Starting phenix.real_space_refine on Thu Sep 18 10:17:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cjy_45636/09_2025/9cjy_45636.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cjy_45636/09_2025/9cjy_45636.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9cjy_45636/09_2025/9cjy_45636.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cjy_45636/09_2025/9cjy_45636.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cjy_45636/09_2025/9cjy_45636.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cjy_45636/09_2025/9cjy_45636.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.031 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 75 5.16 5 C 10201 2.51 5 N 2764 2.21 5 O 3098 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16138 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2505 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 20, 'TRANS': 297} Chain breaks: 1 Chain: "B" Number of atoms: 1350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1350 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 1, 'TRANS': 165} Chain: "C" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2505 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 20, 'TRANS': 297} Chain breaks: 1 Chain: "D" Number of atoms: 1350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1350 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 1, 'TRANS': 165} Chain: "E" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2505 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 20, 'TRANS': 297} Chain breaks: 1 Chain: "F" Number of atoms: 1350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1350 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 1, 'TRANS': 165} Chain: "G" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 895 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain breaks: 1 Chain: "H" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 895 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain breaks: 1 Chain: "I" Number of atoms: 629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 629 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 4, 'TRANS': 77} Chain breaks: 3 Chain: "J" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 895 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain breaks: 1 Chain: "K" Number of atoms: 671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 671 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 4, 'TRANS': 83} Chain breaks: 2 Chain: "L" Number of atoms: 588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 588 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain breaks: 3 Time building chain proxies: 3.55, per 1000 atoms: 0.22 Number of scatterers: 16138 At special positions: 0 Unit cell: (130.98, 132.09, 150.96, 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 75 16.00 O 3098 8.00 N 2764 7.00 C 10201 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS B 137 " distance=2.04 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS D 137 " distance=2.04 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.02 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.03 Simple disulfide: pdb=" SG CYS E 14 " - pdb=" SG CYS F 137 " distance=2.04 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 277 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 76 " distance=2.03 Simple disulfide: pdb=" SG CYS E 97 " - pdb=" SG CYS E 139 " distance=2.03 Simple disulfide: pdb=" SG CYS E 281 " - pdb=" SG CYS E 305 " distance=2.03 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 148 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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 Time building additional restraints: 1.07 Conformation dependent library (CDL) restraints added in 825.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3768 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 41 sheets defined 18.3% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 65 through 70 Processing helix chain 'A' and resid 73 through 77 removed outlier: 3.902A pdb=" N GLU A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 112 removed outlier: 3.511A pdb=" N LEU A 108 " --> pdb=" O ASP A 104 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG A 109 " --> pdb=" O TYR A 105 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N GLU A 110 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLN A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 112 " --> pdb=" O LEU A 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 104 through 112' Processing helix chain 'A' and resid 187 through 196 removed outlier: 3.585A pdb=" N TYR A 195 " --> pdb=" O GLN A 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 57 Processing helix chain 'B' and resid 74 through 126 removed outlier: 3.847A pdb=" N GLU B 78 " --> pdb=" O GLU B 74 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU B 80 " --> pdb=" O ARG B 76 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS B 83 " --> pdb=" O ASN B 79 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N THR B 93 " --> pdb=" O LEU B 89 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LEU B 98 " --> pdb=" O TYR B 94 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU B 105 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU B 108 " --> pdb=" O ASN B 104 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL B 115 " --> pdb=" O HIS B 111 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LYS B 116 " --> pdb=" O ASP B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 155 removed outlier: 4.132A pdb=" N MET B 149 " --> pdb=" O ASN B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 169 removed outlier: 4.608A pdb=" N GLU B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N GLU B 165 " --> pdb=" O LYS B 161 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER B 166 " --> pdb=" O TYR B 162 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS B 167 " --> pdb=" O SER B 163 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU B 168 " --> pdb=" O GLU B 164 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASN B 169 " --> pdb=" O GLU B 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 71 removed outlier: 4.233A pdb=" N LEU C 71 " --> pdb=" O ALA C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 77 removed outlier: 3.751A pdb=" N GLU C 77 " --> pdb=" O PRO C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 112 removed outlier: 3.599A pdb=" N LEU C 108 " --> pdb=" O ASP C 104 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLU C 110 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN C 111 " --> pdb=" O GLU C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'D' and resid 39 through 58 removed outlier: 3.884A pdb=" N LYS D 58 " --> pdb=" O SER D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 126 removed outlier: 3.968A pdb=" N GLU D 78 " --> pdb=" O GLU D 74 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N THR D 93 " --> pdb=" O LEU D 89 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU D 98 " --> pdb=" O TYR D 94 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL D 100 " --> pdb=" O ALA D 96 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLU D 105 " --> pdb=" O LEU D 101 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LEU D 108 " --> pdb=" O ASN