Starting phenix.real_space_refine on Sat Jul 4 19:45:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sjm_54947/07_2026/9sjm_54947.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sjm_54947/07_2026/9sjm_54947.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9sjm_54947/07_2026/9sjm_54947.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sjm_54947/07_2026/9sjm_54947.map" model { file = "/net/cci-nas-00/data/ceres_data/9sjm_54947/07_2026/9sjm_54947.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sjm_54947/07_2026/9sjm_54947.cif" } resolution = 3.13 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= 0.002 sd= 0.028 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: 5 Type Number sf(0) Gaussians P 59 5.49 5 S 114 5.16 5 C 14206 2.51 5 N 3774 2.21 5 O 4438 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 106 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22591 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2691 Classifications: {'peptide': 335} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 17, 'TRANS': 317} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1986 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 8, 'TRANS': 243} Chain: "I" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1161 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 5, 'TRANS': 140} Chain breaks: 1 Chain: "D" Number of atoms: 2603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2603 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 15, 'TRANS': 304} Chain: "E" Number of atoms: 2603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2603 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 15, 'TRANS': 304} Chain: "F" Number of atoms: 2619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2619 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 15, 'TRANS': 306} Chain: "C" Number of atoms: 2612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2612 Classifications: {'peptide': 321} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 304} Chain: "G" Number of atoms: 2619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2619 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 15, 'TRANS': 306} Chain: "H" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2409 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 11, 'TRANS': 283} Chain breaks: 1 Chain: "J" Number of atoms: 1288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1288 Classifications: {'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 19, 'rna2p_pyr': 10, 'rna3p_pur': 18, 'rna3p_pyr': 13} Link IDs: {'rna2p': 29, 'rna3p': 30} Time building chain proxies: 3.75, per 1000 atoms: 0.17 Number of scatterers: 22591 At special positions: 0 Unit cell: (128.325, 147.175, 149.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 114 16.00 P 59 15.00 O 4438 8.00 N 3774 7.00 C 14206 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.66 Conformation dependent library (CDL) restraints added in 672.4 milliseconds 5218 Ramachandran restraints generated. 2609 Oldfield, 0 Emsley, 2609 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5014 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 37 sheets defined 34.9% alpha, 8.3% beta 7 base pairs and 26 stacking pairs defined. Time for finding SS restraints: 2.33 Creating SS restraints... Processing helix chain 'A' and resid 4 through 10 removed outlier: 3.655A pdb=" N ALA A 8 " --> pdb=" O ASN A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 29 removed outlier: 3.870A pdb=" N LYS A 19 " --> pdb=" O PRO A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 86 removed outlier: 3.767A pdb=" N TYR A 86 " --> pdb=" O ASP A 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 83 through 86' Processing helix chain 'A' and resid 87 through 95 removed outlier: 3.522A pdb=" N GLY A 91 " --> pdb=" O LYS A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 109 removed outlier: 3.971A pdb=" N GLN A 108 " --> pdb=" O MET A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 117 Processing helix chain 'A' and resid 117 through 122 Processing helix chain 'A' and resid 124 through 134 Processing helix chain 'A' and resid 166 through 179 removed outlier: 3.820A pdb=" N ARG A 179 " --> pdb=" O ASP A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 199 removed outlier: 4.111A pdb=" N GLY A 199 " --> pdb=" O ALA A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 206 Processing helix chain 'A' and resid 217 through 221 Processing helix chain 'A' and resid 223 through 229 Processing helix chain 'A' and resid 252 through 254 No H-bonds generated for 'chain 'A' and resid 252 through 254' Processing helix chain 'A' and resid 255 through 268 Processing helix chain 'A' and resid 273 through 277 Processing helix chain 'A' and resid 281 through 292 removed outlier: 3.890A pdb=" N TYR A 292 " --> pdb=" O PHE A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 312 Processing helix chain 'A' and resid 325 through 340 removed outlier: 3.661A pdb=" N ARG A 330 " --> pdb=" O GLU A 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 46 removed outlier: 3.538A pdb=" N PHE B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 130 removed outlier: 3.673A pdb=" N CYS B 122 " --> pdb=" O ASP B 118 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS B 123 " --> pdb=" O MET B 119 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU B 130 " --> pdb=" O LYS B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 132 No H-bonds generated for 'chain 'B' and resid 131 through 132' Processing helix chain 'B' and resid 133 through 137 removed outlier: 4.190A pdb=" N GLY B 136 " --> pdb=" O ARG B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 170 Processing helix chain 'B' and resid 174 through 186 removed outlier: 3.767A pdb=" N GLN B 185 " --> pdb=" O HIS B 181 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) Processing helix chain 'I' and resid 15 through 24 removed outlier: 3.787A pdb=" N ILE I 19 " --> pdb=" O SER I 15 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE I 24 " --> pdb=" O ILE I 20 " (cutoff:3.500A) Processing helix chain 'I' and resid 24 through 35 removed outlier: 3.776A pdb=" N SER I 30 " --> pdb=" O PRO I 26 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU I 34 " --> pdb=" O SER I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 72 removed outlier: 3.993A pdb=" N LEU I 68 " --> pdb=" O ASP I 64 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ALA I 69 " --> pdb=" O LYS I 65 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N CYS I 72 " --> pdb=" O LEU I 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 72 through 77 Processing helix chain 'I' and resid 78 through 81 Processing helix chain 'I' and resid 136 through 140 removed outlier: 3.764A pdb=" N CYS I 140 " --> pdb=" O GLN I 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 136 through 140' Processing helix chain 'D' and resid 63 through 71 removed outlier: 3.870A pdb=" N LYS D 69 " --> pdb=" O ASP D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 129 Processing helix chain 'D' and resid 131 through 144 Processing helix chain 'D' and resid 175 through 177 No H-bonds generated for 'chain 'D' and resid 175 through 177' Processing helix chain 'D' and resid 186 through 202 Processing helix chain 'D' and resid 250 through 259 Processing helix chain 'D' and resid 267 through 272 Processing helix chain 'D' and resid 296 through 306 Processing helix chain 'D' and resid 312 through 326 Processing helix chain 'E' and resid 63 through 71 removed outlier: 4.172A pdb=" N LYS E 69 " --> pdb=" O ASP E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 106 removed outlier: 4.052A pdb=" N MET E 106 " --> pdb=" O LYS E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 129 Processing helix chain 'E' and resid 131 through 144 Processing helix chain 'E' and resid 175 through 177 No H-bonds generated for 'chain 'E' and resid 175 through 177' Processing helix chain 'E' and resid 186 through 201 Processing helix chain 'E' and resid 250 through 259 Processing helix chain 'E' and resid 267 through 272 Processing helix chain 'E' and resid 296 through 306 Processing helix chain 'E' and resid 312 through 326 Processing helix chain 'F' and resid 63 through 71 removed outlier: 4.278A pdb=" N LYS F 69 " --> pdb=" O ASP F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 104 No H-bonds generated for 'chain 'F' and resid 102 through 104' Processing helix chain 'F' and resid 111 through 129 Processing helix chain 'F' and resid 131 through 144 Processing helix chain 'F' and resid 175 through 177 No H-bonds generated for 'chain 'F' and resid 175 through 177' Processing helix chain 'F' and resid 186 through 202 removed outlier: 3.577A pdb=" N GLN F 195 " --> pdb=" O GLU F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 260 removed outlier: 3.695A pdb=" N ALA F 257 " --> pdb=" O LYS F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 272 Processing helix chain 'F' and resid 296 through 306 removed outlier: 3.523A pdb=" N ASP F 302 " --> pdb=" O TYR F 298 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG F 303 " --> pdb=" O LYS F 299 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 326 removed outlier: 3.503A pdb=" N TYR F 318 " --> pdb=" O GLU F 314 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG F 325 " --> pdb=" O ALA F 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 40 Processing helix chain 'C' and resid 63 through 71 removed outlier: 4.414A pdb=" N LYS C 69 " --> pdb=" O ASP C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 104 No H-bonds generated for 'chain 'C' and resid 102 through 104' Processing helix chain 'C' and resid 111 through 129 Processing helix chain 'C' and resid 131 through 144 Processing helix chain 'C' and resid 175 through 177 No H-bonds generated for 'chain 'C' and resid 175 through 177' Processing helix chain 'C' and resid 186 through 201 removed outlier: 3.579A pdb=" N GLN C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 259 Processing helix chain 'C' and resid 267 through 272 Processing helix chain 'C' and resid 296 through 306 Processing helix chain 'C' and resid 312 through 326 removed outlier: 3.777A pdb=" N LEU C 323 " --> pdb=" O VAL C 319 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 40 Processing helix chain 'G' and resid 63 through 67 removed outlier: 3.651A pdb=" N LEU G 67 " --> pdb=" O PRO G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 72 removed outlier: 4.113A pdb=" N ILE G 71 " --> pdb=" O GLU G 68 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N MET G 72 " --> pdb=" O LYS G 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 68 through 72' Processing helix chain 'G' and resid 102 through 104 No H-bonds generated for 'chain 'G' and resid 102 through 104' Processing helix chain 'G' and resid 111 through 129 Processing helix chain 'G' and resid 131 through 144 Processing helix chain 'G' and resid 186 through 202 Processing helix chain 'G' and resid 250 through 259 Processing helix chain 'G' and resid 267 through 272 Processing helix chain 'G' and resid 296 through 305 removed outlier: 3.527A pdb=" N ASP G 302 " --> pdb=" O TYR G 298 " (cutoff:3.500A) Processing helix chain 'G' and resid 312 through 326 Processing helix chain 'H' and resid 102 through 104 No H-bonds generated for 'chain 'H' and resid 102 through 104' Processing helix chain 'H' and resid 111 through 129 removed outlier: 3.569A pdb=" N LYS H 121 " --> pdb=" O ALA H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 144 removed outlier: 3.535A pdb=" N ILE H 142 " --> pdb=" O TYR H 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 153 removed outlier: 3.728A pdb=" N LEU H 148 " --> pdb=" O ALA H 145 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ARG H 150 " --> pdb=" O PHE H 147 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS H 153 " --> pdb=" O ARG H 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 186 through 202 Processing helix chain 'H' and resid 230 through 234 removed outlier: 3.536A pdb=" N ASP H 233 " --> pdb=" O THR H 230 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASP H 234 " --> pdb=" O PHE H 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 230 through 234' Processing helix chain 'H' and resid 250 through 258 Processing helix chain 'H' and resid 267 through 272 Processing helix chain 'H' and resid 292 through 295 Processing helix chain 'H' and resid 296 through 306 Processing helix chain 'H' and resid 312 through 326 removed outlier: 3.621A pdb=" N HIS H 317 " --> pdb=" O ILE H 313 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N TYR H 318 " --> pdb=" O GLU H 314 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL H 319 " --> pdb=" O ASP H 315 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 37 Processing sheet with id=AA2, first strand: chain 'A' and resid 148 through 153 removed outlier: 4.351A pdb=" N LYS A 148 " --> pdb=" O ILE A 163 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 158 through 164 current: chain 'B' and resid 101 through 112 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 101 through 112 current: chain 'B' and resid 251 through 253 Processing sheet with id=AA3, first strand: chain 'A' and resid 184 through 186 removed outlier: 3.844A pdb=" N VAL B 24 " --> pdb=" O PHE A 212 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 301 through 305 Processing sheet with id=AA5, first strand: chain 'B' and resid 66 through 68 Processing sheet with id=AA6, first strand: chain 'I' and resid 40 through 42 removed outlier: 3.700A pdb=" N THR I 42 " --> pdb=" O GLU I 59 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N SER I 3 " --> pdb=" O GLU I 89 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N GLU I 89 " --> pdb=" O SER I 3 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE I 5 " --> pdb=" O LYS I 87 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS I 87 " --> pdb=" O ILE I 5 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE I 7 " --> pdb=" O LYS I 85 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 47 through 48 Processing sheet with id=AA8, first strand: chain 'I' and resid 99 through 100 Processing sheet with id=AA9, first strand: chain 'I' and resid 146 through 147 Processing sheet with id=AB1, first strand: chain 'D' and resid 106 through 109 removed outlier: 3.654A pdb=" N SER D 108 " --> pdb=" O SER D 20 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 25 through 27 current: chain 'D' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 45 through 46 current: chain 'D' and resid 167 through 168 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 167 through 168 current: chain 'D' and resid 246 through 249 No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 50 through 51 Processing sheet with id=AB4, first strand: chain 'D' and resid 54 through 57 Processing sheet with id=AB5, first strand: chain 'D' and resid 227 through 228 removed outlier: 4.536A pdb=" N LYS D 239 " --> pdb=" O GLU D 228 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 260 through 262 Processing sheet with id=AB7, first strand: chain 'E' and resid 108 through 109 removed outlier: 3.776A pdb=" N SER E 108 " --> pdb=" O SER E 20 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 25 through 27 current: chain 'E' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 45 through 46 current: chain 'E' and resid 167 through 168 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 167 through 168 current: chain 'E' and resid 246 through 249 No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'E' and resid 50 through 51 removed outlier: 4.297A pdb=" N CYS E 82 " --> pdb=" O VAL E 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 54 through 57 Processing sheet with id=AC2, first strand: chain 'E' and resid 227 through 228 removed outlier: 4.525A pdb=" N LYS E 239 " --> pdb=" O GLU E 228 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 19 through 21 removed outlier: 3.799A pdb=" N SER F 108 " --> pdb=" O SER F 20 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 25 through 27 current: chain 'F' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 45 through 46 current: chain 'F' and resid 167 through 168 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 167 through 168 current: chain 'F' and resid 246 through 249 No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'F' and resid 50 through 51 removed outlier: 4.442A pdb=" N CYS F 82 " --> pdb=" O VAL F 223 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 54 through 57 Processing sheet with id=AC7, first strand: chain 'F' and resid 227 through 228 removed outlier: 4.391A pdb=" N LYS F 239 " --> pdb=" O GLU F 228 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 282 through 283 removed outlier: 3.946A pdb=" N ALA F 283 " --> pdb=" O ILE F 288 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ILE F 288 " --> pdb=" O ALA F 283 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'C' and resid 106 through 109 removed outlier: 3.701A pdb=" N SER C 108 " --> pdb=" O SER C 20 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 25 through 27 current: chain 'C' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 45 through 46 current: chain 'C' and resid 167 through 168 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 167 through 168 current: chain 'C' and resid 246 through 249 No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 50 through 57 removed outlier: 4.288A pdb=" N CYS C 82 " --> pdb=" O VAL C 223 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 19 through 21 Processing sheet with id=AD4, first strand: chain 'G' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 25 through 27 current: chain 'G' and resid 93 through 99 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 93 through 99 current: chain 'G' and resid 167 through 168 No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'G' and resid 50 through 51 removed outlier: 4.417A pdb=" N CYS G 82 " --> pdb=" O VAL G 223 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 54 through 56 Processing sheet with id=AD7, first strand: chain 'G' and resid 90 through 91 Processing sheet with id=AD8, first strand: chain 'H' and resid 106 through 109 removed outlier: 3.611A pdb=" N PHE H 21 " --> pdb=" O GLY H 327 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 25 through 27 current: chain 'H' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 45 through 46 current: chain 'H' and resid 172 through 173 No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'H' and resid 260 through 262 614 hydrogen bonds defined for protein. 1719 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 19 hydrogen bonds 30 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 26 stacking parallelities Total time for adding SS restraints: 3.18 Time building geometry restraints manager: 2.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6860 1.34 - 1.46: 4657 1.46 - 1.58: 11397 1.58 - 1.70: 118 1.70 - 1.82: 181 Bond restraints: 23213 Sorted by residual: bond pdb=" CA SER G 174 " pdb=" CB SER G 174 " ideal model delta sigma weight residual 1.527 1.470 0.057 1.15e-02 7.56e+03 2.45e+01 bond pdb=" N TYR A 232 " pdb=" CA TYR A 232 " ideal model delta sigma weight residual 1.455 1.496 -0.041 1.23e-02 6.61e+03 1.10e+01 bond pdb=" N VAL A 93 " pdb=" CA VAL A 93 " ideal model delta sigma weight residual 1.459 1.498 -0.040 1.25e-02 6.40e+03 1.02e+01 bond pdb=" N LEU A 233 " pdb=" CA LEU A 233 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.29e-02 6.01e+03 9.44e+00 bond pdb=" CA TYR F 318 " pdb=" C TYR F 318 " ideal model delta sigma weight residual 1.523 1.486 0.037 1.37e-02 5.33e+03 7.38e+00 ... (remaining 23208 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 31204 2.32 - 4.65: 385 4.65 - 6.97: 41 6.97 - 9.29: 6 9.29 - 11.61: 5 Bond angle restraints: 31641 Sorted by residual: angle pdb=" N LYS G 175 " pdb=" CA LYS G 175 " pdb=" C LYS G 175 " ideal model delta sigma weight residual 113.43 105.71 7.72 1.26e+00 6.30e-01 3.76e+01 angle pdb=" N TYR A 232 " pdb=" CA TYR A 232 " pdb=" C TYR A 232 " ideal model delta sigma weight residual 108.76 115.87 -7.11 1.58e+00 4.01e-01 2.02e+01 angle pdb=" C LYS A 13 " pdb=" N ILE A 14 " pdb=" CA ILE A 14 " ideal model delta sigma weight residual 120.33 123.89 -3.56 8.00e-01 1.56e+00 1.98e+01 angle pdb=" N LYS I 50 " pdb=" CA LYS I 50 " pdb=" C LYS I 50 " ideal model delta sigma weight residual 114.56 109.25 5.31 1.27e+00 6.20e-01 1.75e+01 angle pdb=" N VAL A 93 " pdb=" CA VAL A 93 " pdb=" C VAL A 93 " ideal model delta sigma weight residual 113.00 107.77 5.23 1.30e+00 5.92e-01 1.62e+01 ... (remaining 31636 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.69: 13174 31.69 - 63.37: 880 63.37 - 95.06: 87 95.06 - 126.75: 1 126.75 - 158.44: 1 Dihedral angle restraints: 14143 sinusoidal: 6381 harmonic: 7762 Sorted by residual: dihedral pdb=" C4' G J 59 " pdb=" C3' G J 59 " pdb=" C2' G J 59 " pdb=" C1' G J 59 " ideal model delta sinusoidal sigma weight residual -35.00 34.90 -69.90 1 8.00e+00 1.56e-02 9.84e+01 dihedral pdb=" C5' G J 59 " pdb=" C4' G J 59 " pdb=" C3' G J 59 " pdb=" O3' G J 59 " ideal model delta sinusoidal sigma weight residual 147.00 78.93 68.07 1 8.00e+00 1.56e-02 9.40e+01 dihedral pdb=" O4' G J 59 " pdb=" C4' G J 59 " pdb=" C3' G J 59 " pdb=" C2' G J 59 " ideal model delta sinusoidal sigma weight residual 24.00 -35.17 59.17 1 8.00e+00 1.56e-02 7.31e+01 ... (remaining 14140 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 3268 0.079 - 0.159: 231 0.159 - 0.238: 8 0.238 - 0.318: 0 0.318 - 0.397: 2 Chirality restraints: 3509 Sorted by residual: chirality pdb=" CB VAL A 103 " pdb=" CA VAL A 103 " pdb=" CG1 VAL A 103 " pdb=" CG2 VAL A 103 " both_signs ideal model delta sigma weight residual False -2.63 -2.23 -0.40 2.00e-01 2.50e+01 3.95e+00 chirality pdb=" C3' G J 59 " pdb=" C4' G J 59 " pdb=" O3' G J 59 " pdb=" C2' G J 59 " both_signs ideal model delta sigma weight residual False -2.74 -2.36 -0.39 2.00e-01 2.50e+01 3.77e+00 chirality pdb=" CB VAL H 139 " pdb=" CA VAL H 139 " pdb=" CG1 VAL H 139 " pdb=" CG2 VAL H 139 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 3506 not shown) Planarity restraints: 3834 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 146 " 1.062 9.50e-02 1.11e+02 4.76e-01 1.37e+02 pdb=" NE ARG H 146 " -0.064 2.00e-02 2.50e+03 pdb=" CZ ARG H 146 