc_final: 0.7669 (t-100) REVERT: F 70 SER cc_start: 0.8862 (m) cc_final: 0.8537 (t) REVERT: F 318 MET cc_start: 0.7127 (tmm) cc_final: 0.6666 (tmm) REVERT: F 338 ARG cc_start: 0.6549 (OUTLIER) cc_final: 0.6194 (ttt180) REVERT: G 21 CYS cc_start: 0.4482 (t) cc_final: 0.4042 (t) REVERT: G 34 SER cc_start: 0.7770 (p) cc_final: 0.7287 (m) REVERT: G 35 TRP cc_start: 0.6707 (OUTLIER) cc_final: 0.5310 (m-90) REVERT: G 98 ASP cc_start: 0.7335 (t0) cc_final: 0.7130 (t0) REVERT: G 112 GLN cc_start: 0.7270 (mm-40) cc_final: 0.6603 (pp30) REVERT: H 17 LEU cc_start: 0.8841 (mp) cc_final: 0.8425 (mp) REVERT: H 31 TYR cc_start: 0.7226 (m-80) cc_final: 0.6825 (m-80) REVERT: H 82 MET cc_start: 0.8749 (ptp) cc_final: 0.8420 (tmm) outliers start: 53 outliers final: 44 residues processed: 252 average time/residue: 0.2517 time to fit residues: 94.0107 Evaluate side-chains 262 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 210 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 88 TYR Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 95 TYR Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain E residue 34 TYR Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 216 HIS Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 4 CYS Chi-restraints excluded: chain F residue 15 CYS Chi-restraints excluded: chain F residue 28 TRP Chi-restraints excluded: chain F residue 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 338 ARG Chi-restraints excluded: chain G residue 35 TRP Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain H residue 46 PHE Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 0.2980 chunk 43 optimal weight: 5.9990 chunk 131 optimal weight: 0.0020 chunk 21 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 143 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 146 optimal weight: 0.0980 chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 overall best weight: 1.0792 ------------------------------------------------------------------------------- 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 ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.164816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.121184 restraints weight = 27167.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.124832 restraints weight = 15857.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.127314 restraints weight = 11234.183| |-----------------------------------------------------------------------------| r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.6233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14488 Z= 0.223 Angle : 0.709 14.266 19666 Z= 0.367 Chirality : 0.044 0.224 2143 Planarity : 0.005 0.075 2528 Dihedral : 5.359 54.315 2030 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.61 % Favored : 91.17 % Rotamer: Outliers : 3.59 % Allowed : 24.10 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (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: -1.61 (0.19), residues: 1800 helix: -1.23 (0.49), residues: 88 sheet: 0.07 (0.25), residues: 463 loop : -1.61 (0.17), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP H 35 HIS 0.003 0.001 HIS E 195 PHE 0.025 0.002 PHE H 36 TYR 0.032 0.002 TYR B 149 ARG 0.004 0.000 ARG C 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3158.13 seconds wall clock time: 59 minutes 27.20 seconds (3567.20 seconds total)