D 104 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL D 115 " --> pdb=" O HIS D 111 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS D 116 " --> pdb=" O ASP D 112 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN D 125 " --> pdb=" O LYS D 121 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU D 126 " --> pdb=" O VAL D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 155 removed outlier: 4.122A pdb=" N MET D 149 " --> pdb=" O ASN D 145 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS D 153 " --> pdb=" O MET D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 170 removed outlier: 4.430A pdb=" N TYR D 162 " --> pdb=" O ASP D 158 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLU D 164 " --> pdb=" O PRO D 160 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N GLU D 165 " --> pdb=" O LYS D 161 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU D 168 " --> pdb=" O GLU D 164 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN D 169 " --> pdb=" O GLU D 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 70 Processing helix chain 'E' and resid 104 through 112 removed outlier: 3.776A pdb=" N LEU E 108 " --> pdb=" O ASP E 104 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG E 109 " --> pdb=" O TYR E 105 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU E 110 " --> pdb=" O GLU E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 196 Processing helix chain 'F' and resid 39 through 57 Processing helix chain 'F' and resid 74 through 126 removed outlier: 3.906A pdb=" N THR F 93 " --> pdb=" O LEU F 89 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLU F 105 " --> pdb=" O LEU F 101 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG F 106 " --> pdb=" O LEU F 102 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU F 108 " --> pdb=" O ASN F 104 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL F 115 " --> pdb=" O HIS F 111 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LYS F 116 " --> pdb=" O ASP F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 155 removed outlier: 3.596A pdb=" N MET F 149 " --> pdb=" O ASN F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 169 removed outlier: 4.361A pdb=" N TYR F 162 " --> pdb=" O ASP F 158 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLU F 164 " --> pdb=" O PRO F 160 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N GLU F 165 " --> pdb=" O LYS F 161 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER F 166 " --> pdb=" O TYR F 162 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS F 167 " --> pdb=" O SER F 163 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU F 168 " --> pdb=" O GLU F 164 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASN F 169 " --> pdb=" O GLU F 165 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 65 removed outlier: 4.109A pdb=" N GLN G 64 " --> pdb=" O GLU G 61 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLY G 65 " --> pdb=" O LYS G 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 61 through 65' Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 41 removed outlier: 3.537A pdb=" N VAL A 40 " --> pdb=" O MET A 316 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 87 through 88 removed outlier: 6.408A pdb=" N ILE A 87 " --> pdb=" O ILE A 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 100 through 102 removed outlier: 3.694A pdb=" N TYR A 232 " --> pdb=" O TYR A 101 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TRP A 180 " --> pdb=" O TYR A 233 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR A 235 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N LEU A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE A 252 " --> pdb=" O GLY A 181 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 117 through 119 removed outlier: 3.865A pdb=" N SER A 117 " --> pdb=" O SER A 261 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER A 261 " --> pdb=" O SER A 117 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU A 117B" --> pdb=" O ALA A 259 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 136 through 141 removed outlier: 4.616A pdb=" N CYS A 139 " --> pdb=" O SER A 146 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 164 through 169 removed outlier: 3.604A pdb=" N VAL A 204 " --> pdb=" O ARG A 211 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 281 through 282 removed outlier: 3.886A pdb=" N ILE A 302 " --> pdb=" O GLN A 282 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 16 through 17 removed outlier: 3.949A pdb=" N GLY C 16 " --> pdb=" O GLY D 23 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AB1, first strand: chain 'C' and resid 87 through 88 removed outlier: 6.436A pdb=" N ILE C 87 " --> pdb=" O ILE C 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 100 through 102 removed outlier: 3.736A pdb=" N TYR C 232 " --> pdb=" O TYR C 101 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TRP C 180 " --> pdb=" O TYR C 233 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR C 235 " --> pdb=" O VAL C 178 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N LEU C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE C 252 " --> pdb=" O GLY C 181 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 117 through 119 removed outlier: 3.540A pdb=" N SER C 117 " --> pdb=" O SER C 261 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU C 117B" --> pdb=" O ALA C 259 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 136 through 141 removed outlier: 4.628A pdb=" N CYS C 139 " --> pdb=" O SER C 146 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 164 through 169 removed outlier: 3.668A pdb=" N VAL C 204 " --> pdb=" O ARG C 211 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG C 211 " --> pdb=" O VAL C 204 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 286 through 288 removed outlier: 4.099A pdb=" N ILE C 288 " --> pdb=" O CYS C 281 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N CYS C 281 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE C 302 " --> pdb=" O GLN C 282 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 16 through 17 removed outlier: 3.528A pdb=" N GLY F 23 " --> pdb=" O GLY E 16 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 39 through 41 Processing sheet with id=AB9, first strand: chain 'E' and resid 51 through 53 removed outlier: 6.082A pdb=" N LEU E 51 " --> pdb=" O ASP E 275 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N CYS E 277 " --> pdb=" O LEU E 51 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 87 through 89 removed outlier: 6.424A pdb=" N ILE E 87 " --> pdb=" O ILE E 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'E' and resid 100 through 102 removed outlier: 3.701A pdb=" N TYR E 232 " --> pdb=" O TYR E 101 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TRP E 180 " --> pdb=" O TYR E 233 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 117 through 118 removed outlier: 3.821A pdb=" N SER E 117 " --> pdb=" O SER E 261 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER E 261 " --> pdb=" O SER E 117 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU E 117B" --> pdb=" O ALA E 259 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AC5, first strand: chain 'E' and resid 151 through 153 Processing sheet with id=AC6, first