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG H 146 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG H 146 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 230 " 0.026 2.00e-02 2.50e+03 4.99e-02 2.49e+01 pdb=" C LYS A 230 " -0.086 2.00e-02 2.50e+03 pdb=" O LYS A 230 " 0.032 2.00e-02 2.50e+03 pdb=" N GLU A 231 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR I 155 " 0.033 2.00e-02 2.50e+03 2.15e-02 9.22e+00 pdb=" CG TYR I 155 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR I 155 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR I 155 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR I 155 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR I 155 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR I 155 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR I 155 " 0.012 2.00e-02 2.50e+03 ... (remaining 3831 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 2551 2.74 - 3.28: 22946 3.28 - 3.82: 40139 3.82 - 4.36: 49746 4.36 - 4.90: 80999 Nonbonded interactions: 196381 Sorted by model distance: nonbonded pdb=" O PHE F 21 " pdb=" O2' U J 23 " model vdw 2.205 3.040 nonbonded pdb=" OH TYR H 265 " pdb=" O PHE H 273 " model vdw 2.207 3.040 nonbonded pdb=" OG SER A 111 " pdb=" OE1 GLU A 113 " model vdw 2.207 3.040 nonbonded pdb=" O PHE G 21 " pdb=" O2' C J 29 " model vdw 2.207 3.040 nonbonded pdb=" NZ LYS D 66 " pdb=" OE1 GLU D 70 " model vdw 2.217 3.120 ... (remaining 196376 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 12 through 52 or resid 79 through 331)) selection = (chain 'D' and (resid 12 through 52 or resid 79 through 331)) selection = (chain 'E' and (resid 12 through 52 or resid 79 through 331)) selection = (chain 'F' and (resid 12 through 52 or resid 79 through 331)) selection = (chain 'G' and (resid 12 through 52 or resid 79 through 331)) selection = (chain 'H' and resid 12 through 331) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.520 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: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 18.180 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 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 : 0.004 0.057 23213 Z= 0.199 Angle : 0.657 11.613 31641 Z= 0.385 Chirality : 0.043 0.397 3509 Planarity : 0.009 0.476 3834 Dihedral : 19.289 158.436 9129 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.52 % Favored : 95.36 % Rotamer: Outliers : 0.51 % Allowed : 27.97 % Favored : 71.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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 are not related in a simple way. whole: -0.56 (0.16), residues: 2609 helix: 0.51 (0.19), residues: 723 sheet: 0.16 (0.25), residues: 464 loop : -1.01 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 284 TYR 0.048 0.001 TYR I 155 PHE 0.034 0.002 PHE I 25 TRP 0.011 0.001 TRP E 149 HIS 0.007 0.001 HIS A 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.20 (23213) covalent geometry : angle 0.65715 / 0.39 (31641) hydrogen bonds : bond 0.25327 / 16.96 ( 633) hydrogen bonds : angle 8.09002 / 5.65 ( 1749) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5218 Ramachandran restraints generated. 2609 Oldfield, 0 Emsley, 2609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5218 Ramachandran restraints generated. 2609 Oldfield, 0 Emsley, 2609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 528 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.6165 (tmm) cc_final: 0.5650 (tmm) REVERT: A 276 LEU cc_start: 0.7132 (mp) cc_final: 0.6869 (tt) REVERT: A 320 MET cc_start: 0.4690 (ptt) cc_final: 0.3829 (tmm) REVERT: B 63 GLU cc_start: 0.7158 (tt0) cc_final: 0.6907 (tt0) REVERT: B 97 MET cc_start: 0.4255 (tmm) cc_final: 0.3751 (tmm) REVERT: B 124 SER cc_start: 0.7930 (t) cc_final: 0.7676 (t) REVERT: B 213 LYS cc_start: 0.7719 (mmtt) cc_final: 0.6786 (mmtt) REVERT: D 23 ARG cc_start: 0.8082 (ptp90) cc_final: 0.7775 (ptt-90) REVERT: D 42 THR cc_start: 0.8621 (p) cc_final: 0.8182 (t) REVERT: D 72 MET cc_start: -0.1415 (mtt) cc_final: -0.2208 (mtt) REVERT: D 103 LYS cc_start: 0.8037 (ttmt) cc_final: 0.7723 (tttm) REVERT: D 104 GLU cc_start: 0.6774 (mp0) cc_final: 0.6443 (mp0) REVERT: D 227 GLN cc_start: 0.8418 (tt0) cc_final: 0.8105 (tt0) REVERT: D 256 ASN cc_start: 0.8111 (t0) cc_final: 0.7703 (t0) REVERT: E 79 SER cc_start: 0.6742 (t) cc_final: 0.6491 (m) REVERT: E 115 ARG cc_start: 0.7733 (ttm110) cc_final: 0.7486 (ttm110) REVERT: E 171 SER cc_start: 0.8592 (p) cc_final: 0.8366 (p) REVERT: E 184 GLU cc_start: 0.7021 (mt-10) cc_final: 0.6672 (mt-10) REVERT: E 198 ASP cc_start: 0.7421 (m-30) cc_final: 0.7208 (m-30) REVERT: E 239 LYS cc_start: 0.8145 (mmtm) cc_final: 0.7915 (mmtm) REVERT: E 243 PHE cc_start: 0.8092 (t80) cc_final: 0.7582 (t80) REVERT: E 280 TYR cc_start: 0.7959 (m-80) cc_final: 0.7689 (m-80) REVERT: F 28 THR cc_start: 0.8355 (p) cc_final: 0.8126 (p) REVERT: F 103 LYS cc_start: 0.8262 (mtpt) cc_final: 0.7950 (mtpp) REVERT: F 123 ASP cc_start: 0.7171 (m-30) cc_final: 0.6557 (m-30) REVERT: F 165 GLU cc_start: 0.7034 (mm-30) cc_final: 0.6811 (mm-30) REVERT: F 256 ASN cc_start: 0.8821 (t0) cc_final: 0.8499 (t0) REVERT: F 265 TYR cc_start: 0.8212 (p90) cc_final: 0.7909 (p90) REVERT: F 328 MET cc_start: 0.6027 (ttp) cc_final: 0.5612 (ttm) REVERT: C 38 LEU cc_start: 0.8014 (mm) cc_final: 0.7784 (mt) REVERT: C 107 TYR cc_start: 0.7796 (m-10) cc_final: 0.7585 (m-80) REVERT: C 136 LYS cc_start: 0.7507 (ttmm) cc_final: 0.7288 (ttmm) REVERT: C 153 LYS cc_start: 0.8060 (mtmt) cc_final: 0.7824 (mtmt) REVERT: C 256 ASN cc_start: 0.7816 (t0) cc_final: 0.7613 (t0) REVERT: G 89 ASP cc_start: 0.7531 (p0) cc_final: 0.7181 (p0) REVERT: G 103 LYS cc_start: 0.8483 (ttpt) cc_final: 0.8249 (ttpt) REVERT: G 123 ASP cc_start: 0.7432 (m-30) cc_final: 0.7152 (m-30) REVERT: G 147 PHE cc_start: 0.7174 (p90) cc_final: 0.6955 (p90) REVERT: G 166 ASP cc_start: 0.7077 (p0) cc_final: 0.6866 (p0) REVERT: G 184 GLU cc_start: 0.7353 (pm20) cc_final: 0.6988 (pm20) REVERT: G 227 GLN cc_start: 0.8352 (tt0) cc_final: 0.7993 (mt0) REVERT: G 300 LEU cc_start: 0.8063 (tt) cc_final: 0.7858 (tt) REVERT: H 132 LEU cc_start: 0.5736 (tp) cc_final: 0.5477 (tp) REVERT: H 133 THR cc_start: 0.7448 (m) cc_final: 0.7070 (p) REVERT: H 144 ASN cc_start: 0.7621 (p0) cc_final: 0.6216 (p0) REVERT: H 146 ARG cc_start: 0.6798 (ttm110) cc_final: 0.6315 (ttm110) REVERT: H 270 THR cc_start: 0.8318 (p) cc_final: 0.7749 (p) REVERT: H 271 TYR cc_start: 0.8010 (m-80) cc_final: 0.7671 (m-80) REVERT: H 303 ARG cc_start: 0.7100 (mtm-85) cc_final: 0.6742 (mtm-85) REVERT: H 320 MET cc_start: 0.7429 (mmt) cc_final: 0.7130 (mmp) outliers start: 12 outliers final: 5 residues processed: 536 average time/residue: 0.1487 time to fit residues: 121.5683 Evaluate side-chains 486 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 481 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain G residue 329 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 HIS A 335 HIS D 140 ASN D 227 GLN ** E 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 279 ASN ** F 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 ASN C 173 ASN C 195 GLN H 34 GLN H 140 ASN ** H 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.187630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.141203 restraints weight = 33657.323| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 2.78 r_work: 0.3596 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 23213 Z= 0.187 Angle : 0.623 8.234 31641 Z= 0.334 Chirality : 0.044 0.276 3509 Planarity : 0.005 0.099 3834 Dihedral : 14.983 151.082 3786 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.50 % Allowed : 26.44 % Favored : 70.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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 are not related in a simple way. whole: -0.49 (0.16), residues: 2609 helix: 0.59 (0.18), residues: 745 sheet: 0.42 (0.26), residues: 445 loop : -1.08 (0.16), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 325 TYR 0.024 0.002 TYR I 155 PHE 0.031 0.002 PHE H 297 TRP 0.008 0.001 TRP D 264 HIS 0.010 0.001 HIS H 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.19 (23213) covalent geometry : angle 0.62289 / 0.33 (31641) hydrogen bonds : bond 0.06066 / 3.92 ( 633) hydrogen bonds : angle 6.17071 / 4.24 ( 1749) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5218 Ramachandran restraints generated. 2609 Oldfield, 0 Emsley, 2609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5218 Ramachandran restraints generated. 2609 Oldfield, 0 Emsley, 2609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 498 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.6147 (tmm) cc_final: 0.5721 (tmm) REVERT: A 95 MET cc_start: 0.6662 (OUTLIER) cc_final: 0.6276 (tpt) REVERT: A 135 MET cc_start: 0.1076 (mmm) cc_final: 0.0785 (mmm) REVERT: A 220 LEU cc_start: 0.8237 (mp) cc_final: 0.8023 (mt) REVERT: A 228 LEU cc_start: 0.7838 (mm) cc_final: 0.7417 (mp) REVERT: A 320 MET cc_start: 0.4674 (ptt) cc_final: 0.4228 (tpp) REVERT: B 119 MET cc_start: 0.6598 (ppp) cc_final: 0.6383 (ppp) REVERT: B 123 LYS cc_start: 0.7759 (mtmm) cc_final: 0.7462 (mtmm) REVERT: B 213 LYS cc_start: 0.7859 (mmtt) cc_final: 0.6924 (mmtt) REVERT: I 1 MET cc_start: -0.1590 (pmm) cc_final: -0.1944 (pmm) REVERT: D 23 ARG cc_start: 0.8256 (ptp90) cc_final: 0.8045 (ptt-90) REVERT: D 29 GLU cc_start: 0.7780 (mp0) cc_final: 0.7230 (mp0) REVERT: D 42 THR cc_start: 0.8713 (p) cc_final: 0.8295 (t) REVERT: D 72 MET cc_start: -0.0636 (mtt) cc_final: -0.1652 (mtt) REVERT: D 103 LYS cc_start: 0.8350 (ttmt) cc_final: 0.8007 (tttm) REVERT: D 104 GLU cc_start: 0.7147 (mp0) cc_final: 0.6803 (mp0) REVERT: D 112 TYR cc_start: 0.8271 (t80) cc_final: 0.7961 (t80) REVERT: D 227 GLN cc_start: 0.8713 (tt0) cc_final: 0.8381 (tt0) REVERT: D 229 MET cc_start: 0.5055 (ttt) cc_final: 0.4746 (ttm) REVERT: D 256 ASN cc_start: 0.8281 (t0) cc_final: 0.7902 (t0) REVERT: D 265 TYR cc_start: 0.8162 (p90) cc_final: 0.7961 (p90) REVERT: D 300 LEU cc_start: 0.8188 (mt) cc_final: 0.7958 (mt) REVERT: D 304 MET cc_start: 0.7803 (ttp) cc_final: 0.7525 (ttm) REVERT: E 79 SER cc_start: 0.7083 (t) cc_final: 0.6861 (m) REVERT: E 124 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7417 (mt-10) REVERT: E 184 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7413 (mt-10) REVERT: E 198 ASP cc_start: 0.7766 (m-30) cc_final: 0.7503 (m-30) REVERT: E 239 LYS cc_start: 0.8414 (mmtm) cc_final: 0.8145 (mmtm) REVERT: E 243 PHE cc_start: 0.8207 (t80) cc_final: 0.7906 (t80) REVERT: F 28 THR cc_start: 0.8485 (p) cc_final: 0.8234 (p) REVERT: F 103 LYS cc_start: 0.8509 (mtpt) cc_final: 0.8141 (mttt) REVERT: F 178 ASN cc_start: 0.7914 (t0) cc_final: 0.7712 (t0) REVERT: F 224 TYR cc_start: 0.8583 (m-80) cc_final: 0.8245 (m-80) REVERT: F 278 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7504 (mm-30) REVERT: F 299 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8468 (mttp) REVERT: C 29 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7357 (mt-10) REVERT: C 72 MET cc_start: -0.1454 (mmt) cc_final: -0.2097 (mmt) REVERT: C 153 LYS cc_start: 0.8259 (mtmt) cc_final: 0.8048 (mtmt) REVERT: C 307 LYS cc_start: 0.8348 (ttpt) cc_final: 0.7823 (ttpt) REVERT: G 89 ASP cc_start: 