strand: chain 'E' and resid 164 through 169 removed outlier: 3.626A pdb=" N VAL E 204 " --> pdb=" O ARG E 211 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 286 through 288 removed outlier: 4.000A pdb=" N ILE E 288 " --> pdb=" O CYS E 281 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N CYS E 281 " --> pdb=" O ILE E 288 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 5 through 6 removed outlier: 3.671A pdb=" N ASP G 72 " --> pdb=" O THR G 77 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 57 through 59 removed outlier: 5.725A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TRP G 36 " --> pdb=" O GLY G 49 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 57 through 59 removed outlier: 5.725A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TRP G 36 " --> pdb=" O GLY G 49 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL G 89 " --> pdb=" O GLN G 39 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL G 109 " --> pdb=" O ALA G 88 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 21 through 23 Processing sheet with id=AD3, first strand: chain 'H' and resid 46 through 51 removed outlier: 5.691A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TRP H 36 " --> pdb=" O GLY H 49 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL H 89 " --> pdb=" O GLN H 39 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 46 through 51 removed outlier: 5.691A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TRP H 36 " --> pdb=" O GLY H 49 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 4 through 6 removed outlier: 3.631A pdb=" N CYS I 23 " --> pdb=" O PHE I 71 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE I 71 " --> pdb=" O CYS I 23 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 45 through 48 removed outlier: 5.356A pdb=" N LEU I 46 " --> pdb=" O GLN I 37 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLN I 37 " --> pdb=" O LEU I 46 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL I 48 " --> pdb=" O TRP I 35 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN I 38 " --> pdb=" O VAL I 85 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL I 85 " --> pdb=" O GLN I 38 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN I 90 " --> pdb=" O THR I 97 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR I 97 " --> pdb=" O GLN I 90 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 35 through 36 removed outlier: 3.686A pdb=" N TRP J 36 " --> pdb=" O GLY J 49 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 38 through 39 removed outlier: 3.590A pdb=" N VAL J 109 " --> pdb=" O ALA J 88 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 70 through 72 removed outlier: 3.611A pdb=" N THR J 70 " --> pdb=" O TYR J 79 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 4 through 5 Processing sheet with id=AE2, first strand: chain 'K' and resid 19 through 22 removed outlier: 3.731A pdb=" N ALA K 19 " --> pdb=" O ILE K 75 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR K 72 " --> pdb=" O SER K 65 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 53 through 54 removed outlier: 3.501A pdb=" N THR K 53 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR K 49 " --> pdb=" O THR K 53 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN K 90 " --> pdb=" O THR K 97 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR K 97 " --> pdb=" O GLN K 90 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.651A pdb=" N THR L 5 " --> pdb=" O ARG L 24 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N CYS L 23 " --> pdb=" O PHE L 71 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'L' and resid 45 through 49 removed outlier: 5.211A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL L 48 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN L 90 " --> pdb=" O THR L 97 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) 412 hydrogen bonds defined for protein. 1110 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.04 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 5260 1.35 - 1.47: 4118 1.47 - 1.59: 7036 1.59 - 1.71: 0 1.71 - 1.83: 102 Bond restraints: 16516 Sorted by residual: bond pdb=" N ASP B 158 " pdb=" CA ASP B 158 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.23e-02 6.61e+03 8.50e+00 bond pdb=" N GLN K 6 " pdb=" CA GLN K 6 " ideal model delta sigma weight residual 1.454 1.488 -0.033 1.16e-02 7.43e+03 8.21e+00 bond pdb=" N TYR B 157 " pdb=" CA TYR B 157 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.27e-02 6.20e+03 7.08e+00 bond pdb=" N SER K 7 " pdb=" CA SER K 7 " ideal model delta sigma weight residual 1.454 1.485 -0.031 1.21e-02 6.83e+03 6.46e+00 bond pdb=" N TYR B 159 " pdb=" CA TYR B 159 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.41e-02 5.03e+03 4.31e+00 ... (remaining 16511 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 21993 1.83 - 3.67: 345 3.67 - 5.50: 49 5.50 - 7.34: 9 7.34 - 9.17: 6 Bond angle restraints: 22402 Sorted by residual: angle pdb=" N VAL I 29 " pdb=" CA VAL I 29 " pdb=" C VAL I 29 " ideal model delta sigma weight residual 113.53 108.86 4.67 9.80e-01 1.04e+00 2.27e+01 angle pdb=" C LEU A 54 " pdb=" CA LEU A 54 " pdb=" CB LEU A 54 " ideal model delta sigma weight residual 117.23 111.71 5.52 1.36e+00 5.41e-01 1.65e+01 angle pdb=" CA GLU E 107 " pdb=" CB GLU E 107 " pdb=" CG GLU E 107 " ideal model delta sigma weight residual 114.10 121.63 -7.53 2.00e+00 2.50e-01 1.42e+01 angle pdb=" CA GLU A 107 " pdb=" CB GLU A 107 " pdb=" CG GLU A 107 " ideal model delta sigma weight residual 114.10 121.17 -7.07 2.00e+00 2.50e-01 1.25e+01 angle pdb=" C LEU E 78 " pdb=" CA LEU E 78 " pdb=" CB LEU E 78 " ideal model delta sigma weight residual 116.54 112.86 3.68 1.15e+00 7.56e-01 1.02e+01 ... (remaining 22397 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 8410 17.89 - 35.77: 1108 35.77 - 53.66: 200 53.66 - 71.55: 40 71.55 - 89.43: 18 Dihedral angle restraints: 9776 sinusoidal: 3885 harmonic: 5891 Sorted by residual: dihedral pdb=" CB CYS A 52 " pdb=" SG CYS A 52 " pdb=" SG CYS A 277 " pdb=" CB CYS A 277 " ideal model delta sinusoidal sigma weight residual -86.00 -28.70 -57.30 1 1.00e+01 1.00e-02 4.41e+01 dihedral pdb=" CB CYS D 144 " pdb=" SG CYS D 144 " pdb=" SG CYS D 148 " pdb=" CB CYS D 148 " ideal model delta sinusoidal sigma weight residual -86.00 -132.25 46.25 1 1.00e+01 1.00e-02 2.96e+01 dihedral pdb=" CB CYS C 14 " pdb=" SG CYS C 14 " pdb=" SG CYS D 137 " pdb=" CB CYS D 137 " ideal model delta sinusoidal sigma weight residual 93.00 47.90 45.10 1 1.00e+01 1.00e-02 2.82e+01 ... (remaining 9773 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 2351 0.106 - 0.211: 71 0.211 - 0.317: 0 0.317 - 0.422: 0 0.422 - 0.528: 1 Chirality restraints: 2423 Sorted by residual: chirality pdb=" CG LEU K 33 " pdb=" CB LEU K 33 " pdb=" CD1 LEU K 33 " pdb=" CD2 LEU K 33 " both_signs ideal model delta sigma weight residual False -2.59 -2.06 -0.53 2.00e-01 2.50e+01 6.96e+00 chirality pdb=" CB ILE C 13 " pdb=" CA ILE C 13 " pdb=" CG1 ILE C 13 " pdb=" CG2 ILE C 13 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.15 2.00e-01 2.50e+01 5.98e-01 chirality pdb=" CA ILE G 52 " pdb=" N ILE G 52 " pdb=" C ILE G 52 " pdb=" CB ILE G 52 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.87e-01 ... (remaining 2420 not shown) Planarity restraints: 2890 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 292 " -0.056 5.00e-02 4.00e+02 8.48e-02 1.15e+01 pdb=" N PRO C 293 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO C 293 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 293 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 107 " -0.012 2.00e-02 2.50e+03 2.38e-02 5.65e+00 pdb=" CD GLU C 107 " 0.041 2.00e-02 2.50e+03 pdb=" OE1 GLU C 107 " -0.015 2.00e-02 2.50e+03 pdb=" OE2 GLU C 107 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR E 283 " 0.035 5.00e-02 4.00e+02 5.26e-02 4.42e+00 pdb=" N PRO E 284 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO E 284 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 284 " 0.029 5.00e-02 4.00e+02 ... (remaining 2887 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2977 2.77 - 3.30: 14670 3.30 - 3.84: 24070 3.84 - 4.37: 25856 4.37 - 4.90: 47687 Nonbonded interactions: 115260 Sorted by model distance: nonbonded pdb=" OH TYR E 86 " pdb=" OE1 GLN E 282 " model vdw 2.239 3.040 nonbonded pdb=" O GLN J 3 " pdb=" OG SER J 25 " model vdw 2.251 3.040 nonbonded pdb=" NE2 GLN D 125 " pdb=" O TYR D 157 " model vdw 2.256 3.120 nonbonded pdb=" OG SER A 138 " pdb=" OE1 GLN A 226 " model vdw 2.266 3.040 nonbonded pdb=" OG SER C 138 " pdb=" OE1 GLN C 226 " model vdw 2.268 3.040 ... (remaining 115255 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' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'J' } ncs_group { reference = (chain 'I' and (resid 2 through 49 or resid 55 or resid 62 through 104)) selection = (chain 'K' and (resid 2 through 8 or resid 19 through 49 or resid 55 or resid 62 \ through 75 or resid 82 through 104)) selection = (chain 'L' and (resid 2 through 8 or resid 19 through 49 or resid 51 through 104 \ )) } 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: 1.690 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: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.460 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 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 0.037 16540 Z= 0.149 Angle : 0.592 9.173 22450 Z= 0.317 Chirality : 0.043 0.528 2423 Planarity : 0.004 0.085 2890 Dihedral : 16.189 89.435 5936 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 0.45 % Allowed : 22.46 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.52 (0.18), residues: 1998 helix: 1.57 (0.32), residues: 294 sheet: -1.00 (0.33), residues: 309 loop : -1.71 (0.15), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 192 TYR 0.018 0.001 TYR A 105 PHE 0.021 0.001 PHE K 71 TRP 0.006 0.001 TRP A 69 HIS 0.007 0.001 HIS H 100B Details of bonding type rmsd covalent geometry : bond 0.00312 (16516) covalent geometry : angle 0.59126 (22402) SS BOND : bond 0.00367 ( 24) SS BOND : angle 0.87952 ( 48) hydrogen bonds : bond 0.24321 ( 406) hydrogen bonds : angle 7.74785 ( 1110) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 235 time to evaluate : 0.475 Fit side-chains REVERT: D 149 MET cc_start: 0.8171 (mmp) cc_final: 0.7856 (mmp) outliers start: 8 outliers final: 7 residues processed: 238 average time/residue: 0.1284 time to fit residues: 45.3851 Evaluate side-chains 237 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 230 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain B residue 138 PHE Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 208 HIS Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain I residue 93 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.3980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 GLN D 95 ASN E 33 ASN E 48 ASN E 282 GLN E 285 GLN G 64 GLN G 100BHIS H 100BHIS K 89 GLN L 6 GLN L 89 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.177563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.151029 restraints weight = 23089.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.151512 restraints weight = 30569.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.152516 restraints weight = 31934.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.154951 restraints weight = 21309.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.155293 restraints weight = 15975.393| |-----------------------------------------------------------------------------| r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 16540 Z= 0.310 Angle : 0.669 8.187 22450 Z= 0.354 Chirality : 0.046 0.153 2423 Planarity : 0.005 0.074 2890 Dihedral : 4.975 34.734 2212 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 4.74 % Allowed : 21.39 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.88 (0.18), residues: 1998 helix: 1.03 (0.31), residues: 303 sheet: -1.48 (0.29), residues: 368 loop : -1.84 (0.16), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 192 TYR 0.023 0.002 TYR K 91 PHE 0.027 0.002 PHE B 110 TRP 0.012 0.002 TRP A 69 HIS 0.008 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00739 (16516) covalent geometry : angle 0.66741 (22402) SS BOND : bond 0.00532 ( 24) SS BOND : angle 1.12902 ( 48) hydrogen bonds : bond 0.07770 ( 406) hydrogen bonds : angle 5.98333 ( 1110) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 233 time to evaluate : 0.596 Fit side-chains revert: symmetry clash REVERT: A 274 MET cc_start: 0.7283 (ppp) cc_final: 0.6921 (ptm) REVERT: B 103 GLU cc_start: 0.7879 (tm-30) cc_final: 0.7628 (tm-30) REVERT: D 159 TYR cc_start: 0.8212 (t80) cc_final: 0.7902 (t80) REVERT: F 69 GLU cc_start: 0.6234 (tt0) cc_final: 0.6009 (tt0) REVERT: H 38 ARG cc_start: 0.8469 (tmm-80) cc_final: 0.7896 (ttp80) REVERT: K 89 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.8252 (tm-30) REVERT: L 89 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.8278 (tm130) outliers start: 84 outliers final: 62 residues processed: 289 average time/residue: 0.1308 time to fit residues: 56.2879 Evaluate side-chains 290 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 226 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 282 GLN Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 24 ASP Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 208 HIS Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 153 LYS Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 269 THR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 79 TYR Chi-restraints excluded: chain I residue 62 PHE Chi-restraints excluded: chain I residue 93 ILE Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 62 PHE Chi-restraints excluded: chain K residue 89 GLN Chi-restraints excluded: chain K residue 104 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 104 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 156 optimal weight: 0.6980 chunk 143 optimal weight: 2.9990 chunk 171 optimal weight: 4.9990 chunk 134 optimal weight: 0.7980 chunk 146 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 160 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 172 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 164 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 95 ASN F 38 GLN G 64 GLN H 100BHIS I 89 GLN J 100BHIS L 89 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.183254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.156975 restraints weight = 23186.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.158595 restraints weight = 29634.