0.7486 (p0) cc_final: 0.7221 (p0) REVERT: G 179 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7854 (tp) REVERT: G 184 GLU cc_start: 0.7478 (pm20) cc_final: 0.7135 (pm20) REVERT: G 256 ASN cc_start: 0.8507 (t0) cc_final: 0.8296 (t0) REVERT: G 300 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7514 (mt) REVERT: H 140 ASN cc_start: 0.6683 (OUTLIER) cc_final: 0.6356 (t160) REVERT: H 150 ARG cc_start: 0.7712 (mtp180) cc_final: 0.7392 (mtp180) REVERT: H 200 PHE cc_start: 0.7908 (m-80) cc_final: 0.7638 (m-80) REVERT: H 303 ARG cc_start: 0.7303 (mtm-85) cc_final: 0.6926 (mtm-85) REVERT: H 309 GLU cc_start: 0.7744 (mm-30) cc_final: 0.7501 (mm-30) outliers start: 82 outliers final: 44 residues processed: 550 average time/residue: 0.1437 time to fit residues: 121.6306 Evaluate side-chains 525 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 475 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain B residue 99 GLN Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 87 LYS Chi-restraints excluded: chain D residue 26 ASN Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 140 ASN Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain E residue 251 SER Chi-restraints excluded: chain E residue 252 GLN Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 72 MET Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 219 CYS Chi-restraints excluded: chain F residue 226 SER Chi-restraints excluded: chain F residue 299 LYS Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 328 MET Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 72 MET Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 104 GLU Chi-restraints excluded: chain G residue 108 SER Chi-restraints excluded: chain G residue 164 ILE Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain G residue 275 ILE Chi-restraints excluded: chain G residue 293 ASP Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain G residue 311 LEU Chi-restraints excluded: chain G residue 329 PHE Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 140 ASN Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 186 ASN Chi-restraints excluded: chain H residue 209 ILE Chi-restraints excluded: chain H residue 316 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 206 optimal weight: 20.0000 chunk 55 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 258 optimal weight: 8.9990 chunk 158 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 188 optimal weight: 0.9980 chunk 186 optimal weight: 0.5980 chunk 170 optimal weight: 0.6980 chunk 165 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 GLN B 95 HIS D 140 ASN E 26 ASN E 120 GLN ** E 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 186 ASN H 34 GLN H 140 ASN H 317 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.187559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.142327 restraints weight = 33521.962| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 2.56 r_work: 0.3607 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3448 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 23213 Z= 0.160 Angle : 0.573 11.446 31641 Z= 0.307 Chirality : 0.042 0.320 3509 Planarity : 0.004 0.059 3834 Dihedral : 14.958 157.911 3786 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.54 % Allowed : 26.70 % Favored : 69.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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 are not related in a simple way. whole: -0.49 (0.16), residues: 2609 helix: 0.66 (0.18), residues: 743 sheet: 0.23 (0.26), residues: 456 loop : -1.06 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 325 TYR 0.024 0.001 TYR F 265 PHE 0.025 0.001 PHE H 297 TRP 0.009 0.001 TRP E 33 HIS 0.009 0.001 HIS H 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (23213) covalent geometry : angle 0.57327 / 0.31 (31641) hydrogen bonds : bond 0.05329 / 3.47 ( 633) hydrogen bonds : angle 5.81644 / 3.99 ( 1749) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5218 Ramachandran restraints generated. 2609 Oldfield, 0 Emsley, 2609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5218 Ramachandran restraints generated. 2609 Oldfield, 0 Emsley, 2609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 493 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.6259 (tmm) cc_final: 0.5792 (tmm) REVERT: A 88 ARG cc_start: 0.5386 (OUTLIER) cc_final: 0.4754 (mtm180) REVERT: A 95 MET cc_start: 0.6743 (tpt) cc_final: 0.6331 (tpt) REVERT: A 320 MET cc_start: 0.4774 (ptt) cc_final: 0.4295 (tpp) REVERT: B 22 ILE cc_start: 0.8215 (pt) cc_final: 0.8015 (pt) REVERT: B 46 LYS cc_start: 0.7646 (mtmt) cc_final: 0.7202 (mtpt) REVERT: B 70 LYS cc_start: 0.5215 (OUTLIER) cc_final: 0.4834 (pttm) REVERT: B 119 MET cc_start: 0.6688 (ppp) cc_final: 0.6417 (ppp) REVERT: B 123 LYS cc_start: 0.7844 (mtmm) cc_final: 0.7471 (mtmm) REVERT: B 143 LYS cc_start: 0.8645 (tttm) cc_final: 0.8429 (ttpp) REVERT: I 1 MET cc_start: -0.1763 (pmm) cc_final: -0.2541 (pmm) REVERT: D 29 GLU cc_start: 0.8032 (mp0) cc_final: 0.7531 (mp0) REVERT: D 72 MET cc_start: -0.0426 (mtt) cc_final: -0.1569 (mtt) REVERT: D 91 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8518 (tp) REVERT: D 103 LYS cc_start: 0.8454 (ttmt) cc_final: 0.8044 (tttm) REVERT: D 104 GLU cc_start: 0.7479 (mp0) cc_final: 0.7133 (mp0) REVERT: D 227 GLN cc_start: 0.8767 (tt0) cc_final: 0.8402 (tt0) REVERT: D 256 ASN cc_start: 0.8309 (t0) cc_final: 0.7919 (t0) REVERT: D 272 GLU cc_start: 0.7387 (mp0) cc_final: 0.7088 (mp0) REVERT: D 300 LEU cc_start: 0.8223 (mt) cc_final: 0.7992 (mt) REVERT: E 79 SER cc_start: 0.7339 (t) cc_final: 0.7135 (m) REVERT: E 124 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7744 (mt-10) REVERT: E 184 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7751 (mt-10) REVERT: E 198 ASP cc_start: 0.7969 (m-30) cc_final: 0.7724 (m-30) REVERT: E 239 LYS cc_start: 0.8492 (mmtm) cc_final: 0.8243 (mmtm) REVERT: F 28 THR cc_start: 0.8556 (p) cc_final: 0.8314 (p) REVERT: F 103 LYS cc_start: 0.8616 (mtpt) cc_final: 0.8258 (mttt) REVERT: F 123 ASP cc_start: 0.7929 (m-30) cc_final: 0.6846 (m-30) REVERT: F 125 TYR cc_start: 0.8343 (t80) cc_final: 0.7881 (t80) REVERT: F 299 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8543 (mttp) REVERT: C 29 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7580 (mt-10) REVERT: C 72 MET cc_start: -0.1103 (mmt) cc_final: -0.1572 (mmt) REVERT: C 153 LYS cc_start: 0.8410 (mtmt) cc_final: 0.8203 (mtmt) REVERT: C 328 MET cc_start: 0.6469 (OUTLIER) cc_final: 0.5936 (mtp) REVERT: G 89 ASP cc_start: 0.7583 (p0) cc_final: 0.7255 (p0) REVERT: G 179 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7969 (tp) REVERT: H 106 MET cc_start: 0.7218 (tpp) cc_final: 0.6548 (tpp) REVERT: H 118 ILE cc_start: 0.7576 (OUTLIER) cc_final: 0.7350 (mt) REVERT: H 150 ARG cc_start: 0.7830 (mtp180) cc_final: 0.7527 (mtp180) REVERT: H 200 PHE cc_start: 0.7990 (m-80) cc_final: 0.6932 (m-80) REVERT: H 271 TYR cc_start: 0.8066 (m-80) cc_final: 0.7755 (m-80) REVERT: H 309 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7615 (mm-30) outliers start: 83 outliers final: 48 residues processed: 537 average time/residue: 0.1406 time to fit residues: 118.9372 Evaluate side-chains 536 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 480 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 88 ARG Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain I residue 41 ILE Chi-restraints excluded: chain D residue 26 ASN Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain E residue 26 ASN Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 171 SER Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 251 SER Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 226 SER Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain F residue 299 LYS Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 328 MET Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 72 MET Chi-restraints excluded: chain G residue 104 GLU Chi-restraints excluded: chain G residue 164 ILE Chi-restraints excluded: chain G residue 172 PHE Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 267 ASP Chi-restraints excluded: chain G residue 275 ILE Chi-restraints excluded: chain G residue 293 ASP Chi-restraints excluded: chain G residue 329 PHE Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 186 ASN Chi-restraints excluded: chain H residue 209 ILE Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 316 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 197 optimal weight: 0.7980 chunk 263 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 219 optimal weight: 0.6980 chunk 13 optimal weight: 0.3980 chunk 140 optimal weight: 7.9990 chunk 85 optimal weight: 0.4980 chunk 131 optimal weight: 4.9990 chunk 154 optimal weight: 1.9990 chunk 17 optimal weight: 0.0470 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 ASN I 137 GLN D 140 ASN E 26 ASN ** E 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.187999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.143189 restraints weight = 33568.288| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 3.09 r_work: 0.3597 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23213 Z= 0.136 Angle : 0.547 7.659 31641 Z= 0.293 Chirality : 0.042 0.329 3509 Planarity : 0.004 0.063 3834 Dihedral : 14.871 160.434 3781 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.62 % Allowed : 26.87 % Favored : 69.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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 are not related in a simple way. whole: -0.49 (0.16), residues: 2609 helix: 0.68 (0.18), residues: 756 sheet: 0.16 (0.26), residues: 461 loop : -1.07 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 23 TYR 0.017 0.001 TYR F 169 PHE 0.020 0.001 PHE H 297 TRP 0.008 0.001 TRP E 33 HIS 0.004 0.001 HIS A 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (23213) covalent geometry : angle 0.54740 / 0.29 (31641) hydrogen bonds : bond 0.04698 / 3.08 ( 633) hydrogen bonds : angle 5.58909 / 3.84 ( 1749) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5218 Ramachandran restraints generated. 2609 Oldfield, 0 Emsley, 2609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5218 Ramachandran restraints generated. 2609 Oldfield, 0 Emsley, 2609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 483 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.6168 (tmm) cc_final: 0.5651 (tmm) REVERT: A 88 ARG cc_start: 0.5383 (OUTLIER) cc_final: 0.4736 (mtm180) REVERT: A 95 MET cc_start: 0.6782 (tpt) cc_final: 0.6393 (tpt) REVERT: A 228 LEU cc_start: 0.7810 (mm) cc_final: 0.7447 (mp) REVERT: A 276 LEU cc_start: 0.6862 (mp) cc_final: 0.6642 (tt) REVERT: A 320 MET cc_start: 0.4716 (ptt) cc_final: 0.4267 (tpp) REVERT: B 70 LYS cc_start: 0.5105 (OUTLIER) cc_final: 0.4698 (pttm) REVERT: B 123 LYS cc_start: 0.7725 (mtmm) cc_final: 0.7504 (mtmm) REVERT: B 129 MET cc_start: 0.8302 (ttm) cc_final: 0.8083 (ttm) REVERT: I 1 MET cc_start: -0.2232 (pmm) cc_final: -0.2738 (pmm) REVERT: D 29 GLU cc_start: 0.7763 (mp0) cc_final: 0.7525 (mm-30) REVERT: D 72 MET cc_start: -0.0457 (mtt) cc_final: -0.1420 (mtt) REVERT: D 103 LYS cc_start: 0.8334 (ttmt) cc_final: 0.7881 (tttm) REVERT: D 104 GLU cc_start: 0.7165 (mp0) cc_final: 0.6844 (mp0) REVERT: D 144 ASN cc_start: 0.8359 (p0) cc_final: 0.8071 (p0) REVERT: D 227 GLN cc_start: 0.8643 (tt0) cc_final: 0.8259 (tt0) REVERT: D 229 MET cc_start: 0.5200 (OUTLIER) cc_final: 0.4634 (ttm) REVERT: D 256 ASN cc_start: 0.8219 (t0) cc_final: 0.7802 (t0) REVERT: D 300 LEU cc_start: 0.8141 (mt) cc_final: 0.7915 (mt) REVERT: E 89 ASP cc_start: 0.8283 (p0) cc_final: 0.8071 (p0) REVERT: E 124 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7446 (mt-10) REVERT: E 198 ASP cc_start: 0.7759 (m-30) cc_final: 0.7473 (m-30) REVERT: E 239 LYS cc_start: 0.8358 (mmtm) cc_final: 0.8158 (mmtp) REVERT: E 290 PHE cc_start: 0.8015 (m-80) cc_final: 0.7774 (m-10) REVERT: F 86 THR cc_start: 0.8123 (p) cc_final: 0.7813 (p) REVERT: F 103 LYS cc_start: 0.8530 (mtpt) cc_final: 0.8150 (mttt) REVERT: F 123 ASP cc_start: 0.7619 (m-30) cc_final: 0.6472 (m-30) REVERT: F 125 TYR cc_start: 0.8297 (t80) cc_final: 0.7697 (t80) REVERT: F 278 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7449 (mm-30) REVERT: F 299 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8476 (mttp) REVERT: C 29 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7349 (mt-10) REVERT: G 121 LYS cc_start: 0.8428 (tppt) cc_final: 0.8111 (mmtm) REVERT: G 179 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7971 (tp) REVERT: G 300 LEU cc_start: 0.8171 (tt) cc_final: 0.7663 (mt) REVERT: H 106 MET cc_start: 0.7085 (tpp) cc_final: 0.6335 (tpp) REVERT: H 150 ARG cc_start: 0.7725 (mtp180) cc_final: 0.7393 (mtp180) REVERT: H 309 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7499 (mm-30) outliers start: 85 outliers final: 61 residues processed: 527 average time/residue: 0.1410 time to fit residues: 117.0673 Evaluate side-chains 536 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 469 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 88 ARG Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain B residue 20 ASN Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 99 GLN Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 137 GLN Chi-restraints excluded: chain D residue 26 ASN Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 140 ASN Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain E residue 26 ASN Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 171 SER Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 251 SER Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 72 MET Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 219 CYS Chi-restraints excluded: chain F residue 226 SER Chi-restraints excluded: chain F residue 249 MET Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain F residue 299 LYS Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 304 MET Chi-restraints excluded: chain C residue 328 MET Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 72 MET Chi-restraints excluded: chain G residue 104 GLU Chi-restraints excluded: chain G residue 108 SER Chi-restraints excluded: chain G residue 164 ILE Chi-restraints excluded: chain G residue 172 PHE Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain G residue 275 ILE Chi-restraints excluded: chain G residue 293 ASP Chi-restraints excluded: chain G residue 329 PHE Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 186 ASN Chi-restraints excluded: chain H residue 209 ILE Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 270 THR Chi-restraints excluded: chain H residue 316 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 31 optimal weight: 9.9990 chunk 1 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 99 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 93 optimal weight: 0.9980 chunk 175 optimal weight: 1.9990 chunk 184 optimal weight: 0.0020 chunk 217 optimal weight: 0.9990 chunk 265 optimal weight: 20.0000 overall best weight: 0.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 ASN D 140 ASN E 195 GLN ** E 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 186 ASN G 195 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.186667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.141698 restraints weight = 33214.070| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 2.91 r_work: 0.3580 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 23213 Z= 0.184 Angle : 0.570 9.417 31641 Z= 0.303 Chirality : 0.043 0.324 3509 Planarity : 0.004 0.061 3834 Dihedral : 14.814 161.869 3781 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 4.09 % Allowed : 26.74 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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 are not related in a simple way. whole: -0.54 (0.16), residues: 2609 helix: 0.67 (0.18), residues: 755 sheet: 0.14 (0.25), residues: 472 loop : -1.13 (0.16), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 23 TYR 0.022 0.001 TYR F 265 PHE 0.020 0.002 PHE G 172 TRP 0.011 0.001 TRP E 33 HIS 0.004 0.001 HIS D 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.18 (23213) covalent geometry : angle 0.56958 / 0.30 (31641) hydrogen bonds : bond 0.04673 / 3.05 ( 633) hydrogen bonds : angle 5.52641 / 3.80 ( 1749) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5218 Ramachandran restraints generated. 2609 Oldfield, 0 Emsley, 2609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5218 Ramachandran restraints generated. 2609 Oldfield, 0 Emsley, 2609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 469 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.6217 (tmm) cc_final: 0.5664 (tmm) REVERT: A 95 MET cc_start: 0.6838 (tpt) cc_final: 0.6438 (tpt) REVERT: A 276 LEU cc_start: 0.6836 (mp) cc_final: 0.6622 (tt) REVERT: A 320 MET cc_start: 0.4674 (ptt) cc_final: 0.4316 (tpp) REVERT: B 61 GLU cc_start: 0.7462 (mt-10) cc_final: 0.7157 (mt-10) REVERT: B 70 LYS cc_start: 0.5152 (OUTLIER) cc_final: 0.4736 (pttm) REVERT: B 123 LYS cc_start: 0.7743 (mtmm) cc_final: 0.7524 (mtmm) REVERT: B 176 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7354 (tt) REVERT: B 213 LYS cc_start: 0.7907 (mmtt) cc_final: 0.7297 (mmtt) REVERT: D 72 MET cc_start: -0.0393 (mtt) cc_final: -0.1121 (mtt) REVERT: D 103 LYS cc_start: 0.8323 (ttmt) cc_final: 0.7999 (tttm) REVERT: D 227 GLN cc_start: 0.8659 (tt0) cc_final: 0.8273 (tt0) REVERT: D 229 MET cc_start: 0.5302 (OUTLIER) cc_final: 0.4415 (ttm) REVERT: D 256 ASN cc_start: 0.8239 (t0) cc_final: 0.7856 (t0) REVERT: D 300 LEU cc_start: 0.8166 (mt) cc_final: 0.7936 (mt) REVERT: E 124 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7417 (mt-10) REVERT: E 221 MET cc_start: 0.8720 (mmt) cc_final: 0.8455 (mmt) REVERT: E 239 LYS cc_start: 0.8382 (mmtm) cc_final: 0.8174 (mmtm) REVERT: E 290 PHE cc_start: 0.8204 (m-80) cc_final: 0.7835 (m-80) REVERT: F 103 LYS cc_start: 0.8566 (mtpt) cc_final: 0.8188 (mttt) REVERT: F 123 ASP cc_start: 0.7581 (m-30) cc_final: 0.6486 (m-30) REVERT: F 227 GLN cc_start: 0.8413 (tt0) cc_final: 0.8184 (tt0) REVERT: F 299 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8485 (mttp) REVERT: C 29 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7367 (mt-10) REVERT: C 72 MET cc_start: -0.0845 (mmt) cc_final: -0.1678 (mmt) REVERT: G 89 ASP cc_start: 0.7594 (p0) cc_final: 0.7327 (p0) REVERT: G 121 LYS cc_start: 0.8442 (tppt) cc_final: 0.8097 (mmtm) REVERT: G 184 GLU cc_start: 0.7439 (pm20) cc_final: 0.7088 (pm20) REVERT: G 300 LEU cc_start: 0.8203 (tt) cc_final: 0.7622 (mt) REVERT: H 23 ARG cc_start: 0.6584 (mtm-85) cc_final: 0.6306 (ttm-80) REVERT: H 106 MET cc_start: 0.7112 (tpp) cc_final: 0.6306 (tpp) REVERT: H 146 ARG cc_start: 0.7764 (mtp-110) cc_final: 0.7365 (mtp-110) REVERT: H 150 ARG cc_start: 0.7746 (mtp180) cc_final: 0.7396 (mtp180) REVERT: H 309 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7552 (mm-30) outliers start: 96 outliers final: 68 residues processed: 523 average time/residue: 0.1362 time to fit residues: 112.5460 Evaluate side-chains 533 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 460 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 20 ASN Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 99 GLN Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 96 TYR Chi-restraints excluded: chain D residue 26 ASN Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 252 GLN Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 72 MET Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 219 CYS Chi-restraints excluded: chain F residue 226 SER Chi-restraints excluded: chain F residue 249 MET Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain F residue 299 LYS Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 304 MET Chi-restraints excluded: chain C residue 328 MET Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 72 MET Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain G residue 104 GLU Chi-restraints excluded: chain G residue 108 SER Chi-restraints excluded: chain G residue 172 PHE Chi-restraints excluded: chain G residue 213 CYS Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain G residue 267 ASP Chi-restraints excluded: chain G residue 275 ILE Chi-restraints excluded: chain G residue 293 ASP Chi-restraints excluded: chain G residue 329 PHE Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 186 ASN Chi-restraints excluded: chain H residue 209 ILE Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 249 MET Chi-restraints excluded: chain H residue 316 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 250 optimal weight: 2.9990 chunk 235 optimal weight: 0.1980 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 242 optimal weight: 4.9990 chunk 261 optimal weight: 4.9990 chunk 129 optimal weight: 0.6980 chunk 236 optimal weight: 6.9990 chunk 97 optimal weight: 0.7980 chunk 176 optimal weight: 0.0670 chunk 120 optimal weight: 0.5980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 ASN I 137 GLN D 140 ASN E 26 ASN ** E 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 308 ASN ** F 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 GLN H 178 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.187941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.142137 restraints weight = 33424.329| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 2.78 r_work: 0.3610 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3445 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23213 Z= 0.129 Angle : 0.544 9.665 31641 Z= 0.288 Chirality : 0.042 0.319 3509 Planarity : 0.004 0.062 3834 Dihedral : 14.766 164.015 3781 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.50 % Allowed : 27.38 % Favored : 69.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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 are not related in a simple way. whole: -0.48 (0.16), residues: 2609 helix: 0.75 (0.18), residues: 764 sheet: 0.17 (0.26), residues: 466 loop : -1.11 (0.16), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 23 TYR 0.018 0.001 TYR G 125 PHE 0.020 0.001 PHE B 19 TRP 0.009 0.001 TRP G 149 HIS 0.003 0.001 HIS A 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (23213) covalent geometry : angle 0.54357 / 0.29 (31641) hydrogen bonds : bond 0.04311 / 2.84 ( 633) hydrogen bonds : angle 5.38185 / 3.70 ( 1749) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5218 Ramachandran restraints generated. 