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.159481 restraints weight = 28380.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.162030 restraints weight = 19203.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.162251 restraints weight = 14551.158| |-----------------------------------------------------------------------------| r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.0981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16540 Z= 0.122 Angle : 0.535 8.771 22450 Z= 0.278 Chirality : 0.043 0.240 2423 Planarity : 0.004 0.066 2890 Dihedral : 4.366 35.843 2206 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.33 % Allowed : 23.02 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.60 (0.18), residues: 1998 helix: 1.29 (0.31), residues: 303 sheet: -1.01 (0.32), residues: 312 loop : -1.73 (0.15), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 192 TYR 0.013 0.001 TYR C 101 PHE 0.016 0.001 PHE D 9 TRP 0.007 0.001 TRP D 92 HIS 0.006 0.001 HIS J 100B Details of bonding type rmsd covalent geometry : bond 0.00277 (16516) covalent geometry : angle 0.53441 (22402) SS BOND : bond 0.00508 ( 24) SS BOND : angle 0.89815 ( 48) hydrogen bonds : bond 0.05782 ( 406) hydrogen bonds : angle 5.32405 ( 1110) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 233 time to evaluate : 0.623 Fit side-chains REVERT: A 274 MET cc_start: 0.7197 (ppp) cc_final: 0.6824 (ptm) REVERT: B 103 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7365 (tm-30) REVERT: C 44 GLU cc_start: 0.8339 (pm20) cc_final: 0.8075 (pm20) REVERT: C 282 GLN cc_start: 0.7414 (mt0) cc_final: 0.7026 (mt0) REVERT: D 159 TYR cc_start: 0.8065 (t80) cc_final: 0.7856 (t80) REVERT: D 170 ARG cc_start: 0.7561 (OUTLIER) cc_final: 0.6860 (ttp-170) REVERT: H 38 ARG cc_start: 0.8352 (tmm-80) cc_final: 0.7835 (ttp80) outliers start: 59 outliers final: 33 residues processed: 276 average time/residue: 0.1303 time to fit residues: 53.8144 Evaluate side-chains 266 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 232 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 24 ASP Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 208 HIS Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain D residue 9 PHE Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 79 TYR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 79 TYR Chi-restraints excluded: chain I residue 93 ILE Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 62 PHE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 93 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 133 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 13 optimal weight: 8.9990 chunk 175 optimal weight: 2.9990 chunk 187 optimal weight: 8.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 GLN A 285 GLN G 64 GLN G 100BHIS H 64 GLN H 100BHIS J 100BHIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.178884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.153081 restraints weight = 23093.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.156177 restraints weight = 31235.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.156776 restraints weight = 25223.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.157337 restraints weight = 17263.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.158216 restraints weight = 15682.013| |-----------------------------------------------------------------------------| r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 16540 Z= 0.257 Angle : 0.619 8.271 22450 Z= 0.324 Chirality : 0.045 0.385 2423 Planarity : 0.004 0.067 2890 Dihedral : 4.707 36.237 2205 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 5.47 % Allowed : 22.23 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.83 (0.18), residues: 1998 helix: 1.08 (0.31), residues: 303 sheet: -1.29 (0.30), residues: 343 loop : -1.85 (0.15), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 192 TYR 0.021 0.002 TYR E 17 PHE 0.023 0.002 PHE B 110 TRP 0.011 0.002 TRP A 69 HIS 0.007 0.001 HIS J 100B Details of bonding type rmsd covalent geometry : bond 0.00614 (16516) covalent geometry : angle 0.61805 (22402) SS BOND : bond 0.00496 ( 24) SS BOND : angle 1.02397 ( 48) hydrogen bonds : bond 0.06960 ( 406) hydrogen bonds : angle 5.44513 ( 1110) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 240 time to evaluate : 0.622 Fit side-chains REVERT: A 274 MET cc_start: 0.7418 (ppp) cc_final: 0.7085 (ptm) REVERT: B 97 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6833 (tp30) REVERT: B 103 GLU cc_start: 0.7909 (tm-30) cc_final: 0.7495 (tm-30) REVERT: C 282 GLN cc_start: 0.7574 (mt0) cc_final: 0.7107 (mt0) REVERT: D 102 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8266 (mp) REVERT: D 159 TYR cc_start: 0.8090 (t80) cc_final: 0.7829 (t80) REVERT: D 170 ARG cc_start: 0.7545 (OUTLIER) cc_final: 0.6898 (ttp-170) REVERT: E 107 GLU cc_start: 0.7540 (tm-30) cc_final: 0.7225 (tm-30) REVERT: E 282 GLN cc_start: 0.7576 (mt0) cc_final: 0.7346 (mt0) REVERT: H 38 ARG cc_start: 0.8444 (tmm-80) cc_final: 0.7885 (ttp80) outliers start: 97 outliers final: 76 residues processed: 306 average time/residue: 0.1246 time to fit residues: 57.3911 Evaluate side-chains 311 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 232 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 282 GLN Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 24 ASP Chi-restraints excluded: chain C residue 27 ASP Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 208 HIS Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain D residue 9 PHE Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 269 THR Chi-restraints excluded: chain F residue 9 PHE Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 79 TYR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain I residue 62 PHE Chi-restraints excluded: chain I residue 93 ILE Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 62 PHE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 71 PHE Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 104 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 191 optimal weight: 5.9990 chunk 142 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 160 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 174 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 GLN D 95 ASN G 64 GLN H 64 GLN H 100BHIS J 64 GLN J 100BHIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.181779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.155725 restraints weight = 22891.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.156440 restraints weight = 29171.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.157407 restraints weight = 30104.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.159638 restraints weight = 20589.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.159939 restraints weight = 15717.567| |-----------------------------------------------------------------------------| r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16540 Z= 0.159 Angle : 0.564 9.942 22450 Z= 0.292 Chirality : 0.043 0.315 2423 Planarity : 0.004 0.063 2890 Dihedral : 4.519 36.587 2205 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 4.29 % Allowed : 23.53 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.77 (0.18), residues: 1998 helix: 1.20 (0.31), residues: 303 sheet: -1.43 (0.27), residues: 397 loop : -1.77 (0.16), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 192 TYR 0.015 0.001 TYR E 17 PHE 0.017 0.001 PHE D 9 TRP 0.007 0.001 TRP C 127 HIS 0.007 0.001 HIS J 100B Details of bonding type rmsd covalent geometry : bond 0.00375 (16516) covalent geometry : angle 0.56293 (22402) SS BOND : bond 0.00438 ( 24) SS BOND : angle 1.05018 ( 48) hydrogen bonds : bond 0.06054 ( 406) hydrogen bonds : angle 5.18095 ( 1110) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 233 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: A 274 MET cc_start: 0.7386 (ppp) cc_final: 0.7055 (ptm) REVERT: B 97 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.6797 (tp30) REVERT: B 103 GLU cc_start: 0.7894 (tm-30) cc_final: 0.7444 (tm-30) REVERT: C 101 TYR cc_start: 0.7657 (t80) cc_final: 0.7451 (t80) REVERT: C 282 GLN cc_start: 0.7441 (mt0) cc_final: 0.6981 (mt0) REVERT: D 102 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8179 (mp) REVERT: D 159 TYR cc_start: 0.8060 (t80) cc_final: 0.7837 (t80) REVERT: D 170 ARG cc_start: 0.7621 (OUTLIER) cc_final: 0.6966 (ttp-170) REVERT: E 107 GLU cc_start: 0.7437 (tm-30) cc_final: 0.6995 (tm-30) REVERT: E 282 GLN cc_start: 0.7503 (mt0) cc_final: 0.7298 (mt0) REVERT: F 72 LYS cc_start: 0.7748 (tptm) cc_final: 0.7376 (pptt) REVERT: H 38 ARG cc_start: 0.8386 (tmm-80) cc_final: 0.7830 (ttp80) outliers start: 76 outliers final: 62 residues processed: 287 average time/residue: 0.1229 time to fit residues: 52.4193 Evaluate side-chains 297 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 232 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 24 ASP Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 208 HIS Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain D residue 9 PHE Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 153 LYS Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain F residue 9 PHE Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 79 TYR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 79 TYR Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain I residue 93 ILE Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 62 PHE Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 104 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 104 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 162 optimal weight: 1.9990 chunk 165 optimal weight: 8.9990 chunk 92 optimal weight: 0.1980 chunk 24 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 chunk 127 optimal weight: 6.9990 chunk 86 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 chunk 121 optimal weight: 3.9990 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 282 GLN A 285 GLN D 95 ASN F 38 GLN F 104 ASN G 64 GLN H 100BHIS J 100BHIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.180959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.154908 restraints weight = 23138.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.156113 restraints weight = 27793.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.157228 restraints weight = 28753.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.158017 restraints weight = 18543.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.158586 restraints weight = 16707.562| |-----------------------------------------------------------------------------| r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16540 Z= 0.146 Angle : 0.553 11.013 22450 Z= 0.284 Chirality : 0.043 0.337 2423 Planarity : 0.004 0.061 2890 Dihedral : 4.402 36.347 2205 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 5.19 % Allowed : 23.31 % Favored : 71.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.71 (0.18), residues: 1998 helix: 1.19 (0.31), residues: 309 sheet: -1.36 (0.27), residues: 405 loop : -1.73 (0.16), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 192 TYR 0.015 0.001 TYR A 105 PHE 0.016 0.001 PHE D 9 TRP 0.006 0.001 TRP E 84 HIS 0.008 0.001 HIS J 100B Details of bonding type rmsd covalent geometry : bond 0.00341 (16516) covalent geometry : angle 0.55169 (22402) SS BOND : bond 0.00385 ( 24) SS BOND : angle 0.91904 ( 48) hydrogen bonds : bond 0.05742 ( 406) hydrogen bonds : angle 5.02984 ( 1110) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 238 time to evaluate : 0.762 Fit side-chains revert: symmetry clash REVERT: A 274 MET cc_start: 0.7394 (ppp) cc_final: 0.7064 (ptm) REVERT: B 97 GLU cc_start: 0.6996 (OUTLIER) cc_final: 0.6786 (tp30) REVERT: B 103 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7423 (tm-30) REVERT: C 282 GLN cc_start: 0.7435 (mt0) cc_final: 0.6985 (mt0) REVERT: D 159 TYR cc_start: 0.8042 (t80) cc_final: 0.7803 (t80) REVERT: D 170 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.6975 (ttp-170) REVERT: E 107 GLU cc_start: 0.7452 (tm-30) cc_final: 0.6960 (tm-30) REVERT: E 282 GLN cc_start: 0.7522 (mt0) cc_final: 0.7234 (mt0) REVERT: F 72 LYS cc_start: 0.7776 (tptm) cc_final: 0.7377 (pptt) REVERT: H 38 ARG cc_start: 0.8369 (tmm-80) cc_final: 0.7809 (ttp80) REVERT: L 4 MET cc_start: 0.8225 (mmt) cc_final: 0.7557 (mtt) outliers start: 92 outliers final: 70 residues processed: 304 average time/residue: 0.1311 time to fit residues: 59.8844 Evaluate side-chains 303 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 231 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 282 GLN Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 24 ASP Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 27 ASP Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 208 HIS Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain D residue 9 PHE Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 153 LYS Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 269 THR Chi-restraints excluded: chain F residue 9 PHE Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 79 TYR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 79 TYR Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 93 ILE Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 62 PHE Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 104 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 69 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 166 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 189 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 184 optimal weight: 0.8980 chunk 92 optimal weight: 6.9990 chunk 164 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 GLN A 285 GLN D 95 ASN H 100BHIS J 100BHIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.182136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.157451 restraints weight = 22946.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.156377 restraints weight = 28056.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.157296 restraints weight = 28506.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.158914 restraints weight = 21082.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.159246 restraints weight = 17406.637| |-----------------------------------------------------------------------------| r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16540 Z= 0.123 Angle : 0.539 9.941 22450 Z= 0.276 Chirality : 0.042 0.261 2423 Planarity : 0.004 0.059 2890 Dihedral : 4.294 38.478 2205 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 4.74 % Allowed : 23.87 % Favored : 71.