2609 Oldfield, 0 Emsley, 2609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5218 Ramachandran restraints generated. 2609 Oldfield, 0 Emsley, 2609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 464 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.6329 (tmm) cc_final: 0.5643 (tmm) REVERT: A 95 MET cc_start: 0.6887 (tpt) cc_final: 0.6504 (tpt) REVERT: A 276 LEU cc_start: 0.6810 (mp) cc_final: 0.6591 (tt) REVERT: A 320 MET cc_start: 0.4795 (ptt) cc_final: 0.4312 (tpp) REVERT: B 61 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7334 (mt-10) REVERT: B 70 LYS cc_start: 0.5243 (OUTLIER) cc_final: 0.4864 (pttm) REVERT: B 176 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.7330 (tt) REVERT: B 213 LYS cc_start: 0.7944 (mmtt) cc_final: 0.7354 (mmtt) REVERT: I 1 MET cc_start: -0.2235 (OUTLIER) cc_final: -0.2633 (pmm) REVERT: D 103 LYS cc_start: 0.8425 (ttmt) cc_final: 0.7991 (tttm) REVERT: D 104 GLU cc_start: 0.7545 (mp0) cc_final: 0.7234 (mp0) REVERT: D 140 ASN cc_start: 0.8434 (OUTLIER) cc_final: 0.8128 (t0) REVERT: D 144 ASN cc_start: 0.8449 (p0) cc_final: 0.8207 (p0) REVERT: D 204 ARG cc_start: 0.8024 (mtp-110) cc_final: 0.7536 (mtp-110) REVERT: D 227 GLN cc_start: 0.8691 (tt0) cc_final: 0.8238 (tt0) REVERT: D 229 MET cc_start: 0.5314 (OUTLIER) cc_final: 0.4578 (ttm) REVERT: D 256 ASN cc_start: 0.8232 (t0) cc_final: 0.7819 (t0) REVERT: D 279 ASN cc_start: 0.8264 (m-40) cc_final: 0.7961 (m-40) REVERT: D 300 LEU cc_start: 0.8195 (mt) cc_final: 0.7962 (mt) REVERT: E 124 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7736 (mt-10) REVERT: E 190 ASN cc_start: 0.7961 (m-40) cc_final: 0.7592 (m-40) REVERT: E 239 LYS cc_start: 0.8494 (mmtm) cc_final: 0.8279 (mmtp) REVERT: E 290 PHE cc_start: 0.8301 (m-80) cc_final: 0.7909 (m-80) REVERT: E 307 LYS cc_start: 0.8771 (tmtt) cc_final: 0.8300 (tmtt) REVERT: F 28 THR cc_start: 0.8539 (p) cc_final: 0.8297 (p) REVERT: F 103 LYS cc_start: 0.8618 (mtpt) cc_final: 0.8370 (mtpp) REVERT: F 123 ASP cc_start: 0.7900 (m-30) cc_final: 0.7247 (m-30) REVERT: F 227 GLN cc_start: 0.8531 (tt0) cc_final: 0.8315 (tt0) REVERT: F 299 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8536 (mttp) REVERT: C 29 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7540 (mt-10) REVERT: C 72 MET cc_start: -0.0781 (mmt) cc_final: -0.1220 (mmt) REVERT: C 91 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7729 (tp) REVERT: C 119 TYR cc_start: 0.7638 (m-10) cc_final: 0.7415 (m-10) REVERT: C 241 PHE cc_start: 0.8806 (t80) cc_final: 0.8144 (t80) REVERT: C 275 ILE cc_start: 0.8459 (pt) cc_final: 0.8165 (tt) REVERT: G 121 LYS cc_start: 0.8486 (tppt) cc_final: 0.8171 (mmtm) REVERT: G 141 ASN cc_start: 0.7753 (m-40) cc_final: 0.7527 (m-40) REVERT: G 184 GLU cc_start: 0.7709 (pm20) cc_final: 0.7320 (pm20) REVERT: G 300 LEU cc_start: 0.8305 (tt) cc_final: 0.7665 (mt) REVERT: H 23 ARG cc_start: 0.6659 (mtm-85) cc_final: 0.6457 (ttm-80) REVERT: H 106 MET cc_start: 0.7288 (tpp) cc_final: 0.6641 (tpp) REVERT: H 146 ARG cc_start: 0.7908 (mtp-110) cc_final: 0.7451 (mtp-110) REVERT: H 150 ARG cc_start: 0.7853 (mtp180) cc_final: 0.7529 (mtp180) REVERT: H 200 PHE cc_start: 0.8042 (m-80) cc_final: 0.7686 (m-80) REVERT: H 304 MET cc_start: 0.7661 (tmm) cc_final: 0.6474 (tpt) REVERT: H 309 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7509 (mm-30) outliers start: 82 outliers final: 62 residues processed: 513 average time/residue: 0.1358 time to fit residues: 110.4308 Evaluate side-chains 535 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 465 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 20 ASN Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 99 GLN Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 96 TYR Chi-restraints excluded: chain I residue 137 GLN Chi-restraints excluded: chain D residue 26 ASN Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 140 ASN Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain E residue 308 ASN Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 72 MET Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 219 CYS Chi-restraints excluded: chain F residue 226 SER Chi-restraints excluded: chain F residue 249 MET Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain F residue 299 LYS Chi-restraints excluded: chain F residue 328 MET Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 304 MET Chi-restraints excluded: chain C residue 328 MET Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 72 MET Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain G residue 104 GLU Chi-restraints excluded: chain G residue 108 SER Chi-restraints excluded: chain G residue 172 PHE Chi-restraints excluded: chain G residue 213 CYS Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain G residue 275 ILE Chi-restraints excluded: chain G residue 293 ASP Chi-restraints excluded: chain G residue 329 PHE Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 186 ASN Chi-restraints excluded: chain H residue 209 ILE Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 249 MET Chi-restraints excluded: chain H residue 316 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 151 optimal weight: 1.9990 chunk 192 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 110 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 chunk 120 optimal weight: 0.4980 chunk 98 optimal weight: 0.0040 chunk 39 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 137 GLN D 140 ASN ** E 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 308 ASN F 80 GLN ** F 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.187767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.142989 restraints weight = 33289.554| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 2.84 r_work: 0.3636 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3473 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23213 Z= 0.153 Angle : 0.551 10.278 31641 Z= 0.291 Chirality : 0.042 0.304 3509 Planarity : 0.004 0.063 3834 Dihedral : 14.704 161.698 3781 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.97 % Allowed : 27.29 % Favored : 68.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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 are not related in a simple way. whole: -0.47 (0.16), residues: 2609 helix: 0.81 (0.18), residues: 754 sheet: 0.17 (0.26), residues: 468 loop : -1.13 (0.16), residues: 1387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 150 TYR 0.017 0.001 TYR G 125 PHE 0.018 0.001 PHE B 19 TRP 0.009 0.001 TRP G 149 HIS 0.004 0.001 HIS D 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (23213) covalent geometry : angle 0.55083 / 0.29 (31641) hydrogen bonds : bond 0.04372 / 2.85 ( 633) hydrogen bonds : angle 5.32783 / 3.64 ( 1749) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5218 Ramachandran restraints generated. 2609 Oldfield, 0 Emsley, 2609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5218 Ramachandran restraints generated. 2609 Oldfield, 0 Emsley, 2609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 472 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.6854 (tpt) cc_final: 0.6435 (tpt) REVERT: A 276 LEU cc_start: 0.6932 (mp) cc_final: 0.6718 (tt) REVERT: A 320 MET cc_start: 0.4794 (ptt) cc_final: 0.4366 (tpp) REVERT: B 26 ILE cc_start: 0.8923 (mm) cc_final: 0.8539 (mt) REVERT: B 61 GLU cc_start: 0.7588 (mt-10) cc_final: 0.7308 (mt-10) REVERT: B 70 LYS cc_start: 0.5245 (OUTLIER) cc_final: 0.4843 (pttm) REVERT: B 123 LYS cc_start: 0.7891 (mtmm) cc_final: 0.7572 (mtmm) REVERT: B 213 LYS cc_start: 0.8017 (mmtt) cc_final: 0.7200 (mmtt) REVERT: B 233 LEU cc_start: 0.7087 (OUTLIER) cc_final: 0.6822 (mm) REVERT: I 1 MET cc_start: -0.2194 (OUTLIER) cc_final: -0.2632 (pmm) REVERT: D 104 GLU cc_start: 0.7437 (mp0) cc_final: 0.7191 (mp0) REVERT: D 140 ASN cc_start: 0.8052 (OUTLIER) cc_final: 0.7460 (m-40) REVERT: D 144 ASN cc_start: 0.8437 (p0) cc_final: 0.8151 (p0) REVERT: D 204 ARG cc_start: 0.7980 (mtp-110) cc_final: 0.7520 (mtp-110) REVERT: D 227 GLN cc_start: 0.8700 (tt0) cc_final: 0.8319 (tt0) REVERT: D 229 MET cc_start: 0.5362 (OUTLIER) cc_final: 0.4551 (ttm) REVERT: D 256 ASN cc_start: 0.8183 (t0) cc_final: 0.7813 (t0) REVERT: D 279 ASN cc_start: 0.8262 (m-40) cc_final: 0.8037 (m-40) REVERT: D 300 LEU cc_start: 0.8291 (mt) cc_final: 0.8080 (mt) REVERT: E 124 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7822 (mt-10) REVERT: E 190 ASN cc_start: 0.8012 (m-40) cc_final: 0.7645 (m-40) REVERT: E 290 PHE cc_start: 0.8317 (m-80) cc_final: 0.7991 (m-80) REVERT: E 307 LYS cc_start: 0.8719 (tmtt) cc_final: 0.8296 (tmtt) REVERT: F 103 LYS cc_start: 0.8584 (mtpt) cc_final: 0.8365 (mtpp) REVERT: F 123 ASP cc_start: 0.7896 (m-30) cc_final: 0.7265 (m-30) REVERT: F 244 GLU cc_start: 0.8798 (mt-10) cc_final: 0.8467 (mt-10) REVERT: F 299 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8563 (mttp) REVERT: C 29 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7501 (mt-10) REVERT: C 72 MET cc_start: -0.0855 (mmt) cc_final: -0.1146 (mmt) REVERT: C 91 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7703 (tp) REVERT: C 241 PHE cc_start: 0.8788 (t80) cc_final: 0.8291 (t80) REVERT: C 275 ILE cc_start: 0.8441 (pt) cc_final: 0.8188 (tt) REVERT: C 305 ILE cc_start: 0.7520 (tt) cc_final: 0.7212 (tt) REVERT: G 121 LYS cc_start: 0.8530 (tppt) cc_final: 0.8222 (mmtm) REVERT: G 184 GLU cc_start: 0.7631 (pm20) cc_final: 0.7300 (pm20) REVERT: G 300 LEU cc_start: 0.8349 (tt) cc_final: 0.7726 (mt) REVERT: H 106 MET cc_start: 0.7213 (tpp) cc_final: 0.6478 (tpp) REVERT: H 146 ARG cc_start: 0.7842 (mtp-110) cc_final: 0.7456 (mtp-110) REVERT: H 150 ARG cc_start: 0.7887 (mtp180) cc_final: 0.7543 (mtp180) REVERT: H 196 ILE cc_start: 0.7771 (mt) cc_final: 0.7531 (tt) REVERT: H 200 PHE cc_start: 0.8066 (m-80) cc_final: 0.7799 (m-80) REVERT: H 303 ARG cc_start: 0.7476 (mtm-85) cc_final: 0.7096 (mtm-85) REVERT: H 304 MET cc_start: 0.7674 (tmm) cc_final: 0.6481 (tpt) REVERT: H 309 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7621 (mm-30) REVERT: H 320 MET cc_start: 0.7657 (mmt) cc_final: 0.7383 (mmp) outliers start: 93 outliers final: 68 residues processed: 531 average time/residue: 0.1370 time to fit residues: 115.0992 Evaluate side-chains 538 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 462 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain B residue 20 ASN Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 99 GLN Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 96 TYR Chi-restraints excluded: chain I residue 137 GLN Chi-restraints excluded: chain D residue 26 ASN Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 140 ASN Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 171 SER Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 72 MET Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 219 CYS Chi-restraints excluded: chain F residue 226 SER Chi-restraints excluded: chain F residue 249 MET Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain F residue 299 LYS Chi-restraints excluded: chain F residue 328 MET Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 304 MET Chi-restraints excluded: chain C residue 328 MET Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 72 MET Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain G residue 104 GLU Chi-restraints excluded: chain G residue 108 SER Chi-restraints excluded: chain G residue 156 GLU Chi-restraints excluded: chain G residue 164 ILE Chi-restraints excluded: chain G residue 172 PHE Chi-restraints excluded: chain G residue 213 CYS Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain G residue 275 ILE Chi-restraints excluded: chain G residue 293 ASP Chi-restraints excluded: chain G residue 329 PHE Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 186 ASN Chi-restraints excluded: chain H residue 209 ILE Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 249 MET Chi-restraints excluded: chain H residue 316 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 200 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 257 optimal weight: 4.9990 chunk 151 optimal weight: 1.9990 chunk 229 optimal weight: 4.9990 chunk 161 optimal weight: 1.9990 chunk 87 optimal weight: 0.0170 chunk 80 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 249 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 overall best weight: 1.3824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 ASN E 195 GLN E 308 ASN ** F 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.185853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.140490 restraints weight = 32922.918| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 2.71 r_work: 0.3590 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 23213 Z= 0.244 Angle : 0.602 10.621 31641 Z= 0.317 Chirality : 0.044 0.275 3509 Planarity : 0.005 0.065 3834 Dihedral : 14.669 155.987 3781 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 4.01 % Allowed : 27.21 % Favored : 68.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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 are not related in a simple way. whole: -0.64 (0.16), residues: 2609 helix: 0.61 (0.18), residues: 762 sheet: 0.07 (0.25), residues: 476 loop : -1.21 (0.16), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 37 TYR 0.017 0.002 TYR B 142 PHE 0.022 0.002 PHE B 19 TRP 0.014 0.002 TRP E 33 HIS 0.006 0.001 HIS D 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00566 / 0.24 (23213) covalent geometry : angle 0.60209 / 0.32 (31641) hydrogen bonds : bond 0.04732 / 3.08 ( 633) hydrogen bonds : angle 5.42124 / 3.70 ( 1749) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5218 Ramachandran restraints generated. 2609 Oldfield, 0 Emsley, 2609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5218 Ramachandran restraints generated. 2609 Oldfield, 0 Emsley, 2609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 472 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.6890 (tpt) cc_final: 0.6497 (tpt) REVERT: A 320 MET cc_start: 0.4642 (ptt) cc_final: 0.4330 (tpp) REVERT: B 26 ILE cc_start: 0.8849 (mm) cc_final: 0.8497 (mt) REVERT: B 61 GLU cc_start: 0.7306 (mt-10) cc_final: 0.7022 (mt-10) REVERT: B 70 LYS cc_start: 0.5173 (OUTLIER) cc_final: 0.4750 (pttm) REVERT: B 133 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7479 (ttp-170) REVERT: B 213 LYS cc_start: 0.8098 (mmtt) cc_final: 0.7252 (mmtt) REVERT: B 233 LEU cc_start: 0.7019 (OUTLIER) cc_final: 0.6755 (mm) REVERT: D 140 ASN cc_start: 0.7819 (OUTLIER) cc_final: 0.7382 (m-40) REVERT: D 144 ASN cc_start: 0.8324 (p0) cc_final: 0.8030 (p0) REVERT: D 229 MET cc_start: 0.5505 (OUTLIER) cc_final: 0.5095 (ttm) REVERT: D 256 ASN cc_start: 0.8177 (t0) cc_final: 0.7837 (t0) REVERT: E 89 ASP cc_start: 0.8310 (p0) cc_final: 0.7944 (p0) REVERT: E 124 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7470 (mt-10) REVERT: E 307 LYS cc_start: 0.8653 (tmtt) cc_final: 0.8222 (tmtt) REVERT: F 87 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8258 (mm-30) REVERT: F 89 ASP cc_start: 0.8043 (p0) cc_final: 0.7508 (p0) REVERT: F 94 ASP cc_start: 0.7813 (m-30) cc_final: 0.7365 (m-30) REVERT: F 123 ASP cc_start: 0.7606 (m-30) cc_final: 0.7362 (m-30) REVERT: F 244 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8487 (mt-10) REVERT: F 299 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8519 (mttp) REVERT: F 311 LEU cc_start: 0.7893 (mt) cc_final: 0.7692 (mt) REVERT: C 29 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7271 (mt-10) REVERT: C 72 MET cc_start: -0.0736 (mmt) cc_final: -0.0962 (mmt) REVERT: C 91 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7590 (tp) REVERT: C 106 MET cc_start: 0.7924 (tpp) cc_final: 0.7326 (ttm) REVERT: C 241 PHE cc_start: 0.8715 (t80) cc_final: 0.8045 (t80) REVERT: C 275 ILE cc_start: 0.8362 (pt) cc_final: 0.8116 (tt) REVERT: C 305 ILE cc_start: 0.7572 (tt) cc_final: 0.7262 (tt) REVERT: G 89 ASP cc_start: 0.7632 (p0) cc_final: 0.7325 (p0) REVERT: G 121 LYS cc_start: 0.8486 (tppt) cc_final: 0.8167 (mmtm) REVERT: G 184 GLU cc_start: 0.7374 (pm20) cc_final: 0.7120 (pm20) REVERT: G 227 GLN cc_start: 0.8719 (tt0) cc_final: 0.8412 (mt0) REVERT: G 300 LEU cc_start: 0.8278 (tt) cc_final: 0.7643 (mt) REVERT: H 106 MET cc_start: 0.7070 (tpp) cc_final: 0.6271 (tpp) REVERT: H 146 ARG cc_start: 0.7705 (mtp-110) cc_final: 0.7279 (mtp-110) REVERT: H 150 ARG cc_start: 0.7758 (mtp180) cc_final: 0.7399 (mtp180) REVERT: H 210 TYR cc_start: 0.6983 (m-80) cc_final: 0.6757 (m-80) REVERT: H 304 MET cc_start: 0.7617 (tmm) cc_final: 0.6438 (tpt) REVERT: H 309 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7475 (mm-30) REVERT: H 320 MET cc_start: 0.7659 (mmt) cc_final: 0.7388 (mmp) outliers start: 94 outliers final: 72 residues processed: 528 average time/residue: 0.1363 time to fit residues: 113.1454 Evaluate side-chains 541 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 461 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain B residue 20 ASN Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 99 GLN Chi-restraints excluded: chain B residue 133 ARG Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 96 TYR Chi-restraints excluded: chain D residue 26 ASN Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 140 ASN Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 252 GLN Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain E residue 308 ASN Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 219 CYS Chi-restraints excluded: chain F residue 226 SER Chi-restraints excluded: chain F residue 249 MET Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain F residue 299 LYS Chi-restraints excluded: chain F residue 305 ILE Chi-restraints excluded: chain F residue 328 MET Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 304 MET Chi-restraints excluded: chain C residue 328 MET Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 72 MET Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 104 GLU Chi-restraints excluded: chain G residue 108 SER Chi-restraints excluded: chain G residue 156 GLU Chi-restraints excluded: chain G residue 164 ILE Chi-restraints excluded: chain G residue 213 CYS Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain G residue 267 ASP Chi-restraints excluded: chain G residue 275 ILE Chi-restraints excluded: chain G residue 293 ASP Chi-restraints excluded: chain G residue 329 PHE Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 186 ASN Chi-restraints excluded: chain H residue 209 ILE Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 249 MET Chi-restraints excluded: chain H residue 316 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 149 optimal weight: 0.6980 chunk 157 optimal weight: 0.6980 chunk 217 optimal weight: 0.9990 chunk 210 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 108 optimal weight: 7.9990 chunk 197 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 71 ASN B 181 HIS I 137 GLN D 140 ASN E 308 ASN ** F 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 GLN G 256 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.186946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.142169 restraints weight = 32935.348| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 2.80 r_work: 0.3616 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3449 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 23213 Z= 0.173 Angle : 0.589 12.804 31641 Z= 0.308 Chirality : 0.045 0.829 3509 Planarity : 0.005 0.068 3834 Dihedral : 14.662 151.866 3781 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.75 % Allowed : 27.46 % Favored : 68.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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 are not related in a simple way. whole: -0.63 (0.16), residues: 2609 helix: 0.70 (0.18), residues: 755 sheet: 0.09 (0.26), residues: 455 loop : -1.24 (0.16), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 150 TYR 0.018 0.001 TYR F 265 PHE 0.035 0.002 PHE G 172 TRP 0.010 0.001 TRP E 33 HIS 0.004 0.001 HIS D 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (23213) covalent geometry : angle 0.58891 / 0.31 (31641) hydrogen bonds : bond 0.04489 / 2.91 ( 633) hydrogen bonds : angle 5.38182 / 3.66 ( 1749) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5218 Ramachandran restraints generated. 2609 Oldfield, 0 Emsley, 2609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5218 Ramachandran restraints generated. 2609 Oldfield, 0 Emsley, 2609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 466 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.6942 (tpt) cc_final: 0.6491 (tpt) REVERT: A 320 MET cc_start: 0.4783 (ptt) cc_final: 0.4380 (tpp) REVERT: B 26 ILE cc_start: 0.8924 (mm) cc_final: 0.8558 (mt) REVERT: B 61 GLU cc_start: 0.7556 (mt-10) cc_final: 0.7257 (mt-10) REVERT: B 70 LYS cc_start: 0.5208 (OUTLIER) cc_final: 0.4808 (pttm) REVERT: B 213 LYS cc_start: 0.8113 (mmtt) cc_final: 0.7304 (mmtt) REVERT: B 233 LEU cc_start: 0.7115 (OUTLIER) cc_final: 0.6835 (mm) REVERT: D 140 ASN cc_start: 0.7922 (OUTLIER) cc_final: 0.7437 (m-40) REVERT: D 144 ASN cc_start: 0.8428 (p0) cc_final: 0.8117 (p0) REVERT: D 227 GLN cc_start: 0.8695 (tt0) cc_final: 0.8291 (tt0) REVERT: D 229 MET cc_start: 0.5579 (OUTLIER) cc_final: 0.5299 (ttm) REVERT: D 256 ASN cc_start: 0.8198 (t0) cc_final: 0.7839 (t0) REVERT: D 279 ASN cc_start: 0.8255 (m-40) cc_final: 0.8033 (m-40) REVERT: E 89 ASP cc_start: 0.8485 (p0) cc_final: 0.8112 (p0) REVERT: E 124 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7798 (mt-10) REVERT: E 290 PHE cc_start: 0.8332 (m-80) cc_final: 0.8021 (m-80) REVERT: E 307 LYS cc_start: 0.8772 (tmtt) cc_final: 0.8343 (tmtt) REVERT: F 87 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8475 (mm-30) REVERT: F 89 ASP cc_start: 0.8189 (p0) cc_final: 0.7641 (p0) REVERT: F 94 ASP cc_start: 0.7997 (m-30) cc_final: 0.7563 (m-30) REVERT: F 103 LYS cc_start: 0.8705 (mtmt) cc_final: 0.8441 (mttm) REVERT: F 123 ASP cc_start: 0.7947 (m-30) cc_final: 0.7619 (m-30) REVERT: F 244 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8594 (mt-10) REVERT: F 299 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8601 (mttp) REVERT: C 29 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7475 (mt-10) REVERT: C 91 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7738 (tp) REVERT: C 106 MET cc_start: 0.7929 (tpp) cc_final: 0.7354 (ttm) REVERT: C 241 PHE cc_start: 0.8786 (t80) cc_final: 0.8240 (t80) REVERT: C 275 ILE cc_start: 0.8459 (pt) cc_final: 0.8208 (tt) REVERT: G 89 ASP cc_start: 0.7711 (p0) cc_final: 0.7423 (p0) REVERT: G 121 LYS cc_start: 0.8560 (tppt) cc_final: 0.8224 (mmtm) REVERT: G 184 GLU cc_start: 0.7611 (pm20) cc_final: 0.7258 (pm20) REVERT: G 227 GLN cc_start: 0.8768 (tt0) cc_final: 0.8486 (mt0) REVERT: G 300 LEU cc_start: 0.8385 (tt) cc_final: 0.7732 (mt) REVERT: H 106 MET cc_start: 0.7251 (tpp) cc_final: 0.6598 (tpp) REVERT: H 121 LYS cc_start: 0.8604 (mmtt) cc_final: 0.8079 (mmtp) REVERT: H 146 ARG cc_start: 0.7865 (mtp-110) cc_final: 0.7463 (mtp-110) REVERT: H 150 ARG cc_start: 0.7890 (mtp180) cc_final: 0.7536 (mtp180) REVERT: H 272 GLU cc_start: 0.7872 (mp0) cc_final: 0.7611 (pm20) REVERT: H 303 ARG cc_start: 0.7423 (mtm-85) cc_final: 0.7049 (mtm-85) REVERT: H 304 MET cc_start: 0.7673 (tmm) cc_final: 0.6429 (tpt) REVERT: H 309 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7562 (mm-30) REVERT: H 320 MET cc_start: 0.7690 (mmt) cc_final: 0.7413 (mmp) outliers start: 88 outliers final: 71 residues processed: 517 average time/residue: 0.1339 time to fit residues: 109.7182 Evaluate side-chains 532 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 454 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain B residue 20 ASN Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 99 GLN Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 96 TYR Chi-restraints excluded: chain I residue 137 GLN Chi-restraints excluded: chain D residue 26 ASN Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 140 ASN Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 171 SER Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 252 GLN Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 219 CYS Chi-restraints excluded: chain F residue 226 SER Chi-restraints excluded: chain F residue 249 MET Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain F residue 299 LYS Chi-restraints excluded: chain F residue 305 ILE Chi-restraints excluded: chain F residue 328 MET Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 304 MET Chi-restraints excluded: chain C residue 328 MET Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 72 MET Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain G residue 104 GLU Chi-restraints excluded: chain G residue 108 SER Chi-restraints excluded: chain G residue 156 GLU Chi-restraints excluded: chain G residue 164 ILE Chi-restraints excluded: chain G residue 172 PHE Chi-restraints excluded: chain G residue 213 CYS Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain G residue 267 ASP Chi-restraints excluded: chain G residue 275 ILE Chi-restraints excluded: chain G residue 329 PHE Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 186 ASN Chi-restraints excluded: chain H residue 209 ILE Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 249 MET Chi-restraints excluded: chain H residue 316 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 20 optimal weight: 0.0870 chunk 142 optimal weight: 0.6980 chunk 137 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 264 optimal weight: 6.9990 chunk 159 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 244 optimal weight: 5.9990 chunk 33 optimal weight: 0.1980 chunk 42 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 137 GLN D 140 ASN E 252 GLN E 308 ASN ** F 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.187795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.142625 restraints weight = 32889.124| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 2.63 r_work: 0.3638 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3476 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23213 Z= 0.135 Angle : 0.577 12.388 31641 Z= 0.301 Chirality : 0.042 0.241 3509 Planarity : 0.005 0.067 3834 Dihedral : 14.639 147.694 3781 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.33 % Allowed : 27.89 % Favored : 68.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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 are not related in a simple way. whole: -0.56 (0.16), residues: 2609 helix: 0.74 (0.18), residues: 757 sheet: 0.13 (0.26), residues: 455 loop : -1.19 (0.16), residues: 1397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 142 TYR 0.019 0.001 TYR F 265 PHE 0.029 0.001 PHE G 172 TRP 0.008 0.001 TRP F 33 HIS 0.006 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (23213) covalent geometry : angle 0.57686 / 0.30 (31641) hydrogen bonds : bond 0.04332 / 2.83 ( 633) hydrogen bonds : angle 5.32292 / 3.61 ( 1749) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5218 Ramachandran restraints generated. 2609 Oldfield, 0 Emsley, 2609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5218 Ramachandran restraints generated. 2609 Oldfield, 0 Emsley, 2609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 456 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.6911 (tpt) cc_final: 0.6463 (tpt) REVERT: A 320 MET cc_start: 0.4721 (ptt) cc_final: 0.4382 (tpp) REVERT: B 26 ILE cc_start: 0.8910 (mm) cc_final: 0.8543 (mt) REVERT: B 61 GLU cc_start: 0.7498 (mt-10) cc_final: 0.7197 (mt-10) REVERT: B 70 LYS cc_start: 0.5194 (OUTLIER) cc_final: 0.4794 (pttm) REVERT: B 233 LEU cc_start: 0.7082 (OUTLIER) cc_final: 0.6817 (mm) REVERT: D 144 ASN cc_start: 0.8382 (p0) cc_final: 0.8062 (p0) REVERT: D 227 GLN cc_start: 0.8681 (tt0) cc_final: 0.8333 (tt0) REVERT: D 256 ASN cc_start: 0.8155 (t0) cc_final: 0.7781 (t0) REVERT: D 279 ASN cc_start: 0.8280 (m-40) cc_final: 0.8053 (m-40) REVERT: D 299 LYS cc_start: 0.8065 (mmmm) cc_final: 0.7740 (mmmm) REVERT: E 116 THR cc_start: 0.8368 (m) cc_final: 0.8121 (m) REVERT: E 124 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7804 (mt-10) REVERT: E 262 ASP cc_start: 0.8238 (t0) cc_final: 0.8036 (t70) REVERT: E 290 PHE cc_start: 0.8316 (m-80) cc_final: 0.8028 (m-80) REVERT: E 307 LYS cc_start: 0.8730 (tmtt) cc_final: 0.8326 (tmtt) REVERT: F 87 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8466 (mm-30) REVERT: F 89 ASP cc_start: 0.8200 (p0) cc_final: 0.7624 (p0) REVERT: F 94 ASP cc_start: 0.7985 (m-30) cc_final: 0.7580 (m-30) REVERT: F 103 LYS cc_start: 0.8659 (mtmt) cc_final: 0.8412 (mttm) REVERT: F 123 ASP cc_start: 0.7915 (m-30) cc_final: 0.7574 (m-30) REVERT: F 244 GLU cc_start: 0.8815 (mt-10) cc_final: 0.8599 (mt-10) REVERT: F 299 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8590 (mttp) REVERT: C 29 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7220 (mp0) REVERT: C 91 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7728 (tp) REVERT: C 106 MET cc_start: 0.7887 (tpp) cc_final: 0.7296 (ttm) REVERT: C 241 PHE cc_start: 0.8776 (t80) cc_final: 0.8222 (t80) REVERT: C 275 ILE cc_start: 0.8460 (pt) cc_final: 0.8208 (tt) REVERT: G 89 ASP cc_start: 0.7650 (p0) cc_final: 0.7358 (p0) REVERT: G 121 LYS cc_start: 0.8556 (tppt) cc_final: 0.8229 (mmtm) REVERT: G 184 GLU cc_start: 0.7591 (pm20) cc_final: 0.7211 (pm20) REVERT: G 227 GLN cc_start: 0.8747 (tt0) cc_final: 0.8464 (mt0) REVERT: G 300 LEU cc_start: 0.8377 (tt) cc_final: 0.7718 (mt) REVERT: H 106 MET cc_start: 0.7207 (tpp) cc_final: 0.6561 (tpp) REVERT: H 118 ILE cc_start: 0.7675 (OUTLIER) cc_final: 0.7434 (mt) REVERT: H 146 ARG cc_start: 0.7857 (mtp-110) cc_final: 0.7468 (mtp-110) REVERT: H 150 ARG cc_start: 0.7865 (mtp180) cc_final: 0.7520 (mtp180) REVERT: H 272 GLU cc_start: 0.7854 (mp0) cc_final: 0.7628 (pm20) REVERT: H 303 ARG cc_start: 0.7442 (mtm-85) cc_final: 0.7054 (mtm-85) REVERT: H 304 MET cc_start: 0.7679 (tmm) cc_final: 0.6447 (tpt) REVERT: H 309 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7590 (mm-30) REVERT: H 320 MET cc_start: 0.7676 (mmt) cc_final: 0.7395 (mmp) outliers start: 78 outliers final: 66 residues processed: 503 average time/residue: 0.1384 time to fit residues: 110.4141 Evaluate side-chains 530 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 458 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 20 ASN Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 99 GLN Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 96 TYR Chi-restraints excluded: chain I residue 137 GLN Chi-restraints excluded: chain D residue 26 ASN Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 140 ASN Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 171 SER Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 252 GLN Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 62 MET Chi-restraints excluded: chain F residue 72 MET Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 219 CYS Chi-restraints excluded: chain F residue 226 SER Chi-restraints excluded: chain F residue 249 MET Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain F residue 299 LYS Chi-restraints excluded: chain F residue 305 ILE Chi-restraints excluded: chain F residue 328 MET Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 304 MET Chi-restraints excluded: chain C residue 328 MET Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 72 MET Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain G residue 104 GLU Chi-restraints excluded: chain G residue 108 SER Chi-restraints excluded: chain G residue 164 ILE Chi-restraints excluded: chain G residue 172 PHE Chi-restraints excluded: chain G residue 213 CYS Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain G residue 275 ILE Chi-restraints excluded: chain G residue 329 PHE Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 186 ASN Chi-restraints excluded: chain H residue 209 ILE Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 249 MET Chi-restraints excluded: chain H residue 316 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 159 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 231 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 75 optimal weight: 0.3980 chunk 126 optimal weight: 0.6980 chunk 172 optimal weight: 1.9990 chunk 210 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 chunk 230 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 ASN ** F 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.187298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.142575 restraints weight = 32949.825| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 2.76 r_work: 0.3631 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3469 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 23213 Z= 0.167 Angle : 0.577 11.742 31641 Z= 0.303 Chirality : 0.042 0.214 3509 Planarity : 0.004 0.067 3834 Dihedral : 14.587 142.457 3781 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.50 % Allowed : 27.89 % Favored : 68.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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 are not related in a simple way. whole: -0.56 (0.16), residues: 2609 helix: 0.74 (0.19), residues: 757 sheet: 0.17 (0.26), residues: 455 loop : -1.19 (0.16), residues: 1397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 23 TYR 0.017 0.001 TYR F 265 PHE 0.029 0.001 PHE G 172 TRP 0.010 0.001 TRP F 149 HIS 0.004 0.001 HIS D 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (23213) covalent geometry : angle 0.57748 / 0.30 (31641) hydrogen bonds : bond 0.04407 / 2.87 ( 633) hydrogen bonds : angle 5.30659 / 3.60 ( 1749) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6315.54 seconds wall clock time: 108 minutes 44.07 seconds (6524.07 seconds total)