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.57 (0.18), residues: 1998 helix: 1.29 (0.31), residues: 309 sheet: -1.16 (0.28), residues: 375 loop : -1.68 (0.16), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 192 TYR 0.019 0.001 TYR C 101 PHE 0.016 0.001 PHE K 71 TRP 0.005 0.001 TRP D 92 HIS 0.008 0.001 HIS J 100B Details of bonding type rmsd covalent geometry : bond 0.00283 (16516) covalent geometry : angle 0.53625 (22402) SS BOND : bond 0.00470 ( 24) SS BOND : angle 1.22553 ( 48) hydrogen bonds : bond 0.05357 ( 406) hydrogen bonds : angle 4.86584 ( 1110) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 235 time to evaluate : 0.648 Fit side-chains revert: symmetry clash REVERT: A 274 MET cc_start: 0.7211 (ppp) cc_final: 0.6877 (ptm) REVERT: B 103 GLU cc_start: 0.7896 (tm-30) cc_final: 0.7400 (tm-30) REVERT: C 282 GLN cc_start: 0.7415 (mt0) cc_final: 0.6943 (mt0) REVERT: D 159 TYR cc_start: 0.8037 (t80) cc_final: 0.7823 (t80) REVERT: D 170 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.6991 (ttp-170) REVERT: E 107 GLU cc_start: 0.7411 (tm-30) cc_final: 0.6908 (tm-30) REVERT: E 282 GLN cc_start: 0.7497 (mt0) cc_final: 0.7217 (mt0) REVERT: F 72 LYS cc_start: 0.7758 (tptm) cc_final: 0.7364 (pptt) REVERT: H 38 ARG cc_start: 0.8354 (tmm-80) cc_final: 0.7796 (ttp80) REVERT: K 21 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7416 (mm) REVERT: L 4 MET cc_start: 0.7988 (mmt) cc_final: 0.7435 (mtt) outliers start: 84 outliers final: 67 residues processed: 292 average time/residue: 0.1298 time to fit residues: 57.1101 Evaluate side-chains 301 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 232 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 282 GLN Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 138 PHE Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 208 HIS Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain D residue 9 PHE Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 153 LYS Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 208 HIS Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain F residue 9 PHE Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 79 TYR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 79 TYR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain I residue 93 ILE Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 62 PHE Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 93 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 chunk 196 optimal weight: 0.8980 chunk 162 optimal weight: 0.4980 chunk 158 optimal weight: 6.9990 chunk 81 optimal weight: 0.9980 chunk 124 optimal weight: 0.0770 chunk 131 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 146 optimal weight: 0.7980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 GLN A 285 GLN D 95 ASN H 64 GLN H 100BHIS J 100BHIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.183304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.157978 restraints weight = 23015.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.157128 restraints weight = 26842.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.158182 restraints weight = 29999.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.158937 restraints weight = 20888.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.159507 restraints weight = 19349.721| |-----------------------------------------------------------------------------| r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16540 Z= 0.110 Angle : 0.527 13.265 22450 Z= 0.268 Chirality : 0.042 0.230 2423 Planarity : 0.004 0.058 2890 Dihedral : 4.198 39.407 2205 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 4.12 % Allowed : 23.98 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.48 (0.18), residues: 1998 helix: 1.37 (0.31), residues: 309 sheet: -1.07 (0.28), residues: 375 loop : -1.63 (0.16), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 192 TYR 0.018 0.001 TYR C 101 PHE 0.014 0.001 PHE D 9 TRP 0.005 0.001 TRP J 36 HIS 0.008 0.001 HIS J 100B Details of bonding type rmsd covalent geometry : bond 0.00250 (16516) covalent geometry : angle 0.52486 (22402) SS BOND : bond 0.00392 ( 24) SS BOND : angle 1.25478 ( 48) hydrogen bonds : bond 0.05051 ( 406) hydrogen bonds : angle 4.75277 ( 1110) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 234 time to evaluate : 0.657 Fit side-chains REVERT: A 274 MET cc_start: 0.7201 (ppp) cc_final: 0.6862 (ptm) REVERT: B 103 GLU cc_start: 0.7899 (tm-30) cc_final: 0.7388 (tm-30) REVERT: C 282 GLN cc_start: 0.7448 (mt0) cc_final: 0.7067 (mt0) REVERT: E 107 GLU cc_start: 0.7385 (tm-30) cc_final: 0.6881 (tm-30) REVERT: E 282 GLN cc_start: 0.7488 (mt0) cc_final: 0.7205 (mt0) REVERT: F 72 LYS cc_start: 0.7737 (tptm) cc_final: 0.7344 (pptt) REVERT: H 38 ARG cc_start: 0.8283 (tmm-80) cc_final: 0.7715 (ttp80) REVERT: K 21 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7391 (mm) outliers start: 73 outliers final: 61 residues processed: 279 average time/residue: 0.1353 time to fit residues: 56.6090 Evaluate side-chains 291 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 229 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 282 GLN Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 138 PHE Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 208 HIS Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain D residue 9 PHE Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 208 HIS Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain F residue 9 PHE Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 79 TYR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 79 TYR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain I residue 93 ILE Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 62 PHE Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 93 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 55 optimal weight: 0.0980 chunk 5 optimal weight: 3.9990 chunk 184 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 153 optimal weight: 0.5980 chunk 168 optimal weight: 10.0000 chunk 188 optimal weight: 3.9990 chunk 60 optimal weight: 7.9990 chunk 173 optimal weight: 10.0000 chunk 170 optimal weight: 3.9990 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 282 GLN A 285 GLN D 95 ASN G 64 GLN H 100BHIS J 100BHIS K 89 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.186226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.155435 restraints weight = 23096.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.156248 restraints weight = 25357.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.157446 restraints weight = 25966.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.158410 restraints weight = 16707.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.159209 restraints weight = 15131.576| |-----------------------------------------------------------------------------| r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 16540 Z= 0.198 Angle : 0.593 12.498 22450 Z= 0.307 Chirality : 0.044 0.251 2423 Planarity : 0.004 0.060 2890 Dihedral : 4.473 38.725 2205 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 4.80 % Allowed : 23.70 % Favored : 71.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.64 (0.18), residues: 1998 helix: 1.32 (0.31), residues: 303 sheet: -1.32 (0.27), residues: 405 loop : -1.69 (0.16), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 192 TYR 0.022 0.002 TYR C 101 PHE 0.018 0.002 PHE F 110 TRP 0.011 0.001 TRP A 69 HIS 0.008 0.001 HIS J 100B Details of bonding type rmsd covalent geometry : bond 0.00471 (16516) covalent geometry : angle 0.59153 (22402) SS BOND : bond 0.00463 ( 24) SS BOND : angle 1.18387 ( 48) hydrogen bonds : bond 0.06128 ( 406) hydrogen bonds : angle 4.94957 ( 1110) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 231 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 274 MET cc_start: 0.7249 (ppp) cc_final: 0.6925 (ptm) REVERT: B 103 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7458 (tm-30) REVERT: C 282 GLN cc_start: 0.7672 (mt0) cc_final: 0.7231 (mt0) REVERT: E 107 GLU cc_start: 0.7521 (tm-30) cc_final: 0.7104 (tm-30) REVERT: E 282 GLN cc_start: 0.7557 (mt0) cc_final: 0.7287 (mt0) REVERT: F 72 LYS cc_start: 0.7839 (tptm) cc_final: 0.7420 (pptt) REVERT: H 38 ARG cc_start: 0.8351 (tmm-80) cc_final: 0.7798 (ttp80) REVERT: K 21 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7390 (mm) outliers start: 85 outliers final: 74 residues processed: 289 average time/residue: 0.1263 time to fit residues: 54.7697 Evaluate side-chains 305 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 230 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 282 GLN Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 24 ASP Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 208 HIS Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain D residue 9 PHE Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 153 LYS Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 208 HIS Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain F residue 9 PHE Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 79 TYR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 79 TYR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 93 ILE Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 100 HIS Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 62 PHE Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 74 optimal weight: 0.8980 chunk 83 optimal weight: 4.9990 chunk 190 optimal weight: 10.0000 chunk 91 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 175 optimal weight: 0.8980 chunk 176 optimal weight: 0.6980 chunk 161 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 GLN D 95 ASN H 100BHIS J 64 GLN J 100BHIS K 89 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.182077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.156455 restraints weight = 22977.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.157919 restraints weight = 26054.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.159110 restraints weight = 26451.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.159619 restraints weight = 17373.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.159988 restraints weight = 16487.999| |-----------------------------------------------------------------------------| r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16540 Z= 0.125 Angle : 0.557 13.149 22450 Z= 0.285 Chirality : 0.042 0.233 2423 Planarity : 0.004 0.059 2890 Dihedral : 4.313 39.398 2205 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 4.06 % Allowed : 24.83 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.53 (0.18), residues: 1998 helix: 1.32 (0.31), residues: 309 sheet: -1.11 (0.28), residues: 375 loop : -1.65 (0.16), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 192 TYR 0.018 0.001 TYR C 101 PHE 0.015 0.001 PHE D 9 TRP 0.006 0.001 TRP C 127 HIS 0.006 0.001 HIS H 100B Details of bonding type rmsd covalent geometry : bond 0.00290 (16516) covalent geometry : angle 0.55532 (22402) SS BOND : bond 0.00410 ( 24) SS BOND : angle 1.11561 ( 48) hydrogen bonds : bond 0.05375 ( 406) hydrogen bonds : angle 4.79127 ( 1110) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 230 time to evaluate : 0.653 Fit side-chains revert: symmetry clash REVERT: B 103 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7411 (tm-30) REVERT: C 282 GLN cc_start: 0.7546 (mt0) cc_final: 0.7105 (mt0) REVERT: E 107 GLU cc_start: 0.7466 (tm-30) cc_final: 0.6965 (tm-30) REVERT: E 282 GLN cc_start: 0.7523 (mt0) cc_final: 0.7237 (mt0) REVERT: F 17 MET cc_start: 0.7745 (mtm) cc_final: 0.7492 (mtm) REVERT: F 72 LYS cc_start: 0.7817 (tptm) cc_final: 0.7389 (pptt) REVERT: H 38 ARG cc_start: 0.8284 (tmm-80) cc_final: 0.7706 (ttp80) REVERT: K 21 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.7342 (mm) outliers start: 72 outliers final: 68 residues processed: 277 average time/residue: 0.1277 time to fit residues: 53.0892 Evaluate side-chains 296 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 227 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 282 GLN Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 208 HIS Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain D residue 9 PHE Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 153 LYS Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 208 HIS Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain F residue 9 PHE Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 79 TYR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 79 TYR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 93 ILE Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 62 PHE Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 93 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 27 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 41 optimal weight: 0.9990 chunk 153 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 chunk 145 optimal weight: 0.8980 chunk 143 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 189 optimal weight: 6.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 GLN D 95 ASN H 100BHIS J 100BHIS K 89 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.179953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.152699 restraints weight = 23053.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.152770 restraints weight = 25202.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.153857 restraints weight = 29930.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.155092 restraints weight = 18707.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.155800 restraints weight = 15993.737| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16540 Z= 0.184 Angle : 0.594 13.408 22450 Z= 0.306 Chirality : 0.043 0.232 2423 Planarity : 0.004 0.069 2890 Dihedral : 4.436 38.466 2205 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 4.57 % Allowed : 24.38 % Favored : 71.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.65 (0.18), residues: 1998 helix: 1.21 (0.31), residues: 309 sheet: -1.19 (0.28), residues: 375 loop : -1.74 (0.16), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 192 TYR 0.020 0.001 TYR C 101 PHE 0.017 0.002 PHE D 9 TRP 0.009 0.001 TRP A 69 HIS 0.008 0.001 HIS J 100B Details of bonding type rmsd covalent geometry : bond 0.00436 (16516) covalent geometry : angle 0.59211 (22402) SS BOND : bond 0.00433 ( 24) SS BOND : angle 1.11944 ( 48) hydrogen bonds : bond 0.05935 ( 406) hydrogen bonds : angle 4.88811 ( 1110) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2298.46 seconds wall clock time: 40 minutes 40.95 seconds (2440.95 seconds total)